toil 8.0.0__tar.gz → 8.2.0__tar.gz

toil-8.2.0/.git-blame-ignore-revs

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+# make format with black 24.10.0 on 2024-10-19
+49d99f17799aa4a4235126bbdfb45f85e6499b27
+# make sort_imports
+a307a57651296e576d55f9159869dc9130da2b7c
+# make remove_unused_import
+1c6217e11a2815476ede1cc3ee584d5da3d5242a
+# make pyupgrade (3.9+)
+00f54f8417b3a0bc5d1ea46650aa2e6ce4792159

toil-8.2.0/.github/PULL_REQUEST_TEMPLATE.md

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+## Changelog Entry
+To be copied to the [draft changelog](https://github.com/DataBiosphere/toil/wiki/Draft-Changelog) by merger:
+
+ * PR submitter writes their recommendation for a changelog entry here
+
+## Reviewer Checklist
+
+<!-- To be kept in sync with docs/contributing/checklists.rst -->
+
+ * [ ] Make sure it is coming from `issues/XXXX-fix-the-thing` in the Toil repo, or from an external repo.
+    * [ ] If it is coming from an external repo, make sure to pull it in for CI with:
+        ```
+        contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
+        ```
+    * [ ] If there is no associated issue, [create one](https://github.com/DataBiosphere/toil/issues/new).
+* [ ] Read through the code changes. Make sure that it doesn't have:
+    * [ ] Addition of trailing whitespace.
+    * [ ] New variable or member names in `camelCase` that want to be in `snake_case`.
+    * [ ] New functions without [type hints](https://docs.python.org/3/library/typing.html).
+    * [ ] New functions or classes without informative docstrings.
+    * [ ] Changes to semantics not reflected in the relevant docstrings.
+    * [ ] New or changed command line options for Toil workflows that are not reflected in `docs/running/{cliOptions,cwl,wdl}.rst` 
+    * [ ] New features without tests.
+* [ ] Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
+* [ ] Finish the review with an overall description of your opinion.
+
+## Merger Checklist
+
+<!-- To be kept in sync with docs/contributing/checklists.rst -->
+
+* [ ] Make sure the PR passed tests, including the Gitlab tests, for the most recent commit in its branch.
+* [ ] Make sure the PR has been reviewed. If not, review it. If it has been reviewed and any requested changes seem to have been addressed, proceed.
+* [ ] Merge with the Github "Squash and merge" feature.
+    * [ ] If there are multiple authors' commits, add [Co-authored-by](https://github.blog/2018-01-29-commit-together-with-co-authors/) to give credit to all contributing authors.
+* [ ] Copy its recommended changelog entry to the [Draft Changelog](https://github.com/DataBiosphere/toil/wiki/Draft-Changelog).
+* [ ] Append the issue number in parentheses to the changelog entry.
+

toil-8.2.0/.github/dependabot.yml

@@ -0,0 +1,23 @@
+# Dependabot configuration file
+# Validate with: check-jsonschema --schemafile https://json.schemastore.org/dependabot-2.0.json .github/dependabot.yml
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+    ignore:
+      # htcondor is not under CI
+      - dependency-name: "htcondor"
+      # Google cloud/storage is not under CI
+      - dependency-name: "apache-libcloud"
+      - dependency-name: "google-cloud-storage"
+      - dependency-name: "google-auth"
+    rebase-strategy: disabled
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    rebase-strategy: disabled
+    
+

toil-8.2.0/.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '27 21 * * 4'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2

toil-8.2.0/.gitignore

@@ -0,0 +1,26 @@
+*.pyc
+/src/*.egg-info
+/build
+/dist
+/docs/_build
+__pycache__
+.eggs/
+.cache/
+.pytest_cache/
+.idea/
+/test-report.xml
+/test-report-*.xml
+venv*
+v3nv/
+tmp/
+/src/toil/test/cwl/spec*
+/src/toil/test/wdl/wdl-conformance-tests
+/cwltool_deps/
+/docs/generated_rst/
+/docker/Dockerfile
+/docker/toil-*.tar.gz
+/src/toil/version.py
+.coverage*
+.mypy_cache
+/contrib/admin/.issue_cache/
+.docker_cache/