Merge pull request #190 from ericpre/simplify_workflow

Simplify GitHub CI workflows by using reusable workflow
hyperspy · Dec 2, 2023 · db3ca53 · db3ca53
2 parents 68606cf + b2b80bf
commit db3ca53
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -1,111 +1,21 @@
-name: Docs
+name: Documentation
 
 on: [push, pull_request]
 
 jobs:
-  build_docs:
-    # This build is to make PR comments for the sphinx warning and check if
-    # web links are not broken 
-    name: Check links and make PR comments
-    runs-on: ubuntu-latest
-    env:
-      DOCS_PATH: ./docs/_build/html/
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Fetch tags upstream
-        # Needs to fetch the tags from upstream to get the
-        # correct version with setuptools_scm
-        run: |
-          git remote add upstream https://github.com/hyperspy/rosettasciio.git
-          git fetch --prune --unshallow
-          git fetch upstream --tags
-
-      - uses: actions/setup-python@v4
-        name: Install Python
-        with:
-          python-version: '3.11'
-
-      - name: Install RosettaSciIO
-        shell: bash -l {0}
-        run: |
-          pip install .'[all, docs]'
-
-      - name: Update packages list
-        shell: bash -l {0}
-        run: |
-          # python generate_supported_format_table.py
-          echo "Table of Supported Format"
-          echo "========================="
-          cat ./docs/user_guide/supported_formats/supported_formats.rst
-
-      # Add sphinx warnings as PR comments
-      - uses: sphinx-doc/sphinx-problem-matcher@master
-
-      - name: Build docs
-        shell: bash -l {0}
-        run: |
-          cd docs
-          make SPHINXOPTS="-W --keep-going" html
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ${{ env.DOCS_PATH }}
-          name: docs_html
-
-      - name: Check links
-        shell: bash -l {0}
-        run: |
-          cd docs
-          make linkcheck
-
-  push_docs:
-    # This build is to push changes to gh-pages branch (https://hyperspy.org/rosettasciio)
-    needs: build_docs
-    name: Push to gh-pages
-    runs-on: ubuntu-latest
-    if: ${{ github.event_name != 'pull_request' && github.repository == 'hyperspy/rosettasciio' }}
+  Build:
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/doc.yml@main
+    with:
+      doc_path: ./doc
+      doc_build_path: ./doc/_build/html/
+      pip_extra_doc: all,doc
+
+  Push:
+    needs: Build
+    if: ${{ github.event_name != 'pull_request' && github.repository_owner == 'hyperspy' }}
     permissions:
       # needs write permission to push the docs to gh-pages
       contents: write
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          ref: gh-pages
-
-      - uses: actions/download-artifact@v3
-        with:
-          name: docs_html
-          path: .
-
-      - name: list files
-        run: |
-          ls
-
-      - name: Git status
-        run: |
-          git status
-          git status -s
-          if [[ $(git status -s) ]]; then
-            HAS_CHANGES='true'
-          else
-            HAS_CHANGES='false'
-          fi
-          echo "HAS_CHANGES=${HAS_CHANGES}" >> $GITHUB_ENV
-
-      - name: Commit files
-        # Skip when there is nothing to commit
-        if: ${{ env.HAS_CHANGES == 'true' }}
-        run: |
-          git config --local user.email "github-actions[bot]@users.noreply.github.com"
-          git config --local user.name "github-actions[bot]"
-          git add -A
-          git commit -m "Update docs build" -a
-
-      - name: Push changes
-        if: ${{ env.HAS_CHANGES == 'true' }}
-        uses: ad-m/github-push-action@d91a481090679876dfc4178fef17f286781251df
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: gh-pages
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/push_doc.yml@main
diff --git a/.github/workflows/package_and_test.yml b/.github/workflows/package_and_test.yml
@@ -0,0 +1,11 @@
+name: Package & Test
+
+on: [push, pull_request]
+
+jobs:
+  package_and_test:
+    name: Package and Test
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/package_and_test.yml@main
+    with:
+      module_name: rsciio
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -40,13 +40,19 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: get repository name
+        shell: bash
+        run: echo "REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}" >> $GITHUB_ENV
 
       - name: Fetch tags upstream
+        if: ${{ github.repository_owner != 'hyperspy' }}
         # Needs to fetch the tags from upstream to get the
         # correct version with setuptools_scm
         run: |
-          git remote add upstream https://github.com/hyperspy/rosettasciio.git
-          git fetch --prune --unshallow
+          git remote add upstream https://github.com/hyperspy/${{ env.REPOSITORY_NAME }}.git
           git fetch upstream --tags
 
       - uses: actions/setup-python@v4

diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,4 @@
-/docs/_build/*
+/doc/_build/*
 /build/*
 /dist/*
 /RosettaSciIO.egg-info/*

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -16,7 +16,7 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+  configuration: doc/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats:
@@ -28,4 +28,4 @@ python:
       path: .
       extra_requirements:
           - all
-          - docs
+          - doc
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -8,6 +8,8 @@ https://rosettasciio.readthedocs.io/en/latest/changes.html
 
 .. towncrier release notes start
 
+.. _changes_0.2:
+
 0.2 (2023-11-09)
 ================
 
@@ -50,6 +52,7 @@ Maintenance
 - Update the test suite and the CI workflows to work with and without exspy installed (`#176 <https://github.com/hyperspy/rosettasciio/issues/176>`_)
 - Add badges that became available after first release (`#177 <https://github.com/hyperspy/rosettasciio/issues/177>`_)
 
+.. _changes_0.1:
 
 0.1 (2023-06-06)
 ================

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -140,8 +140,8 @@ information.
 
 **Documentation** should be added both as **docstring**, as well as to the **user guide**,
 for which a corresponding ``spamandeggs.rst`` file should be created in the directory
-``docs/supported_formats/`` and the format added to the lists in
-``docs/supported_formats/index.rst`` and ``docs/supported_formats/supported_formats.rst``.
+``doc/user_guide/supported_formats/`` and the format added to the lists in
+``doc/user_guide/supported_formats/index.rst`` and ``doc/user_guide/supported_formats/supported_formats.rst``.
 
 A few standard *docstring* components are provided by ``rsciio._docstrings.py`` and should
 be used (see existing plugins).
@@ -159,7 +159,7 @@ The *docstrings* are automatically added in the *user guide* using the following
 The *docstrings* follow `Numpy docstring style <https://numpydoc.readthedocs.io>`_. The
 links to RosettaSciIO API and other Sphinx documented API are checked when building the documentation
 and broken links will raise warnings. In order to identify potentially broken links during pull
-request review, the `Docs <https://github.com/hyperspy/rosettasciio/actions/workflows/docs.yml>`_
+request review, the `Documentation <https://github.com/hyperspy/rosettasciio/actions/workflows/Documentation.yml>`_
 GitHub CI workflow is set to fail when the doc build raises warnings.
 
 .. Note ::

diff --git a/docs/Makefile → doc/Makefile b/docs/Makefile → doc/Makefile
diff --git a/docs/_static/logo_rec_dark_oct22.png → doc/_static/logo_rec_dark_oct22.png b/docs/_static/logo_rec_dark_oct22.png → doc/_static/logo_rec_dark_oct22.png
diff --git a/docs/_static/logo_rec_dark_oct22.svg → doc/_static/logo_rec_dark_oct22.svg b/docs/_static/logo_rec_dark_oct22.svg → doc/_static/logo_rec_dark_oct22.svg
diff --git a/docs/_static/logo_rec_oct22.png → doc/_static/logo_rec_oct22.png b/docs/_static/logo_rec_oct22.png → doc/_static/logo_rec_oct22.png
diff --git a/docs/_static/logo_rec_oct22.svg → doc/_static/logo_rec_oct22.svg b/docs/_static/logo_rec_oct22.svg → doc/_static/logo_rec_oct22.svg
diff --git a/docs/_static/logo_sq.png → doc/_static/logo_sq.png b/docs/_static/logo_sq.png → doc/_static/logo_sq.png
diff --git a/docs/_static/logo_sq.svg → doc/_static/logo_sq.svg b/docs/_static/logo_sq.svg → doc/_static/logo_sq.svg
diff --git a/docs/api/index.rst → doc/api/index.rst b/docs/api/index.rst → doc/api/index.rst
diff --git a/docs/api/utils.rst → doc/api/utils.rst b/docs/api/utils.rst → doc/api/utils.rst
diff --git a/docs/changes.rst → doc/changes.rst b/docs/changes.rst → doc/changes.rst
diff --git a/docs/conf.py → doc/conf.py b/docs/conf.py → doc/conf.py
diff --git a/docs/contributing.rst → doc/contributing.rst b/docs/contributing.rst → doc/contributing.rst
diff --git a/docs/file_specification/edax/ImageIPR.pdf → doc/file_specification/edax/ImageIPR.pdf b/docs/file_specification/edax/ImageIPR.pdf → doc/file_specification/edax/ImageIPR.pdf
diff --git a/.../file_specification/edax/SPECTRUM-V70.pdf → doc/file_specification/edax/SPECTRUM-V70.pdf b/.../file_specification/edax/SPECTRUM-V70.pdf → doc/file_specification/edax/SPECTRUM-V70.pdf
diff --git a/...ification/edax/SpcMap-spd.file.format.pdf → ...ification/edax/SpcMap-spd.file.format.pdf b/...ification/edax/SpcMap-spd.file.format.pdf → ...ification/edax/SpcMap-spd.file.format.pdf
diff --git a/docs/file_specification/index.rst → doc/file_specification/index.rst b/docs/file_specification/index.rst → doc/file_specification/index.rst
diff --git a/docs/file_specification/ripple-specs.rst → doc/file_specification/ripple-specs.rst b/docs/file_specification/ripple-specs.rst → doc/file_specification/ripple-specs.rst
diff --git a/docs/index.rst → doc/index.rst b/docs/index.rst → doc/index.rst
diff --git a/docs/make.bat → doc/make.bat b/docs/make.bat → doc/make.bat
diff --git a/docs/user_guide/index.rst → doc/user_guide/index.rst b/docs/user_guide/index.rst → doc/user_guide/index.rst
diff --git a/docs/user_guide/install.rst → doc/user_guide/install.rst b/docs/user_guide/install.rst → doc/user_guide/install.rst
@@ -73,7 +73,7 @@ The list of *extras*:
 And for development, the following *extras* are available (see ``pyproject.toml`` for more information):
 
 - tests
-- docs
+- doc
 - dev
 
 .. _install-with-conda:

diff --git a/docs/user_guide/interoperability.rst → doc/user_guide/interoperability.rst b/docs/user_guide/interoperability.rst → doc/user_guide/interoperability.rst
diff --git a/...ser_guide/supported_formats/blockfile.rst → ...ser_guide/supported_formats/blockfile.rst b/...ser_guide/supported_formats/blockfile.rst → ...ser_guide/supported_formats/blockfile.rst
diff --git a/docs/user_guide/supported_formats/bruker.rst → doc/user_guide/supported_formats/bruker.rst b/docs/user_guide/supported_formats/bruker.rst → doc/user_guide/supported_formats/bruker.rst
diff --git a/docs/user_guide/supported_formats/de5.rst → doc/user_guide/supported_formats/de5.rst b/docs/user_guide/supported_formats/de5.rst → doc/user_guide/supported_formats/de5.rst
diff --git a/docs/user_guide/supported_formats/dens.rst → doc/user_guide/supported_formats/dens.rst b/docs/user_guide/supported_formats/dens.rst → doc/user_guide/supported_formats/dens.rst
diff --git a/...e/supported_formats/digitalmicrograph.rst → ...e/supported_formats/digitalmicrograph.rst b/...e/supported_formats/digitalmicrograph.rst → ...e/supported_formats/digitalmicrograph.rst
diff --git a/...r_guide/supported_formats/digitalsurf.rst → ...r_guide/supported_formats/digitalsurf.rst b/...r_guide/supported_formats/digitalsurf.rst → ...r_guide/supported_formats/digitalsurf.rst
diff --git a/docs/user_guide/supported_formats/edax.rst → doc/user_guide/supported_formats/edax.rst b/docs/user_guide/supported_formats/edax.rst → doc/user_guide/supported_formats/edax.rst
diff --git a/docs/user_guide/supported_formats/emd.rst → doc/user_guide/supported_formats/emd.rst b/docs/user_guide/supported_formats/emd.rst → doc/user_guide/supported_formats/emd.rst
diff --git a/docs/user_guide/supported_formats/empad.rst → doc/user_guide/supported_formats/empad.rst b/docs/user_guide/supported_formats/empad.rst → doc/user_guide/supported_formats/empad.rst
diff --git a/...ser_guide/supported_formats/hamamatsu.rst → ...ser_guide/supported_formats/hamamatsu.rst b/...ser_guide/supported_formats/hamamatsu.rst → ...ser_guide/supported_formats/hamamatsu.rst
diff --git a/docs/user_guide/supported_formats/hspy.rst → doc/user_guide/supported_formats/hspy.rst b/docs/user_guide/supported_formats/hspy.rst → doc/user_guide/supported_formats/hspy.rst
diff --git a/docs/user_guide/supported_formats/image.rst → doc/user_guide/supported_formats/image.rst b/docs/user_guide/supported_formats/image.rst → doc/user_guide/supported_formats/image.rst
diff --git a/docs/user_guide/supported_formats/index.rst → doc/user_guide/supported_formats/index.rst b/docs/user_guide/supported_formats/index.rst → doc/user_guide/supported_formats/index.rst
diff --git a/docs/user_guide/supported_formats/jeol.rst → doc/user_guide/supported_formats/jeol.rst b/docs/user_guide/supported_formats/jeol.rst → doc/user_guide/supported_formats/jeol.rst
diff --git a/...ser_guide/supported_formats/jobinyvon.rst → ...ser_guide/supported_formats/jobinyvon.rst b/...ser_guide/supported_formats/jobinyvon.rst → ...ser_guide/supported_formats/jobinyvon.rst
diff --git a/docs/user_guide/supported_formats/mrc.rst → doc/user_guide/supported_formats/mrc.rst b/docs/user_guide/supported_formats/mrc.rst → doc/user_guide/supported_formats/mrc.rst
diff --git a/docs/user_guide/supported_formats/mrcz.rst → doc/user_guide/supported_formats/mrcz.rst b/docs/user_guide/supported_formats/mrcz.rst → doc/user_guide/supported_formats/mrcz.rst
diff --git a/docs/user_guide/supported_formats/msa.rst → doc/user_guide/supported_formats/msa.rst b/docs/user_guide/supported_formats/msa.rst → doc/user_guide/supported_formats/msa.rst
diff --git a/docs/user_guide/supported_formats/netcdf.rst → doc/user_guide/supported_formats/netcdf.rst b/docs/user_guide/supported_formats/netcdf.rst → doc/user_guide/supported_formats/netcdf.rst
diff --git a/docs/user_guide/supported_formats/nexus.rst → doc/user_guide/supported_formats/nexus.rst b/docs/user_guide/supported_formats/nexus.rst → doc/user_guide/supported_formats/nexus.rst
diff --git a/...ser_guide/supported_formats/pantarhei.rst → ...ser_guide/supported_formats/pantarhei.rst b/...ser_guide/supported_formats/pantarhei.rst → ...ser_guide/supported_formats/pantarhei.rst
diff --git a/docs/user_guide/supported_formats/phenom.rst → doc/user_guide/supported_formats/phenom.rst b/docs/user_guide/supported_formats/phenom.rst → doc/user_guide/supported_formats/phenom.rst
diff --git a/...er_guide/supported_formats/protochips.rst → ...er_guide/supported_formats/protochips.rst b/...er_guide/supported_formats/protochips.rst → ...er_guide/supported_formats/protochips.rst
diff --git a/...ide/supported_formats/quantumdetector.rst → ...ide/supported_formats/quantumdetector.rst b/...ide/supported_formats/quantumdetector.rst → ...ide/supported_formats/quantumdetector.rst
diff --git a/...user_guide/supported_formats/renishaw.rst → ...user_guide/supported_formats/renishaw.rst b/...user_guide/supported_formats/renishaw.rst → ...user_guide/supported_formats/renishaw.rst
diff --git a/docs/user_guide/supported_formats/ripple.rst → doc/user_guide/supported_formats/ripple.rst b/docs/user_guide/supported_formats/ripple.rst → doc/user_guide/supported_formats/ripple.rst
diff --git a/docs/user_guide/supported_formats/semper.rst → doc/user_guide/supported_formats/semper.rst b/docs/user_guide/supported_formats/semper.rst → doc/user_guide/supported_formats/semper.rst
diff --git a/...e/supported_formats/supported_formats.rst → ...e/supported_formats/supported_formats.rst b/...e/supported_formats/supported_formats.rst → ...e/supported_formats/supported_formats.rst
diff --git a/docs/user_guide/supported_formats/tia.rst → doc/user_guide/supported_formats/tia.rst b/docs/user_guide/supported_formats/tia.rst → doc/user_guide/supported_formats/tia.rst
diff --git a/docs/user_guide/supported_formats/tiff.rst → doc/user_guide/supported_formats/tiff.rst b/docs/user_guide/supported_formats/tiff.rst → doc/user_guide/supported_formats/tiff.rst
diff --git a/...user_guide/supported_formats/trivista.rst → ...user_guide/supported_formats/trivista.rst b/...user_guide/supported_formats/trivista.rst → ...user_guide/supported_formats/trivista.rst
diff --git a/docs/user_guide/supported_formats/tvips.rst → doc/user_guide/supported_formats/tvips.rst b/docs/user_guide/supported_formats/tvips.rst → doc/user_guide/supported_formats/tvips.rst
diff --git a/docs/user_guide/supported_formats/usid.rst → doc/user_guide/supported_formats/usid.rst b/docs/user_guide/supported_formats/usid.rst → doc/user_guide/supported_formats/usid.rst
diff --git a/docs/user_guide/supported_formats/zspy.rst → doc/user_guide/supported_formats/zspy.rst b/docs/user_guide/supported_formats/zspy.rst → doc/user_guide/supported_formats/zspy.rst
diff --git a/pyproject.toml b/pyproject.toml
@@ -63,7 +63,7 @@ tests = [
   "pytest-cov",
   "setuptools_scm",
 ]
-docs = [
+doc = [
   "numpydoc",
   "pooch",
   "pydata-sphinx-theme>=0.13",
@@ -86,7 +86,7 @@ all = [
 ]
 dev = [
   "black",
-  "rosettasciio[docs]",
+  "rosettasciio[doc]",
   "rosettasciio[all]",
   "rosettasciio[tests]"
 ]

diff --git a/upcoming_changes/190.maintenance.rst b/upcoming_changes/190.maintenance.rst
@@ -0,0 +1 @@
+Simplify GitHub CI workflows by using reusable workflow
-Original file line number
+Diff line change
@@ Expand Up / @@ -73,7 +73,7 @@ The list of *extras*: @@
     And for development, the following *extras* are available (see ``pyproject.toml`` for more information):
     - tests
-    - docs
+    - doc
     - dev
     .. _install-with-conda:
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Simplify GitHub CI workflows by using reusable workflow