From 82107b3303b8f64fe50682b90198c03872e28ec4 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 4 Dec 2025 12:02:34 -0800 Subject: [PATCH 1/7] cleaning up workflow --- .binder/overrides.json | 8 -------- .binder/postBuild | 5 ----- .github/workflows/CI.yml | 8 ++++---- .binder/environment.yml => environment.yaml | 3 --- 4 files changed, 4 insertions(+), 20 deletions(-) delete mode 100644 .binder/overrides.json delete mode 100644 .binder/postBuild rename .binder/environment.yml => environment.yaml (91%) diff --git a/.binder/overrides.json b/.binder/overrides.json deleted file mode 100644 index 7748745..0000000 --- a/.binder/overrides.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "@jupyterlab/docmanager-extension:plugin": { - "defaultViewers": { - "markdown": "Markdown Preview" - } - } -} - diff --git a/.binder/postBuild b/.binder/postBuild deleted file mode 100644 index 3a6057f..0000000 --- a/.binder/postBuild +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env bash -set -eux - -mkdir -p ${NB_PYTHON_PREFIX}/share/jupyter/lab/settings -cp .binder/overrides.json ${NB_PYTHON_PREFIX}/share/jupyter/lab/settings diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 21e2725..363c8b0 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -1,4 +1,4 @@ -name: full_tests +name: Full Tests on: push: @@ -33,15 +33,15 @@ jobs: python-version: ["3.12"] steps: - - uses: actions/checkout@v2.4.0 + - uses: actions/checkout@v4 - name: Get current date id: date run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" - - uses: mamba-org/setup-micromamba@v1 + - uses: mamba-org/setup-micromamba@v2 with: - environment-file: .binder/environment.yml + environment-file: environment.yml cache-environment: true cache-downloads: true cache-environment-key: environment-${{ steps.date.outputs.date }} diff --git a/.binder/environment.yml b/environment.yaml similarity index 91% rename from .binder/environment.yml rename to environment.yaml index 5580eb1..bf48654 100644 --- a/.binder/environment.yml +++ b/environment.yaml @@ -3,7 +3,6 @@ channels: - conda-forge dependencies: - MDAnalysis - - click - coverage - ipywidgets - lomap2 @@ -17,12 +16,10 @@ dependencies: - openmm - openmmtools>=0.23.0 - pip - - plugcli - pymbar - pytest - pytest-cov - pytest-xdist - - pydantic - python - rdkit - typing_extensions From 4c7718ddc102f49e435bd54b214dc06b06e7a9ac Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 4 Dec 2025 12:54:12 -0800 Subject: [PATCH 2/7] trim down env yaml --- environment.yaml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/environment.yaml b/environment.yaml index bf48654..0d1f8eb 100644 --- a/environment.yaml +++ b/environment.yaml @@ -2,27 +2,16 @@ name: openfe-notebooks channels: - conda-forge dependencies: - - MDAnalysis - coverage - ipywidgets - - lomap2 - lxml - - mdtraj - nbval - - networkx - nglview - notebook - - openff-forcefields - - openmm - - openmmtools>=0.23.0 - pip - - pymbar - pytest - pytest-cov - pytest-xdist - python - - rdkit - - typing_extensions - gufe>=1.7.0 - openfe>=1.7.0 - - py3dmol From 271bc4fab5250b20165d59bd25fd08ab3663b51e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 4 Dec 2025 13:01:46 -0800 Subject: [PATCH 3/7] update naming --- .github/workflows/{CI.yml => ci.yaml} | 2 +- README.md | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) rename .github/workflows/{CI.yml => ci.yaml} (97%) diff --git a/.github/workflows/CI.yml b/.github/workflows/ci.yaml similarity index 97% rename from .github/workflows/CI.yml rename to .github/workflows/ci.yaml index 363c8b0..036ee84 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/ci.yaml @@ -41,7 +41,7 @@ jobs: - uses: mamba-org/setup-micromamba@v2 with: - environment-file: environment.yml + environment-file: environment.yaml cache-environment: true cache-downloads: true cache-environment-key: environment-${{ steps.date.outputs.date }} diff --git a/README.md b/README.md index d9d1d37..4c257eb 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/) -[![full_tests](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml) +[![CI](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/ci.yaml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml) +[![Docs](https://readthedocs.org/projects/openfe/badge/?version=stable)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/openfe-doc-build.yaml) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/ExampleNotebooks/master.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/ExampleNotebooks/main) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/showcase/openfe_showcase.ipynb) From 4be057f44011c82ee99b8eb8579645d412e06299 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 4 Dec 2025 13:06:45 -0800 Subject: [PATCH 4/7] update docs badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4c257eb..63e61da 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ [![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/) [![CI](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/ci.yaml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml) -[![Docs](https://readthedocs.org/projects/openfe/badge/?version=stable)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/openfe-doc-build.yaml) +[![Docs](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/openfe-doc-build.yaml/badge.svg)](https://docs.openfree.energy/en/stable/?badge=stable) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/ExampleNotebooks/master.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/ExampleNotebooks/main) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/showcase/openfe_showcase.ipynb) From 1688b7efd97d654d7b1b890d6b99d0be0f8c60bd Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 4 Dec 2025 13:09:59 -0800 Subject: [PATCH 5/7] rename for clarity --- .github/workflows/ci.yaml | 2 +- .github/workflows/openfe-doc-build.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 036ee84..0140533 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -1,4 +1,4 @@ -name: Full Tests +name: CI on: push: diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index c77eeef..be3d352 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -1,4 +1,4 @@ -name: Test openfe doc build +name: OpenFE Docs on: workflow_dispatch: From 9410a6b993f40d79fb4050e6583e58e40ad03ef5 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 10 Dec 2025 09:54:28 -0800 Subject: [PATCH 6/7] update environment --- environment.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yaml b/environment.yaml index 0d1f8eb..c2f6347 100644 --- a/environment.yaml +++ b/environment.yaml @@ -13,5 +13,5 @@ dependencies: - pytest-cov - pytest-xdist - python - - gufe>=1.7.0 - - openfe>=1.7.0 + - gufe >=1.7.0, <1.8.0 + - openfe==1.8.0 From a5e9d8f793b2cad4fb547e2a9cdd7ee6db611b14 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 10 Dec 2025 10:05:59 -0800 Subject: [PATCH 7/7] update runner name for clarity --- .github/workflows/openfe-doc-build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index be3d352..b372d61 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -1,4 +1,4 @@ -name: OpenFE Docs +name: Test OpenFE Docs Build on: workflow_dispatch: