diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..3d57836 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,49 @@ +# SPDX-FileCopyrightText: 2026 California Institute of Technology. + +name: Deploy docs + +on: + push: + branches: + - master + workflow_dispatch: + +permissions: + contents: read + pages: write + id-token: write + +concurrency: + group: pages + cancel-in-progress: false + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v7 + + - name: Install the latest version of uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + + - name: Install dependencies + run: uv sync --extra docs + + - name: Build docs + run: uv run zensical build + + - uses: actions/upload-pages-artifact@v5 + with: + path: site/ + + deploy: + needs: build + runs-on: ubuntu-latest + environment: + name: github-pages + url: ${{ steps.deploy.outputs.page_url }} + steps: + - uses: actions/configure-pages@v6 + + - id: deploy + uses: actions/deploy-pages@v5 diff --git a/.gitignore b/.gitignore index 2ed1e34..5c67bc9 100644 --- a/.gitignore +++ b/.gitignore @@ -51,8 +51,8 @@ coverage.xml # Django stuff: *.log -# Sphinx documentation -docs/_build/ +# MkDocs build output +site/ # PyBuilder target/ diff --git a/.readthedocs.yaml b/.readthedocs.yaml deleted file mode 100644 index 4a49353..0000000 --- a/.readthedocs.yaml +++ /dev/null @@ -1,18 +0,0 @@ -# Read the Docs configuration file for Sphinx projects -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - - -# Required -version: 2 - -build: - os: ubuntu-22.04 - tools: - python: "3.12" - -sphinx: - configuration: docs/conf.py - -python: - install: - - requirements: docs/requirements.txt diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 0000000..3dd2d04 --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,21 @@ + + +# Authors + +- Adrian Pawel Baran +- Alan Rubin +- Alexander Ioannidis +- Antoine Lambert +- Bruno Marmol +- Guillaume Viger +- Jiri Kuncar +- Lars Holm Nielsen +- Pedro Gaudencio +- Tibor Simko diff --git a/AUTHORS.rst b/AUTHORS.rst deleted file mode 100644 index d562b11..0000000 --- a/AUTHORS.rst +++ /dev/null @@ -1,22 +0,0 @@ -.. - SPDX-FileCopyrightText: 2015-2019 CERN. - SPDX-License-Identifier: BSD-3-Clause - - In applying this license, CERN does not waive the privileges and immunities - granted to it by virtue of its status as an Intergovernmental Organization - or submit itself to any jurisdiction. - - -Authors -======= - -- Adrian Pawel Baran -- Alan Rubin -- Alexander Ioannidis -- Antoine Lambert -- Bruno Marmol -- Guillaume Viger -- Jiri Kuncar -- Lars Holm Nielsen -- Pedro Gaudencio -- Tibor Simko diff --git a/CHANGES.rst b/CHANGES.md similarity index 70% rename from CHANGES.rst rename to CHANGES.md index 9d65e48..8fadeee 100644 --- a/CHANGES.rst +++ b/CHANGES.md @@ -1,46 +1,45 @@ -.. - SPDX-FileCopyrightText: 2015-2023 CERN. - SPDX-FileCopyrightText: 2022 Northwestern University. - SPDX-License-Identifier: BSD-3-Clause + +# Changes -Changes -======= - -Version v1.6.1 (released 2026-05-28) +## Version v1.6.1 (released 2026-05-28) - setup: replace isbnlib with isbnlib2 -Version v1.6.0 (released 2026-03-19) +## Version v1.6.0 (released 2026-03-19) - refactor: remove DeprecationWarning - feat: add cstr and rrid identifiers - adding tests - feat: add openalex validator -Version v1.5.1 (released 2025-12-15) +## Version v1.5.1 (released 2025-12-15) - feat: add support for wikidata type QID scheme - gh-action: various version bumps -Version v1.5.0 (released 2025-07-14) +## Version v1.5.0 (released 2025-07-14) - chores: replaced importlib_metadata with importlib.metadata -Version 1.4.5 (2025-06-05) +## Version 1.4.5 (2025-06-05) - ark: fix regex to match new ARK identifiers without slash -Version 1.4.4 (2025-06-03) +## Version 1.4.4 (2025-06-03) - swhid: improved SWHID validation - tests: additional tests -Version 1.4.3 (2025-05-12) +## Version 1.4.3 (2025-05-12) - is_url: allow URL parameters (i.e. semicolon) - gnd: improve validation and normalization @@ -48,137 +47,137 @@ Version 1.4.3 (2025-05-12) - pmid: add trailing slash - new: email and sha1 identifiers -Version 1.4.2 (2024-11-01) +## Version 1.4.2 (2024-11-01) - setup: remove pytest-invenio to make imports cleaner - setup: install importlib_metadata for compatibility - bibcode/ads: normalize unicode -Version 1.4.1 (2024-10-18) +## Version 1.4.1 (2024-10-18) - install: add importlib_metadata -Version 1.4.0 (2024-10-17) +## Version 1.4.0 (2024-10-17) - Restructure module to be configurable and readable. - Adds a new entrypoint to register new custom schemes - Adds deprecations for direct imports of schemes -Version 1.3.0 (2024-10-15) (yanked due to undesired flask dependency) +## Version 1.3.0 (2024-10-15) (yanked due to undesired flask dependency) - Restructure module to be configurable and readable. - Adds a new entrypoint to register new custom schemes - Adds deprecations for direct imports of schemes -Version 1.2.1 (2023-03-02) +## Version 1.2.1 (2023-03-02) - Fixes ORCiD validation, by adding the new ISNI block range. -Version 1.2.0 (2023-01-30) +## Version 1.2.0 (2023-01-30) - schemes: add support for viaf and urn -Version 1.1.12 (2022-02-28) +## Version 1.1.12 (2022-02-28) -- Replaces ``isbnid_fork`` with ``isbnlib`` +- Replaces `isbnid_fork` with `isbnlib` -Version 1.1.11 (2022-01-28) +## Version 1.1.11 (2022-01-28) - Normalize pmid + their URL identifiers -Version 1.1.10 (2022-01-11) +## Version 1.1.10 (2022-01-11) - Add purl.fdlp.gov as a valid PURL netloc - Normalize ror identifiers -Version 1.1.9 (2021-08-30) +## Version 1.1.9 (2021-08-30) - Update ARK's NAAN regex per https://datatracker.ietf.org/doc/html/draft-kunze-ark-28#section-2.3. -Version 1.1.8 (2020-08-13) +## Version 1.1.8 (2020-08-13) - Adds support for GEO and ArrayExpress identifiers. -Version 1.1.7 (2020-06-22) +## Version 1.1.7 (2020-06-22) - Updates Software Heritage identifiers - Adds Research Organization Registry identifiers - Fixes DeprctationWarnings by using raw strings for regular expressions -Version 1.1.6 (2020-05-07) +## Version 1.1.6 (2020-05-07) - Deprecates Python versions lower than 3.6.0. Now supporting 3.6.0 and 3.7.0. -Version 1.1.5 (2020-02-26) +## Version 1.1.5 (2020-02-26) - Adds support for Software Heritage identifiers. - Fixes handling of non-digit characters in DOI detection. -Version 1.1.4 (2019-09-27) +## Version 1.1.4 (2019-09-27) - Adds support for ASCL identifiers. - Fixes the ADS identifier regex to also detect lower-case author initials. -Version 1.1.3 (2019-09-17) +## Version 1.1.3 (2019-09-17) - Adds support for HTTPS ORCiD identifiers. -Version 1.1.2 (2019-02-12) +## Version 1.1.2 (2019-02-12) - Adds support for HAL identifiers. -Version 1.1.1 (2018-11-18) +## Version 1.1.1 (2018-11-18) - Changes URL resolution for bibcodes to use https://ui.adsabs.harvard instead of https://adsabs.harvard.edu/abs/. -- Allows choosing HTTP/HTTPS for any generated URL by ``idutils.to_url``. +- Allows choosing HTTP/HTTPS for any generated URL by `idutils.to_url`. -Version 1.1.0 (2018-08-17) +## Version 1.1.0 (2018-08-17) - Adds support for genomic identifiers: SRA, BioProject, BioSample, Ensembl, UniProt, RefSeq, GenBank/RefSeq. - Fixes bug in bibcode detection for non-capitalized journals. -Version 1.0.1 (2018-05-02) +## Version 1.0.1 (2018-05-02) - Fixes bug causing invalid DOIs to be accepted. -Version 1.0.0 (2017-12-07) +## Version 1.0.0 (2017-12-07) - Fixes handling of unicode characters in DOIs. - Adds support for APS style arXiv identifiers. -Version 0.2.4 (2017-01-30) +## Version 0.2.4 (2017-01-30) - Removes `Python 3.3` from a list of supported Python versions and adds `Python 3.6` - Moves from `isbnid (v0.3.4)` to `isbnid_fork (v0.4.4)` library. -Version 0.2.3 (2016-09-21) +## Version 0.2.3 (2016-09-21) - Adds an optional parameter in `idutils.to_url` to use HTTPS scheme for PID providers that support it. - Detects and parses Handles and DOIs without the "http(s)://", and ignores whitespace after scheme tags (eg. "doi: 10.123/456"). -Version 0.2.2 (2016-09-16) +## Version 0.2.2 (2016-09-16) - Fixes issue where a valid ISBN with dashes and spaces could not be normalized. -Version 0.2.1 (2016-06-17) +## Version 0.2.1 (2016-06-17) - Changes ISBN normalization to use `isbnid` instead of `isbnlib`. Now, importing this library will not change the default socket timeout, resulting in unwanted side effects. -Version 0.2.0 (2016-04-07) +## Version 0.2.0 (2016-04-07) - Changes URL resolution for DOIs to use https://doi.org instead of http://dx.doi.org according to https://www.doi.org/doi_handbook/3_Resolution.html#3.8 -Version 0.1.1 (2015-07-22) +## Version 0.1.1 (2015-07-22) - Fixes GND validation and normalization. - Replaces invalid package name in `run-tests.sh` and makes `run-tests.sh` file @@ -188,6 +187,6 @@ Version 0.1.1 (2015-07-22) `docker-compose build` rebuilds the image, `docker-compose run --rm web /code/run-tests.sh` runs the test suite. -Version 0.1.0 (2015-07-02) +## Version 0.1.0 (2015-07-02) - First public release. diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.md similarity index 69% rename from CONTRIBUTING.rst rename to CONTRIBUTING.md index 8392336..a5e5b17 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.md @@ -1,12 +1,10 @@ -Contributing -============ +# Contributing Bug reports, feature requests, and other contributions are welcome. If you find a demonstrable problem that is caused by the code of this library, please: -1. Search for `already reported problems - `_. +1. Search for [already reported problems](https://github.com/inveniosoftware/idutils/issues). 2. Check if the issue has been fixed or is still reproducible on the latest `master` branch. 3. Create an issue with **a test case**. @@ -14,6 +12,6 @@ library, please: If you create a feature branch, you can run the tests to ensure everything is operating correctly: -.. code-block:: console - - $ ./run-tests.sh +```console +$ ./run-tests.sh +``` diff --git a/README.md b/README.md new file mode 100644 index 0000000..c18ce83 --- /dev/null +++ b/README.md @@ -0,0 +1,41 @@ + + +# IDUtils + +[![CI](https://github.com/inveniosoftware/idutils/workflows/CI/badge.svg)](https://github.com/inveniosoftware/idutils/actions?query=workflow%3ACI) +[![Coverage](https://img.shields.io/coveralls/inveniosoftware/idutils.svg)](https://coveralls.io/r/inveniosoftware/idutils) +[![Release](https://img.shields.io/github/tag/inveniosoftware/idutils.svg)](https://github.com/inveniosoftware/idutils/releases) +[![Downloads](https://img.shields.io/pypi/dm/idutils.svg)](https://pypi.python.org/pypi/idutils) +[![License](https://img.shields.io/github/license/inveniosoftware/idutils.svg)](https://github.com/inveniosoftware/idutils/blob/master/LICENSE) + +Small library for validating and normalising persistent identifiers used in +scholarly communication. + +- Free software: Revised BSD license +- Documentation: https://inveniosoftware.github.io/idutils/. + +## Features + +- Validation and normalization of persistent identifiers. +- Detection of persistent identifier scheme. +- Generation of resolving links for persistent identifiers. +- Supported schemes: ISBN10, ISBN13, ISSN, ISTC, DOI, Handle, EAN8, EAN13, ISNI + ORCID, ARK, PURL, LSID, URN, Bibcode, arXiv, PubMed ID, PubMed Central ID, + GND, SRA, BioProject, BioSample, Ensembl, UniProt, RefSeq, GenBank/RefSeq, SWH, + OpenAlex, CSTR, RRID, RAiD. + +## Installation + +The IDUtils package is on PyPI so all you need is: + +```console +$ pip install idutils +``` diff --git a/README.rst b/README.rst deleted file mode 100644 index c063362..0000000 --- a/README.rst +++ /dev/null @@ -1,54 +0,0 @@ -.. - SPDX-FileCopyrightText: 2015 CERN. - SPDX-License-Identifier: BSD-3-Clause - - In applying this license, CERN does not waive the privileges and immunities - granted to it by virtue of its status as an Intergovernmental Organization - or submit itself to any jurisdiction. - - -======= -IDUtils -======= - -.. image:: https://github.com/inveniosoftware/idutils/workflows/CI/badge.svg - :target: https://github.com/inveniosoftware/idutils/actions?query=workflow%3ACI - -.. image:: https://img.shields.io/coveralls/inveniosoftware/idutils.svg - :target: https://coveralls.io/r/inveniosoftware/idutils - -.. image:: https://img.shields.io/github/tag/inveniosoftware/idutils.svg - :target: https://github.com/inveniosoftware/idutils/releases - -.. image:: https://img.shields.io/pypi/dm/idutils.svg - :target: https://pypi.python.org/pypi/idutils - -.. image:: https://img.shields.io/github/license/inveniosoftware/idutils.svg - :target: https://github.com/inveniosoftware/idutils/blob/master/LICENSE - - -Small library for validating and normalising persistent identifiers used in -scholarly communication. - -* Free software: Revised BSD license -* Documentation: https://idutils.readthedocs.io. - -Features -======== - -- Validation and normalization of persistent identifiers. -- Detection of persistent identifier scheme. -- Generation of resolving links for persistent identifiers. -- Supported schemes: ISBN10, ISBN13, ISSN, ISTC, DOI, Handle, EAN8, EAN13, ISNI - ORCID, ARK, PURL, LSID, URN, Bibcode, arXiv, PubMed ID, PubMed Central ID, - GND, SRA, BioProject, BioSample, Ensembl, UniProt, RefSeq, GenBank/RefSeq, SWH, - OpenAlex, CSTR, RRID, RAiD. - -Installation -============ - -The IDUtils package is on PyPI so all you need is: - -.. code-block:: console - - $ pip install idutils diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 43f3caf..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,192 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " applehelp to make an Apple Help Book" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - @echo " coverage to run coverage check of the documentation (if enabled)" - -clean: - rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/cookiecutterproject_name.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/cookiecutterproject_name.qhc" - -applehelp: - $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp - @echo - @echo "Build finished. The help book is in $(BUILDDIR)/applehelp." - @echo "N.B. You won't be able to view it unless you put it in" \ - "~/Library/Documentation/Help or install it in your application" \ - "bundle." - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/cookiecutterproject_name" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/cookiecutterproject_name" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -latexpdfja: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through platex and dvipdfmx..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." - -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." - -coverage: - $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage - @echo "Testing of coverage in the sources finished, look at the " \ - "results in $(BUILDDIR)/coverage/python.txt." - -xml: - $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml - @echo - @echo "Build finished. The XML files are in $(BUILDDIR)/xml." - -pseudoxml: - $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml - @echo - @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/api.md b/docs/api.md new file mode 100644 index 0000000..700af6d --- /dev/null +++ b/docs/api.md @@ -0,0 +1,25 @@ + + +# API Reference + +::: idutils.detectors + options: + filters: + - "!.*" + - "^detect_identifier_schemes$" + +::: idutils.validators + options: + filters: + - "!.*" + - "^is_" + +::: idutils.normalizers + options: + filters: + - "!.*" + - "^normalize_" + - "^to_url$" + diff --git a/docs/changelog.md b/docs/changelog.md new file mode 100644 index 0000000..a1f9eb2 --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1,5 @@ + + +--8<-- "CHANGES.md" diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 68b681b..0000000 --- a/docs/conf.py +++ /dev/null @@ -1,317 +0,0 @@ -# SPDX-FileCopyrightText: 2015, 2016 CERN. -# SPDX-FileCopyrightText: 2022 Graz University of Technology. -# SPDX-License-Identifier: BSD-3-Clause -# -# In applying this license, CERN does not waive the privileges and immunities -# granted to it by virtue of its status as an Intergovernmental Organization -# or submit itself to any jurisdiction. - -"""Sphinx configuration.""" - -import sphinx.environment -from docutils.utils import get_source_line - -from idutils import __version__ - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# sys.path.insert(0, os.path.abspath('.')) - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -# needs_sphinx = '1.0' - -# Do not warn on external images. -suppress_warnings = ["image.nonlocal_uri"] - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.coverage", - "sphinx.ext.doctest", - "sphinx.ext.intersphinx", - "sphinx.ext.viewcode", -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# source_suffix = ['.rst', '.md'] -source_suffix = ".rst" - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = "index" - -# General information about the project. -project = "IDUtils" -copyright = "2016, CERN" -author = "Invenio Software Collaboration" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. - -# The full version, including alpha/beta/rc tags. -release = __version__ - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = "en" - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = [] - -# The reST default role (used for this markup: `text`) to use for all -# documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# A list of ignored prefixes for module index sorting. -# modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -# keep_warnings = False - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - - -# -- Options for HTML output ---------------------------------------------- -html_theme = "alabaster" - -html_theme_options = { - "description": "Small library for validating and normalising persistent " - "identifiers used in scholarly communication.", - "github_user": "inveniosoftware", - "github_repo": "idutils", - "github_button": False, - "github_banner": True, - "show_powered_by": False, - "extra_nav_links": { - "idutils@GitHub": "http://github.com/inveniosoftware/idutils", - "idutils@PyPI": "http://pypi.python.org/pypi/idutils/", - }, -} - -html_sidebars = { - "**": [ - "about.html", - "navigation.html", - "relations.html", - "searchbox.html", - "donate.html", - ] -} - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -# html_static_path = ['_static'] - -# Add any extra paths that contain custom files (such as robots.txt or -# .htaccess) here, relative to this directory. These files are copied -# directly to the root of the documentation. -# html_extra_path = [] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -# html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Language to be used for generating the HTML full-text search index. -# Sphinx supports the following languages: -# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' -# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr' -# html_search_language = 'en' - -# A dictionary with options for the search language support, empty by default. -# Now only 'ja' uses this config value -# html_search_options = {'type': 'default'} - -# The name of a javascript file (relative to the configuration directory) that -# implements a search results scorer. If empty, the default will be used. -# html_search_scorer = 'scorer.js' - -# Output file base name for HTML help builder. -htmlhelp_basename = "idutils_namedoc" - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - #'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). - #'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. - #'preamble': '', - # Latex figure (float) alignment - #'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, "idutils.tex", "idutils Documentation", "Invenio Software", "manual"), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [(master_doc, "idutils", "idutils Documentation", [author], 1)] - -# If true, show URL addresses after external links. -# man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ( - master_doc, - "idutils", - "IDUtils Documentation", - author, - "idutils", - "Small library for validating and normalising persistent identifiers used in scholarly communication.", - "Miscellaneous", - ), -] - -# Documents to append as an appendix to all manuals. -# texinfo_appendices = [] - -# If false, no module index is generated. -# texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -# texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -# texinfo_no_detailmenu = False - - -# Example configuration for intersphinx: refer to the Python standard library. -intersphinx_mapping = {"": ("https://docs.python.org/", None)} diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 0000000..0488e09 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,5 @@ + + +--8<-- "CONTRIBUTING.md" diff --git a/docs/custom-schemes.md b/docs/custom-schemes.md new file mode 100644 index 0000000..f454ef0 --- /dev/null +++ b/docs/custom-schemes.md @@ -0,0 +1,10 @@ + + +# How to add your own schemes + +::: idutils.ext + options: + filters: + - "!^_" diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..b1260b5 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,5 @@ + + +--8<-- "README.md" diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index eee7916..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,63 +0,0 @@ -.. - SPDX-FileCopyrightText: 2015-2018 CERN. - SPDX-FileCopyrightText: 2018 Alan Rubin. - SPDX-License-Identifier: BSD-3-Clause - - In applying this license, CERN does not waive the privileges and immunities - granted to it by virtue of its status as an Intergovernmental Organization - or submit itself to any jurisdiction. - -.. currentmodule:: idutils - -Small library for validating and normalising persistent identifiers used in -scholarly communication. - -* Free software: Revised BSD license -* Documentation: https://idutils.readthedocs.io. - -Features -======== - -- Addition of custom schemes supporting all features of predefined schemes -- Validation and normalization of persistent identifiers. -- Detection of persistent identifier scheme. -- Generation of resolving links for persistent identifiers. -- Supported schemes: ISBN10, ISBN13, ISSN, ISTC, DOI, Handle, EAN8, EAN13, ISNI - ORCID, ARK, PURL, LSID, URN, Bibcode, arXiv, PubMed ID, PubMed Central ID, - GND, SRA, BioProject, BioSample, Ensembl, UniProt, RefSeq, Genome Assembly, - GEO, ArrayExpress. - -Installation -============ - -The IDUtils package is on PyPI so all you need is: - -.. code-block:: console - - $ pip install idutils - - -API -=== - -.. automodule:: idutils - :members: is_isbn10, is_isbn13, is_isbn, is_issn, is_istc, is_doi, is_handle, is_ean8, is_ean13, is_ean, is_isni, is_orcid, is_purl, is_url, is_lsid, is_urn, is_ads, is_arxiv_post_2007, is_arxiv_pre_2007, is_arxiv, is_pmid, is_pmcid, is_gnd, is_sra, is_bioproject, is_biosample, is_ensembl, is_uniprot, is_refseq, is_genome, is_geo, is_arrayexpress_array, is_arrayexpress_experiment, detect_identifier_schemes, normalize_doi, normalize_handle, normalize_ads, normalize_orcid, normalize_gnd, normalize_pmid, normalize_arxiv, normalize_pid, to_url - -.. include:: ../CHANGES.rst - -.. include:: ../CONTRIBUTING.rst - - -How to add your own schemes -=========================== - -.. automodule:: idutils.ext - :members: - - -License -======= - -.. include:: ../LICENSE - -.. include:: ../AUTHORS.rst diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index c037791..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1 +0,0 @@ --e .[docs,tests] diff --git a/idutils/detectors.py b/idutils/detectors.py index fd6ec69..d063661 100644 --- a/idutils/detectors.py +++ b/idutils/detectors.py @@ -26,7 +26,8 @@ def detect_identifier_schemes(val): """Detect persistent identifier scheme for a given value. - .. note:: Some schemes like PMID are very generic. + !!! note + Some schemes like PMID are very generic. """ schemes = [] scheme_validators = IDUTILS_PID_SCHEMES + custom_schemes_registry().pick_scheme_key( diff --git a/idutils/ext.py b/idutils/ext.py index 4d234ce..d9141b2 100644 --- a/idutils/ext.py +++ b/idutils/ext.py @@ -8,38 +8,39 @@ """Extension class to collect and register new schemes via entrypoints. In order to define your own custom schemes you can use the following entrypoint to -register them +register them: -.. code-block:: python +```python +[options.entry_points] +idutils.custom_schemes = + my_new_scheme = my_module.get_scheme_config_func +``` - [options.entry_points] - idutils.custom_schemes = - my_new_scheme = my_module.get_scheme_config_func - -The entry point ``'my_new_scheme = my_module.get_scheme_config_func'`` defines an entry -point named ``my_new_scheme`` pointing to the function ``my_module.get_scheme_config_func`` +The entry point `'my_new_scheme = my_module.get_scheme_config_func'` defines an entry +point named `my_new_scheme` pointing to the function `my_module.get_scheme_config_func` which returns the config for your new registered scheme. That function must return a dictionary with the following format: -.. code-block:: python - - def get_scheme_config_func(): - return { - # See examples in `idutils.validators` file. - "validator": lambda value: True else False, - # Used in `idutils.normalizers.normalize_pid` function. - "normalizer": lambda value: normalized_value, - # See examples in `idutils.detectors.IDUTILS_SCHEME_FILTER` config. - "filter": ["list_of_schemes_to_filter_out"], - # Used in `idutils.normalizers.to_url` function. - "url_generator": lambda scheme, normalized_pid: "normalized_url", - } +```python +def get_scheme_config_func(): + return { + # See examples in `idutils.validators` file. + "validator": lambda value: True else False, + # Used in `idutils.normalizers.normalize_pid` function. + "normalizer": lambda value: normalized_value, + # See examples in `idutils.detectors.IDUTILS_SCHEME_FILTER` config. + "filter": ["list_of_schemes_to_filter_out"], + # Used in `idutils.normalizers.to_url` function. + "url_generator": lambda scheme, normalized_pid: "normalized_url", + } +``` Each key is optional and if not provided a default value is defined in `idutils.ext._set_default_custom_scheme_config()` function. -Note: You can only add new schemes but not override existing ones. +!!! note + You can only add new schemes but not override existing ones. """ import importlib.metadata as m diff --git a/idutils/normalizers.py b/idutils/normalizers.py index c85e81c..0461208 100644 --- a/idutils/normalizers.py +++ b/idutils/normalizers.py @@ -234,13 +234,16 @@ def normalize_pid(val, scheme): def to_url(val, scheme, url_scheme="http"): """Convert a resolvable identifier into a URL for a landing page. - :param val: The identifier's value. - :param scheme: The identifier's scheme. - :param url_scheme: Scheme to use for URL generation, 'http' or 'https'. - :returns: URL for the identifier. + Args: + val: The identifier's value. + scheme: The identifier's scheme. + url_scheme: Scheme to use for URL generation, 'http' or 'https'. - .. versionadded:: 0.3.0 - ``url_scheme`` used for URL generation. + Returns: + URL for the identifier. + + !!! info "New in version 0.3.0" + `url_scheme` used for URL generation. """ pid = normalize_pid(val, scheme) landing_urls = IDUTILS_LANDING_URLS diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..e320848 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,57 @@ +# SPDX-FileCopyrightText: 2026 California Institute of Technology. + +site_name: IDUtils +site_description: Small library for validating and normalising persistent identifiers used in scholarly communication. +site_url: https://inveniosoftware.github.io/idutils +repo_url: https://github.com/inveniosoftware/idutils +repo_name: inveniosoftware/idutils + +theme: + name: material + features: + - navigation.sections + - navigation.top + - search.highlight + palette: + - scheme: default + primary: indigo + accent: indigo + toggle: + icon: material/brightness-7 + name: Switch to dark mode + - scheme: slate + primary: indigo + accent: indigo + toggle: + icon: material/brightness-4 + name: Switch to light mode + +plugins: + - search + - mkdocstrings: + handlers: + python: + options: + docstring_style: google + show_source: true + show_root_heading: true + heading_level: 2 + +nav: + - Home: index.md + - API Reference: api.md + - Custom Schemes: custom-schemes.md + - Changelog: changelog.md + - Contributing: contributing.md + +markdown_extensions: + - admonition + - pymdownx.highlight: + anchor_linenums: true + - pymdownx.superfences + - pymdownx.inlinehilite + - pymdownx.snippets: + base_path: ["."] + check_paths: true + - toc: + permalink: true diff --git a/pyproject.toml b/pyproject.toml index 26010bb..390379c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ [project] name = "idutils" description = "Small library for persistent identifiers used in scholarly communication." -readme = "README.rst" +readme = "README.md" requires-python = ">=3.9" license = "BSD-3-Clause" authors = [ @@ -28,13 +28,15 @@ dynamic = ["version"] Repository = "https://github.com/inveniosoftware/idutils" [project.optional-dependencies] -docs = [] +docs = [ + "zensical", + "mkdocstrings[python]", +] tests = [ "pytest-black-ng>=0.4.0", "pytest-cache>=1.0", "pytest-invenio>=1.4.0", "pytest-runner>=2.6.2", - "sphinx>=4.5", ] [build-system] @@ -56,6 +58,6 @@ profile = "black" add_ignore = "" [tool.pytest.ini_options] -addopts = '--black --isort --pydocstyle --doctest-glob="*.rst" --doctest-modules --cov=idutils --cov-report=term-missing' +addopts = '--black --isort --pydocstyle --doctest-modules --cov=idutils --cov-report=term-missing' testpaths = "tests idutils" live_server_scope = "module" diff --git a/run-tests.sh b/run-tests.sh index 2b0e3a2..4c80b0b 100755 --- a/run-tests.sh +++ b/run-tests.sh @@ -9,5 +9,4 @@ set -o errexit # Quit on unbound symbols set -o nounset -python -m sphinx.cmd.build -qnNW docs docs/_build/html python -m pytest