Merge branch 'master' into ci-fixes

Author: sbryngelson

.github/workflows/docs.yml

@@ -15,6 +15,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Full history for per-page last-updated dates
 
     # We build doxygen from source because of
     # https://github.com/doxygen/doxygen/issues/9016
@@ -35,6 +37,12 @@ jobs:
         cmake -S . -B build -G Ninja --install-prefix="$(pwd)/build/install" -D MFC_DOCUMENTATION=ON
         ninja -C build install
 
+    - name: Verify essential site files
+      run: |
+        for f in index.html 404.html robots.txt; do
+          test -f "build/install/docs/mfc/$f" || { echo "Missing $f"; exit 1; }
+        done
+
     - name: Upload Built Documentation Artifact
       uses: actions/upload-artifact@v4
       with:
@@ -51,20 +59,14 @@ jobs:
         base-url-path: https://mflowcode.github.io/
         path-to-root: build/install/docs/mfc
         include-pdf: false
-        sitemap-format: txt
+        sitemap-format: xml
 
     - name: Output stats
       run: |
         echo "sitemap-path = ${{ steps.sitemap.outputs.sitemap-path }}"
         echo "url-count = ${{ steps.sitemap.outputs.url-count }}"
         echo "excluded-count = ${{ steps.sitemap.outputs.excluded-count }}"
 
-    - name: Linkcheck - Lychee
-      uses: lycheeverse/lychee-action@v2
-      with:
-        args: -c .lychee.toml build/install/docs/mfc/
-        fail: false
-
     - name: Publish Documentation
       if:   github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' &&  (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' )
       run:  |
@@ -81,5 +83,11 @@ jobs:
         git -C ../www commit -m "Docs @ ${GITHUB_SHA::7}" || true
         git -C ../www push
 
+    - name: Linkcheck - Lychee
+      uses: lycheeverse/lychee-action@v2
+      with:
+        args: -c .lychee.toml build/install/docs/mfc/
+        fail: true
+
 # DOC_PUSH_URL should be of the format:
 # --> https://<username>:<token>@github.com/<username>/<repository>

.github/workflows/homebrew-release.yml

@@ -109,13 +109,14 @@ jobs:
 
           echo "Updating formula to v${VERSION}..."
 
-          # Update URL
-          sed -i "s|url \"https://github.com/MFlowCode/MFC/archive/refs/tags/v[^\"]*\.tar\.gz\"|url \"https://github.com/MFlowCode/MFC/archive/refs/tags/v${VERSION}.tar.gz\"|" "$FORMULA"
+          # Update URL (match any GitHub archive URL, not just MFlowCode/MFC,
+          # in case the formula temporarily points at a fork during testing)
+          sed -i "s|url \"https://github.com/[^\"]*/archive/[^\"]*\.tar\.gz\"|url \"https://github.com/MFlowCode/MFC/archive/refs/tags/v${VERSION}.tar.gz\"|" "$FORMULA"
 
           # Update SHA256 (the one right after url, not bottle SHAs)
           # This uses awk to only update the first sha256 after the url line
           awk -v newsha="$SHA256" '
-            /^  url "https:\/\/github.com\/MFlowCode\/MFC/ { found_url=1 }
+            /^  url "https:\/\/github.com\// { found_url=1 }
             found_url && /^  sha256 "/ && !updated {
               sub(/sha256 "[^"]*"/, "sha256 \"" newsha "\"")
               updated=1
@@ -157,13 +158,16 @@ jobs:
           git config user.email "github-actions[bot]@users.noreply.github.com"
 
           git add Formula/mfc.rb
-          git commit -m "Update MFC to v${VERSION}"
 
-          echo "Pushing to homebrew-mfc..."
-          git push origin main
-
-          echo "Successfully pushed formula update!"
-          echo "The bottle.yml workflow in homebrew-mfc will now build bottles automatically."
+          if git diff --cached --quiet; then
+            echo "::notice::Formula already up to date for v${VERSION} — nothing to push."
+          else
+            git commit -m "Update MFC to v${VERSION}"
+            echo "Pushing to homebrew-mfc..."
+            git push origin main
+            echo "Successfully pushed formula update!"
+            echo "The bottle.yml workflow in homebrew-mfc will now build bottles automatically."
+          fi
 
       - name: Dry run summary
         if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.dry_run == 'true' }}

.lychee.toml

@@ -16,5 +16,12 @@ accept = ["200", "429"]
 
 verbose = "error"
 
-# Exclude sitemap from link checking (it contains pre-publish production URLs)
-exclude_path = ["**/sitemap.txt"]
+# Exclude sitemap file from scanning (it contains pre-publish production URLs)
+exclude_path = ["sitemap\\.xml"]
+
+# Exclude URLs that fail due to external issues (broken SSL, pre-deploy only, etc.)
+exclude = [
+    "https://mflowcode\\.github\\.io/sitemap\\.xml",  # Only exists after deployment
+    "https://cpe\\.ext\\.hpe\\.com",                   # HPE Cray docs have broken SSL cert
+    "https://sc22\\.supercomputing\\.org",              # Returns 415 to automated requests
+]

CMakeLists.txt

@@ -806,6 +806,25 @@ if (MFC_DOCUMENTATION)
     GEN_DOCS(post_process  "MFC: Post-Process")
     GEN_DOCS(documentation "MFC")
 
+    # Inject per-page last-updated dates into documentation markdown files.
+    # Runs after auto-generated .md files exist, before Doxygen processes them.
+    # Uses a stamp file so it only runs once per build.
+    add_custom_command(
+        OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/inject-dates.stamp"
+        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/examples.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/case_constraints.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/physics_constraints.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/cli-reference.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/parameters.md"
+        COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/docs/inject-dates.py"
+                "${CMAKE_CURRENT_SOURCE_DIR}"
+        COMMAND "${CMAKE_COMMAND}" -E touch "${CMAKE_CURRENT_BINARY_DIR}/inject-dates.stamp"
+        COMMENT "Injecting page dates into documentation"
+        VERBATIM
+    )
+    add_custom_target(inject_page_dates DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/inject-dates.stamp")
+    add_dependencies(documentation_doxygen inject_page_dates)
+
     # > Copy Resources (main landing page & assets)
     install(DIRECTORY   "${CMAKE_CURRENT_SOURCE_DIR}/docs/res"
             DESTINATION "docs/mfc")
@@ -814,6 +833,7 @@ if (MFC_DOCUMENTATION)
             DESTINATION "docs/mfc")
 
     install(FILES       "${CMAKE_CURRENT_SOURCE_DIR}/docs/index.html"
+                        "${CMAKE_CURRENT_SOURCE_DIR}/docs/404.html"
             DESTINATION "docs/mfc")
 endif()