From dc56870640bc73eb2d0bada8fb6eed4cb9f8ee34 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 29 Sep 2026 14:53:04 -0700 Subject: [PATCH 1/6] update env --- environment.yaml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/environment.yaml b/environment.yaml index 3b9ebb5..1f7208c 100644 --- a/environment.yaml +++ b/environment.yaml @@ -14,7 +14,16 @@ dependencies: - pytest-cov - pytest-xdist - python - - openfe==1.12.0 - - openff-interchange-base != 0.5.1 # https://github.com/openforcefield/openff-interchange/issues/1450 + # - openfe==1.12.0 + + # tmp for dev build until openfe 1.13 is released + - gufe == 1.13.0 + - cinnabar >=0.6.0 + - kartograf ~=2.0 + - konnektor ~=0.5.0 + - openfe-analysis>=0.5.0 + - openmmforcefields >=0.15.1 # min needed for https://github.com/openmm/openmmforcefields/pull/414 + - openmmtools >=0.26 # fix to support membrane barostat: https://github.com/choderalab/openmmtools/pull/798 + - pip: - - git+https://github.com/OpenFreeEnergy/konnektor@v0.5.0 # use conda-forge v0.5.0 after openfe conda-forge release + - git+https://github.com/OpenFreeEnergy/openfe@main # use conda-forge v0.5.0 after openfe conda-forge release From dfa5791e0e796bcfed443e2225d541e1f8206f03 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 29 Sep 2026 15:10:51 -0700 Subject: [PATCH 2/6] update env --- environment.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/environment.yaml b/environment.yaml index 1f7208c..a30a6ca 100644 --- a/environment.yaml +++ b/environment.yaml @@ -13,7 +13,7 @@ dependencies: - pytest - pytest-cov - pytest-xdist - - python + - python=3.13 # - openfe==1.12.0 # tmp for dev build until openfe 1.13 is released @@ -22,8 +22,9 @@ dependencies: - kartograf ~=2.0 - konnektor ~=0.5.0 - openfe-analysis>=0.5.0 + - lomap2>=3.2.1 - openmmforcefields >=0.15.1 # min needed for https://github.com/openmm/openmmforcefields/pull/414 - openmmtools >=0.26 # fix to support membrane barostat: https://github.com/choderalab/openmmtools/pull/798 - pip: - - git+https://github.com/OpenFreeEnergy/openfe@main # use conda-forge v0.5.0 after openfe conda-forge release + - git+https://github.com/OpenFreeEnergy/openfe@main # use conda-forge v1.13.0 after release From f605060907eaf35cbb1390702af089a151b2d08a Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 29 Sep 2026 15:13:46 -0700 Subject: [PATCH 3/6] add plugcli --- environment.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yaml b/environment.yaml index a30a6ca..fb409b9 100644 --- a/environment.yaml +++ b/environment.yaml @@ -25,6 +25,7 @@ dependencies: - lomap2>=3.2.1 - openmmforcefields >=0.15.1 # min needed for https://github.com/openmm/openmmforcefields/pull/414 - openmmtools >=0.26 # fix to support membrane barostat: https://github.com/choderalab/openmmtools/pull/798 + - plugcli - pip: - git+https://github.com/OpenFreeEnergy/openfe@main # use conda-forge v1.13.0 after release From cc889a4d124439c3c22abf28f180360e2388e98b Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 29 Sep 2026 15:18:46 -0700 Subject: [PATCH 4/6] bump to use python 3.13 --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 8517158..5d36ed1 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -31,7 +31,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest", "macos-latest"] - python-version: ["3.12"] + python-version: ["3.13"] steps: - uses: actions/checkout@v4 From a833947b8f288d4e3194e985f447e7803e78788b Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 30 Sep 2026 14:01:39 -0700 Subject: [PATCH 5/6] add extra deps --- environment.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/environment.yaml b/environment.yaml index fb409b9..a3556b0 100644 --- a/environment.yaml +++ b/environment.yaml @@ -23,6 +23,8 @@ dependencies: - konnektor ~=0.5.0 - openfe-analysis>=0.5.0 - lomap2>=3.2.1 + - py3dmol + - pygraphviz - openmmforcefields >=0.15.1 # min needed for https://github.com/openmm/openmmforcefields/pull/414 - openmmtools >=0.26 # fix to support membrane barostat: https://github.com/choderalab/openmmtools/pull/798 - plugcli From 7adb779f41b65fa809dd80bd788fa19b26d64f06 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 2 Oct 2026 13:56:59 -0700 Subject: [PATCH 6/6] add exorcist as dep --- environment.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yaml b/environment.yaml index a3556b0..4ca6a02 100644 --- a/environment.yaml +++ b/environment.yaml @@ -17,6 +17,7 @@ dependencies: # - openfe==1.12.0 # tmp for dev build until openfe 1.13 is released + - exorcist - gufe == 1.13.0 - cinnabar >=0.6.0 - kartograf ~=2.0