pyobo 0.11.2__py3-none-any.whl → 0.12.1__py3-none-any.whl

pyobo-0.11.2.dist-info/METADATA

@@ -1,711 +0,0 @@
-Metadata-Version: 2.1
-Name: pyobo
-Version: 0.11.2
-Summary: A python package for handling and generating OBO
-Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
-Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
-License: MIT License
-        
-        Copyright (c) 2024 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.
-        
-Project-URL: Bug Tracker, https://github.com/biopragmatics/pyobo/issues
-Project-URL: Homepage, https://github.com/biopragmatics/pyobo
-Project-URL: Repository, https://github.com/biopragmatics/pyobo.git
-Project-URL: Documentation, https://pyobo.readthedocs.io
-Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
-Classifier: Development Status :: 4 - Beta
-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: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-Requires-Dist: obonet>=0.3.0
-Requires-Dist: click
-Requires-Dist: tqdm
-Requires-Dist: pyyaml
-Requires-Dist: pandas
-Requires-Dist: requests
-Requires-Dist: protmapper
-Requires-Dist: more_itertools
-Requires-Dist: more_click>=0.0.2
-Requires-Dist: humanize
-Requires-Dist: tabulate
-Requires-Dist: cachier
-Requires-Dist: pystow>=0.2.7
-Requires-Dist: bioversions>=0.5.535
-Requires-Dist: bioregistry>=0.11.23
-Requires-Dist: bioontologies>=0.4.0
-Requires-Dist: zenodo-client>=0.0.5
-Requires-Dist: class_resolver
-Requires-Dist: psycopg2-binary
-Requires-Dist: pydantic>=2.0
-Requires-Dist: requests-ftp
-Requires-Dist: drugbank_downloader
-Requires-Dist: chembl_downloader
-Requires-Dist: umls_downloader>=0.1.3
-Requires-Dist: typing_extensions
-Requires-Dist: rdflib
-Provides-Extra: tests
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: coverage; extra == "tests"
-Provides-Extra: docs
-Requires-Dist: sphinx>=8; extra == "docs"
-Requires-Dist: sphinx-rtd-theme>=3.0; extra == "docs"
-Requires-Dist: sphinx-click; extra == "docs"
-Requires-Dist: sphinx_automodapi; extra == "docs"
-
-<!--
-<p align="center">
-  <img src="https://github.com/biopragmatics/pyobo/raw/main/docs/source/logo.png" height="150">
-</p>
--->
-
-<h1 align="center">
-  PyOBO
-</h1>
-
-<p align="center">
-    <a href="https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml">
-        <img alt="Tests" src="https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml/badge.svg" /></a>
-    <a href="https://pypi.org/project/pyobo">
-        <img alt="PyPI" src="https://img.shields.io/pypi/v/pyobo" /></a>
-    <a href="https://pypi.org/project/pyobo">
-        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/pyobo" /></a>
-    <a href="https://github.com/biopragmatics/pyobo/blob/main/LICENSE">
-        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/pyobo" /></a>
-    <a href='https://pyobo.readthedocs.io/en/latest/?badge=latest'>
-        <img src='https://readthedocs.org/projects/pyobo/badge/?version=latest' alt='Documentation Status' /></a>
-    <a href="https://codecov.io/gh/biopragmatics/pyobo/branch/main">
-        <img src="https://codecov.io/gh/biopragmatics/pyobo/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/biopragmatics/pyobo/blob/main/.github/CODE_OF_CONDUCT.md">
-        <img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
-    <a href="https://doi.org/10.5281/zenodo.3381961">
-        <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3381961.svg" alt="DOI"></a>
-</p>
-
-Tools for biological identifiers, names, synonyms, xrefs, hierarchies, relations, and properties through the
-perspective of OBO.
-
-## Example Usage
-
-Note! PyOBO is no-nonsense. This means that there's no repetitive
-prefixes in identifiers. It also means all identifiers are strings,
-no exceptions.
-
-Note! The first time you run these, they have to download and cache
-all resources. We're not in the business of redistributing data,
-so all scripts should be completely reproducible. There's some
-AWS tools for hosting/downloading pre-compiled versions in
-`pyobo.aws` if you don't have time for that.
-
-Note! PyOBO can perform grounding in a limited number of cases, but
-it is *not* a general solution for named entity recognition (NER) or grounding.
-It's suggested to check `Gilda <https://github.com/indralab/gilda>`_
-for a no-nonsense solution.
-
-### Mapping Identifiers and CURIEs
-
-Get mapping of ChEBI identifiers to names:
-
-```python
-import pyobo
-
-chebi_id_to_name = pyobo.get_id_name_mapping('chebi')
-
-name = chebi_id_to_name['132964']
-assert name == 'fluazifop-P-butyl'
-```
-
-Or, you don't have time for two lines:
-
-```python
-import pyobo
-
-name = pyobo.get_name('chebi', '132964')
-assert name == 'fluazifop-P-butyl'
-```
-
-Get reverse mapping of ChEBI names to identifiers:
-
-```python
-import pyobo
-
-chebi_name_to_id = pyobo.get_name_id_mapping('chebi')
-
-identifier = chebi_name_to_id['fluazifop-P-butyl']
-assert identifier == '132964'
-```
-
-Maybe you live in CURIE world and just want to normalize something like
-`CHEBI:132964`:
-
-```python
-import pyobo
-
-name = pyobo.get_name_by_curie('CHEBI:132964')
-assert name == 'fluazifop-P-butyl'
-```
-
-Sometimes you accidentally got an old CURIE. It can be mapped to the more recent
-one using alternative identifiers listed in the underlying OBO with:
-
-```python
-import pyobo
-
-# Look up DNA-binding transcription factor activity (go:0003700)
-# based on an old id
-primary_curie = pyobo.get_primary_curie('go:0001071')
-assert primary_curie == 'go:0003700'
-
-# If it's already the primary, it just gets returned
-assert 'go:0003700' == pyobo.get_priority_curie('go:0003700')
-```
-
-### Mapping Species
-
-Some resources have species information for their term. Get a mapping of WikiPathway identifiers
-to species (as NCBI taxonomy identifiers):
-
-```python
-import pyobo
-
-wikipathways_id_to_species = pyobo.get_id_species_mapping('wikipathways')
-
-# Apoptosis (Homo sapiens)
-taxonomy_id = wikipathways_id_to_species['WP254']
-assert taxonomy_id == '9606'
-```
-
-Or, you don't have time for two lines:
-
-```python
-import pyobo
-
-# Apoptosis (Homo sapiens)
-taxonomy_id = pyobo.get_species('wikipathways', 'WP254')
-assert taxonomy_id == '9606'
-```
-
-### Grounding
-
-Maybe you've got names/synonyms you want to try and map back to ChEBI synonyms.
-Given the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look
-it up and its preferred label.
-
-```python
-import pyobo
-
-prefix, identifier, name = pyobo.ground('chebi', 'Fusilade II')
-assert prefix == 'chebi'
-assert identifier == '132964'
-assert name == 'fluazifop-P-butyl'
-
-# When failure happens...
-prefix, identifier, name = pyobo.ground('chebi', 'Definitely not a real name')
-assert prefix is None
-assert identifier is None
-assert name is None
-```
-
-If you're not really sure which namespace a name might belong to, you
-can try a few in a row (prioritize by ones that cover the appropriate
-entity type to avoid false positives in case of conflicts):
-
-```python
-import pyobo
-
-# looking for phenotypes/pathways
-prefix, identifier, name = pyobo.ground(['efo', 'go'], 'ERAD')
-assert prefix == 'go'
-assert identifier == '0030433'
-assert name == 'ubiquitin-dependent ERAD pathway'
-```
-
-### Cross-referencing
-
-Get xrefs from ChEBI to PubChem:
-
-```python
-import pyobo
-
-chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs('chebi', 'pubchem.compound')
-
-pubchem_compound_id = chebi_id_to_pubchem_compound_id['132964']
-assert pubchem_compound_id == '3033674'
-```
-
-If you don't have time for two lines:
-
-```python
-import pyobo
-
-pubchem_compound_id = pyobo.get_xref('chebi', '132964', 'pubchem.compound')
-assert pubchem_compound_id == '3033674'
-```
-
-Get xrefs from Entrez to HGNC, but they're only available through HGNC,
-so you need to flip them:
-
-```python
-import pyobo
-
-hgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene')
-ncbigene_id_to_hgnc_id = {
-  ncbigene_id: hgnc_id
-  for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()
-}
-mapt_hgnc = ncbigene_id_to_hgnc_id['4137']
-assert mapt_hgnc == '6893'
-```
-
-Since this is a common pattern, there's a keyword argument `flip`
-that does this for you:
-
-```python
-import pyobo
-
-ncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene', flip=True)
-mapt_hgnc_id = ncbigene_id_to_hgnc_id['4137']
-assert mapt_hgnc_id == '6893'
-```
-
-If you don't have time for two lines (I admit this one is a bit confusing) and
-need to flip it:
-
-```python
-import pyobo
-
-hgnc_id = pyobo.get_xref('hgnc', '4137', 'ncbigene', flip=True)
-assert hgnc_id == '6893'
-```
-
-Remap a CURIE based on pre-defined priority list and [Inspector Javert's Xref
-Database](https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html):
-
-```python
-
-import pyobo
-
-# Map to the best source possible
-mapt_ncbigene = pyobo.get_priority_curie('hgnc:6893')
-assert mapt_ncbigene == 'ncbigene:4137'
-
-# Sometimes you know you're the best. Own it.
-assert 'ncbigene:4137' == pyobo.get_priority_curie('ncbigene:4137')
-```
-
-Find all CURIEs mapped to a given one using Inspector Javert's Xref Database:
-
-```python
-import pyobo
-
-# Get a set of all CURIEs mapped to MAPT
-mapt_curies = pyobo.get_equivalent('hgnc:6893')
-assert 'ncbigene:4137' in mapt_curies
-assert 'ensembl:ENSG00000186868' in mapt_curies
-```
-
-If you don't want to wait to build the database locally for the `pyobo.get_priority_curie` and
-`pyobo.get_equivalent`, you can use the following code to download a release from
-[Zenodo](https://zenodo.org/record/3757266):
-
-```python
-import pyobo.resource_utils
-
-pyobo.resource_utils.ensure_inspector_javert()
-```
-
-### Properties
-
-Get properties, like SMILES. The semantics of these are defined on an OBO-OBO basis.
-
-```python
-import pyobo
-
-# I don't make the rules. I wouldn't have chosen this as the key for this property. It could be any string
-chebi_smiles_property = 'http://purl.obolibrary.org/obo/chebi/smiles'
-chebi_id_to_smiles = pyobo.get_filtered_properties_mapping('chebi', chebi_smiles_property)
-
-smiles = chebi_id_to_smiles['132964']
-assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
-```
-
-If you don't have time for two lines:
-
-```python
-import pyobo
-
-smiles = pyobo.get_property('chebi', '132964', 'http://purl.obolibrary.org/obo/chebi/smiles')
-assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
-```
-
-### Hierarchy
-
-Check if an entity is in the hierarchy:
-
-```python
-import networkx as nx
-import pyobo
-
-# check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
-assert 'go:0008219' in pyobo.get_ancestors('go', '0006915')
-
-# check that go:0070246 ! natural killer cell apoptotic process is a
-# descendant of go:0006915 ! apoptotic process
-apopototic_process_descendants = pyobo.get_descendants('go', '0006915')
-assert 'go:0070246' in apopototic_process_descendants
-```
-
-Get the sub-hierarchy below a given node:
-
-```python
-import pyobo
-
-# get the descendant graph of go:0006915 ! apoptotic process
-apopototic_process_subhierarchy = pyobo.get_subhierarchy('go', '0006915')
-
-# check that go:0070246 ! natural killer cell apoptotic process is a
-# descendant of go:0006915 ! apoptotic process through the subhierarchy
-assert 'go:0070246' in apopototic_process_subhierarchy
-```
-
-Get a hierarchy with properties preloaded in the node data dictionaries:
-
-```python
-import pyobo
-
-prop = 'http://purl.obolibrary.org/obo/chebi/smiles'
-chebi_hierarchy = pyobo.get_hierarchy('chebi', properties=[prop])
-
-assert 'chebi:132964' in chebi_hierarchy
-assert prop in chebi_hierarchy.nodes['chebi:132964']
-assert chebi_hierarchy.nodes['chebi:132964'][prop] == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
-```
-
-### Relations
-
-Get all orthologies (`ro:HOM0000017`) between HGNC and MGI (note: this is one way)
-
-```python
->>> import pyobo
->>> human_mapt_hgnc_id = '6893'
->>> mouse_mapt_mgi_id = '97180'
->>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')
->>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]
-```
-
-If you want to do it in one line, use:
-
-```python
-
->>> import pyobo
->>> human_mapt_hgnc_id = '6893'
->>> mouse_mapt_mgi_id = '97180'
->>> assert mouse_mapt_mgi_id == pyobo.get_relation('hgnc', 'ro:HOM0000017', 'mgi', human_mapt_hgnc_id)
-```
-
-### Writings Tests that Use PyOBO
-
-If you're writing your own code that relies on PyOBO, and unit
-testing it (as you should) in a continuous integration setting,
-you've probably realized that loading all of the resources on each
-build is not so fast. In those scenarios, you can use some of the
-pre-build patches like in the following:
-
-```python
-import unittest
-import pyobo
-from pyobo.mocks import get_mock_id_name_mapping
-
-mock_id_name_mapping = get_mock_id_name_mapping({
-  'chebi': {
-      '132964': 'fluazifop-P-butyl',
-  },
-})
-
-class MyTestCase(unittest.TestCase):
-  def my_test(self):
-      with mock_id_name_mapping:
-          # use functions directly, or use your functions that wrap them
-          pyobo.get_name('chebi', '1234')
-```
-
-
-## Curation of the Bioregistry
-
-In order to normalize references and identify resources, PyOBO uses the
-[Bioregistry](https://github.com/bioregistry/bioregistry). It used to be a part of PyOBO, but has since
-been externalized for more general reuse.
-
-At [src/pyobo/registries/metaregistry.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/registries/metaregistry.json)
-is the curated "metaregistry". This is a source of information that contains
-all sorts of fixes for missing/wrong information in MIRIAM, OLS, and OBO Foundry; entries that don't appear in
-any of them; additional synonym information for each namespace/prefix; rules for normalizing xrefs and CURIEs, etc.
-
-Other entries in the metaregistry:
-
-- The `"remappings"->"full"` entry is a dictionary from strings that might follow `xref:`
-  in a given OBO file that need to be completely replaced, due to incorrect formatting
-- The `"remappings"->"prefix"` entry contains a dictionary of prefixes for xrefs that need
-  to be remapped. Several rules, for example, remove superfluous spaces that occur inside
-  CURIEs or and others address instances of the GOGO issue.
-- The `"blacklists"` entry contains rules for throwing out malformed xrefs based on
-  full string, just prefix, or just suffix.
-
-## Troubleshooting
-
-The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO resources. If you get an error like:
-
-```
-pyobo.getters.MissingOboBuild: OBO Foundry is missing a build for: mondo
-```
-
-Then you should check the corresponding page on the OBO Foundry (in this case, http://www.obofoundry.org/ontology/mondo.html)
-and make update to the `url` entry for that namespace in the Bioregistry.
-
-## 🚀 Installation
-
-The most recent release can be installed from
-[PyPI](https://pypi.org/project/pyobo/) with:
-
-```console
-python3 -m pip install pyobo
-```
-
-The most recent code and data can be installed directly from GitHub with:
-
-```console
-python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
-```
-
-## 👐 Contributing
-
-Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
-[CONTRIBUTING.md](https://github.com/biopragmatics/pyobo/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/biopragmatics/pyobo.git
-cd pyobo
-python3 -m pip install -e .
-```
-
-### 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. Update with the following:
-
-```console
-python3 -m pip install cruft
-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
-`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/biopragmatics/pyobo/actions?query=workflow%3ATests).
-
-### 📖 Building the Documentation
-
-The documentation can be built locally using the following:
-
-```console
-git clone git+https://github.com/biopragmatics/pyobo.git
-cd pyobo
-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`](../../Desktop/pyobo/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`](../../Desktop/pyobo/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`](../../Desktop/pyobo/.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/biopragmatics/pyobo
-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 `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/pyobo/version.py`,
-   and [`docs/source/conf.py`](../../Desktop/pyobo/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/biopragmatics/pyobo/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>