From af4e24070da211b3ca6ddac638e192aaf1f1eba7 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 12 Feb 2026 11:04:37 +1100 Subject: [PATCH 1/8] try using smee-base and no ambertools --- devtools/envs/base.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml index 94c21f8..e569fc5 100644 --- a/devtools/envs/base.yaml +++ b/devtools/envs/base.yaml @@ -9,8 +9,7 @@ dependencies: - pip # Core packages - - smee >=0.10.0 - - pydantic-units # TODO: Remove this line once smee deps are updated + - smee-base >=0.10.0 - pytorch - pyarrow @@ -36,7 +35,6 @@ dependencies: - tensorboardX # Dev / Testing - - ambertools - rdkit - uncertainties From 16f38bb97a715ee01eed01e6b9d8995c6fe40e9e Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 12 Feb 2026 11:35:51 +1100 Subject: [PATCH 2/8] update deps --- devtools/envs/base.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml index e569fc5..7db2e44 100644 --- a/devtools/envs/base.yaml +++ b/devtools/envs/base.yaml @@ -10,6 +10,8 @@ dependencies: # Core packages - smee-base >=0.10.0 + - pydantic + - pydantic-units - pytorch - pyarrow @@ -24,6 +26,7 @@ dependencies: - rdkit - matplotlib-base - panel + - openmm # Examples - jupyter From 4b910b4ed859092fb1e838da8a98ef5dfc0650aa Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 23 Feb 2026 16:45:41 +1100 Subject: [PATCH 3/8] add msgpack and parmed to env --- devtools/envs/base.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml index 694dd51..259b5aa 100644 --- a/devtools/envs/base.yaml +++ b/devtools/envs/base.yaml @@ -10,6 +10,8 @@ dependencies: # Core packages - smee-base >=0.10.0 + - msgpack-python + - parmed - pydantic - pydantic-units - openff-interchange>=0.3.17 From 12ce1b1cce96f9eee76cbaf3fdc6d0bfe805eac7 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 2 Apr 2026 06:08:49 +1100 Subject: [PATCH 4/8] rm pydantic v1 --- .github/workflows/ci.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 2c4276b..0ce4272 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -26,9 +26,6 @@ jobs: make test make docs - mamba install --name descent --yes "pydantic <2" "openff-toolkit>=0.9.2" "openff-interchange>=0.3.17" - make test - - name: CodeCov uses: codecov/codecov-action@v4.1.1 with: From b77cf09bf3745ca27ffabe263d69530708ad7050 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Tue, 7 Apr 2026 09:37:01 +1000 Subject: [PATCH 5/8] mark directory as safe --- .github/workflows/ci.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 0ce4272..ee55b64 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -20,7 +20,12 @@ jobs: - name: Run Tests run: | apt update && apt install -y git make - + # setuptools-scm calls git to determine the version; git refuses to + # run in directories owned by a different user (CVE-2022-24765), which + # happens when actions/checkout runs as a different UID than the + # container's root. Mark the workspace as safe to unblock the build. + git config --global --add safe.directory "$GITHUB_WORKSPACE" + make env make lint make test From 5543377e7025690f113240cc58e5434f50475fb0 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Tue, 7 Apr 2026 12:36:10 +1000 Subject: [PATCH 6/8] remove parmed from env --- devtools/envs/base.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml index 259b5aa..e5e9fdc 100644 --- a/devtools/envs/base.yaml +++ b/devtools/envs/base.yaml @@ -11,7 +11,6 @@ dependencies: # Core packages - smee-base >=0.10.0 - msgpack-python - - parmed - pydantic - pydantic-units - openff-interchange>=0.3.17 From e14275425942cf343a7c65b23c94107edd6891d2 Mon Sep 17 00:00:00 2001 From: Lily Wang <31115101+lilyminium@users.noreply.github.com> Date: Mon, 13 Apr 2026 07:40:57 +1000 Subject: [PATCH 7/8] Update devtools/envs/base.yaml Co-authored-by: Jennifer A Clark --- devtools/envs/base.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml index e5e9fdc..5e60988 100644 --- a/devtools/envs/base.yaml +++ b/devtools/envs/base.yaml @@ -10,7 +10,7 @@ dependencies: # Core packages - smee-base >=0.10.0 - - msgpack-python + - msgpack - pydantic - pydantic-units - openff-interchange>=0.3.17 From 76542cde00253cfab78f42c49f8e49100ada506d Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 13 Apr 2026 07:46:42 +1000 Subject: [PATCH 8/8] Revert "Update devtools/envs/base.yaml" This reverts commit e14275425942cf343a7c65b23c94107edd6891d2. --- devtools/envs/base.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml index 5e60988..e5e9fdc 100644 --- a/devtools/envs/base.yaml +++ b/devtools/envs/base.yaml @@ -10,7 +10,7 @@ dependencies: # Core packages - smee-base >=0.10.0 - - msgpack + - msgpack-python - pydantic - pydantic-units - openff-interchange>=0.3.17