pyobo 0.11.0__tar.gz → 0.11.2__tar.gz

{pyobo-0.11.0/src/pyobo.egg-info → pyobo-0.11.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.11.0
+Version: 0.11.2
 Summary: A python package for handling and generating OBO
 Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
@@ -49,7 +49,6 @@ 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
@@ -63,13 +62,14 @@ 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: bioversions>=0.5.535
+Requires-Dist: bioregistry>=0.11.23
 Requires-Dist: bioontologies>=0.4.0
 Requires-Dist: zenodo-client>=0.0.5
 Requires-Dist: class_resolver
 Requires-Dist: psycopg2-binary
 Requires-Dist: pydantic>=2.0
+Requires-Dist: requests-ftp
 Requires-Dist: drugbank_downloader
 Requires-Dist: chembl_downloader
 Requires-Dist: umls_downloader>=0.1.3
@@ -109,10 +109,12 @@ Requires-Dist: sphinx_automodapi; extra == "docs"
         <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/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
@@ -500,14 +502,14 @@ and make update to the `url` entry for that namespace in the Bioregistry.
 The most recent release can be installed from
 [PyPI](https://pypi.org/project/pyobo/) with:
 
-```shell
-pip install pyobo
+```console
+python3 -m 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
+```console
+python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
 ```
 
 ## 👐 Contributing
@@ -564,10 +566,10 @@ The final section of the README is for if you want to get involved by making a c
 
 To install in development mode, use the following:
 
-```bash
+```console
 git clone git+https://github.com/biopragmatics/pyobo.git
 cd pyobo
-pip install -e .
+python3 -m pip install -e .
 ```
 
 ### Updating Package Boilerplate
@@ -576,8 +578,8 @@ This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
 configuration)
 up-to-date with the upstream cookiecutter package. Update with the following:
 
-```shell
-pip install cruft
+```console
+python3 -m pip install cruft
 cruft update
 ```
 
@@ -586,10 +588,11 @@ available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-pr
 
 ### 🥼 Testing
 
-After cloning the repository and installing `tox` with `pip install tox tox-uv`, 
+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:
 
-```shell
+```console
 tox -e py
 ```
 
@@ -600,12 +603,12 @@ Additionally, these tests are automatically re-run with each commit in a
 
 The documentation can be built locally using the following:
 
-```shell
+```console
 git clone git+https://github.com/biopragmatics/pyobo.git
 cd pyobo
 tox -e docs
 open docs/build/html/index.html
-``` 
+```
 
 The documentation automatically installs the package as well as the `docs`
 extra specified in the [`pyproject.toml`](../../Desktop/pyobo/pyproject.toml). `sphinx` plugins
@@ -661,38 +664,23 @@ You only have to do the following steps once.
 
 #### 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>
+You have to do the following steps once per machine. 
 
-# 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>
+```console
+$ uv tool install keyring
+$ keyring set https://upload.pypi.org/legacy/ __token__
+$ keyring set https://test.pypi.org/legacy/ __token__
 ```
 
-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).
+Note that this deprecates previous workflows using `.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:
+`tox` with `python3 -m pip install tox tox-uv`,
+run the following from the console:
 
-```shell
+```console
 tox -e finish
 ```
 
@@ -703,7 +691,7 @@ This script does the following:
    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).
+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.

{pyobo-0.11.0 → pyobo-0.11.2}/README.md

@@ -23,10 +23,12 @@
         <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/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
@@ -414,14 +416,14 @@ and make update to the `url` entry for that namespace in the Bioregistry.
 The most recent release can be installed from
 [PyPI](https://pypi.org/project/pyobo/) with:
 
-```shell
-pip install pyobo
+```console
+python3 -m 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
+```console
+python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
 ```
 
 ## 👐 Contributing
@@ -478,10 +480,10 @@ The final section of the README is for if you want to get involved by making a c
 
 To install in development mode, use the following:
 
-```bash
+```console
 git clone git+https://github.com/biopragmatics/pyobo.git
 cd pyobo
-pip install -e .
+python3 -m pip install -e .
 ```
 
 ### Updating Package Boilerplate
@@ -490,8 +492,8 @@ This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
 configuration)
 up-to-date with the upstream cookiecutter package. Update with the following:
 
-```shell
-pip install cruft
+```console
+python3 -m pip install cruft
 cruft update
 ```
 
@@ -500,10 +502,11 @@ available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-pr
 
 ### 🥼 Testing
 
-After cloning the repository and installing `tox` with `pip install tox tox-uv`, 
+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:
 
-```shell
+```console
 tox -e py
 ```
 
@@ -514,12 +517,12 @@ Additionally, these tests are automatically re-run with each commit in a
 
 The documentation can be built locally using the following:
 
-```shell
+```console
 git clone git+https://github.com/biopragmatics/pyobo.git
 cd pyobo
 tox -e docs
 open docs/build/html/index.html
-``` 
+```
 
 The documentation automatically installs the package as well as the `docs`
 extra specified in the [`pyproject.toml`](../../Desktop/pyobo/pyproject.toml). `sphinx` plugins
@@ -575,38 +578,23 @@ You only have to do the following steps once.
 
 #### 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>
+You have to do the following steps once per machine. 
 
-# 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>
+```console
+$ uv tool install keyring
+$ keyring set https://upload.pypi.org/legacy/ __token__
+$ keyring set https://test.pypi.org/legacy/ __token__
 ```
 
-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).
+Note that this deprecates previous workflows using `.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:
+`tox` with `python3 -m pip install tox tox-uv`,
+run the following from the console:
 
-```shell
+```console
 tox -e finish
 ```
 
@@ -617,7 +605,7 @@ This script does the following:
    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).
+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.

{pyobo-0.11.0 → pyobo-0.11.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyobo"
-version = "0.11.0"
+version = "0.11.2"
 description = "A python package for handling and generating OBO"
 readme = "README.md"
 authors = [
@@ -68,13 +68,14 @@ dependencies = [
     "tabulate",
     "cachier",
     "pystow>=0.2.7",
-    "bioversions>=0.5.514",
-    "bioregistry>=0.10.20",
+    "bioversions>=0.5.535",
+    "bioregistry>=0.11.23",
     "bioontologies>=0.4.0",
     "zenodo-client>=0.0.5",
     "class_resolver",
     "psycopg2-binary",
     "pydantic>=2.0",
+    "requests-ftp",
     # Resource Downloaders
     "drugbank_downloader",
     "chembl_downloader",
@@ -104,6 +105,12 @@ Documentation = "https://pyobo.readthedocs.io"
 
 [tool.setuptools]
 package-dir = { "" = "src" }
+# This fix is here as a final tombstone before getting rid of setuptools and
+# replacing with uv's build backend. It appears that the setuptools team hasn't
+# prioritized fixing the fully breaking bug in metadata emission described in
+# https://github.com/pypa/setuptools/issues/4759. Luckily, the license
+# is inferred from the trove classifier for MIT license.
+license-files = []
 
 [tool.setuptools.packages.find]
 # this implicitly sets `packages = ":find"`
@@ -243,7 +250,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.11.0"
+current_version = "0.11.2"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{pyobo-0.11.0 → pyobo-0.11.2}/src/pyobo/constants.py

@@ -29,6 +29,7 @@ GLOBAL_SKIP = {
     "resid",  # deprecated
     "adw",  # deprecated
 }
+GLOBAL_CHECK_IDS = False
 
 #: Default prefix
 DEFAULT_PREFIX = "debio"

{pyobo-0.11.0 → pyobo-0.11.2}/src/pyobo/gilda_utils.py

@@ -1,9 +1,10 @@
 """PyOBO's Gilda utilities."""
 
+from __future__ import annotations
+
 import logging
 from collections.abc import Iterable
 from subprocess import CalledProcessError
-from typing import Optional, Union
 
 import bioregistry
 import gilda.api
@@ -37,7 +38,7 @@ def iter_gilda_prediction_tuples(
     prefix: str,
     relation: str = "skos:exactMatch",
     *,
-    grounder: Optional[Grounder] = None,
+    grounder: Grounder | None = None,
     identifiers_are_names: bool = False,
     strict: bool = False,
 ) -> Iterable[tuple[str, str, str, str, str, str, str, str, float]]:
@@ -90,11 +91,11 @@ def normalize_identifier(prefix: str, identifier: str) -> str:
 
 
 def get_grounder(
-    prefixes: Union[str, Iterable[str]],
+    prefixes: str | Iterable[str],
     *,
-    unnamed: Optional[Iterable[str]] = None,
-    grounder_cls: Optional[type[Grounder]] = None,
-    versions: Union[None, str, Iterable[Union[str, None]]] = None,
+    unnamed: Iterable[str] | None = None,
+    grounder_cls: type[Grounder] | None = None,
+    versions: None | str | Iterable[str | None] | dict[str, str] = None,
     strict: bool = True,
     skip_obsolete: bool = False,
     progress: bool = True,
@@ -109,6 +110,8 @@ def get_grounder(
         versions = [None] * len(prefixes)
     elif isinstance(versions, str):
         versions = [versions]
+    elif isinstance(versions, dict):
+        versions = [versions.get(prefix) for prefix in prefixes]
     else:
         versions = list(versions)
     if len(prefixes) != len(versions):
@@ -146,8 +149,8 @@ def _fast_term(
     identifier: str,
     name: str,
     status: str,
-    organism: Optional[str] = None,
-) -> Optional[gilda.term.Term]:
+    organism: str | None = None,
+) -> gilda.term.Term | None:
     try:
         term = gilda.term.Term(
             norm_text=normalize(text),
@@ -168,7 +171,7 @@ def get_gilda_terms(
     prefix: str,
     *,
     identifiers_are_names: bool = False,
-    version: Optional[str] = None,
+    version: str | None = None,
     strict: bool = True,
     skip_obsolete: bool = False,
     progress: bool = True,
@@ -250,7 +253,7 @@ def get_gilda_terms(
 
 
 def get_gilda_term_subset(
-    source: str, ancestors: Union[str, list[str]], **kwargs
+    source: str, ancestors: str | list[str], **kwargs
 ) -> Iterable[gilda.term.Term]:
     """Get a subset of terms."""
     subset = {
@@ -263,7 +266,7 @@ def get_gilda_term_subset(
             yield term
 
 
-def _ensure_list(s: Union[str, list[str]]) -> list[str]:
+def _ensure_list(s: str | list[str]) -> list[str]:
     if isinstance(s, str):
         return [s]
     return s

{pyobo-0.11.0 → pyobo-0.11.2}/src/pyobo/obographs.py

@@ -17,6 +17,7 @@ from bioontologies.obograph import (
     Xref,
 )
 from bioontologies.robot import ParseResults
+from tqdm import tqdm
 
 from pyobo.struct import Obo, Reference, Term
 from pyobo.struct.typedef import definition_source, is_a
@@ -33,11 +34,13 @@ def parse_results_from_obo(obo: Obo) -> ParseResults:
     return ParseResults(graph_document=GraphDocument(graphs=[graph]))
 
 
-def graph_from_obo(obo: Obo) -> Graph:
+def graph_from_obo(obo: Obo, use_tqdm: bool = True) -> Graph:
     """Get an OBO Graph object from a PyOBO object."""
     nodes: list[Node] = []
     edges: list[Edge] = []
-    for term in obo:
+    for term in tqdm(
+        obo, disable=not use_tqdm, unit="term", unit_scale=True, desc=f"[{obo.ontology}] to JSON"
+    ):
         nodes.append(_get_class_node(term))
         edges.extend(_iter_edges(term))
     return Graph(

pyobo-0.11.2/src/pyobo/resources/so.py

@@ -0,0 +1,55 @@
+"""Loading of the relations ontology names."""
+
+from __future__ import annotations
+
+import csv
+import os
+from functools import lru_cache
+
+import requests
+
+__all__ = [
+    "get_so_name",
+    "load_so",
+]
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+SO_PATH = os.path.join(HERE, "so.tsv")
+SO_JSON_URL = "https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/refs/heads/master/Ontology_Files/so-simple.json"
+SO_URI_PREFIX = "http://purl.obolibrary.org/obo/SO_"
+
+
+def get_so_name(so_id: str) -> str | None:
+    """Get the name from the identifier."""
+    return load_so().get(so_id)
+
+
+@lru_cache(maxsize=1)
+def load_so() -> dict[str, str]:
+    """Load the Sequence Ontology names."""
+    if not os.path.exists(SO_PATH):
+        download_so()
+    with open(SO_PATH) as file:
+        return dict(csv.reader(file, delimiter="\t"))
+
+
+def download_so():
+    """Download the latest version of the Relation Ontology."""
+    rows = []
+    res_json = requests.get(SO_JSON_URL).json()
+    for node in res_json["graphs"][0]["nodes"]:
+        uri = node["id"]
+        if not uri.startswith(SO_URI_PREFIX):
+            continue
+        identifier = uri.removeprefix(SO_URI_PREFIX)
+        name = node.get("lbl")
+        if name:
+            rows.append((identifier, name))
+
+    with open(SO_PATH, "w") as file:
+        writer = csv.writer(file, delimiter="\t")
+        writer.writerows(sorted(rows, key=lambda x: int(x[0])))
+
+
+if __name__ == "__main__":
+    download_so()