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

pyobo-0.12.1.dist-info/METADATA

@@ -0,0 +1,671 @@
+Metadata-Version: 2.4
+Name: pyobo
+Version: 0.12.1
+Summary: A python package for handling and generating OBO
+Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
+Author: Charles Tapley Hoyt
+Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+License-File: LICENSE
+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: Natural Language :: English
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Typing :: Typed
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+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>=0.7.0
+Requires-Dist: bioversions>=0.8.0
+Requires-Dist: bioregistry>=0.12.7
+Requires-Dist: bioontologies>=0.7.1
+Requires-Dist: ssslm>=0.0.13
+Requires-Dist: zenodo-client>=0.3.6
+Requires-Dist: class-resolver>=0.6.0
+Requires-Dist: psycopg2-binary
+Requires-Dist: pydantic>=2.0
+Requires-Dist: curies>=0.10.13
+Requires-Dist: python-dateutil
+Requires-Dist: networkx>=3.4
+Requires-Dist: drugbank-downloader
+Requires-Dist: chembl-downloader
+Requires-Dist: umls-downloader>=0.1.3
+Requires-Dist: clinicaltrials-downloader>=0.0.2
+Requires-Dist: nih-reporter-downloader>=0.0.1
+Requires-Dist: typing-extensions
+Requires-Dist: rdflib
+Requires-Dist: ssslm[gilda] ; extra == 'gilda'
+Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
+Maintainer: Charles Tapley Hoyt
+Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+Requires-Python: >=3.10
+Project-URL: Bug Tracker, https://github.com/biopragmatics/pyobo/issues
+Project-URL: Documentation, https://pyobo.readthedocs.io
+Project-URL: Funding, https://github.com/sponsors/cthoyt
+Project-URL: Homepage, https://github.com/biopragmatics/pyobo
+Project-URL: Repository, https://github.com/biopragmatics/pyobo.git
+Provides-Extra: gilda
+Provides-Extra: gilda-slim
+Description-Content-Type: text/markdown
+
+<!--
+<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.
+
+### Mapping Identifiers and CURIEs
+
+Get mapping of ChEBI identifiers to names:
+
+```python
+import pyobo
+
+chebi_id_to_name = pyobo.get_id_name_mapping("chebi")
+assert "fluazifop-P-butyl" == chebi_id_to_name["132964"]
+
+# or more directly
+assert "fluazifop-P-butyl" == pyobo.get_name("chebi", "132964")
+```
+
+Get reverse mapping of ChEBI names to identifiers:
+
+```python
+import pyobo
+
+chebi_name_to_id = pyobo.get_name_id_mapping("chebi")
+assert "132964" == chebi_name_to_id["fluazifop-P-butyl"]
+```
+
+Maybe you live in CURIE world and just want to normalize something like
+`CHEBI:132964`:
+
+```python
+import pyobo
+
+assert "fluazifop-P-butyl" == pyobo.get_name_by_curie("CHEBI:132964")
+```
+
+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
+from pyobo import Reference
+
+# 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 Reference.from_curie("go:0003700") == pyobo.get_primary_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)
+assert "9606" == wikipathways_id_to_species["WP254"]
+```
+
+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
+
+reference = pyobo.ground("chebi", "Fusilade II")
+assert reference.prefix == "chebi"
+assert reference.identifier == "132964"
+assert reference.name == "fluazifop-P-butyl"
+
+# When failure happens...
+reference = pyobo.ground("chebi", "Definitely not a real name")
+assert reference 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
+reference = pyobo.ground(["efo", "go"], "ERAD")
+assert reference.prefix == "go"
+assert reference.identifier == "0030433"
+assert reference.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"
+```
+
+### 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 pyobo
+from pyobo import Reference
+
+# check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
+assert Reference.from_curie("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 Reference.from_curie("go:0070246") in apopototic_process_descendants
+```
+
+Get the sub-hierarchy below a given node:
+
+```python
+import pyobo
+from pyobo import Reference
+
+# 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 Reference.from_curie("go:0070246") in apopototic_process_subhierarchy
+```
+
+Get a hierarchy with properties preloaded in the node data dictionaries:
+
+```python
+import pyobo
+from pyobo import Reference
+
+prop = "http://purl.obolibrary.org/obo/chebi/smiles"
+chebi_hierarchy = pyobo.get_hierarchy("chebi", properties=[prop])
+
+assert Reference.from_curie("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 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")
+```
+
+## Preprocessing CURIEs, URIs, and unqualified identifiers
+
+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/identifier_utils/preprocessing.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/src/pyobo/identifier_utils/preprocessing.json)
+is the curated set of pre-processing rules. These are used in combination with
+the `curies` package to do pre-processing steps on CURIEs, URIs, and unqualified
+identifiers beyond what is possible with the Bioregistry. See
+https://curies.readthedocs.io/en/latest/preprocessing.html.
+
+## 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 uv:
+
+```console
+$ uv pip install pyobo
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install pyobo
+```
+
+The most recent code and data can be installed directly from GitHub with uv:
+
+```console
+$ uv pip install git+https://github.com/biopragmatics/pyobo.git
+```
+
+or with pip:
+
+```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
+$ uv pip install -e .
+```
+
+Alternatively, install using pip:
+
+```console
+$ 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. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
+### 🥼 Testing
+
+After cloning the repository and installing `tox` with
+`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the
+unit tests in the `tests/` folder can be run reproducibly with:
+
+```console
+$ tox -e py
+```
+
+Additionally, these tests are automatically re-run with each commit in a
+[GitHub Action](https://github.com/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`](pyproject.toml). `sphinx` plugins like
+`texext` can be added there. Additionally, they need to be added to the
+`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).
+
+The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
+[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The
+[`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration
+you'll need. You can also set up continuous integration on GitHub to check not
+only that Sphinx can build the documentation in an isolated environment (i.e.,
+with `tox -e docs-test`) but also that
+[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
+
+#### Configuring ReadTheDocs
+
+1. Log in to ReadTheDocs with your GitHub account to install the integration at
+   https://readthedocs.org/accounts/login/?next=/dashboard/
+2. Import your project by navigating to https://readthedocs.org/dashboard/import
+   then clicking the plus icon next to your repository
+3. You can rename the repository on the next screen using a more stylized name
+   (i.e., with spaces and capital letters)
+4. Click next, and you're good to go!
+
+### 📦 Making a Release
+
+#### Configuring Zenodo
+
+[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
+to each release of your package.
+
+1. Log in to Zenodo via GitHub with this link:
+   https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
+   that lists all of your organizations and asks you to approve installing the
+   Zenodo app on GitHub. Click "grant" next to any organizations you want to
+   enable the integration for, then click the big green "approve" button. This
+   step only needs to be done once.
+2. Navigate to https://zenodo.org/account/settings/github/, which lists all of
+   your GitHub repositories (both in your username and any organizations you
+   enabled). Click the on/off toggle for any relevant repositories. When you
+   make a new repository, you'll have to come back to this
+
+After these steps, you're ready to go! After you make "release" on GitHub (steps
+for this are below), you can navigate to
+https://zenodo.org/account/settings/github/repository/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
+`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/pyobo/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/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>