Merge branch 'main' into cofactors

Author: atravitz

.binder/environment.yml

@@ -1,4 +1,4 @@
-name: full_tests
+name: CI
 
 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.yaml
         cache-environment: true
         cache-downloads: true
         cache-environment-key: environment-${{ steps.date.outputs.date }}

.binder/overrides.json

@@ -1,4 +1,4 @@
-name: Test openfe doc build
+name: Test OpenFE Docs Build
 
 on:
   workflow_dispatch:

.binder/postBuild

@@ -228,3 +228,29 @@ $RECYCLE.BIN/
 *.lnk
 
 # End of https://www.toptal.com/developers/gitignore/api/osx,python,jupyternotebooks,windows,linux
+
+# Files generated by example notebooks
+*.zip*
+*.tsv
+*.graphml
+*.tar.gz
+abfe_tutorial/abfe_results/
+abfe_tutorial/abfe_json/
+ahfe_tutorial/ahfe_json/
+cookbook/assets/of3_output/temp_ligands/
+cookbook/assets/of3_output/p_aligned/
+cookbook/dg.png
+cookbook/queries.json
+networks/transformations/
+openmm_md/md_input/
+openmm_md/shared*
+openmm_septop/septop_results/
+openmm_septop/transformations/
+plotting_rbfes_with_cinnabar/cinnabar_input.csv
+plotting_rbfes_with_cinnabar/*.dat
+rbfe_tutorial/transformations/
+showcase/db.json
+showcase/hybrid_system.pdb
+showcase/results/
+showcase/tyk2_edge.png
+showcase/tyk2_json/

.github/workflows/CI.yml .github/workflows/ci.yaml.github/workflows/CI.yml renamed to .github/workflows/ci.yaml

@@ -6,10 +6,10 @@ ci:
 files: (^notebooks)
 repos:
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.9.0
+    rev: 25.12.0
     hooks:
       - id: black
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.9.0
+    rev: 25.12.0
     hooks:
       - id: black-jupyter

.github/workflows/openfe-doc-build.yaml

@@ -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://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)