stepup-queue 1.0.5__tar.gz → 1.0.6__tar.gz

stepup_queue-1.0.6/MANIFEST.in

@@ -0,0 +1,16 @@
+# Exclude documentation and development files
+prune .github
+prune .vscode
+prune docs
+prune overrides
+exclude .editorconfig
+exclude .gitignore
+exclude .markdownlint-cli2.jsonc
+exclude .pre-commit-config.yaml
+exclude mkdocs.yaml
+
+# Exclude tests for now. (Could be useful later for conda package.)
+prune tests
+
+# Exclude common build artifacts and cache files
+global-exclude *.py[cod] __pycache__ *.so

{stepup_queue-1.0.5 → stepup_queue-1.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stepup-queue
-Version: 1.0.5
+Version: 1.0.6
 Summary: StepUp Queue integrates queued jobs into a StepUp workflow.
 Author-email: Toon Verstraelen <toon.verstraelen@ugent.be>
 License-Expression: GPL-3.0-or-later
@@ -19,11 +19,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Software Development :: Build Tools
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: stepup<4.0.0,>=3.0.0
+Requires-Dist: stepup<4.0.0,>=3.1.3
 Provides-Extra: dev
 Requires-Dist: psutil; extra == "dev"
 Requires-Dist: pytest; extra == "dev"

{stepup_queue-1.0.5 → stepup_queue-1.0.6}/pyproject.toml

@@ -23,11 +23,12 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Software Development :: Build Tools",
 ]
 dependencies = [
     # Ensure changes to these dependencies are reflected in .github/requirements-old.txt
-    "stepup>=3.0.0,<4.0.0",
+    "stepup>=3.1.3,<4.0.0",
 ]
 dynamic = ["version"]
 
@@ -88,6 +89,9 @@ ignore = [
     "TRY301",  # https://docs.astral.sh/ruff/rules/raise-within-try/
 ]
 
+[tool.ruff.lint.isort]
+known-first-party = ["stepup"]
+
 [tool.setuptools]
 packages = ["stepup.queue"]
 

{stepup_queue-1.0.5 → stepup_queue-1.0.6}/stepup/queue/api.py

@@ -62,6 +62,9 @@ def sbatch(
 
     See `step()` documentation in StepUp Core for all optional arguments.
     and the return value.
+    Note that the `inp`, `out` and `vol` arguments are extended
+    with the files mentioned above and that any additional files you specify
+    are interpreted relative to the working directory.
 
     Parameters
     ----------

{stepup_queue-1.0.5 → stepup_queue-1.0.6}/stepup/queue/sbatch.py

@@ -36,7 +36,7 @@ SCONTROL_FAILED = "The command `scontrol show job` failed!\n"
 DEBUG = string_to_bool(os.getenv("STEPUP_SBATCH_DEBUG", "0"))
 CACHE_TIMEOUT = int(os.getenv("STEPUP_SBATCH_CACHE_TIMEOUT", "30"))
 POLLING_INTERVAL = int(os.getenv("STEPUP_SBATCH_POLLING_INTERVAL", "10"))
-TIME_MARGIN = int(os.getenv("STEPUP_SBATCH_TIME_MARGIN", "5"))
+TIME_MARGIN = int(os.getenv("STEPUP_SBATCH_TIME_MARGIN", "15"))
 
 
 def submit_once_and_wait(
@@ -185,7 +185,9 @@ def _read_or_poll_status(
         # Call scontrol and parse its response.
         rndsleep()
         status_time, status = get_status(work_thread, jobid, cluster)
-        if status != last_status:
+        # Log only if the status changed, and is not invalid or unlisted.
+        # These two statuses are (potentially) transient and should not be logged.
+        if status != last_status and status not in ["invalid", "unlisted"]:
             log_step(path_log, status)
     done = (status_time > submit_time + TIME_MARGIN) and (
         status not in ["PENDING", "CONFIGURING", "RUNNING", "invalid"]

{stepup_queue-1.0.5 → stepup_queue-1.0.6}/stepup_queue.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stepup-queue
-Version: 1.0.5
+Version: 1.0.6
 Summary: StepUp Queue integrates queued jobs into a StepUp workflow.
 Author-email: Toon Verstraelen <toon.verstraelen@ugent.be>
 License-Expression: GPL-3.0-or-later
@@ -19,11 +19,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Software Development :: Build Tools
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: stepup<4.0.0,>=3.0.0
+Requires-Dist: stepup<4.0.0,>=3.1.3
 Provides-Extra: dev
 Requires-Dist: psutil; extra == "dev"
 Requires-Dist: pytest; extra == "dev"

stepup_queue-1.0.6/stepup_queue.egg-info/SOURCES.txt

@@ -0,0 +1,15 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+stepup/queue/__init__.py
+stepup/queue/actions.py
+stepup/queue/api.py
+stepup/queue/canceljobs.py
+stepup/queue/sbatch.py
+stepup_queue.egg-info/PKG-INFO
+stepup_queue.egg-info/SOURCES.txt
+stepup_queue.egg-info/dependency_links.txt
+stepup_queue.egg-info/entry_points.txt
+stepup_queue.egg-info/requires.txt
+stepup_queue.egg-info/top_level.txt

{stepup_queue-1.0.5 → stepup_queue-1.0.6}/stepup_queue.egg-info/requires.txt

@@ -1,4 +1,4 @@
-stepup<4.0.0,>=3.0.0
+stepup<4.0.0,>=3.1.3
 
 [dev]
 psutil

stepup_queue-1.0.5/.editorconfig

@@ -1,18 +0,0 @@
-# EditorConfig is awesome: https://EditorConfig.org
-
-root = true
-
-[*]
-end_of_line = lf
-insert_final_newline = true
-charset = utf-8
-indent_style = space
-indent_size = 4
-max_line_length = 100
-
-[Makefile]
-indent_style = tab
-
-[{*.json,*.yml,*.yaml}]
-indent_style = space
-indent_size = 2

stepup_queue-1.0.5/.github/requirements-old.txt

@@ -1,2 +0,0 @@
-# Ensure changes to these dependencies are reflected in pyproject.toml
-stepup==3.0.0

stepup_queue-1.0.5/.github/scripts/extract-notes.sh

@@ -1,27 +0,0 @@
-#!/usr/bin/env bash
-# Usage: .github/scripts/extract-notes.sh OWNER/SLUG GITREF
-
-IFS='/'; read -ra REPOSITORY <<<"${1}"
-OWNER=${REPOSITORY[0]}
-SLUG=${REPOSITORY[1]}
-GITREF=${2}
-
-if [[ "${GITREF}" == refs/tags/* ]]; then
-    TAG="${GITREF#refs/tags/}"
-    VERSION="${TAG#v}"
-    MACRO_MESO=$(echo "${VERSION}" | cut -d. -f1,2)
-else
-    TAG="unreleased"
-    VERSION="Unreleased"
-    MACRO_MESO="dev"
-fi
-
-# Extract the release notes from the changelog
-sed -n "/## \[${VERSION}\]/, /## /{ /##/!p }" docs/changelog.md > notes.md
-
-# Add a link to the release notes
-URL="https://${OWNER}.github.io/${SLUG}/${MACRO_MESO}/changelog/#${TAG}"
-echo "See [docs/changelog/#${TAG}](${URL}) for more details." >> notes.md
-
-# Remove leading and trailing empty lines
-sed -e :a -e '/./,$!d;/^\n*$/{$d;N;};/\n$/ba' -i notes.md

stepup_queue-1.0.5/.github/workflows/mkdocs.yaml

@@ -1,72 +0,0 @@
-# This workflow assumes that you deploy the documentation from the gh-pages branch.
-
-name: mkdocs
-on:
-  push:
-    branches:
-      # Run on the main branch ...
-      - main
-    tags:
-      # ... and on release tags ...
-      - 'v*'
-    paths:
-      # ... and only if relevant files have changed.
-      - stepup/**
-      - docs/**
-      - mkdocs.yaml
-      - pyproject.toml
-      - .github/workflows/mkdocs.yaml
-  pull_request:
-  # Run tests on pull requests ...
-    paths:
-      # ... only if relevant files have changed.
-      - stepup/**
-      - docs/**
-      - mkdocs.yaml
-      - pyproject.toml
-      - .github/workflows/mkdocs.yaml
-
-permissions:
-  contents: write
-
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
-concurrency:
-  group: pages
-  cancel-in-progress: false
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      # Get the source
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-
-      # Prepare the environment for building docs.
-      - name: Setup Pages
-        id: pages
-        uses: actions/configure-pages@v5
-      - name: Install development version
-        run: pip install -e .[dev]
-
-      # Update the site using to the gh-pages branch with mike.
-      - name: Get the docs branch
-        run: git fetch --depth=1 origin gh-pages
-      - name: Configure Git user for documentation commit
-        run: |
-          git config --global user.name 'github-actions[bot]'
-          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
-      - name: Build mkdocs
-        run: mike deploy dev
-      - name: Push gh-pages branch with development version of docs
-        if: github.ref == 'refs/heads/main'
-        run: git push origin gh-pages
-      - name: Deploy gh-pages branch with stable version of docs
-        if: startsWith(github.ref, 'refs/tags/v')
-        run: |
-          VERSION="${GITHUB_REF#refs/tags/v}"
-          MACRO_MESO=$(echo "${VERSION}" | cut -d. -f1,2)
-          mike deploy ${MACRO_MESO} -u stable -p

stepup_queue-1.0.5/.github/workflows/pytest.yaml

@@ -1,45 +0,0 @@
-name: pytest
-on:
-  push:
-    branches:
-      # Run tests for change on the main branch ...
-      - main
-    tags-ignore:
-      # ... but not for tags (avoids duplicate work) ...
-      - '**'
-    paths:
-      # ... and only if relevant files have changed.
-      - stepup/**
-      - tests/**
-      - pyproject.toml
-      - .github/workflows/pytest.yaml
-  pull_request:
-    # Run tests on pull requests ...
-    paths:
-      # ... only if relevant files have changed.
-      - stepup/**
-      - tests/**
-      - pyproject.toml
-      - .github/workflows/pytest.yaml
-
-jobs:
-  tests:
-    strategy:
-      matrix:
-        python-version: ['3.11', '3.13']
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install oldest versions of supported dependencies
-        if: ${{ matrix.python-version == '3.11'}}
-        run: pip install -r .github/requirements-old.txt
-      - name: Install development version
-        run: pip install -e .[dev]
-      - name: Run pytest
-        # Enfore strict checks instead of trying to repair fixable issues.
-        # RPC timeout is set shorter to speed up tests in case of failures.
-        run: STEPUP_DEBUG=1 STEPUP_SYNC_RPC_TIMEOUT=10 pytest -vv

stepup_queue-1.0.5/.github/workflows/release.yaml

@@ -1,145 +0,0 @@
-# This workflow is adapted from:
-# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
-
-name: release
-on:
-  push:
-    branches:
-      - main
-    tags:
-      - 'v*'
-
-env:
-  # This is not critical
-  # It is used only for showing URLs in GitHub Actions web interface.
-  PYPI_NAME: stepup-queue
-  TITLE: StepUp Queue
-
-jobs:
-  build:
-    name: Build distribution
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
-    - name: Install pypa/build
-      run: >-
-        python -m pip install build
-    - name: Build package
-      run: >-
-        python -m build
-    - name: Store the distribution packages
-      uses: actions/upload-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Run release notes script
-      run: >-
-        .github/scripts/extract-notes.sh
-        '${{ github.repository }}'
-        '${{ github.ref }}'
-    - name: Store the release notes
-      uses: actions/upload-artifact@v4
-      with:
-        name: release-notes
-        path: notes.md
-
-  publish-to-pypi:
-    name: Publish Python distribution to PyPI
-    if: startsWith(github.ref, 'refs/tags/v')  # only publish to PyPI on tag pushes
-    needs:
-    - build
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/${{ env.PYPI_NAME }}
-    permissions:
-      id-token: write
-
-    steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Publish distribution to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-
-  github-release:
-    name: >-
-      Sign the Python distribution with Sigstore
-      and upload them to GitHub Release
-    needs:
-    - publish-to-pypi
-    runs-on: ubuntu-latest
-
-    permissions:
-      contents: write
-      id-token: write
-
-    steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Download the release notes
-      uses: actions/download-artifact@v4
-      with:
-        name: release-notes
-    - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v3.0.0
-      with:
-        inputs: >-
-          ./dist/*.tar.gz
-          ./dist/*.whl
-    - name: Create GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      run: >-
-        gh release create '${{ github.ref_name }}'
-        --repo '${{ github.repository }}'
-        --title '${{ env.TITLE }} ${{ github.ref_name }}'
-        --notes-file notes.md
-    - name: Upload artifact signatures to GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      # Upload to GitHub Release using the `gh` CLI.
-      # `dist/` contains the built packages, and the
-      # sigstore-produced signatures and certificates.
-      run: >-
-        gh release upload
-        '${{ github.ref_name }}'
-        dist/**
-        --repo '${{ github.repository }}'
-
-  publish-to-testpypi:
-    name: Publish Python distribution to TestPyPI
-    if: ${{ github.ref == 'refs/heads/main' &&  github.repository_owner == 'reproducible-reporting'}}
-    needs:
-    - build
-    runs-on: ubuntu-latest
-
-    environment:
-      name: testpypi
-      url: https://test.pypi.org/p/${{ env.PYPI_NAME }}
-
-    permissions:
-      id-token: write
-
-    steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Publish distribution to TestPyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        repository-url: https://test.pypi.org/legacy/

stepup_queue-1.0.5/.gitignore

@@ -1,29 +0,0 @@
-# Local dev environment
-.envrc
-.idea
-.local
-tmp
-site/
-venv/
-.venv/
-.ruff_cache
-.pytest_cache
-notes.md
-
-# Python and packaging
-__pycache__
-*.egg-info
-dist
-build
-_version.py
-
-# StepUp specifics
-docs/.stepup
-
-# Temporary files
-*.swp
-
-# NodeJS (for markdownlint)
-node_modules/
-package-lock.json
-package.json

stepup_queue-1.0.5/.markdownlint-cli2.jsonc

@@ -1,15 +0,0 @@
-{
-  "config": {
-    "MD013": {
-      "line_length": 100,
-      "heading_line_length": 100,
-      "code_block_line_length": 100
-    },
-    "MD007": { "indent": 4 },
-    "MD033": {
-      "allowed_elements": ["script"]
-    },
-    "MD046": false,
-    "MD052": false
-  }
-}

stepup_queue-1.0.5/.pre-commit-config.yaml

@@ -1,42 +0,0 @@
-repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
-  hooks:
-    - id: check-added-large-files
-    - id: check-ast
-    - id: check-case-conflict
-    - id: check-executables-have-shebangs
-    - id: check-json
-    - id: check-merge-conflict
-    - id: check-symlinks
-    - id: check-toml
-    - id: check-vcs-permalinks
-    - id: debug-statements
-    - id: detect-private-key
-    - id: destroyed-symlinks
-    - id: end-of-file-fixer
-    - id: fix-byte-order-marker
-    - id: mixed-line-ending
-    - id: pretty-format-json
-      args: ["--autofix", "--no-sort-keys"]
-    - id: trailing-whitespace
-- repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.5.5
-  hooks:
-    - id: remove-crlf
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.4
-  hooks:
-    - id: ruff-format
-      exclude: "^docs/examples/slurm-basic/pass/slurmjob.py$"
-    - id: ruff
-      args: ["--fix", "--show-fixes"]
-- repo: https://github.com/DavidAnson/markdownlint-cli2
-  rev: v0.17.2
-  hooks:
-  - id: markdownlint-cli2
-    require_serial: true
-- repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.30.0
-  hooks:
-    - id: check-github-workflows

stepup_queue-1.0.5/docs/changelog.md

@@ -1,69 +0,0 @@
-<!-- markdownlint-disable no-duplicate-heading -->
-
-# Changelog
-
-All notable changes to StepUp Queue will be documented on this page.
-
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
-and this project adheres to [Effort-based Versioning](https://jacobtomlinson.dev/effver/).
-(Changes to features documented as "experimental" will not increment macro and meso version numbers.)
-
-## [Unreleased][]
-
-(no changes yet)
-
-## [1.0.5][] - 2025-05-23 {: #v1.0.4 }
-
-### Changed
-
-- Replaced the old `STEPUP_QUEUE_RESUBMIT_CHANGED_INPUTS` environment variable
-  by the more powerful `STEPUP_QUEUE_ONCHANGE`.
-
-## [1.0.4][] - 2025-05-21 {: #v1.0.4 }
-
-### Fixed
-
-- Minor typo fix in slurm wrapper script.
-- Improved example perpetual workflow job script.
-
-## [1.0.3][] - 2025-05-16 {: #v1.0.3 }
-
-### Fixed
-
-- Fixed errors in the example job scripts.
-- Improved handling of `scontrol` failures.
-
-### Added
-
-## [1.0.2][] - 2025-05-14 {: #v1.0.2 }
-
-### Added
-
-- Option to specify the extension of the job script.
-- Wrap all job scripts to record their return code.
-- Detect when inputs of jobs have changed + optional resubmission.
-- Option to load resource configurations before sbatch is called.
-- More detailed examples, including a self-submitting workflow job.
-
-## [1.0.1][] - 2025-05-11 {: #v1.0.1 }
-
-This is a minor cleanup release, mainly testing the release process.
-
-## [1.0.0][] - 2025-05-11 {: #v1.0.0 }
-
-This is an initial and experimental release of StepUp Queue.
-
-### Added
-
-Initial release of StepUp Queue.
-The initial package is based on the `sbatch-wait` script from Parman.
-It was adapted to integrate well with StepUp Core 3.
-This release also features the `stepup canceljobs` tool, which was not present in Parman.
-
-[Unreleased]: https://github.com/reproducible-reporting/stepup-queue
-[1.0.5]: https://github.com/reproducible-reporting/stepup-queue/releases/tag/v1.0.5
-[1.0.4]: https://github.com/reproducible-reporting/stepup-queue/releases/tag/v1.0.4
-[1.0.3]: https://github.com/reproducible-reporting/stepup-queue/releases/tag/v1.0.3
-[1.0.2]: https://github.com/reproducible-reporting/stepup-queue/releases/tag/v1.0.2
-[1.0.1]: https://github.com/reproducible-reporting/stepup-queue/releases/tag/v1.0.1
-[1.0.0]: https://github.com/reproducible-reporting/stepup-queue/releases/tag/v1.0.0