diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 00000000..8803dce5 --- /dev/null +++ b/.codecov.yml @@ -0,0 +1,18 @@ +coverage: + status: + project: # more options at https://docs.codecov.com/docs/commit-status + default: + target: auto # use the coverage from the base commit, fail if coverage is lower + threshold: 0% # allow the coverage to drop by + +comment: + layout: " diff, flags, files" + behavior: default + require_changes: false + require_base: false # [true :: must have a base report to post] + require_head: false # [true :: must have a head report to post] + hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage] + +# SCons compiles copies of the sources in build/coverage-/, map them back to src/ +fixes: + - "build/coverage-x86_64/::src/" diff --git a/.codespell/ignore_lines.txt b/.codespell/ignore_lines.txt new file mode 100644 index 00000000..07fa7c8c --- /dev/null +++ b/.codespell/ignore_lines.txt @@ -0,0 +1,2 @@ +;; Please include filenames and explanations for each ignored line. +;; See https://docs.openverse.org/meta/codespell.html for docs. diff --git a/.codespell/ignore_words.txt b/.codespell/ignore_words.txt new file mode 100644 index 00000000..04b4fcfa --- /dev/null +++ b/.codespell/ignore_words.txt @@ -0,0 +1,8 @@ +;; Please include explanations for each ignored word (lowercase). +;; See https://docs.openverse.org/meta/codespell.html for docs. + +;; abbreviation for "materials" often used in a journal title +mater + +;; Frobenius norm used in np.linalg.norm +fro diff --git a/.flake8 b/.flake8 new file mode 100644 index 00000000..88077af0 --- /dev/null +++ b/.flake8 @@ -0,0 +1,13 @@ +# As of now, flake8 does not natively support configuration via pyproject.toml +# https://github.com/microsoft/vscode-flake8/issues/135 +[flake8] +exclude = + .git, + __pycache__, + build, + dist, + docs/source/conf.py +max-line-length = 79 +# Ignore some style 'errors' produced while formatting by 'black' +# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings +extend-ignore = E203 diff --git a/.gitattributes b/.gitattributes index 503fc76f..04b6c92b 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,6 +1,4 @@ /.gitattributes export-ignore /.gitignore export-ignore -/.travis* export-ignore -/conda-recipe/ export-ignore /doc export-ignore gitarchive.cfg export-subst diff --git a/.github/ISSUE_TEMPLATE/bug_feature.md b/.github/ISSUE_TEMPLATE/bug_feature.md new file mode 100644 index 00000000..b3454deb --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_feature.md @@ -0,0 +1,16 @@ +--- +name: Bug Report or Feature Request +about: Report a bug or suggest a new feature! +title: "" +labels: "" +assignees: "" +--- + +### Problem + + + +### Proposed solution diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md new file mode 100644 index 00000000..56c5fca3 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/release_checklist.md @@ -0,0 +1,47 @@ +--- +name: Release +about: Checklist and communication channel for PyPI and GitHub release +title: "Ready for PyPI/GitHub release" +labels: "release" +assignees: "" +--- + +### PyPI/GitHub rc-release preparation checklist: + +- [ ] All PRs/issues attached to the release are merged. +- [ ] All the badges on the README are passing. +- [ ] License information is verified as correct. If you are unsure, please comment below. +- [ ] Locally rendered documentation contains all appropriate pages, tutorials, and other human-written text is up-to-date with any changes in the code. +- [ ] All API references are included. To check this, run `conda install scikit-package` and then `package build api-doc`. Review any edits made by rerendering the docs locally. +- [ ] Installation instructions in the README, documentation, and the website are updated. +- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version. +- [ ] Grammar and writing quality are checked (no typos). +- [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release. +- [ ] Dispatch matrix testing to test the release on all Python versions and systems. If you do not have permission to run this workflow, tag the maintainer and say `@maintainer, please dispatch matrix testing workflow`. + +Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here: + +### PyPI/GitHub full-release preparation checklist: + +- [ ] Create a new conda environment and install the rc from PyPI (`pip install ==??`) +- [ ] License information on PyPI is correct. +- [ ] Docs are deployed successfully to `https:///`. +- [ ] Successfully run all tests, tutorial examples or do functional testing. + +Please let the maintainer know that all checks are done and the package is ready for full release. + +### conda-forge release preparation checklist: + + + +- [ ] Ensure that the full release has appeared on PyPI successfully. +- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock. +- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions. +- [ ] Tag the maintainer for conda-forge release. + +### Post-release checklist + + + +- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments. +- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures. diff --git a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md new file mode 100644 index 00000000..1099d862 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md @@ -0,0 +1,15 @@ +### What problem does this PR address? + + + +### What should the reviewer(s) do? + + + + diff --git a/.github/workflows/build-and-publish-docs-on-dispatch.yml b/.github/workflows/build-and-publish-docs-on-dispatch.yml new file mode 100644 index 00000000..1d6992ea --- /dev/null +++ b/.github/workflows/build-and-publish-docs-on-dispatch.yml @@ -0,0 +1,18 @@ +name: Build and Publish Docs on Dispatch + +on: + workflow_dispatch: + +jobs: + get-python-version: + uses: scikit-package/release-scripts/.github/workflows/_get-python-version-latest.yml@v0 + with: + python_version: 0 + + docs: + uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0 + with: + project: libdiffpy + c_extension: true + headless: false + python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }} diff --git a/.github/workflows/check-news-item.yml b/.github/workflows/check-news-item.yml new file mode 100644 index 00000000..fc34d9f5 --- /dev/null +++ b/.github/workflows/check-news-item.yml @@ -0,0 +1,12 @@ +name: Check for News + +on: + pull_request_target: + branches: + - main # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main + +jobs: + check-news-item: + uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0 + with: + project: libdiffpy diff --git a/.github/workflows/matrix-and-codecov.yml b/.github/workflows/matrix-and-codecov.yml new file mode 100644 index 00000000..969d4952 --- /dev/null +++ b/.github/workflows/matrix-and-codecov.yml @@ -0,0 +1,21 @@ +name: Matrix and Codecov + +on: + # push: + # branches: + # - main + release: + types: + - prereleased + - published + workflow_dispatch: + +jobs: + matrix-coverage: + uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0 + with: + project: libdiffpy + c_extension: true + headless: false + secrets: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/release-github-on-tag.yml b/.github/workflows/release-github-on-tag.yml new file mode 100644 index 00000000..a5511623 --- /dev/null +++ b/.github/workflows/release-github-on-tag.yml @@ -0,0 +1,26 @@ +name: Build Wheel and Release + +# Trigger on tag push or manual dispatch. +# Tag and release privilege are verified inside the reusable workflow. +on: + workflow_dispatch: + push: + tags: + - "*" + +jobs: + check-tag-privilege: + uses: scikit-package/release-scripts/.github/workflows/_check-tag-privilege.yml@v0 + with: + maintainer_github_username: sbillinge + + check-pat-token-validity: + uses: scikit-package/release-scripts/.github/workflows/_check-pat-token-validity.yml@v0 + secrets: + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} + + release-github: + needs: [check-tag-privilege, check-pat-token-validity] + uses: scikit-package/release-scripts/.github/workflows/_release-github.yml@v0 + secrets: + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml new file mode 100644 index 00000000..00e87a43 --- /dev/null +++ b/.github/workflows/tests-on-pr.yml @@ -0,0 +1,70 @@ +name: Tests on PR + +on: + pull_request: + workflow_dispatch: + +jobs: + tests-on-pr: + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + + steps: + - name: Check out libdiffpy + uses: actions/checkout@v6 + with: + fetch-depth: 0 + + - name: Initialize miniconda + uses: conda-incubator/setup-miniconda@v3 + with: + activate-environment: test + channels: conda-forge + conda-remove-defaults: "true" + auto-update-conda: true + auto-activate-base: false + + - name: Conda config + run: >- + conda config --set always_yes yes + --set changeps1 no + + - name: Install requirements + run: >- + conda install + --file requirements/build.txt + --file requirements/conda.txt + --file requirements/tests.txt + + - name: Configure SCons for the conda environment + run: | + cat > sconscript.local <<'EOF' + Import('env') + import os + prefix = os.environ['CONDA_PREFIX'] + env.Replace(CXX=os.path.join(prefix, 'bin', 'c++')) + env.Prepend(CCFLAGS=['-isystem' + os.path.join(prefix, 'include')]) + env.Append(LIBPATH=os.path.join(prefix, 'lib')) + env.Append(LINKFLAGS='-Wl,-rpath,' + os.path.join(prefix, 'lib')) + EOF + + - name: Build and run C++ tests with coverage + run: | + "$CONDA_PREFIX/bin/c++" --version + scons build=coverage test + + - name: Generate coverage report + run: >- + gcovr --gcov-executable "$CONDA_PREFIX/bin/gcov" + --root . --filter 'build/coverage-.*/diffpy/' + --xml coverage.xml + + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v5 + with: + files: coverage.xml + verbose: true + fail_ci_if_error: true + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore index 496ca8a9..a73791eb 100644 --- a/.gitignore +++ b/.gitignore @@ -1,32 +1,117 @@ -# Compiled Object files +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Compiled object files *.slo *.lo *.o -# Compiled Dynamic libraries -*.so +# Compiled dynamic libraries *.dylib -# Compiled Static libraries +# Compiled static libraries *.lai *.la -*.a.sconf_temp +*.a # SCons build files -*.pyc -.gdb_history .sconf_temp/ .sconsign.dblite -build -config.log -errors.err /sconscript.local /sconsvars.py +.gdb_history tags -# eclipse +# Source distribution tarball +libdiffpy-*.tar.gz + +# Distribution / packaging +.Python +env/ +build/ +_build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +venv/ +*.egg-info/ +.installed.cfg +*.egg +bin/ +temp/ +tags/ +errors.err + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt +MANIFEST + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Mr Developer +.mr.developer.cfg .project .pydevproject -# source distribution tarball -libdiffpy-*.tar.gz +# Django stuff: +*.log + +# Sphinx documentation +docs/build/ +docs/source/generated/ + +# pytest +.pytest_cache/ + +# PyBuilder +target/ + +# Editor files +# mac +.DS_Store +*~ + +# vim +*.swp +*.swo + +# pycharm +.idea/ + +# VSCode +.vscode/ + +# Ipython Notebook +.ipynb_checkpoints diff --git a/.isort.cfg b/.isort.cfg new file mode 100644 index 00000000..86f162b8 --- /dev/null +++ b/.isort.cfg @@ -0,0 +1,5 @@ +[settings] +# Keep import statement below line_length character limit +line_length = 79 +multi_line_output = 3 +include_trailing_comma = True diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..74f98b2c --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,62 @@ +default_language_version: + python: python3.13 +ci: + autofix_commit_msg: | + [pre-commit.ci] auto fixes from pre-commit hooks + autofix_prs: true + autoupdate_branch: "pre-commit-autoupdate" + autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate" + autoupdate_schedule: monthly + skip: [no-commit-to-branch] + submodules: false +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 + hooks: + - id: check-yaml + - id: end-of-file-fixer + - id: trailing-whitespace + - id: check-case-conflict + - id: check-merge-conflict + - id: check-toml + - id: check-added-large-files + - repo: https://github.com/psf/black + rev: 26.3.1 + hooks: + - id: black + - repo: https://github.com/pycqa/flake8 + rev: 7.3.0 + hooks: + - id: flake8 + - repo: https://github.com/pycqa/isort + rev: 9.0.0a3 + hooks: + - id: isort + args: ["--profile", "black"] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 + hooks: + - id: no-commit-to-branch + name: Prevent Commit to Main Branch + args: ["--branch", "main"] + stages: [pre-commit] + - repo: https://github.com/codespell-project/codespell + rev: v2.4.2 + hooks: + - id: codespell + additional_dependencies: + - tomli + # prettier - multi formatter for .json, .yml, and .md files + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier + additional_dependencies: + - "prettier@^3.2.4" + # docformatter - PEP 257 compliant docstring formatter + - repo: https://github.com/PyCQA/docformatter + rev: v1.7.8 + hooks: + - id: docformatter + additional_dependencies: [tomli] + args: [--in-place, --config, ./pyproject.toml] diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 00000000..aaa88895 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: 2 + +build: + os: "ubuntu-22.04" + tools: + python: "latest" + +python: + install: + - requirements: requirements/docs.txt + +sphinx: + configuration: docs/source/conf.py diff --git a/.travis-sconscript.local b/.travis-sconscript.local deleted file mode 100644 index c7fb22be..00000000 --- a/.travis-sconscript.local +++ /dev/null @@ -1,34 +0,0 @@ -# Customize scons build environment. - -Import('env') - -import os - -# Workaround: DEBUG_CPPFLAGS is defined on Linux, but not on Mac OS X. -# Make sure it is always sensibly defined. -os.environ.setdefault('DEBUG_CPPFLAGS', os.environ['CPPFLAGS']) - -# Apply environment settings for Anaconda compilers -env.Replace(CXX=os.environ['CXX']) -if env['build'] == 'fast': - env.MergeFlags(os.environ['CFLAGS']) - env.MergeFlags(os.environ['CPPFLAGS']) - env.MergeFlags(os.environ['CXXFLAGS']) -else: - env.MergeFlags(os.environ['DEBUG_CFLAGS']) - env.MergeFlags(os.environ['DEBUG_CPPFLAGS']) - env.MergeFlags(os.environ['DEBUG_CXXFLAGS']) -env.MergeFlags(os.environ['LDFLAGS']) - -# Silence copious warnings from the boost headers. -P = os.environ['MYPREFIX'] -env.Prepend(CCFLAGS=['-isystem{}/include'.format(P)]) - -# Define path to the shared libraries from Anaconda environment. -L = P + '/lib' -env.Append(LIBPATH=L) -env.Append(LINKFLAGS='-Wl,-rpath,{!r}'.format(L)) -if env['PLATFORM'] == 'posix': - env.Append(LINKFLAGS='-Wl,-rpath-link,{!r}'.format(L)) - -# vim: ft=python diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index c7af470c..00000000 --- a/.travis.yml +++ /dev/null @@ -1,153 +0,0 @@ -dist: xenial -language: cpp - -os: - - linux - - osx - -env: - - MYUSEMC=true MYPYTHON_VERSION=2.7 - - MYUSEMC=true MYPYTHON_VERSION=3.7 - - MYUSEMC=false - -matrix: - exclude: - - os: osx - env: MYUSEMC=true MYPYTHON_VERSION=2.7 - -git: - depth: 999999 - -branches: - except: - - /^v[0-9]/ - - -before_install: - - MYNAME=libdiffpy - - MYCOMMIT="$(git rev-parse HEAD)" - # travis virtual hosts have 2 cores as per https://goo.gl/DQy4oW - - MYNCPU=2 - - umask 022 - - git fetch origin --tags - - NOSYS=true; NOAPT=true; NOBREW=true; NOMC=true - - if ${MYUSEMC}; then - NOMC=false; - elif [[ ${TRAVIS_OS_NAME} == linux ]]; then - NOAPT=false; NOSYS=false; - MYPIPFLAGS="--user"; - elif [[ ${TRAVIS_OS_NAME} == osx ]]; then - NOBREW=false; NOSYS=false; - MYPIPFLAGS="--user"; - fi - - MYMCREPO=https://repo.anaconda.com/miniconda - - case ${TRAVIS_OS_NAME} in - linux) - MYMCBUNDLE=Miniconda3-latest-Linux-x86_64.sh; - MYCXXCOMPILER=gxx_linux-64 - ;; - osx) - MYMCBUNDLE=Miniconda3-latest-MacOSX-x86_64.sh; - MYCXXCOMPILER=clangxx_osx-64 - ;; - *) - echo "Unsupported operating system." >&2; - exit 2 ;; - esac - - - mkdir -p ~/pkgs - - - $NOMC || pushd ~/pkgs - - $NOMC || wget --timestamping ${MYMCREPO}/${MYMCBUNDLE} - - $NOMC || test -x ~/mc/bin/conda || bash ${MYMCBUNDLE} -b -f -p ~/mc - - $NOMC || popd - - $NOMC || source ~/mc/bin/activate base - - $NOMC || conda update --yes conda - - $NOMC || conda install --yes conda-build conda-verify jinja2 - - $NOMC || conda create --name=testenv --yes $MYCXXCOMPILER - - $NOMC || conda config --add channels diffpy - - - $NOAPT || test "${TRAVIS_OS_NAME}" = "linux" || exit $? - - $NOAPT || sudo apt-get update -qq - - $NOAPT || sudo apt-get install -y - libgsl0-dev libboost-all-dev python-pip - build-essential scons cxxtest - - - $NOBREW || test "${TRAVIS_OS_NAME}" = "osx" || exit $? - - - $NOBREW || brew update - - $NOBREW || brew install gsl - - $NOBREW || brew install scons - - $NOBREW || brew install cxxtest - - $NOBREW || PATH="$(brew --prefix python)/libexec/bin:${PATH}" - - $NOBREW || export CXXTEST="$(brew --prefix cxxtest)"/libexec/bin/cxxtestgen - - - $NOSYS || scons sdist - - $NOSYS || MYTARBUNDLE="$(ls -t "${PWD}"/*.tar.gz | head -1)" - - $NOSYS || pushd ~/pkgs - - $NOSYS || tar xzf "${MYTARBUNDLE}" - - $NOSYS || git clone https://github.com/diffpy/libobjcryst.git - - $NOSYS || popd - - -install: - - $NOMC || conda build --python=${MYPYTHON_VERSION} conda-recipe - - $NOMC || conda render --python=${MYPYTHON_VERSION} --output conda-recipe | - sed 's,.*/,,; s/[.]tar[.]bz2$//; s/-/=/g' > /tmp/mypackage.txt - - $NOMC || source activate base - - $NOMC || conda build purge - - $NOMC || source activate testenv - - $NOMC || conda install --yes --use-local --file=/tmp/mypackage.txt - - $NOMC || conda install --yes cxxtest scons - - $NOMC || MYPREFIX="${HOME}/mc/envs/testenv" - - - MYSUDO= - - $NOAPT || MYSUDO=sudo - - $NOSYS || $MYSUDO scons -j $MYNCPU -C ~/pkgs/libobjcryst install - - $NOSYS || cd ~/pkgs/"$(basename "${MYTARBUNDLE}" .tar.gz)" - - $NOSYS || scons -j $MYNCPU build=fast lib - - $NOSYS || $MYSUDO scons build=fast install - - $NOSYS || scons -Q build=fast --clean lib - - $NOSYS || MYPREFIX=/usr/local - - # Verify version of the installed library. - - MYINCLUDE="${MYPREFIX}/include" - - MYVERSION="${MYINCLUDE}/diffpy/version.hpp" - - MYGIT_REV=$(grep '^#define DIFFPY_GIT_SHA' "$MYVERSION" | cut -d '"' -f 2) - - if [[ "${MYCOMMIT}" != "${MYGIT_REV}" ]]; then - echo "Version mismatch ${MYCOMMIT} vs ${MYGIT_REV}."; - exit 1; - fi - - - $NOMC || export MYPREFIX - # drop linker flags that spuriously remove linkage with libgslcblas - - $NOMC || LDFLAGS="${LDFLAGS/-Wl,-dead_strip_dylibs/}" - - $NOMC || cp .travis-sconscript.local sconscript.local - - scons -j $MYNCPU build=fast prefix="${MYPREFIX}" test_installed=true alltests - - MYALLTESTSFAST=$(ls -t ${PWD}/build/fast*/tests/alltests | head -1) - - scons -j $MYNCPU build=debug lib alltests - # APT and BREW jobs test builds from expanded source archive, but codecov - # requires compilation from a git repository. Tell scons to do so. - - scons -j $MYNCPU -C $TRAVIS_BUILD_DIR build=coverage lib alltests - - -before_script: - - $NOBREW || USER_BASE="$(python -c 'import site; print(site.USER_BASE)')" - - $NOBREW || PATH="${USER_BASE}/bin:${PATH}" - - -script: - - scons -Q build=debug test - - scons -Q build=debug enable_objcryst=false test - - ${MYALLTESTSFAST} - - scons -j $MYNCPU -C $TRAVIS_BUILD_DIR build=coverage test - - -after_success: - - cd $TRAVIS_BUILD_DIR - - pip install $MYPIPFLAGS codecov - - codecov - - -deploy: - - provider: releases - - draft: true diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 00000000..5d0e7bf5 --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,10 @@ +Authors +======= + +Pavol Juhas, Chris Farrow, Simon Billinge, Billinge Group members + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/libdiffpy/graphs/contributors diff --git a/AUTHORS.txt b/AUTHORS.txt deleted file mode 100644 index a0efd439..00000000 --- a/AUTHORS.txt +++ /dev/null @@ -1,9 +0,0 @@ -Authors: - -Pavol Juhas -Chris Farrow -Simon J.L. Billinge - -Contributors: - -https://github.com/diffpy/libdiffpy/graphs/contributors diff --git a/CHANGELOG.md b/CHANGELOG.md deleted file mode 100644 index aea699b4..00000000 --- a/CHANGELOG.md +++ /dev/null @@ -1,41 +0,0 @@ -# Release notes - -## Version 1.4.0 -- 2019-03-09 - -Notable differences from version 1.3.4. - -### Added - -- Test coverage analysis at https://codecov.io/gh/diffpy/libdiffpy. -- Make scons scripts compatible with Python 3 and Python 2. -- Atomic numbers and possible ions for elements 99-103. -- Define libdiffpy version requirements for client Anaconda packages. -- Support free-standing attribute getter and setter functions. -- `uisowidth` and `bisowidth` attributes to `ConstantPeakWidth` class. - This simplifies PDF modeling of structures with uniform isotropic - atom displacements. - - -### Changed - -- Build Anaconda package with Anaconda C++ compiler. -- Adopt language standard c++11. -- Replaced boost unordered set and map types with their STL version. -- Switch to direct serialization of `PeakWidthModel`, `PeakProfile`, - `PDFEnvelope`, `PDFBaseline`, and `ScatteringFactorTable` classes and - derived types. - -### Deprecated - -- `StructureAdapter::customPQConfig` function because it permits unexpected - changes in calculators setup and complicates parallel evaluation. - -### Removed - -- Virtual class inheritance of `BaseDebyeSum` and `DebyePDFCalculator`. - -### Fixed - -- Incorrect results for crystals with off-origin inversion center. -- Incomplete `scons install` when shared library fails to compile. -- Use of invalid iterators when removing `map` items. diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 00000000..44e268d1 --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,45 @@ +============= +Release notes +============= + +.. current developments + +1.4.0 +===== + +Released 2019-03-09. Notable differences from version 1.3.4. + +**Added:** + +* Test coverage analysis at https://codecov.io/gh/diffpy/libdiffpy. +* Make scons scripts compatible with Python 3 and Python 2. +* Atomic numbers and possible ions for elements 99-103. +* Define libdiffpy version requirements for client Anaconda packages. +* Support free-standing attribute getter and setter functions. +* ``uisowidth`` and ``bisowidth`` attributes to ``ConstantPeakWidth`` class. + This simplifies PDF modeling of structures with uniform isotropic + atom displacements. + +**Changed:** + +* Build Anaconda package with Anaconda C++ compiler. +* Adopt language standard c++11. +* Replaced boost unordered set and map types with their STL version. +* Switch to direct serialization of ``PeakWidthModel``, ``PeakProfile``, + ``PDFEnvelope``, ``PDFBaseline``, and ``ScatteringFactorTable`` classes and + derived types. + +**Deprecated:** + +* ``StructureAdapter::customPQConfig`` function because it permits unexpected + changes in calculators setup and complicates parallel evaluation. + +**Fixed:** + +* Incorrect results for crystals with off-origin inversion center. +* Incomplete ``scons install`` when shared library fails to compile. +* Use of invalid iterators when removing ``map`` items. + +**Removed:** + +* Virtual class inheritance of ``BaseDebyeSum`` and ``DebyePDFCalculator``. diff --git a/CODE-OF-CONDUCT.rst b/CODE-OF-CONDUCT.rst new file mode 100644 index 00000000..25fafe27 --- /dev/null +++ b/CODE-OF-CONDUCT.rst @@ -0,0 +1,133 @@ +===================================== + Contributor Covenant Code of Conduct +===================================== + +Our Pledge +---------- + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socioeconomic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +Our Standards +------------- + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +Enforcement Responsibilities +---------------------------- + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +Scope +----- + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +Enforcement +----------- + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +sbillinge@ucsb.edu. All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +Enforcement Guidelines +---------------------- + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +1. Correction +**************** + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +2. Warning +************* + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +3. Temporary Ban +****************** + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +4. Permanent Ban +****************** + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +Attribution +----------- + +This Code of Conduct is adapted from the `Contributor Covenant `_. + +Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder `_. + +For answers to common questions about this code of conduct, see the `FAQ `_. `Translations are available `_ diff --git a/LICENSE.rst b/LICENSE.rst new file mode 100644 index 00000000..fa74e759 --- /dev/null +++ b/LICENSE.rst @@ -0,0 +1,139 @@ +OPEN SOURCE LICENSE AGREEMENT +============================= + +Copyright (c) 2009-2011, University of Tennessee + +Copyright (c) 1989, 1991 Free Software Foundation, Inc. + +Copyright (c) 2006, The Regents of the University of California through Lawrence Berkeley National Laboratory + +Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP") + +Copyright (c) 2006-2007, Board of Trustees of Michigan State University + +Copyright (c) 2008-2012, The Trustees of Columbia University in the City of New York + +Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory + +The "DiffPy-CMI" is distributed subject to the following license conditions: + +.. code-block:: text + + SOFTWARE LICENSE AGREEMENT + + Software: DiffPy-CMI + + + (1) The "Software", below, refers to the aforementioned DiffPy-CMI (in either + source code, or binary form and accompanying documentation). + + Part of the software was derived from the DANSE, ObjCryst++ (with permission), + PyCifRW, Python periodictable, CCTBX, and SasView open source projects, of + which the original Copyrights are contained in each individual file. + + Each licensee is addressed as "you" or "Licensee." + + + (2) The copyright holders shown above and their third-party Licensors hereby + grant licensee a royalty-free nonexclusive license, subject to the limitations + stated herein and U.S. Government license rights. + + + (3) You may modify and make a copy or copies of the software for use within + your organization, if you meet the following conditions: + + (a) Copies in source code must include the copyright notice and this + software license agreement. + + (b) Copies in binary form must include the copyright notice and this + Software License Agreement in the documentation and/or other materials + provided with the copy. + + + (4) You may modify a copy or copies of the Software or any portion of it, thus + forming a work based on the Software, and distribute copies of such work + outside your organization, if you meet all of the following conditions: + + (a) Copies in source code must include the copyright notice and this + Software License Agreement; + + (b) Copies in binary form must include the copyright notice and this + Software License Agreement in the documentation and/or other materials + provided with the copy; + + (c) Modified copies and works based on the Software must carry prominent + notices stating that you changed specified portions of the Software. + + (d) Neither the name of Brookhaven Science Associates or Brookhaven + National Laboratory nor the names of its contributors may be used to + endorse or promote products derived from this software without specific + written permission. + + + (5) Portions of the Software resulted from work developed under a U.S. + Government contract and are subject to the following license: + The Government is granted for itself and others acting on its behalf a + paid-up, nonexclusive, irrevocable worldwide license in this computer software + to reproduce, prepare derivative works, and perform publicly and display + publicly. + + + (6) WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT + WARRANTY OF ANY KIND. THE COPYRIGHT HOLDERS, THEIR THIRD PARTY + LICENSORS, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND + THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING + BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A + PARTICULAR PURPOSE, TITLE OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL + LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF + THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF THE SOFTWARE WOULD NOT INFRINGE + PRIVATELY OWNED RIGHTS, (4) DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION + UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL BE CORRECTED. + + + (7) LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT HOLDERS, THEIR + THIRD PARTY LICENSORS, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF + ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT, INCIDENTAL, + CONSEQUENTIAL, SPECIAL OR PUNITIVE DAMAGES OF ANY KIND OR NATURE, INCLUDING + BUT NOT LIMITED TO LOSS OF PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER, + WHETHER SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT (INCLUDING + NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE, EVEN IF ANY OF SAID PARTIES HAS + BEEN WARNED OF THE POSSIBILITY OF SUCH LOSS OR DAMAGES. + + +Brookhaven National Laboratory Notice +===================================== + +Acknowledgment of sponsorship +----------------------------- + +This software was produced by the Brookhaven National Laboratory, under +Contract DE-AC02-98CH10886 with the Department of Energy. + + +Government disclaimer of liability +---------------------------------- + +Neither the United States nor the United States Department of Energy, nor +any of their employees, makes any warranty, express or implied, or assumes +any legal liability or responsibility for the accuracy, completeness, or +usefulness of any data, apparatus, product, or process disclosed, or +represents that its use would not infringe privately owned rights. + + +Brookhaven disclaimer of liability +---------------------------------- + +Brookhaven National Laboratory makes no representations or warranties, +express or implied, nor assumes any liability for the use of this software. + + +Maintenance of notice +--------------------- + +In the interest of clarity regarding the origin and status of this +software, Brookhaven National Laboratory requests that any recipient of it +maintain this notice affixed to any distribution by the recipient that +contains a copy or derivative of this software. + + +END OF LICENSE diff --git a/LICENSE.txt b/LICENSE.txt deleted file mode 100644 index f6d92af7..00000000 --- a/LICENSE.txt +++ /dev/null @@ -1,137 +0,0 @@ -OPEN SOURCE LICENSE AGREEMENT -============================= - -Copyright (c) 2009-2011, University of Tennessee -Copyright (c) 1989, 1991 Free Software Foundation, Inc. -Copyright (c) 2006, The Regents of the University of California through - Lawrence Berkeley National Laboratory -Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP") -Copyright (c) 2006-2007, Board of Trustees of Michigan State University -Copyright (c) 2008-2012, The Trustees of Columbia University in the City - of New York - -Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National - Laboratory - - -The "DiffPy-CMI" is distributed subject to the following license conditions: - - -SOFTWARE LICENSE AGREEMENT - - Software: DiffPy-CMI - - -(1) The "Software", below, refers to the aforementioned DiffPy-CMI (in either -source code, or binary form and accompanying documentation). - -Part of the software was derived from the DANSE, ObjCryst++ (with permission), -PyCifRW, Python periodictable, CCTBX, and SasView open source projects, of -which the original Copyrights are contained in each individual file. - -Each licensee is addressed as "you" or "Licensee." - - -(2) The copyright holders shown above and their third-party Licensors hereby -grant licensee a royalty-free nonexclusive license, subject to the limitations -stated herein and U.S. Government license rights. - - -(3) You may modify and make a copy or copies of the software for use within -your organization, if you meet the following conditions: - - (a) Copies in source code must include the copyright notice and this - software license agreement. - - (b) Copies in binary form must include the copyright notice and this - Software License Agreement in the documentation and/or other materials - provided with the copy. - - -(4) You may modify a copy or copies of the Software or any portion of it, thus -forming a work based on the Software, and distribute copies of such work -outside your organization, if you meet all of the following conditions: - - (a) Copies in source code must include the copyright notice and this - Software License Agreement; - - (b) Copies in binary form must include the copyright notice and this - Software License Agreement in the documentation and/or other materials - provided with the copy; - - (c) Modified copies and works based on the Software must carry prominent - notices stating that you changed specified portions of the Software. - - (d) Neither the name of Brookhaven Science Associates or Brookhaven - National Laboratory nor the names of its contributors may be used to - endorse or promote products derived from this software without specific - written permission. - - -(5) Portions of the Software resulted from work developed under a U.S. -Government contract and are subject to the following license: -The Government is granted for itself and others acting on its behalf a -paid-up, nonexclusive, irrevocable worldwide license in this computer software -to reproduce, prepare derivative works, and perform publicly and display -publicly. - - -(6) WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT -WARRANTY OF ANY KIND. THE COPYRIGHT HOLDERS, THEIR THIRD PARTY -LICENSORS, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND -THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING -BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A -PARTICULAR PURPOSE, TITLE OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL -LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF -THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF THE SOFTWARE WOULD NOT INFRINGE -PRIVATELY OWNED RIGHTS, (4) DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION -UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL BE CORRECTED. - - -(7) LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT HOLDERS, THEIR -THIRD PARTY LICENSORS, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF -ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT, INCIDENTAL, -CONSEQUENTIAL, SPECIAL OR PUNITIVE DAMAGES OF ANY KIND OR NATURE, INCLUDING -BUT NOT LIMITED TO LOSS OF PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER, -WHETHER SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT (INCLUDING -NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE, EVEN IF ANY OF SAID PARTIES HAS -BEEN WARNED OF THE POSSIBILITY OF SUCH LOSS OR DAMAGES. - - -Brookhaven National Laboratory Notice -===================================== - -Acknowledgment of sponsorship ------------------------------ - -This software was produced by the Brookhaven National Laboratory, under -Contract DE-AC02-98CH10886 with the Department of Energy. - - -Government disclaimer of liability ----------------------------------- - -Neither the United States nor the United States Department of Energy, nor -any of their employees, makes any warranty, express or implied, or assumes -any legal liability or responsibility for the accuracy, completeness, or -usefulness of any data, apparatus, product, or process disclosed, or -represents that its use would not infringe privately owned rights. - - -Brookhaven disclaimer of liability ----------------------------------- - -Brookhaven National Laboratory makes no representations or warranties, -express or implied, nor assumes any liability for the use of this software. - - -Maintenance of notice ---------------------- - -In the interest of clarity regarding the origin and status of this -software, Brookhaven National Laboratory requests that any recipient of it -maintain this notice affixed to any distribution by the recipient that -contains a copy or derivative of this software. - - -END OF LICENSE diff --git a/LICENSE_DANSE.txt b/LICENSE_DANSE.txt index 3e8768db..83c9a71d 100644 --- a/LICENSE_DANSE.txt +++ b/LICENSE_DANSE.txt @@ -6,7 +6,7 @@ the City of New York. All rights reserved. For more information please visit the project web-page: http://www.diffpy.org/ -or email Prof. Simon Billinge at sb2896@columbia.edu +or email Prof. Simon Billinge at sbillinge@ucsb.edu Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions diff --git a/README.md b/README.md deleted file mode 100644 index 4ec67f65..00000000 --- a/README.md +++ /dev/null @@ -1,160 +0,0 @@ -[![Build Status](https://travis-ci.org/diffpy/libdiffpy.svg?branch=master)](https://travis-ci.org/diffpy/libdiffpy) -[![codecov](https://codecov.io/gh/diffpy/libdiffpy/branch/master/graph/badge.svg)](https://codecov.io/gh/diffpy/libdiffpy) - -# libdiffpy - -C++ calculators of PDF, bond valence sum and other pair quantities - -libdiffpy is a C++ library for calculating atomic pair distribution function -(PDF), bond valence sums, atom overlaps for a hard-sphere model, bond -distances and directions up to a specified maximum distance. The atomic -structure models are represented by classes for non-periodic, periodic or -structures with space group symmetries. libdiffpy supports Crystal and -Molecule classes from the [ObjCryst crystallographic library]( -https://sourceforge.net/projects/objcryst). -Calculators support two evaluation models - BASIC, which performs a full -pair-summation every time, and OPTIMIZED, which updates only pair -contributions that have changed since the last evaluation. libdiffpy supports -object serialization and parallel computations using parallel map function. -PDF calculations can be performed in two modes - either as a real-space -summation of peak profiles (PDFCalculator) or as a reciprocal-space Debye -summation and Fourier transform of the total scattering structure function -(DebyePDFCalculator). - -The calculator objects in libdiffpy share a common procedure for iteration -over atom pairs and only specialize the processing of pair contributions. -New calculator classes can thus be readily defined for any quantity that is -obtained by iteration over atom pairs. - -For more information see user manual at -http://www.diffpy.org/doc/libdiffpy. - - -## REQUIREMENTS - -libdiffpy library requires C++ compiler and the following software: - -* `scons` - software constructions tool (1.0 or later) -* `libboost-dev` - Boost C++ libraries development files (1.56 or later) -* `GSL` - GNU Scientific Library for C - -Recommended software: - -* `libobjcryst` - C++ library for free objects for crystallography, - https://github.com/diffpy/libobjcryst -* `cxxtest` - CxxTest Unit Testing Framework, http://cxxtest.com - -The required software is commonly available in the system package manager. -For example, on Ubuntu Linux the required software can be installed using - -```sh -sudo apt-get install \ - build-essential scons libboost-dev libgsl0-dev -``` - -libdiffpy is also available as a pre-compiled package for -[Anaconda Python](https://www.anaconda.com/download). A Python -interface to libdiffpy is provided by Anaconda package diffpy.srreal. - - -## INSTALLATION - -### Installation from sources - -Use sources from the git repository or extract the latest source -bundle from https://github.com/diffpy/libdiffpy/releases/latest. - -```sh -tar xzf libdiffpy-VERSION.tar.gz -cd libdiffpy-VERSION -``` - -To build and install the libdiffpy library use - -```sh -sudo scons -j4 install -``` - -This installs libdiffpy for all users under the `/usr/local` directory. -If administrator (root) access is not available, see the output from -`scons --help` for options to install to a user-writable location. - -To verify libdiffpy installation, compile and run the included -test code [examples/testlib.cpp](examples/testlib.cpp) - -```sh -cd examples -c++ testlib.cpp -ldiffpy -./a.out -``` - -If compilation fails because of missing header files or missing libdiffpy -library, adjust the `CPATH` and `LIBRARY_PATH` environment variables or -use the `-I` or `-L` compiler options. If the shared library libdiffpy -is unavailable at runtime, add a `-Wl,-rpath,SomePath` option to the -c++ command or adjust the `LD_LIBRARY_PATH` environment variable. - -### Installation for Anaconda Python - -The libdiffpy library can be installed from the "diffpy" channel -of Anaconda packages - -```sh -conda config --add channels diffpy -conda install libdiffpy -``` - -libdiffpy is also included in the "diffpy-cmi" collection of packages -for structure analysis - -```sh -conda install diffpy-cmi -``` - -When compiling with the Anaconda version of libdiffpy it is essential to -specify header path, library path and runtime path of the active Anaconda -environment - -```sh -# resolve prefix directory P of the active Anaconda environment -P="$(conda info --json | grep default_prefix | cut -d\" -f4)" -cd examples -c++ testlib.cpp -I$P/include -L$P/lib -Wl,-rpath,$P/lib -ldiffpy -./a.out -``` - -Note the Anaconda package for libdiffpy is built with C++ compilers -provided by Anaconda. This may cause incompatibility with system C++. -In such case please use Anaconda C++ compiler to link with libdiffpy. - - -## DEVELOPMENT - -libdiffpy is an open-source software developed as a part of the -DiffPy-CMI complex modeling initiative at the Brookhaven National -Laboratory. The libdiffpy sources are hosted at -https://github.com/diffpy/libdiffpy. - -Feel free to fork the project and contribute. When developing it is -preferable to compile with `build=develop` option, which compiles the -library with debug information and C-assertions checks: - -```sh -scons -j4 build=develop -``` - -The build script checks for a presence of `sconsvars.py` file, which -can be used to permanently set the `build` variable. The SCons -construction environment can be further customized in a `sconscript.local` -script. The library integrity can be verified by executing unit tests with -`scons -j4 test` (requires the CxxTest framework). - -[Instructions for compiling and modifying source code in development mode](docs/development_instructions.md) - -## CONTACTS - -For more information about libdiffpy please visit the project web-page - -http://www.diffpy.org/ - -or email Prof. Simon Billinge at sb2896@columbia.edu. diff --git a/README.rst b/README.rst new file mode 100644 index 00000000..ae0b1147 --- /dev/null +++ b/README.rst @@ -0,0 +1,200 @@ +|Icon| |title|_ +=============== + +.. |title| replace:: libdiffpy +.. _title: https://diffpy.github.io/libdiffpy + +.. |Icon| image:: https://avatars.githubusercontent.com/diffpy + :target: https://diffpy.github.io/libdiffpy + :height: 100px + +|Forge| |PR| + +|CI| |Tracking| + +.. |CI| image:: https://github.com/diffpy/libdiffpy/actions/workflows/matrix-and-codecov.yml/badge.svg + :target: https://github.com/diffpy/libdiffpy/actions/workflows/matrix-and-codecov.yml + +.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/libdiffpy + :target: https://anaconda.org/conda-forge/libdiffpy + +.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff + :target: https://github.com/diffpy/libdiffpy/pulls + +.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue + :target: https://github.com/diffpy/libdiffpy/issues + +C++ calculators of PDF, bond valence sum and other pair quantities. + +libdiffpy is a C++ library for calculating atomic pair distribution function +(PDF), bond valence sums, atom overlaps for a hard-sphere model, bond +distances and directions up to a specified maximum distance. The atomic +structure models are represented by classes for non-periodic, periodic or +structures with space group symmetries. libdiffpy supports Crystal and +Molecule classes from the `ObjCryst crystallographic library +`_. +Calculators support two evaluation models - BASIC, which performs a full +pair-summation every time, and OPTIMIZED, which updates only pair +contributions that have changed since the last evaluation. libdiffpy supports +object serialization and parallel computations using parallel map function. +PDF calculations can be performed in two modes - either as a real-space +summation of peak profiles (PDFCalculator) or as a reciprocal-space Debye +summation and Fourier transform of the total scattering structure function +(DebyePDFCalculator). + +The calculator objects in libdiffpy share a common procedure for iteration +over atom pairs and only specialize the processing of pair contributions. +New calculator classes can thus be readily defined for any quantity that is +obtained by iteration over atom pairs. + +A Python interface to libdiffpy is provided by the `diffpy.srreal +`_ package. + +For more information about the libdiffpy library, please consult our `online documentation `_. + +Citation +-------- + +If you use libdiffpy in a scientific publication, we would like you to cite this package as + + libdiffpy Package, https://github.com/diffpy/libdiffpy + +Installation +------------ + +The preferred method is to use `Miniconda Python +`_ +and install from the "conda-forge" channel of Conda packages. + +To add "conda-forge" to the conda channels, run the following in a terminal. :: + + conda config --add channels conda-forge + +We want to install our packages in a suitable conda environment. +The following creates and activates a new environment named ``libdiffpy_env`` :: + + conda create -n libdiffpy_env libdiffpy + conda activate libdiffpy_env + +When compiling with the conda version of libdiffpy it is essential to +specify the header path, library path and runtime path of the active conda +environment. To verify the installation, compile and run the included +test code `examples/testlib.cpp `_ :: + + cd examples + c++ testlib.cpp -I$CONDA_PREFIX/include -L$CONDA_PREFIX/lib -Wl,-rpath,$CONDA_PREFIX/lib -ldiffpy + ./a.out + +Note the conda package for libdiffpy is built with C++ compilers +provided by conda-forge. This may cause incompatibility with system C++. +In such case please use the conda-forge C++ compiler to link with libdiffpy. + +Requirements +^^^^^^^^^^^^ + +To build libdiffpy from sources, a C++ compiler and the following software are required: + +* ``scons`` - software constructions tool (1.0 or later) +* ``libboost-dev`` - Boost C++ libraries development files (1.56 or later) +* ``GSL`` - GNU Scientific Library for C + +Recommended software: + +* ``libobjcryst`` - C++ library for free objects for crystallography, + https://github.com/diffpy/libobjcryst +* ``cxxtest`` - CxxTest Unit Testing Framework, http://cxxtest.com + +The required software is commonly available in the system package manager. +For example, on Ubuntu Linux the required software can be installed using :: + + sudo apt-get install build-essential scons libboost-dev libgsl0-dev + +Alternatively, all of the above can be installed into a conda environment from +the ``requirements`` folder :: + + conda create -n libdiffpy_env --file requirements/build.txt --file requirements/conda.txt --file requirements/tests.txt + conda activate libdiffpy_env + +Installation from sources +^^^^^^^^^^^^^^^^^^^^^^^^^ + +Use sources from the git repository or extract the latest source +bundle from https://github.com/diffpy/libdiffpy/releases/latest. :: + + tar xzf libdiffpy-VERSION.tar.gz + cd libdiffpy-VERSION + +To build and install the libdiffpy library use :: + + sudo scons -j4 install + +This installs libdiffpy for all users under the ``/usr/local`` directory. +If administrator (root) access is not available, see the output from +``scons --help`` for options to install to a user-writable location. + +To verify the libdiffpy installation, compile and run the included +test code `examples/testlib.cpp `_ :: + + cd examples + c++ testlib.cpp -ldiffpy + ./a.out + +If compilation fails because of missing header files or missing libdiffpy +library, adjust the ``CPATH`` and ``LIBRARY_PATH`` environment variables or +use the ``-I`` or ``-L`` compiler options. If the shared library libdiffpy +is unavailable at runtime, add a ``-Wl,-rpath,SomePath`` option to the +c++ command or adjust the ``LD_LIBRARY_PATH`` environment variable. + +Getting Started +--------------- + +You may consult our `online documentation `_ for tutorials and API references. + +Support and Contribute +---------------------- + +If you see a bug or want to request a feature, please `report it as an issue `_ and/or `submit a fix as a PR `_. + +Feel free to fork the project and contribute. When developing it is +preferable to compile with the ``build=develop`` option, which compiles the +library with debug information and C-assertions checks :: + + scons -j4 build=develop + +The build script checks for a presence of ``sconsvars.py`` file, which +can be used to permanently set the ``build`` variable. The SCons +construction environment can be further customized in a ``sconscript.local`` +script. The library integrity can be verified by executing unit tests with +``scons test`` (requires the CxxTest framework). + +See also the `instructions for compiling and modifying source code in development mode `_. + +To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit +hooks. + +1. Install pre-commit in your working environment by running ``conda install pre-commit``. + +2. Initialize pre-commit (one time only) ``pre-commit install``. + +Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. +If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should +pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before +trying to commit again. + +Improvements and fixes are always appreciated. + +Before contributing, please read our `Code of Conduct `_. + +Contact +------- + +For more information on libdiffpy please visit the project `web-page `_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu)``. + +Acknowledgements +---------------- + +libdiffpy is an open-source software developed as a part of the +DiffPy-CMI complex modeling initiative at the Brookhaven National +Laboratory. + +``libdiffpy`` is built and maintained with `scikit-package `_. diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh deleted file mode 100644 index 591d6c57..00000000 --- a/conda-recipe/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash - -MYNCPU=$(( (CPU_COUNT > 8) ? 8 : CPU_COUNT )) - -# drop linker flags that spuriously remove linkage with libgslcblas -LDFLAGS="${LDFLAGS/-Wl,-dead_strip_dylibs/}" - -# Apply sconscript.local customizations. -cp ${RECIPE_DIR}/sconscript.local ./ - -# Build and install the library. -scons -j $MYNCPU lib install prefix=$PREFIX diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml deleted file mode 100644 index 30b82637..00000000 --- a/conda-recipe/conda_build_config.yaml +++ /dev/null @@ -1,11 +0,0 @@ -libobjcryst: - - 2026.3.* - -gsl: - - 2.8 - -boost: - - 1.88 - -pin_run_as_build: - libboost: x.x diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml deleted file mode 100644 index e5fd1eb5..00000000 --- a/conda-recipe/meta.yaml +++ /dev/null @@ -1,51 +0,0 @@ -{% set setupdata = load_setup_py_data(from_recipe_dir=True) %} - -package: - name: libdiffpy - version: {{ setupdata['version'] }} - -source: - # git_url: https://github.com/diffpy/libdiffpy.git - git_url: .. - -build: - number: 0 - run_exports: - - {{ pin_subpackage('libdiffpy', max_pin='x.x') }} - -requirements: - build: - - {{ compiler('cxx') }} - - python - - scons - host: - - libboost {{ boost }} - - gsl {{ gsl }} - - libobjcryst {{ libobjcryst }} - - run: - # NOTE libobjcryst is implicitly added by libobjcryst run_exports - - libboost - - {{ pin_compatible('gsl', min_pin='x.x', max_pin='x') }} - -test: - requires: - - {{ compiler('cxx') }} - - cxxtest - - scons - - source_files: - - SConstruct - - site_scons/ - - src/SConscript - - src/SConscript.configure - - src/tests/ - - # commands: - # Execute the run_test.sh script. - -about: - home: https://github.com/diffpy/libdiffpy - summary: C++ calculators of PDF, bond valence sum and other pair quantities. - license: Modified BSD License - license_file: LICENSE.txt diff --git a/conda-recipe/run_test.sh b/conda-recipe/run_test.sh deleted file mode 100644 index ae0d976d..00000000 --- a/conda-recipe/run_test.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -export CPATH="${PREFIX}/include:${CPATH}" -export LIBRARY_PATH="${PREFIX}/lib:${LIBRARY_PATH}" - -MYNCPU=$(( (CPU_COUNT > 8) ? 8 : CPU_COUNT )) - -# Apply sconscript.local customizations. -cp ${RECIPE_DIR}/sconscript.local ./ - -# Build the unit tests program using the installed library. -scons -j $MYNCPU alltests prefix=$PREFIX test_installed=true - -# Execute the unit tests. -MYALLTESTSFAST=$(ls -t ${PWD}/build/fast*/tests/alltests | head -1) -${MYALLTESTSFAST} diff --git a/conda-recipe/sconscript.local b/conda-recipe/sconscript.local deleted file mode 100644 index f8740395..00000000 --- a/conda-recipe/sconscript.local +++ /dev/null @@ -1,18 +0,0 @@ -# Customize scons build environment. - -Import('env') - -import os - -# Apply environment settings for Anaconda compilers -env.Replace(CXX=os.environ['CXX']) -env.MergeFlags(os.environ['CFLAGS']) -env.MergeFlags(os.environ['CPPFLAGS']) -env.MergeFlags(os.environ['CXXFLAGS']) -env.MergeFlags(os.environ['LDFLAGS']) - -# Silence copious warnings from the boost headers. -P = os.environ['PREFIX'] -env.Prepend(CCFLAGS=['-isystem{}/include'.format(P)]) - -# vim: ft=python diff --git a/conda-recipe/setup.py b/conda-recipe/setup.py deleted file mode 100644 index e03b9486..00000000 --- a/conda-recipe/setup.py +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env python - -"""\ -Dummy distutils setup script that provides version data for meta.yaml. -""" - -import os -import sys -from distutils.core import setup - -MYDIR = os.path.dirname(os.path.abspath(__file__)) -SITESCONSDIR = os.path.abspath(os.path.join(MYDIR, '../site_scons')) -sys.path.insert(0, SITESCONSDIR) - -from libdiffpybuildutils import gitinfo - -ginfo = gitinfo() - -setup( - name='libdiffpy', - version=ginfo['version'], -) diff --git a/cookiecutter.json b/cookiecutter.json new file mode 100644 index 00000000..1158d18a --- /dev/null +++ b/cookiecutter.json @@ -0,0 +1,20 @@ +{ + "author_names": "Simon Billinge", + "author_emails": "sbillinge@ucsb.edu", + "maintainer_names": "Simon Billinge", + "maintainer_emails": "sbillinge@ucsb.edu", + "maintainer_github_usernames": "sbillinge", + "contributors": "Pavol Juhas, Chris Farrow, Simon Billinge, Billinge Group members", + "project_name": "libdiffpy", + "license_holders": "libdiffpy contributors", + "github_username_or_orgname": "diffpy", + "github_repo_name": "libdiffpy", + "conda_pypi_package_dist_name": "libdiffpy", + "package_dir_name": "libdiffpy", + "project_short_description": "DiffPy C++ library for calculation of PDF and other real-space quantities", + "project_keywords": "diffraction, PDF, X-ray, neutron", + "minimum_supported_python_version": "3.12", + "maximum_supported_python_version": "3.14", + "project_needs_c_code_compiled": "Yes", + "project_has_gui_tests": "No" +} diff --git a/doc/manual/source/release.rst b/doc/manual/source/release.rst index 7ec4f81d..2f0bd47f 100644 --- a/doc/manual/source/release.rst +++ b/doc/manual/source/release.rst @@ -1,3 +1,3 @@ .. index:: release notes -.. mdinclude:: ../../../CHANGELOG.md +.. include:: ../../../CHANGELOG.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..8234d806 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,194 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build +BASENAME = $(subst .,,$(subst $() $(),,libdiffpy)) + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(BASENAME).qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +# Manual publishing to the gh-pages branch + +GITREPOPATH = $(shell cd $(CURDIR) && git rev-parse --git-dir) +GITREMOTE = origin +GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url) +GITLASTCOMMIT = $(shell git rev-parse --short HEAD) + +publish: + @test -d build/html || \ + ( echo >&2 "Run 'make html' first!"; false ) + git show-ref --verify --quiet refs/heads/gh-pages || \ + git branch --track gh-pages $(GITREMOTE)/gh-pages + test -d build/gh-pages || \ + git clone -s -b gh-pages $(GITREPOPATH) build/gh-pages + cd build/gh-pages && \ + git pull $(GITREMOTEURL) gh-pages + rsync -acv --delete --exclude=.git --exclude=.rsync-exclude \ + --exclude-from=build/gh-pages/.rsync-exclude \ + --link-dest=$(CURDIR)/build/html build/html/ build/gh-pages/ + cd build/gh-pages && \ + git add --all . && \ + git diff --cached --quiet || \ + git commit -m "Sync with the source at $(GITLASTCOMMIT)." + cd build/gh-pages && \ + git push origin gh-pages diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..2be83069 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,36 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build +set SPHINXPROJ=PackagingScientificPython + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% + +:end +popd diff --git a/docs/source/_static/.placeholder b/docs/source/_static/.placeholder new file mode 100644 index 00000000..e69de29b diff --git a/docs/source/api/libdiffpy.rst b/docs/source/api/libdiffpy.rst new file mode 100644 index 00000000..3f7fdd00 --- /dev/null +++ b/docs/source/api/libdiffpy.rst @@ -0,0 +1,11 @@ +:tocdepth: -1 + +|title| +======= + +.. |title| replace:: libdiffpy package + +.. automodule:: libdiffpy + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 00000000..051bfb53 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,322 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# libdiffpy documentation build configuration file, created by # noqa: E501 +# sphinx-quickstart on Thu Jan 30 15:49:41 2014. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import time +from importlib.metadata import version +from pathlib import Path + +# Attempt to import the version dynamically from GitHub tag. +try: + fullversion = version("libdiffpy") +except Exception: + fullversion = "No version found. The correct version will appear in the released version." # noqa: E501 + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use Path().resolve() to make it absolute, like shown here. # noqa: E501 +# sys.path.insert(0, str(Path(".").resolve())) +sys.path.insert(0, str(Path("../..").resolve())) +sys.path.insert(0, str(Path("../../src").resolve())) + +# abbreviations +ab_authors = "Pavol Juhas, Chris Farrow, Simon Billinge, Billinge Group members" + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinx_rtd_theme", + "sphinx_copybutton", + "m2r2", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = [".rst", ".md"] + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "libdiffpy" +copyright = "%Y, libdiffpy contributors" + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. + +# The short X.Y version. +version = "".join(fullversion.split(".post")[:1]) +# The full version, including alpha/beta/rc tags. +release = fullversion + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +today = time.strftime("%B %d, %Y", time.localtime()) +year = today.split()[-1] +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' +# substitute YEAR in the copyright string +copyright = copyright.replace("%Y", year) + +# For sphinx_copybutton extension. +# Do not copy "$" for shell commands in code-blocks. +copybutton_prompt_text = r"^\$ " +copybutton_prompt_is_regexp = True + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ["build"] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# A list of ignored prefixes for module index sorting. +modindex_common_prefix = ["libdiffpy"] + +# Display all warnings for missing links. +nitpicky = True + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_rtd_theme" + +html_context = { + "display_github": True, + "github_user": "diffpy", + "github_repo": "libdiffpy", + "github_version": "main", + "conf_py_path": "/docs/source/", +} + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# +html_theme_options = { + "navigation_with_keys": "true", +} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +# html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +basename = "libdiffpy".replace(" ", "").replace(".", "") +htmlhelp_basename = basename + "doc" + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # 'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + # 'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + # 'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ( + "index", + "libdiffpy.tex", + "libdiffpy Documentation", + ab_authors, + "manual", + ), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ( + "index", + "libdiffpy", + "libdiffpy Documentation", + ab_authors, + 1, + ) +] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ( + "index", + "libdiffpy", + "libdiffpy Documentation", + ab_authors, + "libdiffpy", + "One line description of project.", + "Miscellaneous", + ), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + + +# Example configuration for intersphinx: refer to the Python standard library. +# intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/docs/source/img/.placeholder b/docs/source/img/.placeholder new file mode 100644 index 00000000..e69de29b diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 00000000..e80726b5 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,47 @@ +####### +|title| +####### + +.. |title| replace:: libdiffpy documentation + +``libdiffpy`` - DiffPy C++ library for calculation of PDF and other real-space quantities + +| Software version |release| +| Last updated |today|. + +======= +Authors +======= + +``libdiffpy`` is developed by Pavol Juhas, Chris Farrow, Simon Billinge, Billinge Group members. This project is maintained by Simon Billinge. For a detailed list of contributors see +https://github.com/diffpy/libdiffpy/graphs/contributors. + +============ +Installation +============ + +See the `README `_ +file included with the distribution. + +================ +Acknowledgements +================ + +``libdiffpy`` is built and maintained with `scikit-package `_. + +================= +Table of contents +================= +.. toctree:: + :maxdepth: 2 + + Package API + release + license + +======= +Indices +======= + +* :ref:`genindex` +* :ref:`search` diff --git a/docs/source/license.rst b/docs/source/license.rst new file mode 100644 index 00000000..75f32ed6 --- /dev/null +++ b/docs/source/license.rst @@ -0,0 +1,38 @@ +:tocdepth: -1 + +.. index:: license + +License +####### + +OPEN SOURCE LICENSE AGREEMENT +============================= +BSD 3-Clause License + +Copyright (c) 2026, libdiffpy contributors. +All Rights Reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/docs/source/release.rst b/docs/source/release.rst new file mode 100644 index 00000000..27cd0cc9 --- /dev/null +++ b/docs/source/release.rst @@ -0,0 +1,5 @@ +:tocdepth: -1 + +.. index:: release notes + +.. include:: ../../CHANGELOG.rst diff --git a/docs/source/snippets/.placeholder b/docs/source/snippets/.placeholder new file mode 100644 index 00000000..e69de29b diff --git a/news/TEMPLATE.rst b/news/TEMPLATE.rst new file mode 100644 index 00000000..790d30b1 --- /dev/null +++ b/news/TEMPLATE.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..8cfa9203 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,32 @@ +[tool.codespell] +exclude-file = ".codespell/ignore_lines.txt" +ignore-words = ".codespell/ignore_words.txt" +skip = "*.cif,*.dat" + +[tool.docformatter] +recursive = true +wrap-summaries = 72 +wrap-descriptions = 72 + +[tool.black] +line-length = 79 +include = '\.pyi?$' +exclude = ''' +/( + \.git + | \.hg + | \.mypy_cache + | \.tox + | \.venv + | \.rst + | \.txt + | _build + | buck-out + | build + | dist + + # The following are specific to Black, you probably don't want those. + | blib2to3 + | tests/data +)/ +''' diff --git a/requirements/build.txt b/requirements/build.txt new file mode 100644 index 00000000..802684b1 --- /dev/null +++ b/requirements/build.txt @@ -0,0 +1,2 @@ +cxx-compiler +scons diff --git a/requirements/conda.txt b/requirements/conda.txt new file mode 100644 index 00000000..78514c11 --- /dev/null +++ b/requirements/conda.txt @@ -0,0 +1,3 @@ +libboost-devel +gsl +libobjcryst diff --git a/requirements/docs.txt b/requirements/docs.txt new file mode 100644 index 00000000..1de813f9 --- /dev/null +++ b/requirements/docs.txt @@ -0,0 +1,5 @@ +sphinx +sphinx_rtd_theme +sphinx-copybutton +doctr +m2r2 diff --git a/requirements/tests.txt b/requirements/tests.txt new file mode 100644 index 00000000..a5570111 --- /dev/null +++ b/requirements/tests.txt @@ -0,0 +1,2 @@ +cxxtest +gcovr diff --git a/src/diffpy/Attributes.cpp b/src/diffpy/Attributes.cpp index ab2db890..f555863a 100644 --- a/src/diffpy/Attributes.cpp +++ b/src/diffpy/Attributes.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/Attributes.hpp b/src/diffpy/Attributes.hpp index 31e1e180..af4c074c 100644 --- a/src/diffpy/Attributes.hpp +++ b/src/diffpy/Attributes.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/Attributes.ipp b/src/diffpy/Attributes.ipp index 005c8e31..e35a3ba0 100644 --- a/src/diffpy/Attributes.ipp +++ b/src/diffpy/Attributes.ipp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/EventTicker.cpp b/src/diffpy/EventTicker.cpp index 5caf20fb..c2d30c3e 100644 --- a/src/diffpy/EventTicker.cpp +++ b/src/diffpy/EventTicker.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/EventTicker.hpp b/src/diffpy/EventTicker.hpp index 54d11ef7..cbe394fa 100644 --- a/src/diffpy/EventTicker.hpp +++ b/src/diffpy/EventTicker.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/HasClassRegistry.hpp b/src/diffpy/HasClassRegistry.hpp index 538bd0ad..87832b18 100644 --- a/src/diffpy/HasClassRegistry.hpp +++ b/src/diffpy/HasClassRegistry.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/HasClassRegistry.ipp b/src/diffpy/HasClassRegistry.ipp index afc744c8..10577942 100644 --- a/src/diffpy/HasClassRegistry.ipp +++ b/src/diffpy/HasClassRegistry.ipp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/features.tpl b/src/diffpy/features.tpl index da1e913d..526bdf5f 100644 --- a/src/diffpy/features.tpl +++ b/src/diffpy/features.tpl @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/mathutils.hpp b/src/diffpy/mathutils.hpp index 46894afd..bce53a2a 100644 --- a/src/diffpy/mathutils.hpp +++ b/src/diffpy/mathutils.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/mathutils.ipp b/src/diffpy/mathutils.ipp index c4fc0a44..4181895e 100644 --- a/src/diffpy/mathutils.ipp +++ b/src/diffpy/mathutils.ipp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/runtimepath.cpp b/src/diffpy/runtimepath.cpp index be9bb00a..05551408 100644 --- a/src/diffpy/runtimepath.cpp +++ b/src/diffpy/runtimepath.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/runtimepath.hpp b/src/diffpy/runtimepath.hpp index c894122f..587516c7 100644 --- a/src/diffpy/runtimepath.hpp +++ b/src/diffpy/runtimepath.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/serialization.hpp b/src/diffpy/serialization.hpp index 9d80d14d..e8433ab6 100644 --- a/src/diffpy/serialization.hpp +++ b/src/diffpy/serialization.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/serialization.ipp b/src/diffpy/serialization.ipp index f73d1f6f..f9e6b342 100644 --- a/src/diffpy/serialization.ipp +++ b/src/diffpy/serialization.ipp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/AtomRadiiTable.cpp b/src/diffpy/srreal/AtomRadiiTable.cpp index 20995f69..a28225c2 100644 --- a/src/diffpy/srreal/AtomRadiiTable.cpp +++ b/src/diffpy/srreal/AtomRadiiTable.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/AtomRadiiTable.hpp b/src/diffpy/srreal/AtomRadiiTable.hpp index 830adc40..45af7a72 100644 --- a/src/diffpy/srreal/AtomRadiiTable.hpp +++ b/src/diffpy/srreal/AtomRadiiTable.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/AtomUtils.cpp b/src/diffpy/srreal/AtomUtils.cpp index 37cd41ac..bc39cbed 100644 --- a/src/diffpy/srreal/AtomUtils.cpp +++ b/src/diffpy/srreal/AtomUtils.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/AtomUtils.hpp b/src/diffpy/srreal/AtomUtils.hpp index 30071147..346d7c97 100644 --- a/src/diffpy/srreal/AtomUtils.hpp +++ b/src/diffpy/srreal/AtomUtils.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/AtomicStructureAdapter.cpp b/src/diffpy/srreal/AtomicStructureAdapter.cpp index d4856c81..6d432820 100644 --- a/src/diffpy/srreal/AtomicStructureAdapter.cpp +++ b/src/diffpy/srreal/AtomicStructureAdapter.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/AtomicStructureAdapter.hpp b/src/diffpy/srreal/AtomicStructureAdapter.hpp index e6eb22fa..248d1b11 100644 --- a/src/diffpy/srreal/AtomicStructureAdapter.hpp +++ b/src/diffpy/srreal/AtomicStructureAdapter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BVParam.cpp b/src/diffpy/srreal/BVParam.cpp index 74601708..9db906bd 100644 --- a/src/diffpy/srreal/BVParam.cpp +++ b/src/diffpy/srreal/BVParam.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BVParam.hpp b/src/diffpy/srreal/BVParam.hpp index 061fb98c..ced19a5f 100644 --- a/src/diffpy/srreal/BVParam.hpp +++ b/src/diffpy/srreal/BVParam.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BVParametersTable.cpp b/src/diffpy/srreal/BVParametersTable.cpp index 896cd463..2d53afe4 100644 --- a/src/diffpy/srreal/BVParametersTable.cpp +++ b/src/diffpy/srreal/BVParametersTable.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BVParametersTable.hpp b/src/diffpy/srreal/BVParametersTable.hpp index 9a900f4e..7fd6fb92 100644 --- a/src/diffpy/srreal/BVParametersTable.hpp +++ b/src/diffpy/srreal/BVParametersTable.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BVSCalculator.cpp b/src/diffpy/srreal/BVSCalculator.cpp index 44e5de46..0b3d07ce 100644 --- a/src/diffpy/srreal/BVSCalculator.cpp +++ b/src/diffpy/srreal/BVSCalculator.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BVSCalculator.hpp b/src/diffpy/srreal/BVSCalculator.hpp index c864b31b..86a6f7aa 100644 --- a/src/diffpy/srreal/BVSCalculator.hpp +++ b/src/diffpy/srreal/BVSCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BaseBondGenerator.cpp b/src/diffpy/srreal/BaseBondGenerator.cpp index 6fa3b002..c4374ea2 100644 --- a/src/diffpy/srreal/BaseBondGenerator.cpp +++ b/src/diffpy/srreal/BaseBondGenerator.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BaseBondGenerator.hpp b/src/diffpy/srreal/BaseBondGenerator.hpp index 691c4666..bcee24c4 100644 --- a/src/diffpy/srreal/BaseBondGenerator.hpp +++ b/src/diffpy/srreal/BaseBondGenerator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BaseDebyeSum.cpp b/src/diffpy/srreal/BaseDebyeSum.cpp index e4165694..b60b33c5 100644 --- a/src/diffpy/srreal/BaseDebyeSum.cpp +++ b/src/diffpy/srreal/BaseDebyeSum.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BaseDebyeSum.hpp b/src/diffpy/srreal/BaseDebyeSum.hpp index 5eaea6f5..e70f98df 100644 --- a/src/diffpy/srreal/BaseDebyeSum.hpp +++ b/src/diffpy/srreal/BaseDebyeSum.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BondCalculator.cpp b/src/diffpy/srreal/BondCalculator.cpp index 21e8435a..958a0872 100644 --- a/src/diffpy/srreal/BondCalculator.cpp +++ b/src/diffpy/srreal/BondCalculator.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/BondCalculator.hpp b/src/diffpy/srreal/BondCalculator.hpp index 49c6876f..50aa5799 100644 --- a/src/diffpy/srreal/BondCalculator.hpp +++ b/src/diffpy/srreal/BondCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ConstantPeakWidth.cpp b/src/diffpy/srreal/ConstantPeakWidth.cpp index 32b8bc78..599ca85b 100644 --- a/src/diffpy/srreal/ConstantPeakWidth.cpp +++ b/src/diffpy/srreal/ConstantPeakWidth.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ConstantPeakWidth.hpp b/src/diffpy/srreal/ConstantPeakWidth.hpp index 8c0f552b..a1edceb8 100644 --- a/src/diffpy/srreal/ConstantPeakWidth.hpp +++ b/src/diffpy/srreal/ConstantPeakWidth.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ConstantRadiiTable.cpp b/src/diffpy/srreal/ConstantRadiiTable.cpp index 4a1e3130..ba1145e0 100644 --- a/src/diffpy/srreal/ConstantRadiiTable.cpp +++ b/src/diffpy/srreal/ConstantRadiiTable.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ConstantRadiiTable.hpp b/src/diffpy/srreal/ConstantRadiiTable.hpp index 5a047c75..f2f04684 100644 --- a/src/diffpy/srreal/ConstantRadiiTable.hpp +++ b/src/diffpy/srreal/ConstantRadiiTable.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/CroppedGaussianProfile.cpp b/src/diffpy/srreal/CroppedGaussianProfile.cpp index aabdba0e..19fe7468 100644 --- a/src/diffpy/srreal/CroppedGaussianProfile.cpp +++ b/src/diffpy/srreal/CroppedGaussianProfile.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/CroppedGaussianProfile.hpp b/src/diffpy/srreal/CroppedGaussianProfile.hpp index ed1573ea..a1a92890 100644 --- a/src/diffpy/srreal/CroppedGaussianProfile.hpp +++ b/src/diffpy/srreal/CroppedGaussianProfile.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/CrystalStructureAdapter.cpp b/src/diffpy/srreal/CrystalStructureAdapter.cpp index 6d51c2ed..38ceda6c 100644 --- a/src/diffpy/srreal/CrystalStructureAdapter.cpp +++ b/src/diffpy/srreal/CrystalStructureAdapter.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/CrystalStructureAdapter.hpp b/src/diffpy/srreal/CrystalStructureAdapter.hpp index 423ef48e..767aa805 100644 --- a/src/diffpy/srreal/CrystalStructureAdapter.hpp +++ b/src/diffpy/srreal/CrystalStructureAdapter.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/DebyePDFCalculator.cpp b/src/diffpy/srreal/DebyePDFCalculator.cpp index d77198ec..e200755d 100644 --- a/src/diffpy/srreal/DebyePDFCalculator.cpp +++ b/src/diffpy/srreal/DebyePDFCalculator.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas, Chris Farrow * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/DebyePDFCalculator.hpp b/src/diffpy/srreal/DebyePDFCalculator.hpp index 512e2884..e23b2b5c 100644 --- a/src/diffpy/srreal/DebyePDFCalculator.hpp +++ b/src/diffpy/srreal/DebyePDFCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas, Chris Farrow * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/DebyeWallerPeakWidth.cpp b/src/diffpy/srreal/DebyeWallerPeakWidth.cpp index 10c6bfe6..bb82a6a3 100644 --- a/src/diffpy/srreal/DebyeWallerPeakWidth.cpp +++ b/src/diffpy/srreal/DebyeWallerPeakWidth.cpp @@ -7,7 +7,7 @@ * * File coded by: Christopher Farrow, Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/DebyeWallerPeakWidth.hpp b/src/diffpy/srreal/DebyeWallerPeakWidth.hpp index c900f7f1..7f4a5b08 100644 --- a/src/diffpy/srreal/DebyeWallerPeakWidth.hpp +++ b/src/diffpy/srreal/DebyeWallerPeakWidth.hpp @@ -7,7 +7,7 @@ * * File coded by: Christopher Farrow, Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/EmptyStructureAdapter.cpp b/src/diffpy/srreal/EmptyStructureAdapter.cpp index a5606acb..1dc5b2a5 100644 --- a/src/diffpy/srreal/EmptyStructureAdapter.cpp +++ b/src/diffpy/srreal/EmptyStructureAdapter.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/GaussianProfile.cpp b/src/diffpy/srreal/GaussianProfile.cpp index 97622474..3b833752 100644 --- a/src/diffpy/srreal/GaussianProfile.cpp +++ b/src/diffpy/srreal/GaussianProfile.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/GaussianProfile.hpp b/src/diffpy/srreal/GaussianProfile.hpp index 21b65b65..8885e9bc 100644 --- a/src/diffpy/srreal/GaussianProfile.hpp +++ b/src/diffpy/srreal/GaussianProfile.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/JeongPeakWidth.cpp b/src/diffpy/srreal/JeongPeakWidth.cpp index 7cd9679e..ca2ef297 100644 --- a/src/diffpy/srreal/JeongPeakWidth.cpp +++ b/src/diffpy/srreal/JeongPeakWidth.cpp @@ -7,7 +7,7 @@ * * File coded by: Christopher Farrow, Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/JeongPeakWidth.hpp b/src/diffpy/srreal/JeongPeakWidth.hpp index 1acd9a19..f1606b8b 100644 --- a/src/diffpy/srreal/JeongPeakWidth.hpp +++ b/src/diffpy/srreal/JeongPeakWidth.hpp @@ -7,7 +7,7 @@ * * File coded by: Christopher Farrow, Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/Lattice.cpp b/src/diffpy/srreal/Lattice.cpp index 6fd171d4..3b62e841 100644 --- a/src/diffpy/srreal/Lattice.cpp +++ b/src/diffpy/srreal/Lattice.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/Lattice.hpp b/src/diffpy/srreal/Lattice.hpp index 4e9146c5..b7304662 100644 --- a/src/diffpy/srreal/Lattice.hpp +++ b/src/diffpy/srreal/Lattice.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/LinearBaseline.cpp b/src/diffpy/srreal/LinearBaseline.cpp index 861d82a3..42475228 100644 --- a/src/diffpy/srreal/LinearBaseline.cpp +++ b/src/diffpy/srreal/LinearBaseline.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/LinearBaseline.hpp b/src/diffpy/srreal/LinearBaseline.hpp index ab86aa7a..a4176fd6 100644 --- a/src/diffpy/srreal/LinearBaseline.hpp +++ b/src/diffpy/srreal/LinearBaseline.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/NoMetaStructureAdapter.cpp b/src/diffpy/srreal/NoMetaStructureAdapter.cpp index f5d7366c..1675ed78 100644 --- a/src/diffpy/srreal/NoMetaStructureAdapter.cpp +++ b/src/diffpy/srreal/NoMetaStructureAdapter.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/NoMetaStructureAdapter.hpp b/src/diffpy/srreal/NoMetaStructureAdapter.hpp index da454fcc..c5296a90 100644 --- a/src/diffpy/srreal/NoMetaStructureAdapter.hpp +++ b/src/diffpy/srreal/NoMetaStructureAdapter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/NoSymmetryStructureAdapter.cpp b/src/diffpy/srreal/NoSymmetryStructureAdapter.cpp index 1502f63b..ac7d7781 100644 --- a/src/diffpy/srreal/NoSymmetryStructureAdapter.cpp +++ b/src/diffpy/srreal/NoSymmetryStructureAdapter.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/NoSymmetryStructureAdapter.hpp b/src/diffpy/srreal/NoSymmetryStructureAdapter.hpp index 5d8d87c4..4f9561e4 100644 --- a/src/diffpy/srreal/NoSymmetryStructureAdapter.hpp +++ b/src/diffpy/srreal/NoSymmetryStructureAdapter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ObjCrystStructureAdapter.cpp b/src/diffpy/srreal/ObjCrystStructureAdapter.cpp index 2b5e5660..bee38875 100644 --- a/src/diffpy/srreal/ObjCrystStructureAdapter.cpp +++ b/src/diffpy/srreal/ObjCrystStructureAdapter.cpp @@ -7,7 +7,7 @@ * * File coded by: Chris Farrow * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ObjCrystStructureAdapter.hpp b/src/diffpy/srreal/ObjCrystStructureAdapter.hpp index 0cb21cc7..77268c78 100644 --- a/src/diffpy/srreal/ObjCrystStructureAdapter.hpp +++ b/src/diffpy/srreal/ObjCrystStructureAdapter.hpp @@ -7,7 +7,7 @@ * * File coded by: Chris Farrow * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/OverlapCalculator.cpp b/src/diffpy/srreal/OverlapCalculator.cpp index 4fc638a9..2bf0360c 100644 --- a/src/diffpy/srreal/OverlapCalculator.cpp +++ b/src/diffpy/srreal/OverlapCalculator.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/OverlapCalculator.hpp b/src/diffpy/srreal/OverlapCalculator.hpp index 0a6b5763..820b9f9a 100644 --- a/src/diffpy/srreal/OverlapCalculator.hpp +++ b/src/diffpy/srreal/OverlapCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFBaseline.cpp b/src/diffpy/srreal/PDFBaseline.cpp index 96525875..1c4938f6 100644 --- a/src/diffpy/srreal/PDFBaseline.cpp +++ b/src/diffpy/srreal/PDFBaseline.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFBaseline.hpp b/src/diffpy/srreal/PDFBaseline.hpp index 5329828f..bed16f07 100644 --- a/src/diffpy/srreal/PDFBaseline.hpp +++ b/src/diffpy/srreal/PDFBaseline.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFCalculator.cpp b/src/diffpy/srreal/PDFCalculator.cpp index 47c7189a..262b4cbf 100644 --- a/src/diffpy/srreal/PDFCalculator.cpp +++ b/src/diffpy/srreal/PDFCalculator.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFCalculator.hpp b/src/diffpy/srreal/PDFCalculator.hpp index 79220e0a..9a96b8f1 100644 --- a/src/diffpy/srreal/PDFCalculator.hpp +++ b/src/diffpy/srreal/PDFCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFEnvelope.cpp b/src/diffpy/srreal/PDFEnvelope.cpp index 04023176..8c646107 100644 --- a/src/diffpy/srreal/PDFEnvelope.cpp +++ b/src/diffpy/srreal/PDFEnvelope.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFEnvelope.hpp b/src/diffpy/srreal/PDFEnvelope.hpp index f7035737..5e82036d 100644 --- a/src/diffpy/srreal/PDFEnvelope.hpp +++ b/src/diffpy/srreal/PDFEnvelope.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFUtils.cpp b/src/diffpy/srreal/PDFUtils.cpp index 37a50b67..1a4c540b 100644 --- a/src/diffpy/srreal/PDFUtils.cpp +++ b/src/diffpy/srreal/PDFUtils.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFUtils.hpp b/src/diffpy/srreal/PDFUtils.hpp index 97e2764a..64cb8c86 100644 --- a/src/diffpy/srreal/PDFUtils.hpp +++ b/src/diffpy/srreal/PDFUtils.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PDFUtils.ipp b/src/diffpy/srreal/PDFUtils.ipp index 28d62b5c..26f64b7d 100644 --- a/src/diffpy/srreal/PDFUtils.ipp +++ b/src/diffpy/srreal/PDFUtils.ipp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PQEvaluator.cpp b/src/diffpy/srreal/PQEvaluator.cpp index 71874053..df3b13bd 100644 --- a/src/diffpy/srreal/PQEvaluator.cpp +++ b/src/diffpy/srreal/PQEvaluator.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PQEvaluator.hpp b/src/diffpy/srreal/PQEvaluator.hpp index f446517b..315125f7 100644 --- a/src/diffpy/srreal/PQEvaluator.hpp +++ b/src/diffpy/srreal/PQEvaluator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PairCounter.cpp b/src/diffpy/srreal/PairCounter.cpp index e11c9f91..02e416be 100644 --- a/src/diffpy/srreal/PairCounter.cpp +++ b/src/diffpy/srreal/PairCounter.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PairCounter.hpp b/src/diffpy/srreal/PairCounter.hpp index eef4b92a..6461bff5 100644 --- a/src/diffpy/srreal/PairCounter.hpp +++ b/src/diffpy/srreal/PairCounter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PairQuantity.cpp b/src/diffpy/srreal/PairQuantity.cpp index f420df5d..178c6815 100644 --- a/src/diffpy/srreal/PairQuantity.cpp +++ b/src/diffpy/srreal/PairQuantity.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PairQuantity.hpp b/src/diffpy/srreal/PairQuantity.hpp index b80086ec..ffdf41ac 100644 --- a/src/diffpy/srreal/PairQuantity.hpp +++ b/src/diffpy/srreal/PairQuantity.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PeakProfile.cpp b/src/diffpy/srreal/PeakProfile.cpp index ced61f2b..fdb66200 100644 --- a/src/diffpy/srreal/PeakProfile.cpp +++ b/src/diffpy/srreal/PeakProfile.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PeakProfile.hpp b/src/diffpy/srreal/PeakProfile.hpp index 8f6d4e14..d6fd9ad8 100644 --- a/src/diffpy/srreal/PeakProfile.hpp +++ b/src/diffpy/srreal/PeakProfile.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PeakWidthModel.cpp b/src/diffpy/srreal/PeakWidthModel.cpp index 0418d9e1..999209e8 100644 --- a/src/diffpy/srreal/PeakWidthModel.cpp +++ b/src/diffpy/srreal/PeakWidthModel.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PeakWidthModel.hpp b/src/diffpy/srreal/PeakWidthModel.hpp index 25a589bf..7db9ac70 100644 --- a/src/diffpy/srreal/PeakWidthModel.hpp +++ b/src/diffpy/srreal/PeakWidthModel.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PeriodicStructureAdapter.cpp b/src/diffpy/srreal/PeriodicStructureAdapter.cpp index 29bd4da5..29a20fce 100644 --- a/src/diffpy/srreal/PeriodicStructureAdapter.cpp +++ b/src/diffpy/srreal/PeriodicStructureAdapter.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/PeriodicStructureAdapter.hpp b/src/diffpy/srreal/PeriodicStructureAdapter.hpp index 0d783515..ed540e1c 100644 --- a/src/diffpy/srreal/PeriodicStructureAdapter.hpp +++ b/src/diffpy/srreal/PeriodicStructureAdapter.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/PointsInSphere.cpp b/src/diffpy/srreal/PointsInSphere.cpp index 88c24ef5..4b732026 100644 --- a/src/diffpy/srreal/PointsInSphere.cpp +++ b/src/diffpy/srreal/PointsInSphere.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/PointsInSphere.hpp b/src/diffpy/srreal/PointsInSphere.hpp index 40451aad..27da5b61 100644 --- a/src/diffpy/srreal/PointsInSphere.hpp +++ b/src/diffpy/srreal/PointsInSphere.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/QResolutionEnvelope.cpp b/src/diffpy/srreal/QResolutionEnvelope.cpp index 53049a23..c20d3642 100644 --- a/src/diffpy/srreal/QResolutionEnvelope.cpp +++ b/src/diffpy/srreal/QResolutionEnvelope.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/QResolutionEnvelope.hpp b/src/diffpy/srreal/QResolutionEnvelope.hpp index dccb3b37..52421fc8 100644 --- a/src/diffpy/srreal/QResolutionEnvelope.hpp +++ b/src/diffpy/srreal/QResolutionEnvelope.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/QuantityType.hpp b/src/diffpy/srreal/QuantityType.hpp index 11a1f678..07dda8d7 100644 --- a/src/diffpy/srreal/QuantityType.hpp +++ b/src/diffpy/srreal/QuantityType.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/R3linalg.cpp b/src/diffpy/srreal/R3linalg.cpp index 19a70cc7..c3473a67 100644 --- a/src/diffpy/srreal/R3linalg.cpp +++ b/src/diffpy/srreal/R3linalg.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/R3linalg.hpp b/src/diffpy/srreal/R3linalg.hpp index bffd5c7c..8cd07dbc 100644 --- a/src/diffpy/srreal/R3linalg.hpp +++ b/src/diffpy/srreal/R3linalg.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTElectron.cpp b/src/diffpy/srreal/SFTElectron.cpp index 556aedea..d85bc661 100644 --- a/src/diffpy/srreal/SFTElectron.cpp +++ b/src/diffpy/srreal/SFTElectron.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTElectron.hpp b/src/diffpy/srreal/SFTElectron.hpp index 86b158dd..f77cd34d 100644 --- a/src/diffpy/srreal/SFTElectron.hpp +++ b/src/diffpy/srreal/SFTElectron.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTElectronNumber.cpp b/src/diffpy/srreal/SFTElectronNumber.cpp index 47f65d8e..a200171c 100644 --- a/src/diffpy/srreal/SFTElectronNumber.cpp +++ b/src/diffpy/srreal/SFTElectronNumber.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTElectronNumber.hpp b/src/diffpy/srreal/SFTElectronNumber.hpp index 3736861b..306d1d9d 100644 --- a/src/diffpy/srreal/SFTElectronNumber.hpp +++ b/src/diffpy/srreal/SFTElectronNumber.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTNeutron.cpp b/src/diffpy/srreal/SFTNeutron.cpp index 96d9af20..72ec80c3 100644 --- a/src/diffpy/srreal/SFTNeutron.cpp +++ b/src/diffpy/srreal/SFTNeutron.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTNeutron.hpp b/src/diffpy/srreal/SFTNeutron.hpp index d2264dc6..a2fb2ad3 100644 --- a/src/diffpy/srreal/SFTNeutron.hpp +++ b/src/diffpy/srreal/SFTNeutron.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTXray.cpp b/src/diffpy/srreal/SFTXray.cpp index 9d24562a..3b589b93 100644 --- a/src/diffpy/srreal/SFTXray.cpp +++ b/src/diffpy/srreal/SFTXray.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SFTXray.hpp b/src/diffpy/srreal/SFTXray.hpp index 833ff611..e29d27de 100644 --- a/src/diffpy/srreal/SFTXray.hpp +++ b/src/diffpy/srreal/SFTXray.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ScaleEnvelope.cpp b/src/diffpy/srreal/ScaleEnvelope.cpp index 65dab37a..2e3f2685 100644 --- a/src/diffpy/srreal/ScaleEnvelope.cpp +++ b/src/diffpy/srreal/ScaleEnvelope.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ScaleEnvelope.hpp b/src/diffpy/srreal/ScaleEnvelope.hpp index a01bb462..b02ef37a 100644 --- a/src/diffpy/srreal/ScaleEnvelope.hpp +++ b/src/diffpy/srreal/ScaleEnvelope.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ScatteringFactorTable.cpp b/src/diffpy/srreal/ScatteringFactorTable.cpp index b5c4872a..26109dfd 100644 --- a/src/diffpy/srreal/ScatteringFactorTable.cpp +++ b/src/diffpy/srreal/ScatteringFactorTable.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ScatteringFactorTable.hpp b/src/diffpy/srreal/ScatteringFactorTable.hpp index e876748d..a81d5831 100644 --- a/src/diffpy/srreal/ScatteringFactorTable.hpp +++ b/src/diffpy/srreal/ScatteringFactorTable.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SphericalShapeEnvelope.cpp b/src/diffpy/srreal/SphericalShapeEnvelope.cpp index c7f7388c..f5c2e0d8 100644 --- a/src/diffpy/srreal/SphericalShapeEnvelope.cpp +++ b/src/diffpy/srreal/SphericalShapeEnvelope.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/SphericalShapeEnvelope.hpp b/src/diffpy/srreal/SphericalShapeEnvelope.hpp index 67ba9740..eeecae77 100644 --- a/src/diffpy/srreal/SphericalShapeEnvelope.hpp +++ b/src/diffpy/srreal/SphericalShapeEnvelope.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/StepCutEnvelope.cpp b/src/diffpy/srreal/StepCutEnvelope.cpp index 0c186693..700cf781 100644 --- a/src/diffpy/srreal/StepCutEnvelope.cpp +++ b/src/diffpy/srreal/StepCutEnvelope.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/StepCutEnvelope.hpp b/src/diffpy/srreal/StepCutEnvelope.hpp index 597b5a64..b32c796e 100644 --- a/src/diffpy/srreal/StepCutEnvelope.hpp +++ b/src/diffpy/srreal/StepCutEnvelope.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/StructureAdapter.cpp b/src/diffpy/srreal/StructureAdapter.cpp index d3468ea4..954c27d7 100644 --- a/src/diffpy/srreal/StructureAdapter.cpp +++ b/src/diffpy/srreal/StructureAdapter.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/StructureAdapter.hpp b/src/diffpy/srreal/StructureAdapter.hpp index 3d047b11..e4840767 100644 --- a/src/diffpy/srreal/StructureAdapter.hpp +++ b/src/diffpy/srreal/StructureAdapter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/StructureDifference.cpp b/src/diffpy/srreal/StructureDifference.cpp index 90a57cb6..53759441 100644 --- a/src/diffpy/srreal/StructureDifference.cpp +++ b/src/diffpy/srreal/StructureDifference.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/StructureDifference.hpp b/src/diffpy/srreal/StructureDifference.hpp index 4be27e58..ee3a1b47 100644 --- a/src/diffpy/srreal/StructureDifference.hpp +++ b/src/diffpy/srreal/StructureDifference.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/ZeroBaseline.cpp b/src/diffpy/srreal/ZeroBaseline.cpp index eede7bd5..9415fe15 100644 --- a/src/diffpy/srreal/ZeroBaseline.cpp +++ b/src/diffpy/srreal/ZeroBaseline.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/ZeroBaseline.hpp b/src/diffpy/srreal/ZeroBaseline.hpp index 06ba3978..70ba54f7 100644 --- a/src/diffpy/srreal/ZeroBaseline.hpp +++ b/src/diffpy/srreal/ZeroBaseline.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/srreal/forwardtypes.hpp b/src/diffpy/srreal/forwardtypes.hpp index acaafa1e..0384ee9c 100644 --- a/src/diffpy/srreal/forwardtypes.hpp +++ b/src/diffpy/srreal/forwardtypes.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/scatteringfactordata.cpp b/src/diffpy/srreal/scatteringfactordata.cpp index 808a47e2..d33e2533 100644 --- a/src/diffpy/srreal/scatteringfactordata.cpp +++ b/src/diffpy/srreal/scatteringfactordata.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/srreal/scatteringfactordata.hpp b/src/diffpy/srreal/scatteringfactordata.hpp index 1844002f..bae6e603 100644 --- a/src/diffpy/srreal/scatteringfactordata.hpp +++ b/src/diffpy/srreal/scatteringfactordata.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/validators.hpp b/src/diffpy/validators.hpp index 6c6907d0..4f40684e 100644 --- a/src/diffpy/validators.hpp +++ b/src/diffpy/validators.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/diffpy/version.cpp b/src/diffpy/version.cpp index 803f0a6b..ba4f9f8e 100644 --- a/src/diffpy/version.cpp +++ b/src/diffpy/version.cpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/diffpy/version.tpl b/src/diffpy/version.tpl index 548fb3ab..06b0093a 100644 --- a/src/diffpy/version.tpl +++ b/src/diffpy/version.tpl @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestAtomRadiiTable.hpp b/src/tests/TestAtomRadiiTable.hpp index 392f8fd2..6a5fce87 100644 --- a/src/tests/TestAtomRadiiTable.hpp +++ b/src/tests/TestAtomRadiiTable.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestAtomicStructureAdapter.hpp b/src/tests/TestAtomicStructureAdapter.hpp index 80cf2922..85113634 100644 --- a/src/tests/TestAtomicStructureAdapter.hpp +++ b/src/tests/TestAtomicStructureAdapter.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestAttributes.hpp b/src/tests/TestAttributes.hpp index 992dc4c4..1183b9f2 100644 --- a/src/tests/TestAttributes.hpp +++ b/src/tests/TestAttributes.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestBVParametersTable.hpp b/src/tests/TestBVParametersTable.hpp index 41a985e8..38df3a90 100644 --- a/src/tests/TestBVParametersTable.hpp +++ b/src/tests/TestBVParametersTable.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestBVSCalculator.hpp b/src/tests/TestBVSCalculator.hpp index 511a0f4d..1b268030 100644 --- a/src/tests/TestBVSCalculator.hpp +++ b/src/tests/TestBVSCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestBVSObjCryst.hpp b/src/tests/TestBVSObjCryst.hpp index 84830445..ab3a7968 100644 --- a/src/tests/TestBVSObjCryst.hpp +++ b/src/tests/TestBVSObjCryst.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestDebyePDFCalculator.hpp b/src/tests/TestDebyePDFCalculator.hpp index 51cc251c..2c78ee69 100644 --- a/src/tests/TestDebyePDFCalculator.hpp +++ b/src/tests/TestDebyePDFCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestEmptyStructureAdapter.hpp b/src/tests/TestEmptyStructureAdapter.hpp index 932dde17..89e2af2b 100644 --- a/src/tests/TestEmptyStructureAdapter.hpp +++ b/src/tests/TestEmptyStructureAdapter.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestHasClassRegistry.hpp b/src/tests/TestHasClassRegistry.hpp index 8f325a0e..8ce9aac5 100644 --- a/src/tests/TestHasClassRegistry.hpp +++ b/src/tests/TestHasClassRegistry.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestLattice.hpp b/src/tests/TestLattice.hpp index 5752aa2f..2c66c0ad 100644 --- a/src/tests/TestLattice.hpp +++ b/src/tests/TestLattice.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestNoMetaStructureAdapter.hpp b/src/tests/TestNoMetaStructureAdapter.hpp index aabf5dd0..6fdb1920 100644 --- a/src/tests/TestNoMetaStructureAdapter.hpp +++ b/src/tests/TestNoMetaStructureAdapter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestObjCrystStructureAdapter.hpp b/src/tests/TestObjCrystStructureAdapter.hpp index cd4bf902..7428a03b 100644 --- a/src/tests/TestObjCrystStructureAdapter.hpp +++ b/src/tests/TestObjCrystStructureAdapter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestOverlapCalculator.hpp b/src/tests/TestOverlapCalculator.hpp index 53654bfe..69a379d7 100644 --- a/src/tests/TestOverlapCalculator.hpp +++ b/src/tests/TestOverlapCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestPDFBaseline.hpp b/src/tests/TestPDFBaseline.hpp index 34494f9e..3d7b38d6 100644 --- a/src/tests/TestPDFBaseline.hpp +++ b/src/tests/TestPDFBaseline.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestPDFCalculator.hpp b/src/tests/TestPDFCalculator.hpp index c14d6397..0a5c4ada 100644 --- a/src/tests/TestPDFCalculator.hpp +++ b/src/tests/TestPDFCalculator.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestPQEvaluator.hpp b/src/tests/TestPQEvaluator.hpp index 688729af..ed99ded3 100644 --- a/src/tests/TestPQEvaluator.hpp +++ b/src/tests/TestPQEvaluator.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestPairCounter.hpp b/src/tests/TestPairCounter.hpp index e697086c..1ec6c390 100644 --- a/src/tests/TestPairCounter.hpp +++ b/src/tests/TestPairCounter.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestPeakProfile.hpp b/src/tests/TestPeakProfile.hpp index 44b9875f..fba070c0 100644 --- a/src/tests/TestPeakProfile.hpp +++ b/src/tests/TestPeakProfile.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestPeakWidthModel.hpp b/src/tests/TestPeakWidthModel.hpp index d42e0200..846b81ae 100644 --- a/src/tests/TestPeakWidthModel.hpp +++ b/src/tests/TestPeakWidthModel.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestPeriodicStructureAdapter.hpp b/src/tests/TestPeriodicStructureAdapter.hpp index 19979d16..935e7ec4 100644 --- a/src/tests/TestPeriodicStructureAdapter.hpp +++ b/src/tests/TestPeriodicStructureAdapter.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestPointsInSphere.hpp b/src/tests/TestPointsInSphere.hpp index 6be10856..ffaec7e3 100644 --- a/src/tests/TestPointsInSphere.hpp +++ b/src/tests/TestPointsInSphere.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ************************************************************************ diff --git a/src/tests/TestR3linalg.hpp b/src/tests/TestR3linalg.hpp index 8f779dfb..7a3da835 100644 --- a/src/tests/TestR3linalg.hpp +++ b/src/tests/TestR3linalg.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestRuntimePath.hpp b/src/tests/TestRuntimePath.hpp index 36b52189..644732e3 100644 --- a/src/tests/TestRuntimePath.hpp +++ b/src/tests/TestRuntimePath.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/TestScatteringFactorTable.hpp b/src/tests/TestScatteringFactorTable.hpp index 5c517a2d..2315ba46 100644 --- a/src/tests/TestScatteringFactorTable.hpp +++ b/src/tests/TestScatteringFactorTable.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestSphericalShapeEnvelope.hpp b/src/tests/TestSphericalShapeEnvelope.hpp index 2bf667c8..d8b602d1 100644 --- a/src/tests/TestSphericalShapeEnvelope.hpp +++ b/src/tests/TestSphericalShapeEnvelope.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/TestStepCutEnvelope.hpp b/src/tests/TestStepCutEnvelope.hpp index ffb49a0f..d3be0593 100644 --- a/src/tests/TestStepCutEnvelope.hpp +++ b/src/tests/TestStepCutEnvelope.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/objcryst_helpers.cpp b/src/tests/objcryst_helpers.cpp index 76a61df1..88c06ffa 100644 --- a/src/tests/objcryst_helpers.cpp +++ b/src/tests/objcryst_helpers.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/objcryst_helpers.hpp b/src/tests/objcryst_helpers.hpp index 55d0e35e..3fcfa1d9 100644 --- a/src/tests/objcryst_helpers.hpp +++ b/src/tests/objcryst_helpers.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/serialization_helpers.hpp b/src/tests/serialization_helpers.hpp index 4e689474..e656a9e0 100644 --- a/src/tests/serialization_helpers.hpp +++ b/src/tests/serialization_helpers.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/test_custompqconfig.hpp b/src/tests/test_custompqconfig.hpp index a71ec108..5478f3fe 100644 --- a/src/tests/test_custompqconfig.hpp +++ b/src/tests/test_custompqconfig.hpp @@ -7,8 +7,8 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. -* See LICENSE.txt for license information. +* See AUTHORS.rst for a list of people who contributed. +* See LICENSE.rst for license information. * ****************************************************************************** * diff --git a/src/tests/test_helpers.cpp b/src/tests/test_helpers.cpp index d8f5bdf9..0781ada4 100644 --- a/src/tests/test_helpers.cpp +++ b/src/tests/test_helpers.cpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ****************************************************************************** diff --git a/src/tests/test_helpers.hpp b/src/tests/test_helpers.hpp index f1fd3c23..ef0d2430 100644 --- a/src/tests/test_helpers.hpp +++ b/src/tests/test_helpers.hpp @@ -7,7 +7,7 @@ * * File coded by: Pavol Juhas * -* See AUTHORS.txt for a list of people who contributed. +* See AUTHORS.rst for a list of people who contributed. * See LICENSE_DANSE.txt for license information. * ******************************************************************************