obographs 0.0.1__tar.gz

obographs-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Charles Tapley Hoyt
+
+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.

obographs-0.0.1/PKG-INFO

@@ -0,0 +1,351 @@
+Metadata-Version: 2.4
+Name: obographs
+Version: 0.0.1
+Summary: A python data model for OBO Graphs
+Keywords: snekpack,cookiecutter
+Author: Charles Tapley Hoyt
+Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+License-File: LICENSE
+Classifier: Development Status :: 1 - Planning
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Framework :: Pytest
+Classifier: Framework :: tox
+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 :: Only
+Classifier: Typing :: Typed
+Requires-Dist: pydantic
+Requires-Dist: sphinx>=8 ; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme>=3.0 ; extra == 'docs'
+Requires-Dist: sphinx-automodapi ; extra == 'docs'
+Requires-Dist: autodoc-pydantic ; extra == 'docs'
+Requires-Dist: requests ; extra == 'network'
+Requires-Dist: pytest ; extra == 'tests'
+Requires-Dist: coverage[toml] ; extra == 'tests'
+Maintainer: Charles Tapley Hoyt
+Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+Requires-Python: >=3.10
+Project-URL: Bug Tracker, https://github.com/cthoyt/obographs/issues
+Project-URL: Documentation, https://obographs.readthedocs.io
+Project-URL: Funding, https://github.com/sponsors/cthoyt
+Project-URL: Homepage, https://github.com/cthoyt/obographs
+Project-URL: Repository, https://github.com/cthoyt/obographs.git
+Provides-Extra: docs
+Provides-Extra: network
+Provides-Extra: tests
+Description-Content-Type: text/markdown
+
+<!--
+<p align="center">
+  <img src="https://github.com/cthoyt/obographs/raw/main/docs/source/logo.png" height="150">
+</p>
+-->
+
+<h1 align="center">
+  OBO Graphs
+</h1>
+
+<p align="center">
+    <a href="https://github.com/cthoyt/obographs/actions/workflows/tests.yml">
+        <img alt="Tests" src="https://github.com/cthoyt/obographs/actions/workflows/tests.yml/badge.svg" /></a>
+    <a href="https://pypi.org/project/obographs">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/obographs" /></a>
+    <a href="https://pypi.org/project/obographs">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/obographs" /></a>
+    <a href="https://github.com/cthoyt/obographs/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/obographs" /></a>
+    <a href='https://obographs.readthedocs.io/en/latest/?badge=latest'>
+        <img src='https://readthedocs.org/projects/obographs/badge/?version=latest' alt='Documentation Status' /></a>
+    <a href="https://codecov.io/gh/cthoyt/obographs/branch/main">
+        <img src="https://codecov.io/gh/cthoyt/obographs/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/cthoyt/obographs/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://zenodo.org/badge/latestdoi/XXXXXX">
+        <img src="https://zenodo.org/badge/XXXXXX.svg" alt="DOI"></a>
+    -->
+</p>
+
+A Python data model for [OBO Graphs](https://github.com/geneontology/obographs).
+
+## 💪 Getting Started
+
+This package enables reading a remote OBO Graph JSON file into a Pydantic-backed
+data model.
+
+```python
+import obographs
+
+url = "https://raw.githubusercontent.com/geneontology/obographs/refs/heads/master/examples/abox.json"
+graph_document = obographs.read(url)
+```
+
+Note that the OBO Graph JSON schema uses non-pythonic names. The underlying data
+model does not attempt to give better names to the fields.
+
+## 🚀 Installation
+
+The most recent release can be installed from
+[PyPI](https://pypi.org/project/obographs/) with uv:
+
+```console
+$ uv pip install obographs
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install obographs
+```
+
+The most recent code and data can be installed directly from GitHub with uv:
+
+```console
+$ uv --preview pip install git+https://github.com/cthoyt/obographs.git
+```
+
+or with pip:
+
+```console
+$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/cthoyt/obographs.git
+```
+
+Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
+backend becomes a stable feature.
+
+## 👐 Contributing
+
+Contributions, whether filing an issue, making a pull request, or forking, are
+appreciated. See
+[CONTRIBUTING.md](https://github.com/cthoyt/obographs/blob/master/.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/cthoyt/obographs.git
+$ cd obographs
+$ uv --preview pip install -e .
+```
+
+Alternatively, install using pip:
+
+```console
+$ UV_PREVIEW=1 python3 -m pip install -e .
+```
+
+Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
+backend becomes a stable feature.
+
+### 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).
+
+### 🥼 Testing
+
+After cloning the repository and installing `tox` with
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the
+unit tests in the `tests/` folder can be run reproducibly with:
+
+```console
+$ tox -e py
+```
+
+Additionally, these tests are automatically re-run with each commit in a
+[GitHub Action](https://github.com/cthoyt/obographs/actions?query=workflow%3ATests).
+
+### 📖 Building the Documentation
+
+The documentation can be built locally using the following:
+
+```console
+$ git clone git+https://github.com/cthoyt/obographs.git
+$ cd obographs
+$ tox -e 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 `tox -e docs-test`) but also that
+[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
+
+#### Configuring ReadTheDocs
+
+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!
+
+### 📦 Making a Release
+
+#### Configuring Zenodo
+
+[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
+to each release of your package.
+
+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/cthoyt/obographs to see
+the DOI for the release and link to the Zenodo record for it.
+
+#### Registering with the Python Package Index (PyPI)
+
+You only have to do the following steps once.
+
+1. Register for an account on the
+   [Python Package Index (PyPI)](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
+
+#### Configuring your machine's connection to PyPI
+
+You have to do the following steps 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`.
+
+#### Uploading to PyPI
+
+After installing the package in development mode and installing `tox` with
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run
+the following from the console:
+
+```console
+$ tox -e 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/obographs/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/cthoyt/obographs/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.
+
+</details>

obographs-0.0.1/README.md

@@ -0,0 +1,306 @@
+<!--
+<p align="center">
+  <img src="https://github.com/cthoyt/obographs/raw/main/docs/source/logo.png" height="150">
+</p>
+-->
+
+<h1 align="center">
+  OBO Graphs
+</h1>
+
+<p align="center">
+    <a href="https://github.com/cthoyt/obographs/actions/workflows/tests.yml">
+        <img alt="Tests" src="https://github.com/cthoyt/obographs/actions/workflows/tests.yml/badge.svg" /></a>
+    <a href="https://pypi.org/project/obographs">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/obographs" /></a>
+    <a href="https://pypi.org/project/obographs">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/obographs" /></a>
+    <a href="https://github.com/cthoyt/obographs/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/obographs" /></a>
+    <a href='https://obographs.readthedocs.io/en/latest/?badge=latest'>
+        <img src='https://readthedocs.org/projects/obographs/badge/?version=latest' alt='Documentation Status' /></a>
+    <a href="https://codecov.io/gh/cthoyt/obographs/branch/main">
+        <img src="https://codecov.io/gh/cthoyt/obographs/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/cthoyt/obographs/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://zenodo.org/badge/latestdoi/XXXXXX">
+        <img src="https://zenodo.org/badge/XXXXXX.svg" alt="DOI"></a>
+    -->
+</p>
+
+A Python data model for [OBO Graphs](https://github.com/geneontology/obographs).
+
+## 💪 Getting Started
+
+This package enables reading a remote OBO Graph JSON file into a Pydantic-backed
+data model.
+
+```python
+import obographs
+
+url = "https://raw.githubusercontent.com/geneontology/obographs/refs/heads/master/examples/abox.json"
+graph_document = obographs.read(url)
+```
+
+Note that the OBO Graph JSON schema uses non-pythonic names. The underlying data
+model does not attempt to give better names to the fields.
+
+## 🚀 Installation
+
+The most recent release can be installed from
+[PyPI](https://pypi.org/project/obographs/) with uv:
+
+```console
+$ uv pip install obographs
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install obographs
+```
+
+The most recent code and data can be installed directly from GitHub with uv:
+
+```console
+$ uv --preview pip install git+https://github.com/cthoyt/obographs.git
+```
+
+or with pip:
+
+```console
+$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/cthoyt/obographs.git
+```
+
+Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
+backend becomes a stable feature.
+
+## 👐 Contributing
+
+Contributions, whether filing an issue, making a pull request, or forking, are
+appreciated. See
+[CONTRIBUTING.md](https://github.com/cthoyt/obographs/blob/master/.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/cthoyt/obographs.git
+$ cd obographs
+$ uv --preview pip install -e .
+```
+
+Alternatively, install using pip:
+
+```console
+$ UV_PREVIEW=1 python3 -m pip install -e .
+```
+
+Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
+backend becomes a stable feature.
+
+### 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).
+
+### 🥼 Testing
+
+After cloning the repository and installing `tox` with
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the
+unit tests in the `tests/` folder can be run reproducibly with:
+
+```console
+$ tox -e py
+```
+
+Additionally, these tests are automatically re-run with each commit in a
+[GitHub Action](https://github.com/cthoyt/obographs/actions?query=workflow%3ATests).
+
+### 📖 Building the Documentation
+
+The documentation can be built locally using the following:
+
+```console
+$ git clone git+https://github.com/cthoyt/obographs.git
+$ cd obographs
+$ tox -e 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 `tox -e docs-test`) but also that
+[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
+
+#### Configuring ReadTheDocs
+
+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!
+
+### 📦 Making a Release
+
+#### Configuring Zenodo
+
+[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
+to each release of your package.
+
+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/cthoyt/obographs to see
+the DOI for the release and link to the Zenodo record for it.
+
+#### Registering with the Python Package Index (PyPI)
+
+You only have to do the following steps once.
+
+1. Register for an account on the
+   [Python Package Index (PyPI)](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
+
+#### Configuring your machine's connection to PyPI
+
+You have to do the following steps 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`.
+
+#### Uploading to PyPI
+
+After installing the package in development mode and installing `tox` with
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run
+the following from the console:
+
+```console
+$ tox -e 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/obographs/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/cthoyt/obographs/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.
+
+</details>

obographs-0.0.1/pyproject.toml

@@ -0,0 +1,222 @@
+[build-system]
+requires = ["uv>=0.5.13,<0.6.0"]
+# The uv backend entered preview mode in https://github.com/astral-sh/uv/pull/8886/files
+# with the 0.5.0 release. See also https://github.com/astral-sh/uv/issues/3957 for tracking.
+build-backend = "uv"
+
+[project]
+name = "obographs"
+version = "0.0.1"
+description = "A python data model for OBO Graphs"
+readme = "README.md"
+authors = [
+    { name = "Charles Tapley Hoyt", email = "cthoyt@gmail.com" }
+]
+maintainers = [
+    { name = "Charles Tapley Hoyt", email = "cthoyt@gmail.com" }
+]
+
+# See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#classifiers
+# Search tags using the controlled vocabulary at https://pypi.org/classifiers
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Framework :: Pytest",
+    "Framework :: tox",
+    "Framework :: Sphinx",
+    "Natural Language :: English",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3 :: Only",
+    "Typing :: Typed",
+    # TODO add your topics from the Trove controlled vocabulary (see https://pypi.org/classifiers)
+]
+keywords = [
+    "snekpack", # please keep this keyword to credit the cookiecutter-snekpack template
+    "cookiecutter",
+    # TODO add your own free-text keywords
+]
+
+# License Information.
+# See PEP-639 at https://peps.python.org/pep-0639/#add-license-files-key
+license-files = [
+    "LICENSE",
+]
+
+requires-python = ">=3.10"
+dependencies = [
+    "pydantic",
+]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+    "coverage[toml]",
+]
+docs = [
+    "sphinx>=8",
+    "sphinx-rtd-theme>=3.0",
+    "sphinx_automodapi",
+    "autodoc_pydantic",
+]
+network = [
+    "requests",
+]
+
+# See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#urls
+# and also https://packaging.python.org/en/latest/specifications/well-known-project-urls/
+[project.urls]
+"Bug Tracker" = "https://github.com/cthoyt/obographs/issues"
+Homepage = "https://github.com/cthoyt/obographs"
+Repository = "https://github.com/cthoyt/obographs.git"
+Documentation = "https://obographs.readthedocs.io"
+Funding = "https://github.com/sponsors/cthoyt"
+
+[project.scripts]
+obographs = "obographs.cli:main"
+
+[tool.cruft]
+skip = [
+    "**/__init__.py",
+    "tests/*"
+]
+
+# MyPy, see https://mypy.readthedocs.io/en/stable/config_file.html
+[tool.mypy]
+plugins = [
+    "pydantic.mypy",
+]
+
+# Doc8, see https://doc8.readthedocs.io/en/stable/readme.html#ini-file-usage
+[tool.doc8]
+max-line-length = 120
+
+# Pytest, see https://docs.pytest.org/en/stable/reference/customize.html#pyproject-toml
+[tool.pytest.ini_options]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+]
+
+# Coverage, see https://coverage.readthedocs.io/en/latest/config.html
+[tool.coverage.run]
+branch = true
+source = [
+    "obographs",
+]
+omit = [
+    "tests/*",
+    "docs/*",
+]
+
+[tool.coverage.paths]
+source = [
+    "src/obographs",
+    ".tox/*/lib/python*/site-packages/obographs",
+]
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+    "pragma: no cover",
+    "raise NotImplementedError",
+    "if __name__ == \"__main__\":",
+    "if TYPE_CHECKING:",
+    "def __str__",
+    "def __repr__",
+]
+
+[tool.ruff]
+line-length = 100
+extend-include = ["*.ipynb"]
+
+[tool.ruff.lint]
+# See https://docs.astral.sh/ruff/rules
+extend-select = [
+    "F", # pyflakes
+    "E", # pycodestyle errors
+    "W", # pycodestyle warnings
+    "C90", # mccabe
+    "I", # isort
+    "UP", # pyupgrade
+    "D", # pydocstyle
+    "DOC", # pydoclint
+    "B", # bugbear
+    "S", # bandit
+    "T20", # print
+    "N", # pep8 naming
+    "ERA", # eradicate commented out code
+    "NPY", # numpy checks
+    "RUF", # ruff rules
+    "C4", # comprehensions
+]
+ignore = [
+    "D105", # Missing docstring in magic method
+    "E203", # Black conflicts with the following
+]
+
+# See https://docs.astral.sh/ruff/settings/#per-file-ignores
+[tool.ruff.lint.per-file-ignores]
+# Ignore security issues in the version.py, which are inconsistent
+"src/obographs/version.py" = ["S603", "S607"]
+# Ignore commented out code in Sphinx configuration file
+"docs/source/conf.py" = ["ERA001"]
+# Prints are okay in notebooks
+"notebooks/**/*.ipynb" = ["T201"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "pep257"
+
+[tool.ruff.lint.isort]
+relative-imports-order = "closest-to-furthest"
+known-third-party = [
+    "tqdm",
+]
+known-first-party = [
+    "obographs",
+    "tests",
+]
+
+[tool.ruff.format]
+# see https://docs.astral.sh/ruff/settings/#format_docstring-code-format
+docstring-code-format = true
+
+[tool.bumpversion]
+current_version = "0.0.1"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
+serialize = [
+    "{major}.{minor}.{patch}-{release}+{build}",
+    "{major}.{minor}.{patch}+{build}",
+    "{major}.{minor}.{patch}-{release}",
+    "{major}.{minor}.{patch}",
+]
+commit = true
+tag = false
+
+[tool.bumpversion.parts.release]
+optional_value = "production"
+first_value = "dev"
+values = [
+    "dev",
+    "production",
+]
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = "version = \"{current_version}\""
+replace = "version = \"{new_version}\""
+
+[[tool.bumpversion.files]]
+filename = "docs/source/conf.py"
+search = "release = \"{current_version}\""
+replace = "release = \"{new_version}\""
+
+[[tool.bumpversion.files]]
+filename = "src/obographs/version.py"
+search = "VERSION = \"{current_version}\""
+replace = "VERSION = \"{new_version}\""

obographs-0.0.1/src/obographs/__init__.py

@@ -0,0 +1,14 @@
+"""A python data model for OBO Graphs."""
+
+from .model import Graph, GraphDocument, Meta, Node, Property, Synonym, Xref, read
+
+__all__ = [
+    "Graph",
+    "GraphDocument",
+    "Meta",
+    "Node",
+    "Property",
+    "Synonym",
+    "Xref",
+    "read",
+]

obographs-0.0.1/src/obographs/model.py

@@ -0,0 +1,212 @@
+"""Data structures for representing OBO Graphs.
+
+.. seealso::
+
+    - the defining repository https://github.com/geneontology/obographs
+    - the JSON schema
+      https://github.com/geneontology/obographs/blob/master/schema/obographs-schema.json
+"""
+
+from __future__ import annotations
+
+import json
+import logging
+from collections import defaultdict
+from pathlib import Path
+from typing import Any, Literal, TypeAlias, overload
+
+from pydantic import BaseModel, Field
+
+__all__ = [
+    "Definition",
+    "Edge",
+    "Graph",
+    "GraphDocument",
+    "Meta",
+    "Node",
+    "Property",
+    "Synonym",
+    "Xref",
+    "read",
+]
+
+logger = logging.getLogger(__name__)
+
+OBO_URI_PREFIX = "http://purl.obolibrary.org/obo/"
+OBO_URI_PREFIX_LEN = len(OBO_URI_PREFIX)
+
+SynonymPredicate: TypeAlias = Literal[
+    "hasExactSynonym",
+    "hasBroadSynonym",
+    "hasNarrowSynonym",
+    "hasRelatedSynonym",
+]
+NodeType: TypeAlias = Literal["CLASS", "PROPERTY", "INDIVIDUAL"]
+
+TimeoutHint = int | float | None
+
+#: A mapping from OBO flat file format internal synonym types to OBO in OWL vocabulary
+#: identifiers. See https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html
+OBO_SYNONYM_TO_OIO: dict[str, SynonymPredicate] = {
+    "EXACT": "hasExactSynonym",
+    "BROAD": "hasBroadSynonym",
+    "NARROW": "hasNarrowSynonym",
+    "RELATED": "hasRelatedSynonym",
+}
+
+
+class Property(BaseModel):
+    """Represent a property inside a metadata element."""
+
+    pred: str = Field(...)
+    val: str = Field(
+        ...,
+    )
+
+
+class Definition(BaseModel):
+    """Represents a definition for a node."""
+
+    val: str | None = Field(default=None)
+    xrefs: list[str] | None = Field(default=None)  # Just a list of CURIEs/IRIs
+
+
+class Xref(BaseModel):
+    """Represents a cross-reference."""
+
+    val: str = Field(...)
+
+
+class Synonym(BaseModel):
+    """Represents a synonym inside an object meta."""
+
+    val: str | None = Field(default=None)
+    pred: str = Field(default="hasExactSynonym")
+    synonymType: str | None = Field(examples=["OMO:0003000"])  # noqa:N815
+    xrefs: list[str] = Field(
+        default_factory=list,
+        description="A list of CURIEs/IRIs for provenance for the synonym",
+    )
+
+
+class Meta(BaseModel):
+    """Represents the metadata about a node or ontology."""
+
+    definition: Definition | None = None
+    subsets: list[str] | None = None
+    xrefs: list[Xref] | None = None
+    synonyms: list[Synonym] | None = None
+    comments: list[str] | None = None
+    version: str | None = None
+    basicPropertyValues: list[Property] | None = Field(None)  # noqa:N815
+    deprecated: bool = False
+
+
+class Edge(BaseModel):
+    """Represents an edge in an OBO Graph."""
+
+    sub: str = Field(..., examples=["http://purl.obolibrary.org/obo/CHEBI_99998"])
+    pred: str = Field(..., examples=["is_a"])
+    obj: str = Field(..., examples=["http://purl.obolibrary.org/obo/CHEBI_24995"])
+    meta: Meta | None = None
+
+
+class Node(BaseModel):
+    """Represents a node in an OBO Graph."""
+
+    id: str = Field(..., description="The IRI for the node")
+    lbl: str | None = Field(None, description="The name of the node")
+    meta: Meta | None = None
+    type: NodeType = Field(..., description="Type of node")
+
+
+class Graph(BaseModel):
+    """A graph corresponds to an ontology."""
+
+    id: str | None = None
+    meta: Meta | None = None
+    nodes: list[Node] = Field(default_factory=list)
+    edges: list[Edge] = Field(default_factory=list)
+    equivalentNodesSets: list[Any] = Field(default_factory=list)  # noqa:N815
+    logicalDefinitionAxioms: list[Any] = Field(default_factory=list)  # noqa:N815
+    domainRangeAxioms: list[Any] = Field(default_factory=list)  # noqa:N815
+    propertyChainAxioms: list[Any] = Field(default_factory=list)  # noqa:N815
+
+
+class GraphDocument(BaseModel):
+    """Represents a list of OBO graphs."""
+
+    graphs: list[Graph]
+
+
+def get_id_to_node(graph: Graph) -> dict[str, Node]:
+    """Get a dictionary from node ID to nodes."""
+    return {node.id: node for node in graph.nodes or []}
+
+
+def get_id_to_edges(graph: Graph) -> dict[str, list[tuple[str, str]]]:
+    """Get a dictionary from node ID to nodes."""
+    dd = defaultdict(set)
+    for edge in graph.edges or []:
+        dd[edge.sub].add((edge.pred, edge.obj))
+    return {node_id: list(predicate_object_pairs) for node_id, predicate_object_pairs in dd.items()}
+
+
+# docstr-coverage:excused `overload`
+@overload
+def read(
+    source: str, *, timeout: TimeoutHint = ..., squeeze: Literal[False] = ...
+) -> GraphDocument: ...
+
+
+# docstr-coverage:excused `overload`
+@overload
+def read(source: str, *, timeout: TimeoutHint = ..., squeeze: Literal[True] = ...) -> Graph: ...
+
+
+def read(
+    source: str, *, timeout: TimeoutHint = None, squeeze: bool = True
+) -> Graph | GraphDocument:
+    """Read an OBO Graph document.
+
+    :param source: A file path or URL to an OBO Graph JSON
+    :param timeout: The timeout for getting a URL
+    :param squeeze: By default, will unpack the first graph from a graph document that
+        only has a single graph and return a :class:`Graph` object. If `true` and
+        multiple graphs are received, will raise an error. Set this to `false` to return
+        a GraphDocument containing all graphs.
+
+    :returns: A graph or graph document
+
+    :raises ValueError: If squeeze is set to true and multiple graphs are received
+    """
+    if (isinstance(source, str) and source.startswith("https://")) or source.startswith("http://"):
+        import requests
+
+        if source.endswith(".gz"):
+            raise NotImplementedError
+        else:
+            res = requests.get(source, timeout=timeout)
+            res_json = res.json()
+            graph_document = GraphDocument.model_validate(res_json)
+
+    elif isinstance(source, str | Path):
+        path = Path(source).expanduser().resolve()
+        if path.is_file():
+            if path.suffix.endswith(".gz"):
+                raise NotImplementedError
+            else:
+                with path.open() as file:
+                    graph_document = GraphDocument.model_validate(json.load(file))
+    else:
+        raise TypeError(f"Unhandled source: {source}")
+
+    if not squeeze:
+        return graph_document
+    elif len(graph_document.graphs) != 1:
+        raise ValueError(
+            f"graph document has {len(graph_document.graphs)} graphs, "
+            f"so can not squeeze. set squeeze=False"
+        )
+    else:
+        return graph_document.graphs[0]

obographs-0.0.1/src/obographs/py.typed

@@ -0,0 +1 @@
+

obographs-0.0.1/src/obographs/version.py

@@ -0,0 +1,39 @@
+"""Version information for :mod:`obographs`.
+
+Run with ``python -m obographs.version``
+"""
+
+import os
+from subprocess import CalledProcessError, check_output
+
+__all__ = [
+    "VERSION",
+    "get_git_hash",
+    "get_version",
+]
+
+VERSION = "0.0.1"
+
+
+def get_git_hash() -> str:
+    """Get the :mod:`obographs` git hash."""
+    with open(os.devnull, "w") as devnull:
+        try:
+            ret = check_output(
+                ["git", "rev-parse", "HEAD"],
+                cwd=os.path.dirname(__file__),
+                stderr=devnull,
+            )
+        except CalledProcessError:
+            return "UNHASHED"
+        else:
+            return ret.strip().decode("utf-8")[:8]
+
+
+def get_version(with_git_hash: bool = False) -> str:
+    """Get the :mod:`obographs` version string, including a git hash."""
+    return f"{VERSION}-{get_git_hash()}" if with_git_hash else VERSION
+
+
+if __name__ == "__main__":
+    print(get_version(with_git_hash=True))  # noqa:T201