pyobo 0.10.12__py3-none-any.whl → 0.11.0__py3-none-any.whl

pyobo-0.11.0.dist-info/METADATA

@@ -0,0 +1,723 @@
+Metadata-Version: 2.1
+Name: pyobo
+Version: 0.11.0
+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
+License-File: LICENSE
+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 >=0.5.514
+Requires-Dist: bioregistry >=0.10.20
+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: drugbank-downloader
+Requires-Dist: chembl-downloader
+Requires-Dist: umls-downloader >=0.1.3
+Requires-Dist: typing-extensions
+Requires-Dist: rdflib
+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'
+Provides-Extra: tests
+Requires-Dist: pytest ; extra == 'tests'
+Requires-Dist: coverage ; extra == 'tests'
+
+<!--
+<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/psf/black'>
+        <img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' /></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>
+</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:
+
+```shell
+pip install pyobo
+```
+
+The most recent code and data can be installed directly from GitHub with:
+
+```shell
+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:
+
+```bash
+git clone git+https://github.com/biopragmatics/pyobo.git
+cd pyobo
+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:
+
+```shell
+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 `pip install tox tox-uv`, 
+the unit tests in the `tests/` folder can be run reproducibly with:
+
+```shell
+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:
+
+```shell
+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. Create a file in your home directory called
+`.pypirc` and include the following:
+
+```ini
+[distutils]
+index-servers =
+    pypi
+    testpypi
+
+[pypi]
+username = __token__
+password = <the API token you just got>
+
+# This block is optional in case you want to be able to make test releases to the Test PyPI server
+[testpypi]
+repository = https://test.pypi.org/legacy/
+username = __token__
+password = <an API token from test PyPI>
+```
+
+Note that since PyPI is requiring token-based authentication, we use `__token__` as the user, verbatim.
+If you already have a `.pypirc` file with a `[distutils]` section, just make sure that there is an `index-servers`
+key and that `pypi` is in its associated list. More information on configuring the `.pypirc` file can
+be found [here](https://packaging.python.org/en/latest/specifications/pypirc).
+
+#### Uploading to PyPI
+
+After installing the package in development mode and installing
+`tox` with `pip install tox tox-uv`,
+run the following from the shell:
+
+```shell
+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 [`twine`](https://github.com/pypa/twine).
+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>