{"id":21731112,"url":"https://github.com/biopragmatics/pyobo","last_synced_at":"2025-04-04T19:12:02.760Z","repository":{"id":39888931,"uuid":"203449095","full_name":"biopragmatics/pyobo","owner":"biopragmatics","description":"📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures","archived":false,"fork":false,"pushed_at":"2025-03-27T09:05:21.000Z","size":24889,"stargazers_count":62,"open_issues_count":47,"forks_count":16,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-28T18:15:28.918Z","etag":null,"topics":["bioinformatics","biopragmatics","bioregistry","obo","obofoundry","ontologies"],"latest_commit_sha":null,"homepage":"https://pyobo.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biopragmatics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":".github/FUNDING.yml","license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null},"funding":{"github":"cthoyt"}},"created_at":"2019-08-20T20:24:49.000Z","updated_at":"2025-03-27T09:05:25.000Z","dependencies_parsed_at":"2023-09-26T14:12:50.090Z","dependency_job_id":"435dbbf8-9bf0-46a3-a4ec-ed445fe04120","html_url":"https://github.com/biopragmatics/pyobo","commit_stats":{"total_commits":1156,"total_committers":9,"mean_commits":"128.44444444444446","dds":"0.038927335640138394","last_synced_commit":"67f4da3988aca3ab4483c4a32bb31f896e371c25"},"previous_names":["biopragmatics/pyobo","pyobo/pyobo"],"tags_count":68,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopragmatics%2Fpyobo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopragmatics%2Fpyobo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopragmatics%2Fpyobo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biopragmatics%2Fpyobo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biopragmatics","download_url":"https://codeload.github.com/biopragmatics/pyobo/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247234922,"owners_count":20905854,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","biopragmatics","bioregistry","obo","obofoundry","ontologies"],"created_at":"2024-11-26T04:19:47.867Z","updated_at":"2025-04-04T19:12:02.740Z","avatar_url":"https://github.com/biopragmatics.png","language":"Python","funding_links":["https://github.com/sponsors/cthoyt"],"categories":[],"sub_categories":[],"readme":"\u003c!--\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/biopragmatics/pyobo/raw/main/docs/source/logo.png\" height=\"150\"\u003e\n\u003c/p\u003e\n--\u003e\n\n\u003ch1 align=\"center\"\u003e\n  PyOBO\n\u003c/h1\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml\"\u003e\n        \u003cimg alt=\"Tests\" src=\"https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml/badge.svg\" /\u003e\u003c/a\u003e\n    \u003ca href=\"https://pypi.org/project/pyobo\"\u003e\n        \u003cimg alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/pyobo\" /\u003e\u003c/a\u003e\n    \u003ca href=\"https://pypi.org/project/pyobo\"\u003e\n        \u003cimg alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/pyobo\" /\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/biopragmatics/pyobo/blob/main/LICENSE\"\u003e\n        \u003cimg alt=\"PyPI - License\" src=\"https://img.shields.io/pypi/l/pyobo\" /\u003e\u003c/a\u003e\n    \u003ca href='https://pyobo.readthedocs.io/en/latest/?badge=latest'\u003e\n        \u003cimg src='https://readthedocs.org/projects/pyobo/badge/?version=latest' alt='Documentation Status' /\u003e\u003c/a\u003e\n    \u003ca href=\"https://codecov.io/gh/biopragmatics/pyobo/branch/main\"\u003e\n        \u003cimg src=\"https://codecov.io/gh/biopragmatics/pyobo/branch/main/graph/badge.svg\" alt=\"Codecov status\" /\u003e\u003c/a\u003e  \n    \u003ca href=\"https://github.com/cthoyt/cookiecutter-python-package\"\u003e\n        \u003cimg alt=\"Cookiecutter template from @cthoyt\" src=\"https://img.shields.io/badge/Cookiecutter-snekpack-blue\" /\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/astral-sh/ruff\"\u003e\n        \u003cimg 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%;\"\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/biopragmatics/pyobo/blob/main/.github/CODE_OF_CONDUCT.md\"\u003e\n        \u003cimg src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" alt=\"Contributor Covenant\"/\u003e\u003c/a\u003e\n    \u003ca href=\"https://doi.org/10.5281/zenodo.3381961\"\u003e\n        \u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.3381961.svg\" alt=\"DOI\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\nTools for biological identifiers, names, synonyms, xrefs, hierarchies,\nrelations, and properties through the perspective of OBO.\n\n## Example Usage\n\nNote! PyOBO is no-nonsense. This means that there's no repetitive prefixes in\nidentifiers. It also means all identifiers are strings, no exceptions.\n\nNote! The first time you run these, they have to download and cache all\nresources. We're not in the business of redistributing data, so all scripts\nshould be completely reproducible. There's some AWS tools for\nhosting/downloading pre-compiled versions in `pyobo.aws` if you don't have time\nfor that.\n\nNote! PyOBO can perform grounding in a limited number of cases, but it is _not_\na general solution for named entity recognition (NER) or grounding. It's\nsuggested to check `Gilda \u003chttps://github.com/indralab/gilda\u003e`\\_ for a\nno-nonsense solution.\n\n### Mapping Identifiers and CURIEs\n\nGet mapping of ChEBI identifiers to names:\n\n```python\nimport pyobo\n\nchebi_id_to_name = pyobo.get_id_name_mapping('chebi')\n\nname = chebi_id_to_name['132964']\nassert name == 'fluazifop-P-butyl'\n```\n\nOr, you don't have time for two lines:\n\n```python\nimport pyobo\n\nname = pyobo.get_name('chebi', '132964')\nassert name == 'fluazifop-P-butyl'\n```\n\nGet reverse mapping of ChEBI names to identifiers:\n\n```python\nimport pyobo\n\nchebi_name_to_id = pyobo.get_name_id_mapping('chebi')\n\nidentifier = chebi_name_to_id['fluazifop-P-butyl']\nassert identifier == '132964'\n```\n\nMaybe you live in CURIE world and just want to normalize something like\n`CHEBI:132964`:\n\n```python\nimport pyobo\n\nname = pyobo.get_name_by_curie('CHEBI:132964')\nassert name == 'fluazifop-P-butyl'\n```\n\nSometimes you accidentally got an old CURIE. It can be mapped to the more recent\none using alternative identifiers listed in the underlying OBO with:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\n# Look up DNA-binding transcription factor activity (go:0003700)\n# based on an old id\nprimary_curie = pyobo.get_primary_curie('go:0001071')\nassert primary_curie == 'go:0003700'\n\n# If it's already the primary, it just gets returned\nassert Reference.from_curie('go:0003700') == pyobo.get_primary_curie('go:0003700')\n```\n\n### Mapping Species\n\nSome resources have species information for their term. Get a mapping of\nWikiPathway identifiers to species (as NCBI taxonomy identifiers):\n\n```python\nimport pyobo\n\nwikipathways_id_to_species = pyobo.get_id_species_mapping('wikipathways')\n\n# Apoptosis (Homo sapiens)\ntaxonomy_id = wikipathways_id_to_species['WP254']\nassert taxonomy_id == '9606'\n```\n\nOr, you don't have time for two lines:\n\n```python\nimport pyobo\n\n# Apoptosis (Homo sapiens)\ntaxonomy_id = pyobo.get_species('wikipathways', 'WP254')\nassert taxonomy_id == '9606'\n```\n\n### Grounding\n\nMaybe you've got names/synonyms you want to try and map back to ChEBI synonyms.\nGiven the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look\nit up and its preferred label.\n\n```python\nimport pyobo\n\nprefix, identifier, name = pyobo.ground('chebi', 'Fusilade II')\nassert prefix == 'chebi'\nassert identifier == '132964'\nassert name == 'fluazifop-P-butyl'\n\n# When failure happens...\nprefix, identifier, name = pyobo.ground('chebi', 'Definitely not a real name')\nassert prefix is None\nassert identifier is None\nassert name is None\n```\n\nIf you're not really sure which namespace a name might belong to, you can try a\nfew in a row (prioritize by ones that cover the appropriate entity type to avoid\nfalse positives in case of conflicts):\n\n```python\nimport pyobo\n\n# looking for phenotypes/pathways\nprefix, identifier, name = pyobo.ground(['efo', 'go'], 'ERAD')\nassert prefix == 'go'\nassert identifier == '0030433'\nassert name == 'ubiquitin-dependent ERAD pathway'\n```\n\n### Cross-referencing\n\nGet xrefs from ChEBI to PubChem:\n\n```python\nimport pyobo\n\nchebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs('chebi', 'pubchem.compound')\n\npubchem_compound_id = chebi_id_to_pubchem_compound_id['132964']\nassert pubchem_compound_id == '3033674'\n```\n\nIf you don't have time for two lines:\n\n```python\nimport pyobo\n\npubchem_compound_id = pyobo.get_xref('chebi', '132964', 'pubchem.compound')\nassert pubchem_compound_id == '3033674'\n```\n\nGet xrefs from Entrez to HGNC, but they're only available through HGNC, so you\nneed to flip them:\n\n```python\nimport pyobo\n\nhgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene')\nncbigene_id_to_hgnc_id = {\n  ncbigene_id: hgnc_id\n  for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()\n}\nmapt_hgnc = ncbigene_id_to_hgnc_id['4137']\nassert mapt_hgnc == '6893'\n```\n\nSince this is a common pattern, there's a keyword argument `flip` that does this\nfor you:\n\n```python\nimport pyobo\n\nncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene', flip=True)\nmapt_hgnc_id = ncbigene_id_to_hgnc_id['4137']\nassert mapt_hgnc_id == '6893'\n```\n\nIf you don't have time for two lines (I admit this one is a bit confusing) and\nneed to flip it:\n\n```python\nimport pyobo\n\nhgnc_id = pyobo.get_xref('hgnc', '4137', 'ncbigene', flip=True)\nassert hgnc_id == '6893'\n```\n\n### Properties\n\nGet properties, like SMILES. The semantics of these are defined on an OBO-OBO\nbasis.\n\n```python\nimport pyobo\n\n# I don't make the rules. I wouldn't have chosen this as the key for this property. It could be any string\nchebi_smiles_property = 'http://purl.obolibrary.org/obo/chebi/smiles'\nchebi_id_to_smiles = pyobo.get_filtered_properties_mapping('chebi', chebi_smiles_property)\n\nsmiles = chebi_id_to_smiles['132964']\nassert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'\n```\n\nIf you don't have time for two lines:\n\n```python\nimport pyobo\n\nsmiles = pyobo.get_property('chebi', '132964', 'http://purl.obolibrary.org/obo/chebi/smiles')\nassert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'\n```\n\n### Hierarchy\n\nCheck if an entity is in the hierarchy:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\n# check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process\nassert Reference.from_curie('go:0008219') in pyobo.get_ancestors('go', '0006915')\n\n# check that go:0070246 ! natural killer cell apoptotic process is a\n# descendant of go:0006915 ! apoptotic process\napopototic_process_descendants = pyobo.get_descendants('go', '0006915')\nassert Reference.from_curie('go:0070246') in apopototic_process_descendants\n```\n\nGet the sub-hierarchy below a given node:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\n# get the descendant graph of go:0006915 ! apoptotic process\napopototic_process_subhierarchy = pyobo.get_subhierarchy('go', '0006915')\n\n# check that go:0070246 ! natural killer cell apoptotic process is a\n# descendant of go:0006915 ! apoptotic process through the subhierarchy\nassert Reference.from_curie('go:0070246') in apopototic_process_subhierarchy\n```\n\nGet a hierarchy with properties preloaded in the node data dictionaries:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\nprop = 'http://purl.obolibrary.org/obo/chebi/smiles'\nchebi_hierarchy = pyobo.get_hierarchy('chebi', properties=[prop])\n\nassert Reference.from_curie('chebi:132964') in chebi_hierarchy\nassert prop in chebi_hierarchy.nodes['chebi:132964']\nassert 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'\n```\n\n### Relations\n\nGet all orthologies (`ro:HOM0000017`) between HGNC and MGI (note: this is one\nway)\n\n```python\n\u003e\u003e\u003e import pyobo\n\u003e\u003e\u003e human_mapt_hgnc_id = '6893'\n\u003e\u003e\u003e mouse_mapt_mgi_id = '97180'\n\u003e\u003e\u003e hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')\n\u003e\u003e\u003e assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]\n```\n\nIf you want to do it in one line, use:\n\n```python\n\n\u003e\u003e\u003e import pyobo\n\u003e\u003e\u003e human_mapt_hgnc_id = '6893'\n\u003e\u003e\u003e mouse_mapt_mgi_id = '97180'\n\u003e\u003e\u003e assert mouse_mapt_mgi_id == pyobo.get_relation('hgnc', 'ro:HOM0000017', 'mgi', human_mapt_hgnc_id)\n```\n\n### Writings Tests that Use PyOBO\n\nIf you're writing your own code that relies on PyOBO, and unit testing it (as\nyou should) in a continuous integration setting, you've probably realized that\nloading all the resources on each build is not so fast. In those scenarios, you\ncan use some of the pre-build patches like in the following:\n\n```python\nimport unittest\nimport pyobo\nfrom pyobo.mocks import get_mock_id_name_mapping\n\nmock_id_name_mapping = get_mock_id_name_mapping({\n  'chebi': {\n      '132964': 'fluazifop-P-butyl',\n  },\n})\n\nclass MyTestCase(unittest.TestCase):\n  def my_test(self):\n      with mock_id_name_mapping:\n          # use functions directly, or use your functions that wrap them\n          pyobo.get_name('chebi', '1234')\n```\n\n## Curation of the Bioregistry\n\nIn order to normalize references and identify resources, PyOBO uses the\n[Bioregistry](https://github.com/bioregistry/bioregistry). It used to be a part\nof PyOBO, but has since been externalized for more general reuse.\n\nAt\n[src/pyobo/registries/metaregistry.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/registries/metaregistry.json)\nis the curated \"metaregistry\". This is a source of information that contains all\nsorts of fixes for missing/wrong information in MIRIAM, OLS, and OBO Foundry;\nentries that don't appear in any of them; additional synonym information for\neach namespace/prefix; rules for normalizing xrefs and CURIEs, etc.\n\nOther entries in the metaregistry:\n\n- The `\"remappings\"-\u003e\"full\"` entry is a dictionary from strings that might\n  follow `xref:` in a given OBO file that need to be completely replaced, due to\n  incorrect formatting\n- The `\"remappings\"-\u003e\"prefix\"` entry contains a dictionary of prefixes for xrefs\n  that need to be remapped. Several rules, for example, remove superfluous\n  spaces that occur inside CURIEs or and others address instances of the GOGO\n  issue.\n- The `\"blacklists\"` entry contains rules for throwing out malformed xrefs based\n  on full string, just prefix, or just suffix.\n\n## Troubleshooting\n\nThe OBO Foundry seems to be pretty unstable with respect to the URLs to OBO\nresources. If you get an error like:\n\n```\npyobo.getters.MissingOboBuild: OBO Foundry is missing a build for: mondo\n```\n\nThen you should check the corresponding page on the OBO Foundry (in this case,\nhttp://www.obofoundry.org/ontology/mondo.html) and make update to the `url`\nentry for that namespace in the Bioregistry.\n\n## 🚀 Installation\n\nThe most recent release can be installed from\n[PyPI](https://pypi.org/project/pyobo/) with uv:\n\n```console\npython3 -m pip install pyobo\n$ uv pip install pyobo\n```\n\nor with pip:\n\n```console\n$ python3 -m pip install pyobo\n```\n\nThe most recent code and data can be installed directly from GitHub with uv:\n\n```console\n$ uv pip install git+https://github.com/biopragmatics/pyobo.git\n```\n\nor with pip:\n\n```console\n$ python3 -m pip install git+https://github.com/biopragmatics/pyobo.git\n```\n\n## 👐 Contributing\n\nContributions, whether filing an issue, making a pull request, or forking, are\nappreciated. See\n[CONTRIBUTING.md](https://github.com/biopragmatics/pyobo/blob/master/.github/CONTRIBUTING.md)\nfor more information on getting involved.\n\n## 👋 Attribution\n\n### ⚖️ License\n\nThe code in this package is licensed under the MIT License.\n\n\u003c!--\n### 📖 Citation\n\nCitation goes here!\n--\u003e\n\n\u003c!--\n### 🎁 Support\n\nThis project has been supported by the following organizations (in alphabetical order):\n\n- [Biopragmatics Lab](https://biopragmatics.github.io)\n\n--\u003e\n\n\u003c!--\n### 💰 Funding\n\nThis project has been supported by the following grants:\n\n| Funding Body  | Program                                                      | Grant Number |\n|---------------|--------------------------------------------------------------|--------------|\n| Funder        | [Grant Name (GRANT-ACRONYM)](https://example.com/grant-link) | ABCXYZ       |\n--\u003e\n\n### 🍪 Cookiecutter\n\nThis package was created with\n[@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using\n[@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)\ntemplate.\n\n## 🛠️ For Developers\n\n\u003cdetails\u003e\n  \u003csummary\u003eSee developer instructions\u003c/summary\u003e\n\nThe final section of the README is for if you want to get involved by making a\ncode contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```console\n$ git clone git+https://github.com/biopragmatics/pyobo.git\n$ cd pyobo\n$ uv pip install -e .\n```\n\nAlternatively, install using pip:\n\n```console\n$ python3 -m pip install -e .\n```\n\n### Updating Package Boilerplate\n\nThis project uses `cruft` to keep boilerplate (i.e., configuration, contribution\nguidelines, documentation configuration) up-to-date with the upstream\ncookiecutter package. Install cruft with either `uv tool install cruft` or\n`python3 -m pip install cruft` then run:\n\n```console\n$ cruft update\n```\n\nMore info on Cruft's update command is available\n[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).\n\n### 🥼 Testing\n\nAfter cloning the repository and installing `tox` with\n`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the\nunit tests in the `tests/` folder can be run reproducibly with:\n\n```console\n$ tox -e py\n```\n\nAdditionally, these tests are automatically re-run with each commit in a\n[GitHub Action](https://github.com/biopragmatics/pyobo/actions?query=workflow%3ATests).\n\n### 📖 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```console\n$ git clone git+https://github.com/biopragmatics/pyobo.git\n$ cd pyobo\n$ tox -e docs\n$ open docs/build/html/index.html\n```\n\nThe documentation automatically installs the package as well as the `docs` extra\nspecified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like\n`texext` can be added there. Additionally, they need to be added to the\n`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).\n\nThe documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using\n[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The\n[`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration\nyou'll need. You can also set up continuous integration on GitHub to check not\nonly that Sphinx can build the documentation in an isolated environment (i.e.,\nwith `tox -e docs-test`) but also that\n[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).\n\n#### Configuring ReadTheDocs\n\n1. Log in to ReadTheDocs with your GitHub account to install the integration at\n   https://readthedocs.org/accounts/login/?next=/dashboard/\n2. Import your project by navigating to https://readthedocs.org/dashboard/import\n   then clicking the plus icon next to your repository\n3. You can rename the repository on the next screen using a more stylized name\n   (i.e., with spaces and capital letters)\n4. Click next, and you're good to go!\n\n### 📦 Making a Release\n\n#### Configuring Zenodo\n\n[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI\nto each release of your package.\n\n1. Log in to Zenodo via GitHub with this link:\n   https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page\n   that lists all of your organizations and asks you to approve installing the\n   Zenodo app on GitHub. Click \"grant\" next to any organizations you want to\n   enable the integration for, then click the big green \"approve\" button. This\n   step only needs to be done once.\n2. Navigate to https://zenodo.org/account/settings/github/, which lists all of\n   your GitHub repositories (both in your username and any organizations you\n   enabled). Click the on/off toggle for any relevant repositories. When you\n   make a new repository, you'll have to come back to this\n\nAfter these steps, you're ready to go! After you make \"release\" on GitHub (steps\nfor this are below), you can navigate to\nhttps://zenodo.org/account/settings/github/repository/biopragmatics/pyobo to see\nthe DOI for the release and link to the Zenodo record for it.\n\n#### Registering with the Python Package Index (PyPI)\n\nYou only have to do the following steps once.\n\n1. Register for an account on the\n   [Python Package Index (PyPI)](https://pypi.org/account/register)\n2. Navigate to https://pypi.org/manage/account and make sure you have verified\n   your email address. A verification email might not have been sent by default,\n   so you might have to click the \"options\" dropdown next to your address to get\n   to the \"re-send verification email\" button\n3. 2-Factor authentication is required for PyPI since the end of 2023 (see this\n   [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)).\n   This means you have to first issue account recovery codes, then set up\n   2-factor authentication\n4. Issue an API token from https://pypi.org/manage/account/token\n\n#### Configuring your machine's connection to PyPI\n\nYou have to do the following steps once per machine.\n\n```console\n$ uv tool install keyring\n$ keyring set https://upload.pypi.org/legacy/ __token__\n$ keyring set https://test.pypi.org/legacy/ __token__\n```\n\nNote that this deprecates previous workflows using `.pypirc`.\n\n#### Uploading to PyPI\n\nAfter installing the package in development mode and installing `tox` with\n`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run\nthe following from the console:\n\n```console\n$ tox -e finish\n```\n\nThis script does the following:\n\n1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to\n   switch the version number in the `pyproject.toml`, `CITATION.cff`,\n   `src/pyobo/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to\n   not have the `-dev` suffix\n2. Packages the code in both a tar archive and a wheel using\n   [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)\n3. Uploads to PyPI using\n   [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).\n4. Push to GitHub. You'll need to make a release going with the commit where the\n   version was bumped.\n5. Bump the version to the next patch. If you made big changes and want to bump\n   the version by minor, you can use `tox -e bumpversion -- minor` after.\n\n#### Releasing on GitHub\n\n1. Navigate to https://github.com/biopragmatics/pyobo/releases/new to draft a\n   new release\n2. Click the \"Choose a Tag\" dropdown and select the tag corresponding to the\n   release you just made\n3. Click the \"Generate Release Notes\" button to get a quick outline of recent\n   changes. Modify the title and description as you see fit\n4. Click the big green \"Publish Release\" button\n\nThis will trigger Zenodo to assign a DOI to your release as well.\n\n\u003c/details\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopragmatics%2Fpyobo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiopragmatics%2Fpyobo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopragmatics%2Fpyobo/lists"}