robot_obo_tool 0.0.1__tar.gz

robot_obo_tool-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 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.

robot_obo_tool-0.0.1/PKG-INFO

@@ -0,0 +1,383 @@
+Metadata-Version: 2.4
+Name: robot_obo_tool
+Version: 0.0.1
+Summary: A wrapper around ROBOT
+Keywords: snekpack,cookiecutter,ontologies,obo,robot,open biomedical ontologies
+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 :: 3.14
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Typing :: Typed
+Requires-Dist: pystow
+Maintainer: Charles Tapley Hoyt
+Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+Requires-Python: >=3.10
+Project-URL: Bug Tracker, https://github.com/cthoyt/robot-obo-tool/issues
+Project-URL: Homepage, https://github.com/cthoyt/robot-obo-tool
+Project-URL: Repository, https://github.com/cthoyt/robot-obo-tool.git
+Project-URL: Documentation, https://robot_obo_tool.readthedocs.io
+Project-URL: Funding, https://github.com/sponsors/cthoyt
+Description-Content-Type: text/markdown
+
+<!--
+<p align="center">
+  <img src="https://github.com/cthoyt/robot-obo-tool/raw/main/docs/source/logo.png" height="150">
+</p>
+-->
+
+<h1 align="center">
+  ROBOT is an OBO Tool
+</h1>
+
+<p align="center">
+    <a href="https://github.com/cthoyt/robot-obo-tool/actions/workflows/tests.yml">
+        <img alt="Tests" src="https://github.com/cthoyt/robot-obo-tool/actions/workflows/tests.yml/badge.svg" /></a>
+    <a href="https://pypi.org/project/robot_obo_tool">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/robot_obo_tool" /></a>
+    <a href="https://pypi.org/project/robot_obo_tool">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/robot_obo_tool" /></a>
+    <a href="https://github.com/cthoyt/robot-obo-tool/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/robot_obo_tool" /></a>
+    <a href='https://robot_obo_tool.readthedocs.io/en/latest/?badge=latest'>
+        <img src='https://readthedocs.org/projects/robot_obo_tool/badge/?version=latest' alt='Documentation Status' /></a>
+    <a href="https://codecov.io/gh/cthoyt/robot-obo-tool/branch/main">
+        <img src="https://codecov.io/gh/cthoyt/robot-obo-tool/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/robot-obo-tool/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>
+
+A Python wrapper around [ROBOT](https://robot.obolibrary.org/) that automates
+downloading the Java JAR and wraps calls via the console using `subprocess`.
+
+## 💪 Getting Started
+
+The `convert` can be called like in:
+
+```python
+import robot_obo_tool
+
+robot_obo_tool.convert(
+   "https://raw.githubusercontent.com/pato-ontology/pato/master/pato.owl",
+   "pato.obo",
+   check=False,  # remove pesky errors for incorrect OWL
+)
+```
+
+Other ROBOT commands don't (yet) have a wrapper, but you can directly call ROBOT
+with `call()`:
+
+```python
+import robot_obo_tool
+
+robot_obo_tool.call(
+   "convert",
+   "-I"
+   "https://raw.githubusercontent.com/pato-ontology/pato/master/pato.owl",
+   "-o",
+   "pato.obo",
+   "--check=false",
+)
+```
+
+## 🚀 Installation
+
+The most recent release can be installed from
+[PyPI](https://pypi.org/project/robot_obo_tool/) with uv:
+
+```console
+$ uv pip install robot_obo_tool
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install robot_obo_tool
+```
+
+The most recent code and data can be installed directly from GitHub with uv:
+
+```console
+$ uv pip install git+https://github.com/cthoyt/robot-obo-tool.git
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install git+https://github.com/cthoyt/robot-obo-tool.git
+```
+
+## 👐 Contributing
+
+Contributions, whether filing an issue, making a pull request, or forking, are
+appreciated. See
+[CONTRIBUTING.md](https://github.com/cthoyt/robot-obo-tool/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/robot-obo-tool.git
+$ cd robot-obo-tool
+$ 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 `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/robot-obo-tool/actions?query=workflow%3ATests).
+
+### 📖 Building the Documentation
+
+The documentation can be built locally using the following:
+
+```console
+$ git clone git+https://github.com/cthoyt/robot-obo-tool.git
+$ cd robot-obo-tool
+$ 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).
+
+</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/cthoyt/robot-obo-tool 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 `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/robot_obo_tool/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/robot-obo-tool/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>

robot_obo_tool-0.0.1/README.md

@@ -0,0 +1,347 @@
+<!--
+<p align="center">
+  <img src="https://github.com/cthoyt/robot-obo-tool/raw/main/docs/source/logo.png" height="150">
+</p>
+-->
+
+<h1 align="center">
+  ROBOT is an OBO Tool
+</h1>
+
+<p align="center">
+    <a href="https://github.com/cthoyt/robot-obo-tool/actions/workflows/tests.yml">
+        <img alt="Tests" src="https://github.com/cthoyt/robot-obo-tool/actions/workflows/tests.yml/badge.svg" /></a>
+    <a href="https://pypi.org/project/robot_obo_tool">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/robot_obo_tool" /></a>
+    <a href="https://pypi.org/project/robot_obo_tool">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/robot_obo_tool" /></a>
+    <a href="https://github.com/cthoyt/robot-obo-tool/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/robot_obo_tool" /></a>
+    <a href='https://robot_obo_tool.readthedocs.io/en/latest/?badge=latest'>
+        <img src='https://readthedocs.org/projects/robot_obo_tool/badge/?version=latest' alt='Documentation Status' /></a>
+    <a href="https://codecov.io/gh/cthoyt/robot-obo-tool/branch/main">
+        <img src="https://codecov.io/gh/cthoyt/robot-obo-tool/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/robot-obo-tool/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>
+
+A Python wrapper around [ROBOT](https://robot.obolibrary.org/) that automates
+downloading the Java JAR and wraps calls via the console using `subprocess`.
+
+## 💪 Getting Started
+
+The `convert` can be called like in:
+
+```python
+import robot_obo_tool
+
+robot_obo_tool.convert(
+   "https://raw.githubusercontent.com/pato-ontology/pato/master/pato.owl",
+   "pato.obo",
+   check=False,  # remove pesky errors for incorrect OWL
+)
+```
+
+Other ROBOT commands don't (yet) have a wrapper, but you can directly call ROBOT
+with `call()`:
+
+```python
+import robot_obo_tool
+
+robot_obo_tool.call(
+   "convert",
+   "-I"
+   "https://raw.githubusercontent.com/pato-ontology/pato/master/pato.owl",
+   "-o",
+   "pato.obo",
+   "--check=false",
+)
+```
+
+## 🚀 Installation
+
+The most recent release can be installed from
+[PyPI](https://pypi.org/project/robot_obo_tool/) with uv:
+
+```console
+$ uv pip install robot_obo_tool
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install robot_obo_tool
+```
+
+The most recent code and data can be installed directly from GitHub with uv:
+
+```console
+$ uv pip install git+https://github.com/cthoyt/robot-obo-tool.git
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install git+https://github.com/cthoyt/robot-obo-tool.git
+```
+
+## 👐 Contributing
+
+Contributions, whether filing an issue, making a pull request, or forking, are
+appreciated. See
+[CONTRIBUTING.md](https://github.com/cthoyt/robot-obo-tool/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/robot-obo-tool.git
+$ cd robot-obo-tool
+$ 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 `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/robot-obo-tool/actions?query=workflow%3ATests).
+
+### 📖 Building the Documentation
+
+The documentation can be built locally using the following:
+
+```console
+$ git clone git+https://github.com/cthoyt/robot-obo-tool.git
+$ cd robot-obo-tool
+$ 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).
+
+</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/cthoyt/robot-obo-tool 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 `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/robot_obo_tool/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/robot-obo-tool/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>

robot_obo_tool-0.0.1/pyproject.toml

@@ -0,0 +1,254 @@
+[build-system]
+requires = ["uv_build>=0.9.6,<1.0"]
+build-backend = "uv_build"
+
+[project]
+name = "robot_obo_tool"
+version = "0.0.1"
+description = "A wrapper around ROBOT"
+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 :: 3.14",
+    "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",
+    "ontologies",
+    "obo",
+    "robot",
+    "open biomedical ontologies",
+]
+
+# License Information.
+# See PEP-639 at https://peps.python.org/pep-0639/#add-license-files-key
+license-files = [
+    "LICENSE",
+]
+
+requires-python = ">=3.10"
+dependencies = [
+    "pystow",
+]
+
+# see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups
+[dependency-groups]
+tests = [
+    "pytest",
+    "coverage[toml]",
+]
+docs = [
+    "sphinx>=8,<9",
+    "sphinx-rtd-theme>=3.0",
+    "sphinx_automodapi",
+]
+lint = [
+    "ruff",
+]
+typing = [
+    { include-group = "tests" },
+    "mypy",
+]
+docs-lint = [
+    { include-group = "docs" },
+    "doc8",
+]
+format-docs = [
+    { include-group = "docs" },
+    "docstrfmt",
+]
+doctests = [
+    "xdoctest",
+    "pygments",
+]
+pyroma = [
+    "pyroma",
+    "pygments",
+]
+
+# see https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#dependencies-optional-dependencies
+[project.optional-dependencies]
+
+
+# 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/robot-obo-tool/issues"
+Homepage = "https://github.com/cthoyt/robot-obo-tool"
+Repository = "https://github.com/cthoyt/robot-obo-tool.git"
+Documentation = "https://robot_obo_tool.readthedocs.io"
+Funding = "https://github.com/sponsors/cthoyt"
+
+
+
+[tool.cruft]
+skip = [
+    "**/__init__.py",
+    "tests/*"
+]
+
+# MyPy, see https://mypy.readthedocs.io/en/stable/config_file.html
+[tool.mypy]
+plugins = [
+]
+
+# 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 = [
+    "robot_obo_tool",
+]
+omit = [
+    "tests/*",
+    "docs/*",
+    "src/robot_obo_tool/version.py",
+    "src/robot_obo_tool/__main__.py",
+    "src/robot_obo_tool/cli.py",
+]
+
+[tool.coverage.paths]
+source = [
+    "src/robot_obo_tool",
+    ".tox/*/lib/python*/site-packages/robot_obo_tool",
+]
+
+[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/robot_obo_tool/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 = [
+    "robot_obo_tool",
+    "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/robot_obo_tool/version.py"
+search = "VERSION = \"{current_version}\""
+replace = "VERSION = \"{new_version}\""
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+search = "version: {current_version}"
+replace = "version: {new_version}"

robot_obo_tool-0.0.1/src/robot_obo_tool/__init__.py

@@ -0,0 +1,12 @@
+"""A wrapper around ROBOT."""
+
+from .api import ROBOT_VERSION, ROBOTError, call, convert, ensure_jar, is_available
+
+__all__ = [
+    "ROBOT_VERSION",
+    "ROBOTError",
+    "call",
+    "convert",
+    "ensure_jar",
+    "is_available",
+]

robot_obo_tool-0.0.1/src/robot_obo_tool/api.py

@@ -0,0 +1,232 @@
+"""A wrapper around ROBOT functionality.
+
+.. seealso:: https://robot.obolibrary.org
+"""
+
+import logging
+import os
+import subprocess
+from pathlib import Path
+from shutil import which
+from subprocess import check_output
+from textwrap import indent, shorten
+from typing import Literal
+
+import pystow
+
+__all__ = [
+    "ROBOT_VERSION",
+    "ROBOTError",
+    "call",
+    "convert",
+    "ensure_jar",
+    "is_available",
+]
+
+logger = logging.getLogger(__name__)
+
+#: The default ROBOT version to download
+ROBOT_VERSION = "1.9.8"
+ROBOT_MODULE = pystow.module("robot")
+
+
+def ensure_jar(*, version: str | None = None) -> Path:
+    """Ensure the ROBOT JAR is cached."""
+    if version is None:
+        version = ROBOT_VERSION
+    url = f"https://github.com/ontodev/robot/releases/download/v{version}/robot.jar"
+    return ROBOT_MODULE.ensure(url=url, version=version)
+
+
+def is_available(*, version: str | None = None) -> bool:
+    """Check if ROBOT is available."""
+    if which("java") is None:
+        # suggested in https://stackoverflow.com/questions/11210104/check-if-a-program-exists-from-a-python-script
+        logger.error("java is not on the PATH")
+        return False
+
+    try:
+        check_output(["java", "--help"])  # noqa: S607
+    except Exception:
+        logger.error(
+            "java --help failed - this means the java runtime environment (JRE) "
+            "might not be configured properly"
+        )
+        return False
+
+    robot_jar_path = ensure_jar(version=version)
+    if not robot_jar_path.is_file():
+        logger.error("ROBOT was not successfully downloaded to %s", robot_jar_path)
+        # ROBOT was unsuccessfully downloaded
+        return False
+
+    try:
+        call("--help")
+    except Exception:
+        logger.error("ROBOT was downloaded to %s but could not be run with --help", robot_jar_path)
+        return False
+
+    return True
+
+
+def call(*args: str, version: str | None = None) -> str:
+    """Run a ROBOT command and return the output as a string."""
+    rr = ["java", "-jar", str(ensure_jar(version=version)), *args]
+    logger.debug("Running shell command: %s", rr)
+    try:
+        ret = check_output(  # noqa:S603
+            rr,
+            cwd=os.path.dirname(__file__),
+            stderr=subprocess.PIPE,
+        )
+    except subprocess.CalledProcessError as e:
+        raise ROBOTError(
+            command=e.cmd,
+            return_code=e.returncode,
+            output=e.output.decode() if e.output is not None else None,
+            stderr=e.stderr.decode() if e.stderr is not None else None,
+        ) from None
+
+    return ret.decode()
+
+
+def convert(
+    input_path: str | Path,
+    output_path: str | Path,
+    input_flag: Literal["-i", "-I"] | None = None,
+    *,
+    merge: bool = False,
+    fmt: str | None = None,
+    check: bool = True,
+    reason: bool = False,
+    extra_args: list[str] | None = None,
+    debug: bool = False,
+    version: str | None = None,
+) -> str:
+    """Convert an OBO file to an OWL file with ROBOT.
+
+    :param input_path: Either a local file path or IRI. If a local file path
+        is used, pass ``"-i"`` to ``flag``. If an IRI is used, pass ``"-I"``
+        to ``flag``.
+    :param output_path: The local file path to save the converted ontology to.
+        Will infer format from the extension, otherwise, use the ``fmt`` param.
+    :param input_flag: The flag to denote if the file is local or remote.
+        Tries to infer from input string if none is given
+    :param merge: Use ROBOT's merge command to squash all graphs together
+    :param fmt: Explicitly set the format
+    :param check:
+        By default, the OBO writer strictly enforces
+        `document structure rules <http://owlcollab.github.io/oboformat/doc/obo-syntax.html#4>`.
+        If an ontology violates these, the convert to OBO operation will fail.
+        These checks can be ignored by setting this to false.
+    :param reason:
+        Turn on ontology reasoning
+    :param extra_args:
+        Extra positional arguments to pass in the command line
+    :param debug:
+        Turn on -vvv
+    :param version: the version of ROBOT to use
+    :return: Output from standard out from running ROBOT
+    """
+    if input_flag is None:
+        input_flag = "-I" if _is_remote(input_path) else "-i"
+
+    args: list[str] = []
+
+    if merge and not reason:
+        args.extend(["merge", str(input_flag), str(input_path), "convert"])
+    elif merge and reason:
+        args.extend(
+            [
+                "merge",
+                str(input_flag),
+                str(input_path),
+                "reason",
+                "convert",
+            ]
+        )
+    elif not merge and reason:
+        args.extend(
+            [
+                "reason",
+                str(input_flag),
+                str(input_path),
+                "convert",
+            ]
+        )
+    else:
+        args.extend(
+            [
+                "convert",
+                str(input_flag),
+                str(input_path),
+            ]
+        )
+
+    args.extend(("-o", str(output_path)))
+    if extra_args:
+        args.extend(extra_args)
+    if not check:
+        args.append("--check=false")
+    if fmt:
+        args.extend(("--format", fmt))
+    if debug:
+        args.append("-vvv")
+
+    return call(*args, version=version)
+
+
+#: Prefixes that denote remote resources
+PROTOCOLS = {
+    "https://",
+    "http://",
+    "ftp://",
+    "ftps://",
+}
+
+
+def _is_remote(url: str | Path) -> bool:
+    return isinstance(url, str) and any(url.startswith(protocol) for protocol in PROTOCOLS)
+
+
+class ROBOTError(Exception):
+    """Custom error for ROBOT command failures that includes output preview."""
+
+    def __init__(
+        self,
+        command: list[str],
+        return_code: int,
+        output: str | None = None,
+        stderr: str | None = None,
+        preview_length: int = 500,
+    ) -> None:
+        """Initialize a wrapper around a ROBOT exception.
+
+        :param command: The command that was executed and failed
+        :param return_code: The exit code returned by the command
+        :param output: The stdout/stderr output from the command execution
+        :param preview_length:
+            Maximum number of characters to include in the
+            error message preview. Default is 500 characters.
+
+        The error message will contain the command, return code, and a preview
+        of the output truncated to preview_length characters.
+        """
+        self.command = command
+        self.return_code = return_code
+        self.stdout = output or "<no stdout>"
+        self.preview_length = preview_length
+        self.stderr = stderr or "<no stderr>"
+
+        # Create the error message
+        command_str = " ".join(command)
+        stdout_preview = indent(shorten(self.stdout, preview_length), "  ")
+        stderr_preview = indent(shorten(self.stderr, preview_length), "  ")
+
+        message = (
+            f"Command `{command_str}` returned non-zero exit status {return_code}.\n\n"
+            f"stderr:\n\n{stderr_preview}"
+            f"\n\nstdout:\n\n{stdout_preview}"
+        )
+
+        super().__init__(message)

robot_obo_tool-0.0.1/src/robot_obo_tool/py.typed

@@ -0,0 +1 @@
+

robot_obo_tool-0.0.1/src/robot_obo_tool/version.py

@@ -0,0 +1,39 @@
+"""Version information for :mod:`robot_obo_tool`.
+
+Run with ``python -m robot_obo_tool.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:`robot_obo_tool` 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:`robot_obo_tool` 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