backmerge after hotfix #178

rozyczko · 2025-06-12T07:23:49Z

Interestingly, there is a large discrepancy between master and develop, despite develop being pushed to master for the 0.4.0 release

* initial conversion to the new parameter syntax Remaining issue with unit conversion (deg -> us) Remaining Descriptor conversion * added new Descriptors and fixed ruff * use ruff 0.9, since 0.8.x didn't give good enough info * rely on `new_param` branch of EXC * assure exp names are correct * Update README for logo links and project info * Add CI workflow for documentation build and deploy * Update development workflow * Update docs and improve formatting * Fix issues after reviewing PR * assign interface when necessary * Fix path in mkdocs.yml creation step * _pd_calib.2theta_offset in parameters for display proper handling of error format in experiment cif * minor changes for multiphase * added optional to some phase params to make possible editing CIF in place modified setup for the cryspy job object * fix offset setup * added error parser for integers * fixed reading of errors in phase cif * tof stuff from new_param_tof * changes after merging DescriptorAny in EasyCrystallography * added updated version of dataBlockToCif * Fixed TOF profile calcs. Fixed typos * minor fixes and performance impromevents * fix for multiphase scale issue not being properly set up after fitting * add fix for exp names, not just tof. fix phase generation for cases when arguments don't contain atoms/cell adjusted fitting results * Added bridge link for intermediate updates Updated dependency for easyScience * fixed phase update for multiphase cases * minor fix for ToF * fixes for experiment update --------- Co-authored-by: Andrew Sazonov <[email protected]> Co-authored-by: Andrew Sazonov <[email protected]>

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github-advanced-security · 2025-06-12T07:34:50Z

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.github/workflows/build-docs.yml

+        with:
+          python-version: '3.12'
+
+      - name: Upgrade package installer for Python
+        run: python -m pip install --upgrade pip
+
+      # Install MkDocs -- static site generator
+      # https://www.mkdocs.org
+      - name: Install MkDocs and its dependencies
+        run: >
+          pip install mkdocs mkdocs-material 'mkdocs-autorefs<1.3.0'
+          mkdocs-jupyter mkdocs-plugin-inline-svg
+          mkdocs-markdownextradata-plugin mkdocstrings-python
+
+      # Install EasyDiffraction Library to run Jupyter notebooks
+      # Install with the 'charts' and 'docs' extras
+      - name: Install EasyDiffraction Library and its dependencies
+        run: pip install 'easydiffraction[charts]'
+
+      # Download and add the extra files from the easyscience/assets-docs repository
+      - name: Get easyscience/assets-docs files
+        run: |
+          git clone https://github.com/easyscience/assets-docs.git
+          cp -R assets-docs/docs/assets/ docs/assets/
+          cp -R assets-docs/includes/ includes/
+          cp -R assets-docs/overrides/ overrides/
+
+      # Download and add the extra files from the easyscience/assets-branding repository
+      - name: Get easyscience/assets-branding files
+        run: |
+          git clone https://github.com/easyscience/assets-branding.git
+          mkdir -p docs/assets/images/
+          cp assets-branding/easydiffraction/logos/ed-logo-2_dark.svg docs/assets/images/
+          cp assets-branding/easydiffraction/logos/ed-logo-2_light.svg docs/assets/images/
+          cp assets-branding/easydiffraction/icons/ed-icon_256x256.png docs/assets/images/favicon.png
+          mkdir -p overrides/.icons/
+          cp assets-branding/easydiffraction/icons/ed-icon_bw.svg overrides/.icons/easydiffraction.svg
+          cp assets-branding/easyscience-org/icons/eso-icon_bw.svg overrides/.icons/easyscience.svg
+
+      # Copy Jupyter notebooks from the project to the docs folder
+      # The notebooks are used to generate the documentation
+      - name:
+          Copy Jupyter notebooks from ${{ env.NOTEBOOKS_DIR }}/ to docs/${{
+          env.NOTEBOOKS_DIR }}/
+        run: cp -R ${{ env.NOTEBOOKS_DIR }}/ docs/${{ env.NOTEBOOKS_DIR }}/
+
+      # The following step is needed to avoid the following message during the build:
+      # "Matplotlib is building the font cache; this may take a moment"
+      - name: Pre-build site step
+        run: python -c "import easydiffraction"
+
+      # Create the mkdocs.yml configuration file
+      # The file is created by merging two files:
+      # - assets-docs/mkdocs.yml - the common configuration (theme, plugins, etc.)
+      # - docs/mkdocs.yml - the project-specific configuration (project name, TOC, etc.)
+      - name: Create mkdocs.yml file
+        run: cat assets-docs/mkdocs.yml docs/mkdocs.yml > mkdocs.yml
+
+      # Build the static files
+      # Input: docs/ directory containing the Markdown files
+      # Output: site/ directory containing the generated HTML files
+      - name: Build site with MkDocs
+        run: |
+          export JUPYTER_PLATFORM_DIRS=1
+          mkdocs build
+
+      # Set up the Pages action to configure the static files to be deployed
+      # NOTE: The repository must have GitHub Pages enabled and configured to build using GitHub Actions
+      # This can be done via https://github.com/easyscience/diffraction-lib/settings/pages
+      # Select: Build and deploy - Source - GitHub Actions
+      - name: Setup GitHub Pages
+        uses: actions/configure-pages@v5
+
+      # Upload the static files from the site/ directory to be used in the next job
+      # This artifact is named github-pages and is a single gzip archive containing a single tar file
+      # The artifact is then used in the next job by actions/deploy-pages to deploy the static files to GitHub Pages
+      # Unfortunately, the artifact is not available for download, so extra steps below are needed to do similar things
+      - name:
+          Upload built site as artifact for
+          easyscience.github.io/diffraction-lib (all branches)
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/
+
+      # Upload the static files from the site/ directory to be used in the next job
+      # This extra step is needed to allow the download of the artifact in the next job
+      # for pushing its content to the branch named 'easydiffraction.org'
+      - name:
+          Upload built site as artifact for gh_pages and easydiffraction.org
+          (master branch)
+        if: ${{ env.CI_BRANCH == 'master' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifact # name of the artifact (without the extension zip)
+          path: site/
+          if-no-files-found: 'error'
+          compression-level: 0
+
+  # Job 2: Deploy the static files
+  deploy-docs:


To fix the issue, we need to add a permissions block to the build-docs job in the workflow file. This block should explicitly set the permissions required for the job, which in this case is likely limited to contents: read. This ensures that the GITHUB_TOKEN used in the job has only the minimal permissions necessary to complete the tasks.

The changes should be made in the .github/workflows/build-docs.yml file, specifically within the build-docs job definition. No additional imports, methods, or definitions are required.

rozyczko and others added 2 commits April 4, 2025 19:15

Added missing conversion field (#177)

daff336

github-actions bot requested changes Jun 12, 2025

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rozyczko added chore Changes to the build process or auxiliary tools and libraries such as documentation generation [scope] maintenance Code/tooling cleanup, no feature or bugfix (major.minor.PATCH) [priority] high Should be prioritized soon labels Jun 12, 2025

github-actions bot approved these changes Jun 12, 2025

View reviewed changes

github-advanced-security bot found potential problems Jun 12, 2025

View reviewed changes

@@ -24,2 +24,4 @@
                 runs-on: macos-14 # Use macOS to switch to dark mode for Plotly charts
+                permissions:
+                  contents: read

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backmerge after hotfix #178

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rozyczko commented Jun 12, 2025 •

edited

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rozyczko commented Jun 12, 2025 •

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