Fix test workflow to run tests in nested test directories

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
   "name": "stdlib - OSS Development",
-  "image": "mcr.microsoft.com/devcontainers/universal:2",
+  "image": "mcr.microsoft.com/devcontainers/javascript-node",
   "features": {
     "ghcr.io/rocker-org/devcontainer-features/r-apt:0": {},
     "ghcr.io/julialang/devcontainer-features/julia:1": {},

.devcontainer/post-create

@@ -24,4 +24,4 @@ make init
 sudo apt-get update
 sudo apt-get install -y gfortran
 
-make install-deps-r
+#make install-deps-r

.github/workflows/autoclose.yml

@@ -37,11 +37,6 @@ jobs:
     # Only run this job if the pull request has a specific label:
     if: "${{ github.event.label.name == 'autoclose: EditorConfig' }}"
 
-    # Define job permissions:
-    permissions:
-      contents: read
-      pull-requests: write
-
     # Define the type of virtual host machine:
     runs-on: ubuntu-latest
 
@@ -58,7 +53,7 @@ jobs:
           BODY: |
             Thank you for working on this pull request. However, we cannot accept your contribution as this pull request does not follow our [contributing guidelines](https://github.com/stdlib-js/stdlib/blob/develop/CONTRIBUTING.md).
 
-            Per the guidelines outlined in our [development guide](https://github.com/stdlib-js/stdlib/blob/develop/docs/development.md), you should download and setup [EditorConfig](http://editorconfig.org/) to ensure that files are automatically configured to use expected indentation and line endings.
+            Per the guidelines outlined in our [development guide](https://github.com/stdlib-js/stdlib/blob/develop/docs/contributing/development.md), you should download and setup [EditorConfig](http://editorconfig.org/) to ensure that files are automatically configured to use expected indentation and line endings.
 
             If you would prefer to avoid manual setup, you could also consider using a pre-configured [development container](https://github.com/stdlib-js/stdlib/tree/develop/.devcontainer) for use locally or in GitHub Codespaces.
 
@@ -73,11 +68,6 @@ jobs:
     # Only run this job if the pull request has a specific label:
     if: "${{ github.event.label.name == 'autoclose: Contributor Guidelines' }}"
 
-    # Define job permissions:
-    permissions:
-      contents: read
-      pull-requests: write
-
     # Define the type of virtual host machine:
     runs-on: ubuntu-latest
 
@@ -94,7 +84,7 @@ jobs:
           BODY: |
             Thank you for working on this pull request. However, we cannot accept your contribution as this pull request does not follow our [contributing guidelines](https://github.com/stdlib-js/stdlib/blob/develop/CONTRIBUTING.md).
 
-            Per the guidelines outlined in our [development guide](https://github.com/stdlib-js/stdlib/blob/develop/docs/development.md), you should have setup your local development environment such that automated development processes for linting, license verification, and unit testing can run prior to authoring commits and pushing changes. We encourage you to refer to that guide **before** continuing to work on this pull request.
+            Per the guidelines outlined in our [development guide](https://github.com/stdlib-js/stdlib/blob/develop/docs/contributing/development.md), you should have setup your local development environment such that automated development processes for linting, license verification, and unit testing can run prior to authoring commits and pushing changes. We encourage you to refer to that guide **before** continuing to work on this pull request.
 
             If you would prefer to avoid manual setup, you could also consider using a pre-configured [development container](https://github.com/stdlib-js/stdlib/tree/develop/.devcontainer) for use locally or in GitHub Codespaces.
 
@@ -109,11 +99,6 @@ jobs:
     # Only run this job if the pull request has a specific label:
     if: "${{ github.event.label.name == 'autoclose: Project Conventions' }}"
 
-    # Define job permissions:
-    permissions:
-      contents: read
-      pull-requests: write
-
     # Define the type of virtual host machine:
     runs-on: ubuntu-latest
 
@@ -149,11 +134,6 @@ jobs:
     # Only run this job if the pull request has a specific label:
     if: "${{ github.event.label.name == 'autoclose: Spam' }}"
 
-    # Define job permissions:
-    permissions:
-      contents: read
-      pull-requests: write
-
     # Define the type of virtual host machine:
     runs-on: ubuntu-latest
 
@@ -189,12 +169,6 @@ jobs:
     # Only run this job if the pull request has a specific label:
     if: "${{ github.event.label.name == 'autoclose: Stale' }}"
 
-    # Define job permissions:
-    permissions:
-      contents: read
-      issues: write
-      pull-requests: write
-
     # Define the type of virtual host machine:
     runs-on: ubuntu-latest
 
@@ -211,3 +185,39 @@ jobs:
             This pull request has been automatically closed because it has been inactive for an extended period after changes were requested. If you still wish to pursue this contribution, feel free to reopen the pull request or submit a new one.
 
             We appreciate your interest in contributing to stdlib!
+
+  # Define a job which closes a pull request if a PR has an inappropriate Git history:
+  git_history:
+
+    # Define job name:
+    name: 'Check for Git History label'
+
+    # Only run this job if the pull request has a specific label:
+    if: "${{ github.event.label.name == 'autoclose: Git History' }}"
+
+    # Define the type of virtual host machine:
+    runs-on: ubuntu-latest
+
+    # Define the sequence of job steps:
+    steps:
+
+      # Close the pull request:
+      - name: 'Close pull request'
+        run: gh pr close "$NUMBER" --comment "$BODY"
+        env:
+          GH_TOKEN: ${{ secrets.STDLIB_BOT_PAT_REPO_WRITE }}
+          GH_REPO: ${{ github.repository }}
+          NUMBER: ${{ github.event.pull_request.number }}
+          BODY: |
+            Thank you for working on this pull request. However, we cannot accept your contribution due to Git history issues.
+
+            Some common issues include:
+
+            -   Merge conflicts
+            -   Inappropriate commit messages
+            -   Unrelated commits
+            -   Including changes from merged branches that weren't intended for this PR
+
+            We recommend opening a new pull request with only the intended changes.
+
+            Thank you for your interest in stdlib, and we look forward to your future contributions.

.github/workflows/check_commit_metadata.yml

@@ -0,0 +1,75 @@
+#/
+# @license Apache-2.0
+#
+# Copyright (c) 2025 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: check_commit_metadata
+
+# Workflow triggers:
+on:
+  # Trigger on pull request events:
+  pull_request_target:
+    types:
+      - opened
+
+# Global permissions:
+permissions:
+  # Allow read-only access to the repository contents:
+  contents: read
+
+# Workflow jobs:
+jobs:
+
+  # Define a job for checking the commit metadata for whether local development is properly setup...
+  check_commit_metadata:
+
+    # Define a display name:
+    name: 'Check Commit Metadata'
+
+    # Define the type of virtual host machine:
+    runs-on: ubuntu-latest
+
+    # Temporarily disable the entire workflow:
+    if: false
+
+    # Define the sequence of job steps...
+    steps:
+      # Checkout the repository:
+      - name: 'Checkout repository'
+        # Pin action to full length commit SHA
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          # Ensure we have access to the scripts directory:
+          sparse-checkout: |
+              .github/workflows/scripts
+          sparse-checkout-cone-mode: false
+        timeout-minutes: 10
+
+      # Extract commit metadata from commit messages as JSON:
+      - name: 'Extract commit metadata'
+        id: extract-metadata
+        # Pin action to full length commit SHA
+        uses: stdlib-js/metadata-action@3ccf68f24c51ae23470319e8e5619d539df8212b # v3.0.0
+
+      # Check commit metadata:
+      - name: 'Check commit metadata'
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          COMMIT_METADATA: ${{ steps.extract-metadata.outputs.metadata }}
+          GITHUB_TOKEN: ${{ secrets.STDLIB_BOT_PAT_REPO_WRITE }}
+        run: |
+          . "$GITHUB_WORKSPACE/.github/workflows/scripts/check_commit_metadata" $PR_NUMBER $COMMIT_METADATA

.github/workflows/check_contributing_guidelines_acceptance.yml

@@ -19,39 +19,11 @@
 # Workflow name:
 name: check_contributing_guidelines_acceptance
 
-# Workflow triggers:
-on:
-  # Allow the workflow to be triggered by other workflows
-  workflow_call:
-    # Define the input parameters for the workflow:
-    inputs:
-      pull_request_number:
-        description: 'Pull request number'
-        required: true
-        type: number
-      user:
-        required: true
-        type: string
-    # Define the secrets accessible by the workflow:
-    secrets:
-      STDLIB_BOT_GITHUB_TOKEN:
-        description: 'stdlib-bot GitHub token to create pull request comments'
-        required: true
-
-  # Trigger on pull request events:
-  pull_request_target:
-    types:
-      - opened
-      - reopened
-
 # Global permissions:
 permissions:
   # Allow read-only access to the repository contents:
   contents: read
 
-  # Allow write access to pull requests:
-  pull-requests: write
-
 # Workflow jobs:
 jobs:
 
@@ -74,14 +46,10 @@ jobs:
         # Pin action to full length commit SHA
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
-          # Specify whether to remove untracked files before checking out the repository:
-          clean: true
-
-          # Limit clone depth to the most recent commit:
-          fetch-depth: 1
-
-          # Specify whether to download Git-LFS files:
-          lfs: false
+          # Ensure we have access to the scripts directory:
+          sparse-checkout: |
+              .github/workflows/scripts
+          sparse-checkout-cone-mode: false
         timeout-minutes: 10
 
       # Check contributing guidelines acceptance:

.github/workflows/check_licenses.yml

@@ -128,7 +128,7 @@ jobs:
       # Upload the log file:
       - name: 'Upload log file'
         # Pin action to full length commit SHA
-        uses: actions/upload-artifact@65c4c4a1ddee5b72f698fdd19549f0f0fb45cf08 # v4.6.0
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4.6.1
         if: always()
         with:
           # Define a name for the uploaded artifact:

.github/workflows/create_address_commit_comment_issues.yml

@@ -55,14 +55,10 @@ jobs:
         # Pin action to full length commit SHA
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
-          # Specify whether to remove untracked files before checking out the repository:
-          clean: false
-
-          # Limit clone depth to the most recent commit:
-          fetch-depth: 1
-
-          # Specify whether to download Git-LFS files:
-          lfs: false
+          # Ensure we have access to the scripts directory:
+          sparse-checkout: |
+              .github/workflows/scripts
+          sparse-checkout-cone-mode: false
         timeout-minutes: 10
 
       # Create issues from commit comments:

.github/workflows/first_time_greeting.yml

@@ -19,8 +19,6 @@
 # Workflow name:
 name: first_time_greeting
 
-# Workflow triggers:
-on: [pull_request_target, issues]
 
 # Global permissions:
 permissions:

.github/workflows/generate_pr_commit_message.yml

@@ -30,12 +30,6 @@ permissions:
   # Allow read-only access to the repository contents:
   contents: read
 
-  # Allow write access to issues, assignees, labels, and milestones:
-  issues: write
-
-  # Allow write access to pull requests:
-  pull-requests: write
-
 # Workflow jobs:
 jobs:
 
@@ -62,8 +56,10 @@ jobs:
         # Pin action to full length commit SHA
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
-          # Fetch all commits to ensure we have the full commit history:
-          fetch-depth: 0
+          # Ensure we have access to the scripts directory:
+          sparse-checkout: |
+            .github/workflows/scripts
+          sparse-checkout-cone-mode: false
 
       # Generate commit message:
       - name: 'Generate commit message'

.github/workflows/good_first_issue.yml

@@ -40,7 +40,6 @@ jobs:
     # Define job permissions:
     permissions:
       contents: read
-      pull-requests: write
 
     # Define the type of virtual host machine:
     runs-on: ubuntu-latest
@@ -65,7 +64,7 @@ jobs:
             1.  **You cannot "claim" issues.** People new to open source often want to "claim" or be assigned an issue before beginning work. The typical rationale is that people want to avoid wasted work in the event that someone else ends up working the issue. However, this practice is not effective in open source, as it often leads to "issue squatting", in which an individual asks to be assigned, is granted their request, and then never ends up working on the issue. Accordingly, you are encouraged to communicate your intent to address this issue, ideally by providing a rough outline as to how you plan to address the issue or asking clarifying questions, but, at the end of the day, we will take running code and rough consensus in order to move forward quickly.
             2.  **We have a very high bar for contributions.** We have very high standards for contributions and expect all contributions—whether new features, tests, or documentation—to be rigorous, thorough, and complete. Once a pull request is merged into stdlib, that contribution immediately becomes the collective responsibility of all maintainers of stdlib. When we merge code into stdlib, we are saying that we, the maintainers, commit to reviewing subsequent changes and making bugfixes to the code. Hence, in order to ensure future maintainability, this naturally leads to a higher standard of contribution.
 
-            Before working on this issue and opening a pull request, please read the project's [contributing guidelines](https://github.com/stdlib-js/stdlib/blob/develop/CONTRIBUTING.md). These guidelines and the associated [development guide](https://github.com/stdlib-js/stdlib/blob/develop/docs/development.md) provide important information, including links to stdlib's [Code of Conduct](https://github.com/stdlib-js/stdlib/blob/develop/CODE_OF_CONDUCT.md), license policy, and steps for setting up your local development environment.
+            Before working on this issue and opening a pull request, please read the project's [contributing guidelines](https://github.com/stdlib-js/stdlib/blob/develop/CONTRIBUTING.md). These guidelines and the associated [development guide](https://github.com/stdlib-js/stdlib/blob/develop/docs/contributing/development.md) provide important information, including links to stdlib's [Code of Conduct](https://github.com/stdlib-js/stdlib/blob/develop/CODE_OF_CONDUCT.md), license policy, and steps for setting up your local development environment.
 
             To reiterate, we **strongly** encourage you to refer to our contributing guides **before** beginning work on this issue. Failure to follow our guidelines significantly decreases the likelihood that you'll successfully contribute to stdlib and may result in automatic closure of a pull request without review.