biocommons.python_package 0.0.8__py3-none-any.whl

biocommons/python_package/__init__.py

@@ -0,0 +1,11 @@
+"""biocommons.python_package package"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+from .marvin import get_quote as get_quote_from_marvin  # noqa: F401
+
+try:
+    __version__ = version(__package__)
+except PackageNotFoundError:  # pragma: no cover
+    # package is not installed
+    __version__ = None

biocommons/python_package/__main__.py

@@ -0,0 +1,30 @@
+"""biocommons.python_package.__main__"""
+
+import logging
+import time
+
+from . import marvin
+
+_logger = logging.getLogger(__name__)
+
+
+def main():  # pragma: no cover
+    """marvin.example main"""
+    import coloredlogs  # noqa: PLC0415
+
+    logging.Formatter.converter = time.gmtime
+    coloredlogs.install(
+        level="INFO",
+        fmt="%(asctime)s [%(process)d] %(name)s:%(lineno)d %(levelname)s %(message)s",
+        datefmt="%FT%T.%f%z",
+    )
+
+    quote = marvin.get_quote()
+    _logger.warning("Got quote from Marvin (len=%s)", len(quote))
+
+    print("Marvin says:")
+    print(quote)
+
+
+if __name__ == "__main__":
+    main()

biocommons/python_package/_data/quotes.yaml

@@ -0,0 +1,47 @@
+quotes:
+  - >-
+    Here I am, brain the size of a planet, and they tell me to take
+    you up to the bridge. Call that job satisfaction? 'Cos I don't.
+
+  - >-
+    I think you ought to know I'm feeling very depressed.
+
+  - >-
+    You think you've got problems? What are you supposed to do if you
+    are a manically depressed robot? No, don't try to answer that. I'm
+    fifty thousand times more intelligent than you and even I don't
+    know the answer. It gives me a headache just trying to think down
+    to your level.
+
+  - >-
+    There's only one life-form as intelligent as me within thirty
+    parsecs of here and that's me.
+
+  - >-
+    I wish you'd just tell me rather trying to engage my enthusiasm
+    because I haven't got one.
+
+  - >-
+    And then, of course, I've got this terrible pain in all the diodes
+    down my left side.
+
+  - |
+    Now the world has gone to bed,
+    Darkness won't engulf my head,
+    I can see by infra-red,
+    How I hate the night,
+    Now I lay me down to sleep,
+    Try to count electric sheep,
+    Sweet dream wishes you can keep,
+    How I hate the night.
+
+  - >-
+    The first ten million years were the worst, and the second ten
+    million years, they were the worst too. The third ten million
+    years I didn't enjoy at all. After that I went into a bit of a
+    decline.
+
+  - >-
+    "I Don't blame you," said Marvin and counted five hundred and
+    ninety-seven thousand million sheep before falling asleep again a
+    second later.

biocommons/python_package/marvin.py

@@ -0,0 +1,43 @@
+"""random quotes from Marvin the depressed robot
+
+The secret is to bang the rocks together.
+
+"""
+
+import importlib.resources
+import logging
+import random
+
+import yaml
+
+_logger = logging.getLogger(__name__)
+
+
+quotes_stream = importlib.resources.files(__package__).joinpath("_data/quotes.yaml").read_text()
+quotes = yaml.load(quotes_stream, Loader=yaml.SafeLoader)["quotes"]
+
+
+def is_alive() -> bool:
+    """tests whether Marvin is alive
+
+    >>> is_alive() is True
+    True
+
+    """
+    return True
+
+
+def get_quote() -> str:
+    """return random Marvin quote
+
+    eg> get_quote()
+    "There's only one life-form as intelligent..."
+
+    """
+    _logger.info("Getting quote from Marvin")
+
+    quote = random.choice(quotes)  # noqa: S311
+
+    _logger.info("Got quote from Marvin (len=%s)", len(quote))
+
+    return quote

biocommons/python_package/marvin_adjacent_test.py

@@ -0,0 +1,8 @@
+"""biocommons.python_package test, adjacent to code"""
+
+from .marvin import get_quote
+
+
+def test_get_quote():
+    """test get_quote"""
+    assert get_quote() is not None  # noqa: S101

biocommons_python_package-0.0.8.dist-info/METADATA

@@ -0,0 +1,141 @@
+Metadata-Version: 2.4
+Name: biocommons.python_package
+Version: 0.0.8
+Summary: biocommons.python_package package (namespaced)
+Author-email: biocommons contributors <biocommons-dev@googlegroups.com>
+License-Expression: Apache-2.0
+Project-URL: Changelog, https://github.com/biocommons/python-package/releases
+Project-URL: Documentation, https://biocommons.github.io/python-package/
+Project-URL: Homepage, https://github.com/biocommons/python-package/
+Project-URL: Issues, https://github.com/biocommons/python-package/issues/
+Project-URL: Repository, https://github.com/biocommons/python-package/
+Keywords: biocommons,bioinformatics,computational biology,genome variation,genomics,hgvs,variation
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+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: Programming Language :: Python :: 3.15
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: coloredlogs>=15.0.1
+Requires-Dist: pyyaml>=6.0.3
+Provides-Extra: example
+Requires-Dist: pyyaml>=6.0.3; extra == "example"
+Dynamic: license-file
+
+# biocommons.python_package
+
+[![Release](https://img.shields.io/github/v/release/biocommons/python-package)](https://img.shields.io/github/v/release/biocommons/python-package)
+[![Build status](https://img.shields.io/github/actions/workflow/status/biocommons/python-package/main.yml?branch=main)](https://github.com/biocommons/python-package/actions/workflows/main.yml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/biocommons/python-package/branch/main/graph/badge.svg)](https://codecov.io/gh/biocommons/python-package)
+[![Commit activity](https://img.shields.io/github/commit-activity/m/biocommons/python-package)](https://img.shields.io/github/commit-activity/m/biocommons/python-package)
+[![License](https://img.shields.io/github/license/biocommons/python-package)](https://img.shields.io/github/license/biocommons/python-package)
+
+## Package Description
+
+This project is a product of the [biocommons](https://biocommons.org/) community.
+
+- **Github repository**: <https://github.com/biocommons/python-package/>
+- **Documentation** <https://biocommons.github.io/python-package/>
+
+## Getting Help
+
+- 🐛 **Bug reports**: [Open an issue](../../issues/new?template=bug_report.md)
+- 💡 **Feature requests**: [Open an issue](../../issues/new?template=feature_request.md)
+- ❓ **Questions**: [Ask in biocommons/discussions](https://github.com/biocommons/discussions)
+- 💬 **General discussion**: [biocommons/discussions](https://github.com/biocommons/discussions)
+
+## Python Package Installation
+
+Install from PyPI with `pip install biocommons.python_package` or `uv pip install biocommons.python_package`, then try it:
+
+    $ source venv/bin/activate
+
+    $ python3 -m biocommons.python_package
+    Marvin says:
+    There's only one life-form as intelligent as me within thirty parsecs...
+
+    $ marvin-quote
+    Marvin says:
+    You think you've got problems? What are you supposed to do if you...
+
+    $ ipython
+    >>> from biocommons.python_package import __version__, get_quote_from_marvin
+    >>> __version__
+    '0.1.dev8+gd5519a8.d20211123'
+    >>> get_quote()
+    "The first ten million years were the worst, ...
+
+
+## Developer Setup
+
+### Install Prerequisites
+
+These tools are required to get started:
+
+- [git](https://git-scm.com/): Version control system
+- [GNU make](https://www.gnu.org/software/make/): Current mechanism for consistent invocation of developer tools.
+- [uv](https://docs.astral.sh/uv/): An extremely fast Python package and project manager, written in Rust.
+
+#### MacOS or Linux Systems
+
+- [Install brew](https://brew.sh/)
+- `brew install git make uv`
+
+#### Linux (Debian-based systems)
+
+You may also install using distribution packages:
+
+    sudo apt install git make
+
+Then install uv using the [uv installation instructions](https://docs.astral.sh/uv/getting-started/installation/).
+
+### One-time developer setup
+
+Create a Python virtual environment, install dependencies, install git hooks (prek), and install an editable package:
+
+    make devready
+
+### Development
+
+**N.B.** Developers are strongly encouraged to use `make` to invoke tools to
+ensure consistency with the CI/CD pipelines.  Type `make` to see a list of
+supported targets.  A subset are listed here:
+
+    » make
+    🌟🌟 biocommons conventional make targets 🌟🌟
+
+    Using these targets promots consistency between local development and ci/cd commands.
+
+    usage: make [target ...]
+
+    BASIC USAGE
+    help                Display help message
+
+    SETUP, INSTALLATION, PACKAGING
+    devready            Prepare local dev env: Create virtual env, install the git hooks (prek)
+    build               Build package
+    publish             publish package to PyPI
+
+    FORMATTING, TESTING, AND CODE QUALITY
+    cqa                 Run code quality assessments
+    test                Test the code with pytest
+
+    DOCUMENTATION
+    docs-serve          Build and serve the documentation
+    docs-test           Test if documentation can be built without warnings or errors
+
+    CLEANUP
+    clean               Remove temporary and backup files
+    cleaner             Remove files and directories that are easily rebuilt
+    cleanest            Remove all files that can be rebuilt
+    distclean           Remove untracked files and other detritus

biocommons_python_package-0.0.8.dist-info/RECORD

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biocommons_python_package-0.0.8.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

biocommons_python_package-0.0.8.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+marvin-quote = biocommons.python_package.__main__:main

biocommons_python_package-0.0.8.dist-info/licenses/LICENSE.txt

@@ -0,0 +1,201 @@
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biocommons_python_package-0.0.8.dist-info/top_level.txt

@@ -0,0 +1 @@
+biocommons

biocommons_python_package-0.0.8.dist-info/zip-safe

@@ -0,0 +1 @@
+