Merge branch 'of3_septop_example' of github.com:OpenFreeEnergy/ExampleNotebooks into of3_septop_example

Author: hannahbaumann

.binder/environment.yml

@@ -1,6 +1,5 @@
 name: openfe-notebooks
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
   - MDAnalysis
@@ -27,6 +26,6 @@ dependencies:
   - python
   - rdkit
   - typing_extensions
-  - gufe>=1.4.1
-  - openfe~=1.2
+  - gufe>=1.7.0
+  - openfe>=1.7.0
   - py3dmol

.github/workflows/CI.yml

@@ -29,10 +29,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # Note: we temporarily pin to macos-12 to avoid compatibility issues
-        # between AT22+ and macos-13+ runners
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.12"]
 
     steps:
     - uses: actions/checkout@v2.4.0
@@ -65,4 +63,4 @@ jobs:
 
     - name: Run example notebooks
       run: |
-        python -m pytest -v setup/ showcase/ cookbook/ openmm_rbfe/ networks/ --nbval-lax --nbval-cell-timeout=3000 -n auto --dist loadscope
+        python -m pytest -v --nbval-lax --nbval-cell-timeout=3000 -n auto --dist loadscope

.github/workflows/binder-badge.yaml .github/workflows/colab-badge.yaml.github/workflows/binder-badge.yaml renamed to .github/workflows/colab-badge.yaml

@@ -17,11 +17,11 @@ jobs:
         script: |
           var PR_HEAD_USERREPO = process.env.PR_HEAD_USERREPO;
           var PR_HEAD_REF = process.env.PR_HEAD_REF;
-          github.issues.createComment({
+          github.rest.issues.createComment({
             issue_number: context.issue.number,
             owner: context.repo.owner,
             repo: context.repo.repo,
-            body: `[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/${PR_HEAD_REF}/showcase)) :point_left: Launch a Colab session on branch ``${PR_HEAD_REF}``.
+            body: `[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/${PR_HEAD_REF}/showcase) :point_left: Launch a Colab session on branch _${PR_HEAD_REF}_`
           })
       env:
         PR_HEAD_REF: ${{ github.event.pull_request.head.ref }}

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

@@ -0,0 +1,59 @@
+name: Test openfe doc build
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    # nightly tests, 2 am
+    - cron: "0 2 * * *"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0} 
+
+jobs:
+  test-conda-build:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout openfe
+        uses: actions/checkout@v4
+        with:
+          repository: OpenFreeEnergy/openfe
+          path: openfe
+
+      - name: Checkout ExampleNotebooks repository
+        uses: actions/checkout@v4
+        with:
+          path: openfe/docs/ExampleNotebooks
+
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
+      
+      - name: Install doc environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: openfe/docs/environment.yaml
+          cache-environment: true
+          cache-downloads: true
+          cache-environment-key: environment-${{ steps.date.outputs.date }}
+          cache-downloads-key: downloads-${{ steps.date.outputs.date }}
+          init-shell: bash
+
+      - name: Build the docs
+        run: |
+          cd openfe
+          # install so that we can get a version metadata we use in docs
+          pip install . --no-deps
+          cd docs
+          make html

README.md

@@ -6,9 +6,9 @@
 # OpenFE Notebooks
 
 Collection of notebooks for the Open FreeEnergy project.
-These can be ran in the browser via the Binder links.
+These can be run in the browser via the Colab links.
 
-| Binder link | Description |
+| Colab link | Description |
 | --- | --- |
 | [![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) | Start here.  This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the `openfe` package. |
 
@@ -21,7 +21,7 @@ Then you can download a copy of the notebooks:
 
 - `wget -O OpenFEExampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/main`
 - or (depending on your platform)
-- `curl -L -k -o OpenFEEXampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/main`
+- `curl -L -k -o OpenFEExampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/main`
 
 Unpack, then navigate to the downloaded notebooks: