From 16d86d08c38b001946577b9be77edf8f7a8839b6 Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Sat, 21 Oct 2023 18:22:49 -0400
Subject: [PATCH] fix doc deployment

- fix #132
- updated doc workflow with more recent code from mdaencore's docs.yaml:
  - modern parameters for conda-incubator/setup-miniconda@v2
  - use Python 3.11 for building docs
  - use ci/environment.yaml
- now also build on PR (as a test), only deploy on merge
- canonical package name of sphinx-sitemap in environment (prefer dash to
  underscore)
- updated requirements.txt (at least pro-forma, not sure if we use it)
---
 .github/workflows/docs.yaml | 35 ++++++++++++++---------------------
 ci/environment.yaml         |  2 +-
 ci/requirements.txt         |  2 ++
 3 files changed, 17 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index 6394d1e..c013b16 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -3,6 +3,9 @@ on:
   push:
     branches:
       - master
+  pull_request:
+    branches:
+      - master
 
 concurrency:
   group: "${{ github.ref }}-${{ github.head_ref }}"
@@ -18,44 +21,34 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
-        fetch-depth: 0         
-
+        fetch-depth: 0
+        
     - name: setup_miniconda
       uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.9
+        python-version: 3.11
+        environment-file: ci/environment.yaml
         auto-update-conda: true
         channel-priority: flexible
         channels: conda-forge
-        add-pip-as-python-dependency: true
-        mamba-version: "*"
-
-    - name: install package deps
-      run: |
-        mamba install numpy scipy pytest pytest-cov codecov sphinx
-        pip install sphinx-sitemap sphinx-rtd-theme
-
-    - name: check install
-      run: |
-        which python
-        which pip
-        conda info
-        conda list
-
+        miniforge-variant: Mambaforge
+        use-mamba: true
+        
     - name: install package
       run: |
         pip install -v .
 
     - name: build docs
       run: |
-        python setup.py build_sphinx
+        cd doc && sphinx-build -b html source build
 
     - name: deploy docs
       uses: peaceiris/actions-gh-pages@v3
+      if: github.event_name != 'pull_request'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./build/sphinx/html
+        publish_dir: ./doc/build
         user_name: 'github-actions'
         user_email: 'github-action@users.noreply.github.com'
diff --git a/ci/environment.yaml b/ci/environment.yaml
index 9a3355f..5e29a52 100644
--- a/ci/environment.yaml
+++ b/ci/environment.yaml
@@ -10,4 +10,4 @@ dependencies:
   # documentation
   - mdanalysis-sphinx-theme >=1.0.1
   - pip:
-    - sphinx_sitemap
\ No newline at end of file
+    - sphinx-sitemap
\ No newline at end of file
diff --git a/ci/requirements.txt b/ci/requirements.txt
index 2bbd2a1..39273b6 100644
--- a/ci/requirements.txt
+++ b/ci/requirements.txt
@@ -1,3 +1,5 @@
 numpy
 scipy
+mrcfile
+mdanalysis-sphinx-theme >=1.0.1
 sphinx-sitemap