Merge branch 'main' into add-federated-queries-test-with-docker

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.4-dev
+current_version = 0.7.5-dev
 commit = True
 tag = False
 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-]+)*))?

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.7", "3.11" ]
+        python-version: [ "3.8", "3.11" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -34,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.7", "3.11" ]
+        python-version: [ "3.8", "3.11" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -57,7 +57,8 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.7", "3.11" ]
+        python-version: [ "3.8", "3.11" ]
+        pydantic: [ "1", "2" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -74,7 +75,10 @@ jobs:
         run: pip install tox
       - name: Test with pytest and generate coverage file
         run:
-          tox run -e py
+          tox run -e py-pydantic${{ matrix.pydantic }}
+      - name: Doctests
+        run:
+          tox run -e doctests
       - name: Upload coverage report to codecov
         uses: codecov/codecov-action@v1
         if: success()

MANIFEST.in

@@ -10,6 +10,7 @@ prune docs/source/api
 recursive-include docs/source *.py
 recursive-include docs/source *.rst
 recursive-include docs/source *.png
+recursive-include docs/source *.svg
 
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
 

README.md

@@ -44,131 +44,22 @@
 Idiomatic conversion between URIs and compact URIs (CURIEs).
 
 ```python
-from curies import Converter
+import curies
 
-converter = Converter.from_prefix_map({
+converter = curies.load_prefix_map({
     "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
-    "MONDO": "http://purl.obolibrary.org/obo/MONDO_",
-    "GO": "http://purl.obolibrary.org/obo/GO_",
     # ... and so on
-    "OBO": "http://purl.obolibrary.org/obo/",
 })
 
 >>> converter.compress("http://purl.obolibrary.org/obo/CHEBI_1")
 'CHEBI:1'
 
 >>> converter.expand("CHEBI:1")
 'http://purl.obolibrary.org/obo/CHEBI_1'
-
-# Unparsable
->>> assert converter.compress("http://example.com/missing:0000000") is None
->>> assert converter.expand("missing:0000000") is None
 ```
 
-When some URI prefixes are partially overlapping (e.g.,
-`http://purl.obolibrary.org/obo/GO_` for `GO` and
-`http://purl.obolibrary.org/obo/` for ``OBO``), the longest
-URI prefix will always be matched. For example, compressing
-`http://purl.obolibrary.org/obo/GO_0032571`
-will return `GO:0032571` instead of `OBO:GO_0032571`.
-
 Full documentation is available at [curies.readthedocs.io](https://curies.readthedocs.io).
 
-### Standardization
-
-The `curies.Converter` data structure supports prefix and URI prefix synonyms.
-The following exampl demonstrates
-using these synonyms to support standardizing prefixes, CURIEs, and URIs. Note below,
-the colloquial prefix `gomf`, sometimes used to represent the subspace in the
-[Gene Ontology (GO)](https://obofoundry.org/ontology/go) corresponding to molecular
-functions, is upgraded to the preferred prefix, `GO`.
-
-```python
-from curies import Converter, Record
-
-converter = Converter([
-    Record(
-        prefix="GO",
-        prefix_synonyms=["gomf", "gocc", "gobp", "go", ...],
-        uri_prefix="http://purl.obolibrary.org/obo/GO_",
-        uri_prefix_synonyms=[
-            "http://amigo.geneontology.org/amigo/term/GO:",
-            "https://identifiers.org/GO:",
-            ...
-        ],
-    ),
-    # And so on
-    ...
-])
-
->>> converter.standardize_prefix("gomf")
-'GO'
->>> converter.standardize_curie('gomf:0032571')
-'GO:0032571'
->>> converter.standardize_uri('http://amigo.geneontology.org/amigo/term/GO:0032571')
-'http://purl.obolibrary.org/obo/GO_0032571'
-```
-
-Note: non-standard URIs can still be parsed with `converter.parse_uri()` and compressed
-into CURIEs with `converter.compress()`.
-
-### Loading Prefix Maps
-
-All loader function work on local file paths, remote URLs, and pre-loaded
-data structures. For example, a converter can be instantiated from a web-based
-resource in JSON-LD format:
-
-```python
-from curies import Converter
-
-url = "https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/semweb.context.jsonld"
-converter = Converter.from_jsonld(url)
-```
-
-Several converters can be instantiated from pre-defined web-based resources:
-
-```python
-import curies
-
-# Uses the Bioregistry, an integrative, comprehensive registry
-bioregistry_converter = curies.get_bioregistry_converter()
-
-# Uses the OBO Foundry, a registry of ontologies
-obo_converter = curies.get_obo_converter()
-
-# Uses the Monarch Initative's project-specific context
-monarch_converter = curies.get_monarch_converter()
-```
-
-### Bulk Operations
-
-Apply in bulk to a `pandas.DataFrame` with `Converter.pd_expand` and
-`Converter.pd_compress`:
-
-```python
-import curies
-import pandas as pd
-
-df = pd.read_csv(...)
-obo_converter = curies.get_obo_converter()
-obo_converter.pd_compress(df, column=0)
-obo_converter.pd_expand(df, column=0)
-```
-
-Apply in bulk to a CSV file with `Converter.file_expand` and
-`Converter.file_compress` (defaults to using tab separator):
-
-```python
-import curies
-
-path = ...
-obo_converter = curies.get_obo_converter()
-# modifies file in place
-obo_converter.file_compress(path, column=0)
-# modifies file in place
-obo_converter.file_expand(path, column=0)
-```
-
 ### CLI Usage
 
 This package comes with a built-in CLI for running a resolver web application or a IRI mapper web application:
@@ -200,6 +91,7 @@ Other packages that convert between CURIEs and URIs:
 - https://github.com/geneontology/curie-util-py (Python)
 - https://github.com/geneontology/curie-util-es5 (Node.js)
 - https://github.com/endoli/curie.rs (Rust)
+- https://github.com/cthoyt/curies4j (Java)
 
 ## 🚀 Installation
 
@@ -210,6 +102,10 @@ The most recent release can be installed from
 $ pip install curies
 ```
 
+This package currently supports both Pydantic v1 and v2. See the
+[Pydantic migration guide](https://docs.pydantic.dev/2.0/migration/)
+for updating your code.
+
 ## 👐 Contributing
 
 Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See

docs/source/api.rst

@@ -0,0 +1,5 @@
+API Reference
+-------------
+.. automodapi:: curies
+   :no-inheritance-diagram:
+   :no-heading:

docs/source/conf.py

@@ -27,7 +27,7 @@
 author = "Charles Tapley Hoyt"
 
 # The full version, including alpha/beta/rc tags.
-release = "0.5.4-dev"
+release = "0.7.5-dev"
 
 # The short X.Y version.
 parsed_version = re.match(
@@ -63,7 +63,6 @@
     "sphinx.ext.todo",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
-    "sphinx_autodoc_typehints",
     "sphinx_automodapi.automodapi",
     "sphinx_automodapi.smart_resolver",
     # 'texext',
@@ -226,10 +225,11 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    "https://docs.python.org/3/": None,
+    "python": ("https://docs.python.org/3", None),
     "bioregistry": ("https://bioregistry.readthedocs.io/en/stable/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),
     "flask": ("https://flask.palletsprojects.com/", None),
+    "pydantic": ("https://docs.pydantic.dev/latest/", None),
     # "fastapi": ("https://fastapi.tiangolo.com/", None),
     # "gunicorn": ("https://docs.gunicorn.org/", None),
     # "uvicorn": ("https://www.uvicorn.org/", None),