mapkgsutils 0.0.2__tar.gz

mapkgsutils-0.0.2/LICENSE

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+MIT License
+
+Copyright (c) 2026 Javier Millan Acosta
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mapkgsutils-0.0.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: mapkgsutils
+Version: 0.0.2
+Summary: Utils shared by several mapping set generation tools for biomedical databases
+Keywords: snekpack,cookiecutter
+Author: Javier Millan Acosta
+Author-email: Javier Millan Acosta <javier.millanacosta@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 1 - Planning
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Framework :: Pytest
+Classifier: Framework :: Sphinx
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+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 :: Only
+Classifier: Typing :: Typed
+Requires-Dist: more-itertools
+Requires-Dist: tqdm
+Requires-Dist: click
+Requires-Dist: more-click
+Requires-Dist: typing-extensions
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyyaml
+Requires-Dist: sssom==0.4.21
+Requires-Dist: sssom-schema==1.1.0a5
+Requires-Dist: curies>=0.7.0
+Requires-Dist: polars>=0.20.0
+Requires-Dist: polars-runtime-32
+Requires-Dist: pandas
+Requires-Dist: numpy
+Requires-Dist: httpx>=0.24.0
+Maintainer: Javier Millan Acosta
+Maintainer-email: Javier Millan Acosta <javier.millanacosta@gmail.com>
+Requires-Python: >=3.10
+Project-URL: Bug Tracker, https://github.com//mapkgsutils/issues
+Project-URL: Homepage, https://github.com//mapkgsutils
+Project-URL: Repository, https://github.com//mapkgsutils.git
+Project-URL: Documentation, https://mapkgsutils.readthedocs.io
+Project-URL: Funding, https://github.com/sponsors/jmillanacosta
+Description-Content-Type: text/markdown
+
+<!--
+<p align="center">
+  <img src="https://github.com//mapkgsutils/raw/main/docs/source/logo.png" height="150">
+</p>
+-->
+
+<h1 align="center">
+  MaPkgsUtilS
+</h1>
+
+<p align="center">
+    <a href="https://github.com//mapkgsutils/actions/workflows/tests.yml">
+        <img alt="Tests" src="https://github.com//mapkgsutils/actions/workflows/tests.yml/badge.svg" /></a>
+    <a href="https://pypi.org/project/mapkgsutils">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/mapkgsutils" /></a>
+    <a href="https://pypi.org/project/mapkgsutils">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/mapkgsutils" /></a>
+    <a href="https://github.com//mapkgsutils/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/mapkgsutils" /></a>
+    <a href='https://mapkgsutils.readthedocs.io/en/latest/?badge=latest'>
+        <img src='https://readthedocs.org/projects/mapkgsutils/badge/?version=latest' alt='Documentation Status' /></a>
+    <a href="https://codecov.io/gh//mapkgsutils/branch/main">
+        <img src="https://codecov.io/gh//mapkgsutils/branch/main/graph/badge.svg" alt="Codecov status" /></a>  
+    <a href="https://github.com/cthoyt/cookiecutter-python-package">
+        <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /></a>
+    <a href="https://github.com/astral-sh/ruff">
+        <img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff" style="max-width:100%;"></a>
+    <a href="https://github.com//mapkgsutils/blob/main/.github/CODE_OF_CONDUCT.md">
+        <img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
+    <!-- uncomment if you archive on zenodo
+    <a href="https://doi.org/10.5281/zenodo.XXXXXX">
+        <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.XXXXXX.svg" alt="DOI"></a>
+    -->
+</p>
+
+Utils shared by several mapping set generation tools for biomedical databases.
+
+## 💪 Getting Started
+
+> TODO show in a very small amount of space the **MOST** useful thing your
+> package can do. Make it as short as possible! You have an entire set of docs
+> for later.
+
+### Command Line Interface
+
+The `mapkgsutils` command line tool is automatically installed. It can be used
+from the console with the `--help` flag to show all subcommands:
+
+```console
+$ mapkgsutils --help
+```
+
+> TODO show the most useful thing the CLI does! The CLI will have documentation
+> auto-generated by `sphinx`.
+
+## 🚀 Installation
+
+<!-- Uncomment this section after your first ``just finish``
+The most recent release can be installed from
+[PyPI](https://pypi.org/project/mapkgsutils/) with uv:
+
+```console
+$ uv pip install mapkgsutils
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install mapkgsutils
+```
+-->
+
+The most recent code and data can be installed directly from GitHub with uv:
+
+```console
+$ uv pip install git+https://github.com//mapkgsutils.git
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install git+https://github.com//mapkgsutils.git
+```
+
+## 👐 Contributing
+
+Contributions, whether filing an issue, making a pull request, or forking, are
+appreciated. See
+[CONTRIBUTING.md](https://github.com//mapkgsutils/blob/main/.github/CONTRIBUTING.md)
+for more information on getting involved.
+
+## 👋 Attribution
+
+### ⚖️ License
+
+The code in this package is licensed under the MIT License.
+
+<!--
+### 📖 Citation
+
+Citation goes here!
+-->
+
+<!--
+### 🎁 Support
+
+This project has been supported by the following organizations (in alphabetical order):
+
+- [Biopragmatics Lab](https://biopragmatics.github.io)
+
+-->
+
+<!--
+### 💰 Funding
+
+This project has been supported by the following grants:
+
+| Funding Body  | Program                                                      | Grant Number |
+|---------------|--------------------------------------------------------------|--------------|
+| Funder        | [Grant Name (GRANT-ACRONYM)](https://example.com/grant-link) | ABCXYZ       |
+-->
+
+### 🍪 Cookiecutter
+
+This package was created with
+[@audreyfeldroy](https://github.com/audreyfeldroy)'s
+[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using
+[@cthoyt](https://github.com/cthoyt)'s
+[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
+template.
+
+## 🛠️ For Developers
+
+<details>
+  <summary>See developer instructions</summary>
+
+The final section of the README is for if you want to get involved by making a
+code contribution.
+
+### Development Installation
+
+To install in development mode, use the following:
+
+```console
+$ git clone git+https://github.com//mapkgsutils.git
+$ cd mapkgsutils
+$ uv pip install -e .
+```
+
+Alternatively, install using pip:
+
+```console
+$ python3 -m pip install -e .
+```
+
+### Pre-commit
+
+You can optionally use [pre-commit](https://pre-commit.com) to automate running
+key code quality checks on each commit. Enable it with:
+
+```console
+$ uvx pre-commit install
+```
+
+Or using `pip`:
+
+```console
+$ pip install pre-commit
+$ pre-commit install
+```
+
+### 🥼 Testing
+
+After cloning the repository and installing `just` with
+`uv tool install rust-just` or `python3 -m pip install rust-just`, the unit
+tests in the `tests/` folder can be run reproducibly with:
+
+```console
+$ just test
+```
+
+Additionally, these tests are automatically re-run with each commit in a
+[GitHub Action](https://github.com//mapkgsutils/actions?query=workflow%3ATests).
+
+### 📖 Building the Documentation
+
+The documentation can be built locally using the following:
+
+```console
+$ git clone git+https://github.com//mapkgsutils.git
+$ cd mapkgsutils
+$ just docs
+$ open docs/build/html/index.html
+```
+
+The documentation automatically installs the package as well as the `docs` extra
+specified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like
+`texext` can be added there. Additionally, they need to be added to the
+`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).
+
+The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
+[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The
+[`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration
+you'll need. You can also set up continuous integration on GitHub to check not
+only that Sphinx can build the documentation in an isolated environment (i.e.,
+with `just docs-test`) but also that
+[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
+
+</details>
+
+## 🧑‍💻 For Maintainers
+
+<details>
+  <summary>See maintainer instructions</summary>
+
+### Initial Configuration
+
+#### Configuring ReadTheDocs
+
+[ReadTheDocs](https://readthedocs.org) is an external documentation hosting
+service that integrates with GitHub's CI/CD. Do the following for each
+repository:
+
+1. Log in to ReadTheDocs with your GitHub account to install the integration at
+   https://readthedocs.org/accounts/login/?next=/dashboard/
+2. Import your project by navigating to https://readthedocs.org/dashboard/import
+   then clicking the plus icon next to your repository
+3. You can rename the repository on the next screen using a more stylized name
+   (i.e., with spaces and capital letters)
+4. Click next, and you're good to go!
+
+#### Configuring Archival on Zenodo
+
+[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
+to each release of your package. Do the following for each repository:
+
+1. Log in to Zenodo via GitHub with this link:
+   https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
+   that lists all of your organizations and asks you to approve installing the
+   Zenodo app on GitHub. Click "grant" next to any organizations you want to
+   enable the integration for, then click the big green "approve" button. This
+   step only needs to be done once.
+2. Navigate to https://zenodo.org/account/settings/github/, which lists all of
+   your GitHub repositories (both in your username and any organizations you
+   enabled). Click the on/off toggle for any relevant repositories. When you
+   make a new repository, you'll have to come back to this
+
+After these steps, you're ready to go! After you make "release" on GitHub (steps
+for this are below), you can navigate to
+https://zenodo.org/account/settings/github/repository//mapkgsutils to see the
+DOI for the release and link to the Zenodo record for it.
+
+#### Registering with the Python Package Index (PyPI)
+
+The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can
+be easily installed with `pip`, `uv`, and equivalent tools.
+
+1. Register for an account [here](https://pypi.org/account/register)
+2. Navigate to https://pypi.org/manage/account and make sure you have verified
+   your email address. A verification email might not have been sent by default,
+   so you might have to click the "options" dropdown next to your address to get
+   to the "re-send verification email" button
+3. 2-Factor authentication is required for PyPI since the end of 2023 (see this
+   [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)).
+   This means you have to first issue account recovery codes, then set up
+   2-factor authentication
+4. Issue an API token from https://pypi.org/manage/account/token
+
+This only needs to be done once per developer.
+
+#### Configuring your machine's connection to PyPI
+
+This needs to be done once per machine.
+
+```console
+$ uv tool install keyring
+$ keyring set https://upload.pypi.org/legacy/ __token__
+$ keyring set https://test.pypi.org/legacy/ __token__
+```
+
+Note that this deprecates previous workflows using `.pypirc`.
+
+### 📦 Making a Release
+
+#### Uploading to PyPI
+
+After installing the package in development mode and installing `just` with
+`uv tool install rust-just` or `python3 -m pip install rust-just`, run the
+following from the console:
+
+```console
+$ just finish
+```
+
+This script does the following:
+
+1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to
+   switch the version number in the `pyproject.toml`,`CITATION.cff`,
+   `src/mapkgsutils/version.py`, and
+   [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
+2. Packages the code in both a tar archive and a wheel using
+   [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)
+3. Uploads to PyPI using
+   [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).
+4. Push to GitHub. You'll need to make a release going with the commit where the
+   version was bumped.
+5. Bump the version to the next patch. If you made big changes and want to bump
+   the version by minor, you can use `tox -e bumpversion -- minor` after.
+
+#### Releasing on GitHub
+
+1. Navigate to https://github.com//mapkgsutils/releases/new to draft a new
+   release
+2. Click the "Choose a Tag" dropdown and select the tag corresponding to the
+   release you just made
+3. Click the "Generate Release Notes" button to get a quick outline of recent
+   changes. Modify the title and description as you see fit
+4. Click the big green "Publish Release" button
+
+This will trigger Zenodo to assign a DOI to your release as well.
+
+### Updating Package Boilerplate
+
+This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
+guidelines, documentation configuration) up-to-date with the upstream
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
+</details>