From a6882c458df218cfd0f3a47f86aad9deb2b7f74e Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Mar 2026 10:48:46 -0500 Subject: [PATCH 1/6] Bump dependencies --- devtools/conda-envs/examples_env.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/devtools/conda-envs/examples_env.yml b/devtools/conda-envs/examples_env.yml index 7b0050d8e..e8fc23014 100644 --- a/devtools/conda-envs/examples_env.yml +++ b/devtools/conda-envs/examples_env.yml @@ -3,9 +3,9 @@ channels: - conda-forge dependencies: # Examples - - openff-toolkit-examples>=0.16.9 - - openff-interchange ~=0.4.2 - - openff-nagl + - openff-toolkit-examples =0.18 + - openff-interchange =0.5 + - openff-nagl =0.5 # openff-fragmenter # Runtime - pip @@ -26,7 +26,7 @@ dependencies: - rich - jax - parmed - - nglview ~=3.0.6 + - nglview - psi4 # NAGL training dependencies # hopefully will be replaced by openff-nagl-training in future From 56f6888329fc3fea3d1c8233b684ced3fe869237 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Mar 2026 11:25:52 -0500 Subject: [PATCH 2/6] Bump/update some deps --- devtools/conda-envs/examples_env.yml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/devtools/conda-envs/examples_env.yml b/devtools/conda-envs/examples_env.yml index e8fc23014..d74e413db 100644 --- a/devtools/conda-envs/examples_env.yml +++ b/devtools/conda-envs/examples_env.yml @@ -10,6 +10,7 @@ dependencies: # Runtime - pip - python=3.11 + - setuptools_scm # needed for get-tag-from-github automation - jupyterlab>=4 - ipywidgets>=8 # Cookbook @@ -20,19 +21,19 @@ dependencies: - packaging # Other deps - openff-qcsubmit - - openmmforcefields ~=0.14.2 + - openmmforcefields =0.15 - gromacs >=2021=nompi* - lammps - rich - jax - - parmed + - parmed >=4.3.1 - nglview - psi4 - # NAGL training dependencies + # NAGL training dependencies - constraints are just to help solver # hopefully will be replaced by openff-nagl-training in future - - pyarrow - - openff-recharge + - pyarrow =17 + - openff-recharge =0.5.3 - dask-jobqueue - - dgl + - dgl =2.3.0 # torchdata.datapipes was removed in 0.10.0 - torchdata<=0.9.0 From 5151b22659f55363cc343c555dc3417aeed43a6c Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Mar 2026 11:26:54 -0500 Subject: [PATCH 3/6] Also cache downloads --- .github/workflows/cookbook_preproc.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/cookbook_preproc.yaml b/.github/workflows/cookbook_preproc.yaml index 88fc42e52..9b2c73cf0 100644 --- a/.github/workflows/cookbook_preproc.yaml +++ b/.github/workflows/cookbook_preproc.yaml @@ -92,6 +92,7 @@ jobs: uses: mamba-org/setup-micromamba@v2 with: environment-file: devtools/conda-envs/examples_env.yml + cache-downloads: false - name: Pre-process and execute notebooks run: | From fb13b18eb960f44dd204850d3afc8716dd8a4988 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 27 Mar 2026 08:01:10 -0500 Subject: [PATCH 4/6] Bump Psi4 --- devtools/conda-envs/examples_env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/examples_env.yml b/devtools/conda-envs/examples_env.yml index d74e413db..c487e867b 100644 --- a/devtools/conda-envs/examples_env.yml +++ b/devtools/conda-envs/examples_env.yml @@ -28,7 +28,7 @@ dependencies: - jax - parmed >=4.3.1 - nglview - - psi4 + - psi4 >=1.10 # NAGL training dependencies - constraints are just to help solver # hopefully will be replaced by openff-nagl-training in future - pyarrow =17 From a03aae4c0134ed1c7fcbabcfccff0f8c595ca9e3 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 27 Mar 2026 09:18:55 -0500 Subject: [PATCH 5/6] Help out solver a bit --- .github/workflows/cookbook_preproc.yaml | 2 +- devtools/conda-envs/examples_env.yml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/cookbook_preproc.yaml b/.github/workflows/cookbook_preproc.yaml index 9b2c73cf0..2a3ad6db8 100644 --- a/.github/workflows/cookbook_preproc.yaml +++ b/.github/workflows/cookbook_preproc.yaml @@ -92,7 +92,7 @@ jobs: uses: mamba-org/setup-micromamba@v2 with: environment-file: devtools/conda-envs/examples_env.yml - cache-downloads: false + cache-downloads: true - name: Pre-process and execute notebooks run: | diff --git a/devtools/conda-envs/examples_env.yml b/devtools/conda-envs/examples_env.yml index c487e867b..9e4da6f97 100644 --- a/devtools/conda-envs/examples_env.yml +++ b/devtools/conda-envs/examples_env.yml @@ -10,9 +10,8 @@ dependencies: # Runtime - pip - python=3.11 - - setuptools_scm # needed for get-tag-from-github automation - - jupyterlab>=4 - - ipywidgets>=8 + - jupyterlab + - ipywidgets # Cookbook - gitpython - nbconvert @@ -28,7 +27,8 @@ dependencies: - jax - parmed >=4.3.1 - nglview - - psi4 >=1.10 + - psi4 =1.9.1 + - libint <3 # NAGL training dependencies - constraints are just to help solver # hopefully will be replaced by openff-nagl-training in future - pyarrow =17 From 403192262555c7209505ea50f4147127b1ba9ae4 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 27 Mar 2026 09:54:43 -0500 Subject: [PATCH 6/6] Debug --- devtools/conda-envs/examples_env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/examples_env.yml b/devtools/conda-envs/examples_env.yml index 9e4da6f97..3314b2e39 100644 --- a/devtools/conda-envs/examples_env.yml +++ b/devtools/conda-envs/examples_env.yml @@ -28,7 +28,7 @@ dependencies: - parmed >=4.3.1 - nglview - psi4 =1.9.1 - - libint <3 + - libint =2.9 # NAGL training dependencies - constraints are just to help solver # hopefully will be replaced by openff-nagl-training in future - pyarrow =17