From cc5768fd7669a09b3ee7e48481ec952a8e4f46df Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Mon, 4 May 2026 13:23:06 -0500 Subject: [PATCH 1/4] Update environment --- devtools/conda-envs/full-stack.yaml | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/devtools/conda-envs/full-stack.yaml b/devtools/conda-envs/full-stack.yaml index 34eca62..07f7f1e 100644 --- a/devtools/conda-envs/full-stack.yaml +++ b/devtools/conda-envs/full-stack.yaml @@ -1,19 +1,18 @@ name: full-stack-tests channels: - - openeye - conda-forge dependencies: - python - - setuptools =81 + - setuptools - pip - numpy >=2.4 - - pydantic >=2,<3,!=2.12 + - pydantic =2.11 - pint >=0.25 - openff-toolkit >=0.18 - openff-fragmenter - openff-interchange >=0.5 - - openff-packmol >=0.1 - - pymbar + - openff-packmol =0.1=pyhc364b38_1 + - pymbar =4 - pytest - pytest-randomly - pytest-xdist @@ -23,25 +22,25 @@ dependencies: - toml - bson - msgpack-python - - openeye-toolkits >=2025 - - rdkit !=2024.03.6,!=2024.09.1 + - openeye::openeye-toolkits >=2025 + - rdkit >=2025.09.5 - intermol # Recharge - qcelemental - - qcportal >=0.59 + - qcportal - qcengine - geometric - - openff-qcsubmit + - openff-qcsubmit >=0.57 - qcarchivetesting - qcfractalcompute - h5py - - psi4 =1.9 + - psi4 - openff-nagl - - gromacs >=2024 - # https://github.com/conda-forge/lammps-feedstock/issues/207 - - lammps >=2023.08.02 - - openmpi =4 +# - gromacs >=2026 +# # https://github.com/conda-forge/lammps-feedstock/issues/207 +# # lammps # >=2023.08.02 +# - openmpi =5 From b87f1651c07eaac6958398fa04c48081e6ddf9cb Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Mon, 4 May 2026 16:26:47 -0500 Subject: [PATCH 2/4] Refactor to not assume AmberTools installed --- devtools/conda-envs/full-stack.yaml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/devtools/conda-envs/full-stack.yaml b/devtools/conda-envs/full-stack.yaml index 07f7f1e..5cc8476 100644 --- a/devtools/conda-envs/full-stack.yaml +++ b/devtools/conda-envs/full-stack.yaml @@ -8,9 +8,9 @@ dependencies: - numpy >=2.4 - pydantic =2.11 - pint >=0.25 - - openff-toolkit >=0.18 - - openff-fragmenter - - openff-interchange >=0.5 + - openff-toolkit-base >=0.18 + - openff-fragmenter-base + - openff-interchange-base >=0.5 - openff-packmol =0.1=pyhc364b38_1 - pymbar =4 - pytest @@ -23,7 +23,7 @@ dependencies: - bson - msgpack-python - openeye::openeye-toolkits >=2025 - - rdkit >=2025.09.5 + - rdkit - intermol # Recharge @@ -40,7 +40,5 @@ dependencies: - openff-nagl -# - gromacs >=2026 -# # https://github.com/conda-forge/lammps-feedstock/issues/207 -# # lammps # >=2023.08.02 -# - openmpi =5 + - gromacs + - lammps From 092467803af9260909a1c3d95472984d3e9c6d51 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Mon, 4 May 2026 16:37:11 -0500 Subject: [PATCH 3/4] Add OpenMM --- devtools/conda-envs/full-stack.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/conda-envs/full-stack.yaml b/devtools/conda-envs/full-stack.yaml index 5cc8476..da1aa5a 100644 --- a/devtools/conda-envs/full-stack.yaml +++ b/devtools/conda-envs/full-stack.yaml @@ -12,6 +12,7 @@ dependencies: - openff-fragmenter-base - openff-interchange-base >=0.5 - openff-packmol =0.1=pyhc364b38_1 + - openmm - pymbar =4 - pytest - pytest-randomly From 62092b6a68caa28b191e6b3355d68b2f25593ccc Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 5 May 2026 08:14:17 -0500 Subject: [PATCH 4/4] No engines --- devtools/conda-envs/full-stack.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/devtools/conda-envs/full-stack.yaml b/devtools/conda-envs/full-stack.yaml index da1aa5a..588655c 100644 --- a/devtools/conda-envs/full-stack.yaml +++ b/devtools/conda-envs/full-stack.yaml @@ -24,16 +24,16 @@ dependencies: - bson - msgpack-python - openeye::openeye-toolkits >=2025 - - rdkit + - rdkit >=2026.03.2 - intermol # Recharge - qcelemental - - qcportal - qcengine - geometric - openff-qcsubmit >=0.57 + - qcportal >=0.63 - qcarchivetesting - qcfractalcompute - h5py @@ -41,5 +41,5 @@ dependencies: - openff-nagl - - gromacs - - lammps + # gromacs + # lammps