pyobo 0.11.2__tar.gz → 0.12.0__tar.gz

{pyobo-0.11.2/src/pyobo.egg-info → pyobo-0.12.0}/PKG-INFO

@@ -1,36 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pyobo
-Version: 0.11.2
+Version: 0.12.0
 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
+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
@@ -39,16 +14,16 @@ 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 :: 3.9
 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-Python: >=3.9
-Description-Content-Type: text/markdown
 Requires-Dist: obonet>=0.3.0
 Requires-Dist: click
 Requires-Dist: tqdm
@@ -56,33 +31,51 @@ 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: 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: pystow>=0.7.0
+Requires-Dist: bioversions>=0.7.0
+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: requests-ftp
-Requires-Dist: drugbank_downloader
-Requires-Dist: chembl_downloader
-Requires-Dist: umls_downloader>=0.1.3
-Requires-Dist: typing_extensions
+Requires-Dist: curies>=0.10.10
+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
-Provides-Extra: tests
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: coverage; extra == "tests"
+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'
+Requires-Dist: ssslm[gilda] ; extra == 'gilda'
+Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
+Requires-Dist: pytest ; extra == 'tests'
+Requires-Dist: coverage[toml] ; extra == 'tests'
+Maintainer: Charles Tapley Hoyt
+Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+Requires-Python: >=3.10
+Project-URL: Bug Tracker, https://github.com/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: 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: gilda
+Provides-Extra: gilda-slim
+Provides-Extra: tests
+Description-Content-Type: text/markdown
 
 <!--
 <p align="center">
@@ -117,25 +110,24 @@ Requires-Dist: sphinx_automodapi; extra == "docs"
         <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.
+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! 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! 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.
+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
 
@@ -185,6 +177,7 @@ 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
@@ -192,13 +185,13 @@ 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')
+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):
+Some resources have species information for their term. Get a mapping of
+WikiPathway identifiers to species (as NCBI taxonomy identifiers):
 
 ```python
 import pyobo
@@ -229,30 +222,28 @@ 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'
+reference = pyobo.ground('chebi', 'Fusilade II')
+assert reference.prefix == 'chebi'
+assert reference.identifier == '132964'
+assert reference.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
+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):
+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'
+reference = pyobo.ground(['efo', 'go'], 'ERAD')
+assert reference.prefix == 'go'
+assert reference.identifier == '0030433'
+assert reference.name == 'ubiquitin-dependent ERAD pathway'
 ```
 
 ### Cross-referencing
@@ -277,8 +268,8 @@ 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:
+Get xrefs from Entrez to HGNC, but they're only available through HGNC, so you
+need to flip them:
 
 ```python
 import pyobo
@@ -292,8 +283,8 @@ 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:
+Since this is a common pattern, there's a keyword argument `flip` that does this
+for you:
 
 ```python
 import pyobo
@@ -313,45 +304,10 @@ 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.
+Get properties, like SMILES. The semantics of these are defined on an OBO-OBO
+basis.
 
 ```python
 import pyobo
@@ -378,47 +334,50 @@ assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
 Check if an entity is in the hierarchy:
 
 ```python
-import networkx as nx
 import pyobo
+from pyobo import Reference
 
 # check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
-assert 'go:0008219' in pyobo.get_ancestors('go', '0006915')
+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 'go:0070246' in apopototic_process_descendants
+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 'go:0070246' in apopototic_process_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 'chebi:132964' in chebi_hierarchy
+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)
+Get all orthologies (`ro:HOM0000017`) between HGNC and MGI (note: this is one
+way)
 
 ```python
 >>> import pyobo
@@ -440,11 +399,10 @@ If you want to do it in one line, use:
 
 ### 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:
+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
@@ -464,57 +422,75 @@ class MyTestCase(unittest.TestCase):
           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.
+[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.
+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.
+- 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:
+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.
+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:
+[PyPI](https://pypi.org/project/pyobo/) with uv:
 
 ```console
-python3 -m pip install pyobo
+$ uv pip install pyobo
 ```
 
-The most recent code and data can be installed directly from GitHub with:
+or with pip:
 
 ```console
-python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
+$ 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
+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.
 
@@ -551,49 +527,59 @@ This project has been supported by the following grants:
 
 ### 🍪 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.
+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.
+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 .
+$ 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. Update with the following:
+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
-python3 -m pip install cruft
-cruft update
+$ cruft update
 ```
 
-More info on Cruft's update command is
-available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+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:
+`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
+$ tox -e py
 ```
 
 Additionally, these tests are automatically re-run with each commit in a
@@ -604,67 +590,77 @@ Additionally, these tests are automatically re-run with each commit in a
 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
+$ 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 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`](../../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).
+[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)
+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.
+[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
+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
+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.
+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
+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. 
+You have to do the following steps once per machine.
 
 ```console
 $ uv tool install keyring
@@ -676,34 +672,37 @@ 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:
+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
+$ 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
+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.
+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
+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.