snakemake-logger-plugin-rich 0.1.0__tar.gz

snakemake_logger_plugin_rich-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,137 @@
+name: release
+
+on:
+  push:
+    tags:
+      - "[0-9]+.[0-9]+.[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+a[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+b[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+rc[0-9]+"
+
+env:
+  PACKAGE_NAME: "snakemake-logger-plugin-rich"
+  OWNER: "cademirch"
+
+jobs:
+  details:
+    runs-on: ubuntu-latest
+    outputs:
+      new_version: ${{ steps.release.outputs.new_version }}
+      suffix: ${{ steps.release.outputs.suffix }}
+      tag_name: ${{ steps.release.outputs.tag_name }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Extract tag and Details
+        id: release
+        run: |
+          if [ "${{ github.ref_type }}" = "tag" ]; then
+            TAG_NAME=${GITHUB_REF#refs/tags/}
+            NEW_VERSION=$(echo $TAG_NAME | awk -F'-' '{print $1}')
+            SUFFIX=$(echo $TAG_NAME | grep -oP '[a-z]+[0-9]+' || echo "")
+            echo "new_version=$NEW_VERSION" >> "$GITHUB_OUTPUT"
+            echo "suffix=$SUFFIX" >> "$GITHUB_OUTPUT"
+            echo "tag_name=$TAG_NAME" >> "$GITHUB_OUTPUT"
+            echo "Version is $NEW_VERSION"
+            echo "Suffix is $SUFFIX"
+            echo "Tag name is $TAG_NAME"
+          else
+            echo "No tag found"
+            exit 1
+          fi
+
+  check_pypi:
+    needs: details
+    runs-on: ubuntu-latest
+    steps:
+      - name: Fetch information from PyPI
+        run: |
+          response=$(curl -s https://pypi.org/pypi/${{ env.PACKAGE_NAME }}/json || echo "{}")
+          latest_previous_version=$(echo $response | grep -oP '"releases":\{"\K[^"]+' | sort -rV | head -n 1)
+          if [ -z "$latest_previous_version" ]; then
+            echo "Package not found on PyPI."
+            latest_previous_version="0.0.0"
+          fi
+          echo "Latest version on PyPI: $latest_previous_version"
+          echo "latest_previous_version=$latest_previous_version" >> $GITHUB_ENV
+
+      - name: Compare versions and exit if not newer
+        run: |
+          NEW_VERSION=${{ needs.details.outputs.new_version }}
+          LATEST_VERSION=$latest_previous_version
+          if [ "$(printf '%s\n' "$LATEST_VERSION" "$NEW_VERSION" | sort -rV | head -n 1)" != "$NEW_VERSION" ] || [ "$NEW_VERSION" == "$LATEST_VERSION" ]; then
+            echo "The new version $NEW_VERSION is not greater than the latest version $LATEST_VERSION on PyPI."
+            exit 1
+          else
+            echo "The new version $NEW_VERSION is greater than the latest version $LATEST_VERSION on PyPI."
+          fi
+
+  setup_and_build:
+    needs: [details, check_pypi]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+      
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Build source and wheel distribution
+        run: |
+          uv build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+  pypi_publish:
+    name: Upload release to PyPI
+    needs: [setup_and_build, details]
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github_release:
+    name: Create GitHub Release
+    needs: [setup_and_build, details]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub Release
+        id: create_release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          gh release create ${{ needs.details.outputs.tag_name }} dist/* --title ${{ needs.details.outputs.tag_name }} --generate-notes

snakemake_logger_plugin_rich-0.1.0/.gitignore

@@ -0,0 +1,163 @@
+### Generated by gibo (https://github.com/simonwhitaker/gibo)
+### https://raw.github.com/github/gitignore/4488915eec0b3a45b5c63ead28f286819c0917de/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

snakemake_logger_plugin_rich-0.1.0/.python-version

@@ -0,0 +1 @@
+3.12

snakemake_logger_plugin_rich-0.1.0/CHANGELOG.md

@@ -0,0 +1,5 @@
+# Changelog
+
+## [0.1.0] - 2024-11-03
+
+- Initial release.

snakemake_logger_plugin_rich-0.1.0/PKG-INFO

@@ -0,0 +1,15 @@
+Metadata-Version: 2.3
+Name: snakemake-logger-plugin-rich
+Version: 0.1.0
+Summary: Log plugin for snakemake using Rich
+Requires-Python: >=3.12
+Requires-Dist: rich>=13.9.4
+Requires-Dist: snakemake-interface-executor-plugins>=9.3.2
+Requires-Dist: snakemake-interface-logger-plugins>=0.1.0
+Description-Content-Type: text/markdown
+
+# Snakemake Rich Logger Plugin
+
+Proof of concept logger plugin that uses [rich](https://github.com/Textualize/rich) for terminal styling and progress bar. 
+
+Log formatting still needs lots of work but the progress bar works well.

snakemake_logger_plugin_rich-0.1.0/README.md

@@ -0,0 +1,5 @@
+# Snakemake Rich Logger Plugin
+
+Proof of concept logger plugin that uses [rich](https://github.com/Textualize/rich) for terminal styling and progress bar. 
+
+Log formatting still needs lots of work but the progress bar works well.

snakemake_logger_plugin_rich-0.1.0/pyproject.toml

@@ -0,0 +1,15 @@
+[project]
+name = "snakemake-logger-plugin-rich"
+version = "0.1.0"
+description = "Log plugin for snakemake using Rich"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "rich>=13.9.4",
+    "snakemake-interface-executor-plugins>=9.3.2",
+    "snakemake-interface-logger-plugins>=0.1.0",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

snakemake_logger_plugin_rich-0.1.0/src/snakemake_logger_plugin_rich/__init__.py

@@ -0,0 +1,46 @@
+from snakemake_interface_logger_plugins.base import LoggerPluginBase
+from snakemake_logger_plugin_rich.handler import RichLogHandler
+from logging import Handler, Formatter
+
+
+class LoggerPlugin(LoggerPluginBase):
+    def __post__init(self) -> None:
+        """
+        Any additional setup after initialization.
+        """
+
+    def create_handler(
+        self,
+        quiet,
+        printshellcmds: bool,
+        printreason: bool,
+        debug_dag: bool,
+        nocolor: bool,
+        stdout: bool,
+        debug: bool,
+        mode,
+        show_failed_logs: bool,
+        dryrun: bool,
+    ) -> Handler:
+        """
+        Creates and returns an instance of RichLogHandler, configured with plugin settings.
+        """
+        # Initialize RichLogHandler with plugin settings
+        handler = RichLogHandler(
+            quiet=quiet,
+            printshellcmds=printshellcmds,
+            printreason=printreason,
+            debug_dag=debug_dag,
+            nocolor=nocolor,
+            stdout=stdout,
+            debug=debug,
+            mode=mode,
+            show_failed_logs=show_failed_logs,
+            dryrun=dryrun,
+            show_time=True,
+            show_path=False,
+            markup=False,
+        )
+        FORMAT = Formatter("%(message)s")
+        handler.setFormatter(FORMAT)
+        return handler

snakemake_logger_plugin_rich-0.1.0/src/snakemake_logger_plugin_rich/handler.py

@@ -0,0 +1,139 @@
+import logging
+from rich.logging import RichHandler
+from rich.progress import (
+    BarColumn,
+    MofNCompleteColumn,
+    Progress,
+    TextColumn,
+    TimeElapsedColumn,
+    TimeRemainingColumn,
+)
+from rich.console import Console
+from typing import Optional
+from snakemake_interface_executor_plugins.settings import ExecMode
+
+
+class RichLogHandler(RichHandler):
+    """
+    A custom Rich handler for Snakemake logging with a persistent progress bar at the bottom.
+    """
+
+    def __init__(
+        self,
+        quiet=None,
+        printshellcmds: Optional[bool] = None,
+        printreason: Optional[bool] = None,
+        debug_dag: Optional[bool] = None,
+        nocolor: Optional[bool] = None,
+        stdout: Optional[bool] = None,
+        debug: Optional[bool] = None,
+        mode=None,
+        show_failed_logs: Optional[bool] = None,
+        dryrun: Optional[bool] = None,
+        *args,
+        **kwargs,
+    ):
+        console = Console(stderr=not stdout)
+        super().__init__(*args, **kwargs, console=console)
+
+        # Store additional configurations
+        self.quiet = quiet
+        self.printshellcmds = printshellcmds
+        self.printreason = printreason
+        self.debug_dag = debug_dag
+        self.nocolor = nocolor
+        self.stdout = stdout
+        self.debug = debug
+        self.mode = mode
+        self.show_failed_logs = show_failed_logs
+        self.dryrun = dryrun
+        self.stream = True
+
+        # Initialize the progress bar only if mode is not SUBPROCESS and not dryrun
+        if self.mode != ExecMode.SUBPROCESS and not self.dryrun:
+            self.progress = Progress(
+                TextColumn("[progress.percentage]{task.percentage:>3.0f}%"),
+                BarColumn(),
+                MofNCompleteColumn(),
+                TextColumn("•"),
+                TimeElapsedColumn(),
+                TextColumn("•"),
+                TimeRemainingColumn(),
+                console=console,
+                auto_refresh=True,
+            )
+            self.progress_task = None
+            self.total_steps = 1  # To avoid division errors if not set
+        else:
+            self.progress = None
+            self.progress_task = None
+
+    def start_progress_bar(self, total_steps):
+        """
+        Initialize and start the progress bar for a Snakemake job if progress is enabled.
+        """
+        if self.progress:
+            self.total_steps = total_steps
+            self.progress_task = self.progress.add_task(
+                "Processing...", total=total_steps
+            )
+
+    def get_level(self, record: logging.LogRecord) -> str:
+        """
+        Gets snakemake log level from a log record. If there is no snakemake log level,
+        returns the log record's level name.
+
+        Args:
+            record (logging.LogRecord)
+        Returns:
+            str: The log level
+
+        """
+        level = record.__dict__.get("level", None)
+
+        if level is None:
+            level = record.levelname
+
+        return level.lower()
+
+    def update_progress(self, done_steps):
+        """
+        Update the progress bar with the number of completed steps.
+        """
+        if self.progress and self.progress_task is not None:
+            self.progress.update(self.progress_task, completed=done_steps)
+
+    def emit(self, record):
+        """
+        Emit log messages with Rich formatting and update the progress bar if necessary.
+        """
+        message = self.format(record)
+        level = self.get_level(record)
+
+        if level == "progress" and self.progress:
+            done_steps = getattr(record, "done", 0)
+            total_steps = getattr(record, "total", self.total_steps)
+            if self.progress_task is None:
+                # Start progress bar if this is the first progress log
+                self.total_steps = total_steps
+                self.progress_task = self.progress.add_task(
+                    "Processing...", total=total_steps
+                )
+                self.progress.start()
+            # Update the progress bar
+            self.progress.update(self.progress_task, completed=done_steps)
+        if level == "run_info":
+            record.message.replace("\n", "")
+        else:
+            super().emit(record)
+
+    def close(self):
+        """
+        Ensure progress bar is stopped and cleaned up on handler close.
+        """
+        if self.progress:
+            self.progress.stop()
+            if self.progress_task is not None:
+                self.progress.remove_task(self.progress_task)
+                self.progress_task = None
+        super().close()

snakemake_logger_plugin_rich-0.1.0/uv.lock

@@ -0,0 +1,128 @@
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+
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