Merge remote-tracking branch 'upstream/develop' into develop

Author: stdlib-bot

.github/workflows/cleanup_coverage.yml

@@ -0,0 +1,78 @@
+#/
+# @license Apache-2.0
+#
+# Copyright (c) 2024 The Stdlib Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#/
+
+# Workflow name:
+name: cleanup_coverage
+
+# Workflow triggers:
+on:
+
+  # Trigger the workflow when a pull request is closed (e.g., merged or closed without merging):
+  pull_request_target:
+    types:
+      - closed
+
+# Workflow jobs:
+jobs:
+
+  # Define a job to perform coverage cleanup...
+  cleanup:
+
+    # Define a display name:
+    name: 'Cleanup coverage'
+
+    # Define the type of virtual host machine:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Delete the 'pr-<number>' branch from the 'stdlib-js/www-test-code-coverage' repository:
+      - name: 'Delete coverage branch for PR'
+        env:
+          REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+        run: |
+          curl -X DELETE -H "Authorization: token $REPO_GITHUB_TOKEN" \
+            "https://api.github.com/repos/stdlib-js/www-test-code-coverage/git/refs/heads/pr-${PR_NUMBER}" \
+            || echo "Branch pr-${PR_NUMBER} does not exist or could not be deleted."
+
+      # Find and update the '## Coverage Report' comment in the PR
+      - name: 'Update coverage comment in PR'
+        # Pin action to full length commit SHA
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7.0.1
+        with:
+          github-token: ${{ secrets.CHATBOT_GITHUB_TOKEN }}
+          script: |
+            const prNumber = context.payload.pull_request.number;
+            const { data: comments } = await github.rest.issues.listComments({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: prNumber,
+            });
+            const coverageComment = comments.find( comment => comment.body && comment.body.includes( '## Coverage Report' ) );
+            if ( coverageComment ) {
+              // Replace URLs with plain text in the coverage report comment body:
+              const updatedBody = coverageComment.body.replace( /<a href="[^"]+">([^<]+)<\/a>/g, '$1' );
+              await github.rest.issues.updateComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                comment_id: coverageComment.id,
+                body: updatedBody,
+              });
+            } else {
+              console.log( 'No Coverage Report comment found.' );
+            }

.github/workflows/pr_merge_develop.yml

@@ -108,8 +108,18 @@ jobs:
           BRANCH_NAME: ${{ steps.pr-details.outputs.branch }}
           REPO_NAME: ${{ steps.pr-details.outputs.repository }}
         run: |
+          # Configure Git user:
           git config --local user.email "[email protected]"
           git config --local user.name "stdlib-bot"
-          git fetch origin develop:develop
-          git merge develop --no-edit
+
+          # Add upstream remote pointing to the original repository:
+          git remote add upstream https://github.com/stdlib-js/stdlib.git
+
+          # Fetch the develop branch from upstream:
+          git fetch upstream develop
+
+          # Merge upstream develop into the current branch:
+          git merge upstream/develop --no-edit
+
+          # Push the updated branch back to the forked repository:
           git push "https://$USER_NAME:[email protected]/$REPO_NAME.git" $BRANCH_NAME

.github/workflows/pr_rebase_develop.yml

@@ -108,8 +108,18 @@ jobs:
           BRANCH_NAME: ${{ steps.pr-details.outputs.branch }}
           REPO_NAME: ${{ steps.pr-details.outputs.repository }}
         run: |
+          # Configure Git user:
           git config --local user.email "[email protected]"
           git config --local user.name "stdlib-bot"
-          git fetch origin develop:develop
-          git rebase develop
+
+          # Add upstream remote pointing to the original repository:
+          git remote add upstream https://github.com/stdlib-js/stdlib.git
+
+          # Fetch the develop branch from upstream:
+          git fetch upstream develop
+
+          # Rebase current branch onto upstream develop:
+          git rebase upstream/develop
+
+          # Force push the updated branch back to the forked repository:
           git push --force-with-lease "https://$USER_NAME:[email protected]/$REPO_NAME.git" $BRANCH_NAME

.github/workflows/run_tests_coverage.yml

@@ -131,11 +131,22 @@ jobs:
         if: github.event_name != 'workflow_dispatch'
         id: changed-directories
         continue-on-error: true
+        env:
+          STDLIB_BOT_GITHUB_TOKEN: ${{ secrets.STDLIB_BOT_GITHUB_TOKEN }}
         run: |
           if [ -n "${{ github.event.pull_request.number }}" ]; then
             # Get the list of changed files in pull request:
-            ancestor_commit=$(git merge-base ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }})
-            files=$(git diff --diff-filter=AM --name-only $ancestor_commit ${{ github.event.pull_request.head.sha }})
+            page=1
+            files=""
+            while true; do
+                changed_files=$(curl -s -H "Accept: application/vnd.github.v3+json" -H "Authorization: Bearer $STDLIB_BOT_GITHUB_TOKEN" "https://api.github.com/repos/stdlib-js/stdlib/pulls/${{ github.event.pull_request.number }}/files?page=$page&per_page=100" | jq -r '.[] | .filename')
+                if [ -z "$changed_files" ]; then
+                    break
+                fi
+                files="$files $changed_files"
+                page=$((page+1))
+            done
+            files=$(echo "$files" | tr '\n' ' ' | sed 's/ $//')
           else
             # Get changed files by comparing the current commit to the commit before the push event or with its parent:
             if [ "${{ github.event.before }}" == "0000000000000000000000000000000000000000" ]; then
@@ -167,6 +178,15 @@ jobs:
           else
             directories="${{ steps.changed-directories.outputs.directories }}"
           fi
+
+          # Append suffix to coverage base URL for PRs:
+          if [ -n "${{ github.event.pull_request.number }}" ]; then
+            PR_NUMBER=${{ github.event.pull_request.number }}
+            export COVERAGE_BASE_URL="https://coverage.stdlib.io/pr-${PR_NUMBER}"
+          else
+            export COVERAGE_BASE_URL="https://coverage.stdlib.io"
+          fi
+
           . "$GITHUB_WORKSPACE/.github/workflows/scripts/run_tests_coverage" "$directories"
         timeout-minutes: 30
 

.github/workflows/scripts/run_tests_coverage

@@ -42,6 +42,9 @@ set -o pipefail
 
 # VARIABLES #
 
+# Define the base URL for coverage reports, defaulting to 'https://coverage.stdlib.io':
+coverage_base_url="${COVERAGE_BASE_URL:-https://coverage.stdlib.io}"
+
 # Get the list of changed files:
 changed="$*"
 
@@ -159,11 +162,11 @@ main() {
 	for package in ${directories}; do
 		# For each package, extract coverage values from the respective coverage report:
 		pkg=`echo $package | sed -E 's/^.*stdlib\///'`
-		
+
 		if [ -f "lib/node_modules/@stdlib/${pkg}/binding.gyp" ]; then
 			NODE_ADDONS_PATTERN="${pkg}" make install-node-addons
 		fi
-		
+
 		make test-javascript-cov TESTS_FILTER=".*/${pkg}/test/.*"
 
 		if [ ! -f reports/coverage/lcov-report/${pkg}/lib/index.html ]; then
@@ -187,7 +190,7 @@ main() {
 		pkg_functions_cov_fraction=${pkg_cov_fractions[2]}
 		pkg_lines_cov_fraction=${pkg_cov_fractions[3]}
 
-		old_cov_report=$(curl -s --fail "https://coverage.stdlib.io/${pkg}/lib/index.html" 2>/dev/null || true)
+		old_cov_report=$(curl -s --fail "${coverage_base_url}/${pkg}/lib/index.html" 2>/dev/null || true)
 		if [ -z "$old_cov_report" ]; then
 			old_statements_cov=0
 			old_branches_cov=0
@@ -208,7 +211,7 @@ main() {
 
 		pkg_cov="| $pkg_statements_cov_fraction <br> $cov_change_statements | $pkg_branches_cov_fraction <br> $cov_change_branches | $pkg_functions_cov_fraction <br> $cov_change_functions | $pkg_lines_cov_fraction <br> $cov_change_lines |"
 
-		pkg_url="https://coverage.stdlib.io/${pkg}/index.html"
+		pkg_url="${coverage_base_url}/${pkg}/index.html"
 		pkg_link="<a href="$pkg_url">$pkg</a>"
 		coverage="$coverage\n| $pkg_link $pkg_cov"
 

lib/node_modules/@stdlib/blas/base/ccopy/README.md

@@ -245,7 +245,7 @@ Copies values from `X` into `Y`.
 const float x[] = { 1.0f, 2.0f, 3.0f, 4.0f }; // interleaved real and imaginary components
 float y[] = { 0.0f, 0.0f, 0.0f, 0.0f };
 
-c_ccopy( 2, (void *)x, 1, (void *)Y, 1 );
+c_ccopy( 2, (void *)x, 1, (void *)y, 1 );
 ```
 
 The function accepts the following arguments:
@@ -260,6 +260,31 @@ The function accepts the following arguments:
 void c_ccopy( const CBLAS_INT N, const void *X, const CBLAS_INT strideX, void *Y, const CBLAS_INT strideY );
 ```
 
+#### c_ccopy_ndarray( N, \*X, strideX, offsetX, \*Y, strideY, offsetY )
+
+Copies values from `X` into `Y` using alternative indexing semantics.
+
+```c
+const float x[] = { 1.0f, 2.0f, 3.0f, 4.0f }; // interleaved real and imaginary components
+float y[] = { 0.0f, 0.0f, 0.0f, 0.0f };
+
+c_ccopy_ndarray( 2, (void *)x, 1, 0, (void *)y, 1, 0 );
+```
+
+The function accepts the following arguments:
+
+-   **N**: `[in] CBLAS_INT` number of indexed elements.
+-   **X**: `[in] void*` input array.
+-   **strideX**: `[in] CBLAS_INT` index increment for `X`.
+-   **offsetX**: `[in] CBLAS_INT` starting index for `X`.
+-   **Y**: `[out] void*` output array.
+-   **strideY**: `[in] CBLAS_INT` index increment for `Y`.
+-   **offsetY**: `[in] CBLAS_INT` starting index for `Y`.
+
+```c
+void c_ccopy_ndarray( const CBLAS_INT N, const void *X, const CBLAS_INT strideX, const CBLAS_INT offsetX, void *Y, const CBLAS_INT strideY, const CBLAS_INT offsetY );
+```
+
 </section>
 
 <!-- /.usage -->
@@ -301,6 +326,14 @@ int main( void ) {
     for ( int i = 0; i < N; i++ ) {
         printf( "y[ %i ] = %f + %fj\n", i, y[ i*2 ], y[ (i*2)+1 ] );
     }
+
+    // Copy elements using alternative indexing semantics:
+    c_ccopy_ndarray( N, (void *)x, -strideX, N-1, (void *)y, strideY, N-1 );
+
+    // Print the result:
+    for ( int i = 0; i < N; i++ ) {
+        printf( "y[ %i ] = %f + %fj\n", i, y[ i*2 ], y[ (i*2)+1 ] );
+    }
 }
 ```
 

lib/node_modules/@stdlib/blas/base/ccopy/benchmark/c/benchmark.length.c

@@ -94,7 +94,7 @@ static float rand_float( void ) {
 * @param len          array length
 * @return elapsed time in seconds
 */
-static double benchmark( int iterations, int len ) {
+static double benchmark1( int iterations, int len ) {
 	double elapsed;
 	float x[ len*2 ];
 	float y[ len*2 ];
@@ -122,6 +122,41 @@ static double benchmark( int iterations, int len ) {
 	return elapsed;
 }
 
+/**
+* Runs a benchmark.
+*
+* @param iterations   number of iterations
+* @param len          array length
+* @return elapsed time in seconds
+*/
+static double benchmark2( int iterations, int len ) {
+	double elapsed;
+	float x[ len*2 ];
+	float y[ len*2 ];
+	double t;
+	int i;
+
+	for ( i = 0; i < len; i++ ) {
+		x[ i ] = ( rand_float()*10000.0f ) - 5000.0f;
+		x[ i+1 ] = ( rand_float()*10000.0f ) - 5000.0f;
+		y[ i ] = 0.0f;
+		y[ i+1 ] = 0.0f;
+	}
+	t = tic();
+	for ( i = 0; i < iterations; i++ ) {
+		c_ccopy_ndarray( len, (void *)x, 1, 0, (void *)y, 1, 0 );
+		if ( y[ 0 ] != y[ 0 ] ) {
+			printf( "should not return NaN\n" );
+			break;
+		}
+	}
+	elapsed = tic() - t;
+	if ( y[ 0 ] != y[ 0 ] ) {
+		printf( "should not return NaN\n" );
+	}
+	return elapsed;
+}
+
 /**
 * Main execution sequence.
 */
@@ -144,7 +179,14 @@ int main( void ) {
 		for ( j = 0; j < REPEATS; j++ ) {
 			count += 1;
 			printf( "# c::%s:len=%d\n", NAME, len );
-			elapsed = benchmark( iter, len );
+			elapsed = benchmark1( iter, len );
+			print_results( iter, elapsed );
+			printf( "ok %d benchmark finished\n", count );
+		}
+		for ( j = 0; j < REPEATS; j++ ) {
+			count += 1;
+			printf( "# c::%s:ndarray:len=%d\n", NAME, len );
+			elapsed = benchmark2( iter, len );
 			print_results( iter, elapsed );
 			printf( "ok %d benchmark finished\n", count );
 		}

lib/node_modules/@stdlib/blas/base/ccopy/examples/c/example.c

@@ -38,4 +38,12 @@ int main( void ) {
 	for ( int i = 0; i < N; i++ ) {
 		printf( "y[ %i ] = %f + %fj\n", i, y[ i*2 ], y[ (i*2)+1 ] );
 	}
+
+	// Copy elements using alternative indexing semantics:
+	c_ccopy_ndarray( N, (void *)x, -strideX, N-1, (void *)y, strideY, N-1 );
+
+	// Print the result:
+	for ( int i = 0; i < N; i++ ) {
+		printf( "y[ %i ] = %f + %fj\n", i, y[ i*2 ], y[ (i*2)+1 ] );
+	}
 }

lib/node_modules/@stdlib/blas/base/ccopy/include/stdlib/blas/base/ccopy.h

@@ -36,6 +36,11 @@ extern "C" {
 */
 void API_SUFFIX(c_ccopy)( const CBLAS_INT N, const void *X, const CBLAS_INT strideX, void *Y, const CBLAS_INT strideY );
 
+/**
+* Copies values from one complex single-precision floating-point vector to another complex single-precision floating-point vector using alternative indexing semantics.
+*/
+void API_SUFFIX(c_ccopy_ndarray)( const CBLAS_INT N, const void *X, const CBLAS_INT strideX, const CBLAS_INT offsetX, void *Y, const CBLAS_INT strideY, const CBLAS_INT offsetY );
+
 #ifdef __cplusplus
 }
 #endif