Merge branch 'develop' into strsv/ndarray

Author: MeKaustubh07

.devcontainer/post-create

@@ -18,10 +18,31 @@
 
 # Script to set up a development environment.
 
-make install
-make init
+arch="$(uname -m)"
 
 sudo apt-get update
-sudo apt-get install -y gfortran
+
+# On ARM64, pin gcc/g++/gfortran to version 12 to avoid a GCC 16 and binutils version mismatch:
+if [ "${arch}" = "aarch64" ]; then
+	sudo apt-get install -y gfortran-12
+	sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-12 100
+	sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-12 100
+	sudo update-alternatives --install /usr/bin/cc cc /usr/bin/gcc-12 100
+	sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-12 100
+else
+	sudo apt-get install -y gfortran
+fi
+
+make install
+make init
 
 make install-deps-r
+
+# On ARM64, replace the wrong-architecture shellcheck binary with the correct one:
+if [ "${arch}" = "aarch64" ]; then
+	sc_version="$(shellcheck --version 2>/dev/null | grep '^version:' | awk '{print $2}')"
+	if [ -n "${sc_version}" ]; then
+		curl -sL "https://github.com/koalaman/shellcheck/releases/download/v${sc_version}/shellcheck-v${sc_version}.linux.aarch64.tar.xz" \
+			| sudo tar xJ --strip-components=1 -C /usr/local/bin "shellcheck-v${sc_version}/shellcheck"
+	fi
+fi

.github/workflows/generate_pr_commit_message.yml

@@ -21,9 +21,11 @@ name: generate_pr_commit_message
 
 # Workflow triggers:
 on:
-  pull_request_target:
-    types:
-      - labeled
+  workflow_dispatch:
+
+  # pull_request_target:
+    # types:
+      # - labeled
 
 # Global permissions:
 permissions:

.github/workflows/lint_changed_files.yml

@@ -305,7 +305,7 @@ jobs:
       - name: 'Setup R'
         if: ( success() || failure() ) && steps.check-r-files.outputs.files != ''
         # Pin action to full length commit SHA
-        uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
+        uses: r-lib/actions/setup-r@d3c5be51b12e724e68f33216ca3c148b66d5f0b6 # v2.12.1
         with:
           r-version: '4.3.3'
 

.github/workflows/lint_random_files.yml

@@ -113,8 +113,21 @@ jobs:
           node-version: '20' # 'lts/*'
         timeout-minutes: 5
 
+      # Restore cache if up-to-date:
+      - name: 'Restore cache if up-to-date'
+        # Pin action to full length commit SHA
+        uses: actions/cache/restore@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5
+        id: cache
+        with:
+          path: |
+            ${{ github.workspace }}/node_modules
+          key: ${{ runner.os }}-node-${{ hashFiles('**/package.json') }}
+          restore-keys: |
+            ${{ runner.os }}-node-
+
       # Install dependencies (accounting for possible network failures, etc, when installing node module dependencies):
       - name: 'Install dependencies'
+        if: steps.cache.outputs.cache-hit != 'true'
         run: |
           make install-node-modules || make install-node-modules || make install-node-modules
         timeout-minutes: 15
@@ -206,17 +219,34 @@ jobs:
         id: lint-editorconfig
         env:
           FILES: ${{ steps.random-files.outputs.files }}
+
+          # Provide a token so that the editorconfig-checker binary download is authenticated, thus avoiding rate limiting:
+          GITHUB_TOKEN: ${{ github.token }}
         run: |
           set -o pipefail
           files=$(echo "$FILES" | tr ',' ' ')
           make lint-editorconfig-files FILES="${files}" 2>&1 | tee lint_editorconfig_errors.txt
 
+      # Save cache after editorconfig-checker binary has been downloaded:
+      - name: 'Save cache after editorconfig-checker binary has been downloaded'
+        if: always() && steps.cache.outputs.cache-hit != 'true'
+        uses: actions/cache/save@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5
+        with:
+          path: ${{ github.workspace }}/node_modules
+          key: ${{ steps.cache.outputs.cache-primary-key }}
+
       # Create sub-issue for EditorConfig lint failures:
       - name: 'Create sub-issue for EditorConfig lint failures'
         if: failure() && contains(steps.lint-editorconfig.outcome, 'failure')
         env:
           GITHUB_TOKEN: ${{ secrets.STDLIB_BOT_PAT_REPO_WRITE }}
         run: |
+          # Guard against creating spurious issues when the lint step failed due to an infrastructure error (e.g., failing to download the editorconfig-checker binary due to rate limiting) rather than actual lint errors:
+          if grep -q 'Failed to download binary' lint_editorconfig_errors.txt 2>/dev/null; then
+            echo 'EditorConfig lint step failed due to an infrastructure error (e.g., failed binary download). Skipping issue creation.'
+            exit 0
+          fi
+
           strip_ansi() {
             sed -r 's/\x1B\[[0-9;]*[mK]//g'
           }
@@ -406,7 +436,7 @@ jobs:
       - name: 'Setup R'
         if: ( github.event.inputs.r != 'false' ) && ( success() || failure() )
         # Pin action to full length commit SHA
-        uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
+        uses: r-lib/actions/setup-r@d3c5be51b12e724e68f33216ca3c148b66d5f0b6 # v2.12.1
         with:
           r-version: '4.3.3'
 

.github/workflows/markdown_equations.yml

@@ -59,8 +59,11 @@ jobs:
           # Specify whether to remove untracked files before checking out the repository:
           clean: true
 
-          # Limit clone depth to the most recent 100 commits:
-          fetch-depth: 100
+          # Fetch full history to find when SVGs were last modified:
+          fetch-depth: 0
+
+          # Use a blobless clone to speed up the checkout:
+          filter: blob:none
 
           # Specify whether to download Git-LFS files:
           lfs: false
@@ -171,7 +174,7 @@ jobs:
             git commit -m "docs: update Markdown equation elements"
             echo "changed=true" >> $GITHUB_OUTPUT
           fi
-        timeout-minutes: 15
+        timeout-minutes: 60
 
       # Delete remote PR branch to ensure a clean push when the branch has diverged:
       - name: 'Delete remote PR branch'

.github/workflows/markdown_links.yml

@@ -119,18 +119,22 @@ jobs:
 
       # Check whether links are included in `docs/links/database.json` and use the correct identifier:
       - name: 'Check links against database'
-        env:
-          ALL_LINKS: ${{ steps.results.outputs.all_links }}
         run: |
           # Determine root directory:
           root=$(git rev-parse --show-toplevel)
 
           # Define the path to a utility for validating links:
           validate="${root}/lib/node_modules/@stdlib/_tools/links/validate/bin/cli"
 
+          # Write the discovered links to a file, as the list may be too large to pass via an environment variable:
+          all_links_file="${RUNNER_TEMP}/all_links.json"
+          cat > "${all_links_file}" <<'STDLIB_ALL_LINKS_EOF'
+          ${{ steps.results.outputs.all_links }}
+          STDLIB_ALL_LINKS_EOF
+
           echo "## Link Validation" >> $GITHUB_STEP_SUMMARY
 
-          output=$(echo "$ALL_LINKS" | ${validate})
+          output=$(${validate} < "${all_links_file}")
           if [[ "${output}" != "All links are valid." ]]; then
             echo "| URL | ID | Error |" >> $GITHUB_STEP_SUMMARY
             echo "| --- | -- | ----- |" >> $GITHUB_STEP_SUMMARY
@@ -144,12 +148,13 @@ jobs:
 
       # Log the results:
       - name: 'Log results'
-        env:
-          FAILURES: ${{ steps.results.outputs.failures }}
-          WARNINGS: ${{ steps.results.outputs.warnings }}
         run: |
-          echo "$FAILURES" >> "${{ env.LOG_FILE_FAILURES }}"
-          echo "$WARNINGS" >> "${{ env.LOG_FILE_WARNINGS }}"
+          cat >> "${{ env.LOG_FILE_FAILURES }}" <<'STDLIB_FAILURES_EOF'
+          ${{ steps.results.outputs.failures }}
+          STDLIB_FAILURES_EOF
+          cat >> "${{ env.LOG_FILE_WARNINGS }}" <<'STDLIB_WARNINGS_EOF'
+          ${{ steps.results.outputs.warnings }}
+          STDLIB_WARNINGS_EOF
         timeout-minutes: 2
 
       # Fail the workflow if the status is not "success":
@@ -172,10 +177,15 @@ jobs:
         if: failure() && contains(steps.check-status.outcome, 'failure')
         env:
           GITHUB_TOKEN: ${{ secrets.STDLIB_BOT_PAT_REPO_WRITE }}
-          FAILURES: ${{ steps.results.outputs.failures }}
         run: |
+          # Write the failures list to a file, as it may be too large to pass via an environment variable or command-line argument:
+          failures_file="${RUNNER_TEMP}/failures.json"
+          cat > "${failures_file}" <<'STDLIB_FAILURES_EOF'
+          ${{ steps.results.outputs.failures }}
+          STDLIB_FAILURES_EOF
+
           "$GITHUB_WORKSPACE/.github/workflows/scripts/markdown_links/create_broken_link_issues" \
-            "$FAILURES" \
+            "${failures_file}" \
             "9112"
         timeout-minutes: 30
 

.github/workflows/markdown_src_attributes.yml

@@ -97,17 +97,18 @@ jobs:
 
       # Log the results:
       - name: 'Log results'
-        env:
-          FAILURES: ${{ steps.results.outputs.failures }}
-          WARNINGS: ${{ steps.results.outputs.warnings }}
         run: |
-          echo "$FAILURES" >> "${{ env.LOG_FILE_FAILURES }}"
-          echo "$WARNINGS" >> "${{ env.LOG_FILE_WARNINGS }}"
+          cat >> "${{ env.LOG_FILE_FAILURES }}" <<'STDLIB_FAILURES_EOF'
+          ${{ steps.results.outputs.failures }}
+          STDLIB_FAILURES_EOF
+          cat >> "${{ env.LOG_FILE_WARNINGS }}" <<'STDLIB_WARNINGS_EOF'
+          ${{ steps.results.outputs.warnings }}
+          STDLIB_WARNINGS_EOF
         timeout-minutes: 2
 
       # Fail the workflow if the status is not "success":
       - name: 'Check status'
-        if: ${{ steps.results.outputs.status }} != 'success'
+        if: ${{ steps.results.outputs.status != 'success' }}
         run: |
           exit 1
 

.github/workflows/random_benchmarks.yml

@@ -88,6 +88,12 @@ jobs:
           make benchmark-random-javascript RANDOM_SELECTION_SIZE=50 BUILD_ADDONS=1
         timeout-minutes: 60
 
+      # Install Cephes dependencies (required by C benchmarks which compare against the Cephes math library; accounting for possible network failures when downloading):
+      - name: 'Install Cephes dependencies'
+        run: |
+          make install-deps-cephes || make install-deps-cephes || make install-deps-cephes
+        timeout-minutes: 15
+
       # Run C benchmarks:
       - name: 'Run C benchmarks'
         run: |

.github/workflows/run_affected_benchmarks.yml

@@ -131,7 +131,7 @@ jobs:
               files=$(git diff --diff-filter=AM --name-only ${{ github.event.before }} ${{ github.event.after }})
             fi
           fi
-          directories=$(for file in $files; do dirname $file; done | uniq | tr '\n' ' ' | sed 's/ $//')
+          directories=$(for file in $files; do dirname $file; done | sort -u | tr '\n' ' ' | sed 's/ $//')
           echo "directories=${directories}" >> $GITHUB_OUTPUT
 
       # Get list of changed directories from workflow dispatch event:

.github/workflows/run_affected_tests.yml

@@ -163,7 +163,7 @@ jobs:
               files=$(git diff --diff-filter=AM --name-only ${{ github.event.before }} ${{ github.event.after }})
             fi
           fi
-          directories=$(for file in $files; do dirname $file; done | uniq | tr '\n' ' ' | sed 's/ $//')
+          directories=$(for file in $files; do dirname $file; done | sort -u | tr '\n' ' ' | sed 's/ $//')
           echo "directories=${directories}" >> $GITHUB_OUTPUT
 
       # Get list of changed directories from workflow dispatch event: