Store source files under /tmp to avoid permission issues on GHA

microbiomedata · Dec 5, 2024 · 3b4b9dc · 3b4b9dc
1 parent 0386f9f
commit 3b4b9dc
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Showing 3 changed files with 20 additions and 19 deletions.
diff --git a/.github/workflows/fetch-and-compile-workflow-documentation.yml b/.github/workflows/fetch-and-compile-workflow-documentation.yml
@@ -20,18 +20,18 @@ jobs:
         with: { python-version: '3.12' }
       - name: Install dependencies of workflow documentation
         run: python -m pip install sphinx sphinx_rtd_theme pillow
-        # Note: This shell script will store the chapters in `/src/*`.
+        # Note: This shell script will store the chapters under `/tmp/book/src/`.
       - name: Fetch documentation sources and arrange into chapters
         run: |
           chmod +x ./src/workflow_docs/fetch_docs_sources.sh
           ./src/workflow_docs/fetch_docs_sources.sh
       - name: Introduce additional source documents and a configuration file
         run: |
-          cp src/workflow_docs/overview.rst /src/overview.rst
-          cp src/workflow_docs/index.rst    /src/index.rst
-          cp src/workflow_docs/conf.py      /src/conf.py
+          cp src/workflow_docs/overview.rst /tmp/book/src/chapters/overview.rst
+          cp src/workflow_docs/index.rst    /tmp/book/src/index.rst
+          cp src/workflow_docs/conf.py      /tmp/book/src/conf.py
       - name: Compile source documents into HTML
-        run: sphinx-build --builder html /src ${{ github.workspace }}/_dist
+        run: sphinx-build --builder html /tmp/book/src ${{ github.workspace }}/_dist
         # Upload the result as an "artifact" so it can then be downloaded and used by another job.
       - name: Save the HTML for publishing later  # Docs: https://github.com/actions/upload-artifact
         uses: actions/upload-artifact@v4

diff --git a/src/workflow_docs/Dockerfile b/src/workflow_docs/Dockerfile
@@ -26,9 +26,10 @@ RUN chmod +x /tmp/fetch_docs_sources.sh
 RUN /tmp/fetch_docs_sources.sh
 
 # Introduce additional source documents and a configuration file.
-COPY overview.rst /src/chapters/overview.rst
-COPY index.rst    /src/index.rst
-COPY conf.py      /src/conf.py
+# Note: The above shell script will have created `/tmp/book/src/chapters/`.
+COPY overview.rst /tmp/book/src/chapters/overview.rst
+COPY index.rst    /tmp/book/src/index.rst
+COPY conf.py      /tmp/book/src/conf.py
 
 # Compile source documents into HTML.
 #
@@ -38,7 +39,7 @@ COPY conf.py      /src/conf.py
 #
 # Reference: https://www.sphinx-doc.org/en/master/man/sphinx-build.html
 #
-RUN sphinx-build --builder html /src /html
+RUN sphinx-build --builder html /tmp/book/src /html
 
 EXPOSE 8000
 

diff --git a/src/workflow_docs/fetch_docs_sources.sh b/src/workflow_docs/fetch_docs_sources.sh
@@ -21,13 +21,13 @@ git clone --no-checkout --depth=1 --single-branch --branch=master --filter=tree:
 git clone --no-checkout --depth=1 --single-branch --branch=master --filter=tree:0 https://github.com/microbiomedata/enviroMS /tmp/clones/enviroMS                   && cd /tmp/clones/enviroMS          && git sparse-checkout set --no-cone /docs && git checkout
 
 # Arrange the "docs" directories into chapters.
-mkdir -p /src/chapters
-mv /tmp/clones/ReadsQC/docs           /src/chapters/1_RQC
-mv /tmp/clones/ReadbasedAnalysis/docs /src/chapters/2_ReadAnalysis
-mv /tmp/clones/metaAssembly/docs      /src/chapters/3_MetaGAssembly
-mv /tmp/clones/mg_annotation/docs     /src/chapters/4_MetaGAnnotation
-mv /tmp/clones/metaMAGs/docs          /src/chapters/5_MAG
-mv /tmp/clones/metaT/docs             /src/chapters/6_MetaT
-mv /tmp/clones/metaPro/docs           /src/chapters/7_Metaproteomics
-mv /tmp/clones/metaMS/docs            /src/chapters/8_Metabolomics
-mv /tmp/clones/enviroMS/docs          /src/chapters/9_NOM
+mkdir -p /tmp/book/src/chapters
+mv /tmp/clones/ReadsQC/docs           /tmp/book/src/chapters/1_RQC
+mv /tmp/clones/ReadbasedAnalysis/docs /tmp/book/src/chapters/2_ReadAnalysis
+mv /tmp/clones/metaAssembly/docs      /tmp/book/src/chapters/3_MetaGAssembly
+mv /tmp/clones/mg_annotation/docs     /tmp/book/src/chapters/4_MetaGAnnotation
+mv /tmp/clones/metaMAGs/docs          /tmp/book/src/chapters/5_MAG
+mv /tmp/clones/metaT/docs             /tmp/book/src/chapters/6_MetaT
+mv /tmp/clones/metaPro/docs           /tmp/book/src/chapters/7_Metaproteomics
+mv /tmp/clones/metaMS/docs            /tmp/book/src/chapters/8_Metabolomics
+mv /tmp/clones/enviroMS/docs          /tmp/book/src/chapters/9_NOM