👷 Build docs and check links

* Configure linkcheck
* Fix external links

.github/workflows/docs.yml

@@ -0,0 +1,27 @@
+# SPDX-FileCopyrightText: 2023 Veit Schiele
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+name: ci
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  docs:
+    name: Build docs and check links
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: pandoc/actions/setup@v1
+    - uses: ts-graphviz/setup-graphviz@v2
+    - uses: actions/setup-python@v5
+      with:
+        cache: pip
+        # Keep in sync with .readthedocs.yaml
+        python-version-file: .python-version
+    - run: python -m pip install -e ".[docs]"
+    - run: python -m sphinx -nb html docs/ docs/_build/html
+    - run: python -m sphinx -b linkcheck docs/ docs/_build/html

.python-version

@@ -0,0 +1 @@
+3.12

README.rst

@@ -10,20 +10,20 @@ Quick start
 Status
 ------
 
-.. image:: https://img.shields.io/github/contributors/veit/python4datascience.svg
+.. image:: https://img.shields.io/github/contributors/cusyio/python4datascience.svg
    :alt: Contributors
-   :target: https://github.com/veit/python4datascience/graphs/contributors
-.. image:: https://img.shields.io/github/license/veit/Python4DataScience.svg
+   :target: https://github.com/cusyio/python4datascience/graphs/contributors
+.. image:: https://img.shields.io/github/license/cusyio/Python4DataScience.svg
    :alt: License
-   :target: https://github.com/veit/python4datascience/blob/main/LICENSE
-.. image:: https://results.pre-commit.ci/badge/github/veit/Python4DataScience/main.svg
-   :target: https://results.pre-commit.ci/latest/github/veit/python4datascience/main
+   :target: https://github.com/cusyio/python4datascience/blob/main/LICENSE
+.. image:: https://results.pre-commit.ci/badge/github/cusyio/Python4DataScience/main.svg
+   :target: https://results.pre-commit.ci/repo/github/649815375
    :alt: pre-commit.ci status
 .. image:: https://readthedocs.org/projects/python4datascience/badge/?version=latest
    :alt: Docs
-   :target: https://python4datascience.readthedocs.io/en/latest/
+   :target: https://www.python4data.science/en/latest/
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo..12593850.svg
-   :target: https://doi.org/10.5281/zenodo..12593850
+   :target: https://doi.org/10.5281/zenodo.12593850
 .. image:: https://img.shields.io/badge/dynamic/json?label=Mastodon&query=totalItems&url=https%3A%2F%2Fmastodon.social%2F@Python4DataScience%2Ffollowers.json&logo=mastodon
    :alt: Mastodon
    :target: https://mastodon.social/@Python4DataScience
@@ -48,7 +48,7 @@ Installation
 
    .. code-block:: console
 
-    $ curl -O https://codeload.github.com/veit/python4datascience/zip/main
+    $ curl -O https://codeload.github.com/cusyio/python4datascience/zip/main
     $ unzip main
     Archive:  main
     …
@@ -160,20 +160,21 @@ Installation
 Follow us
 ---------
 
-* `GitHub <https://github.com/veit/python4datascience>`_
+* `GitHub <https://github.com/cusyio/python4datascience>`_
 * `Mastodon <https://mastodon.social/@Python4DataScience>`_
 
 Pull-Requests
 -------------
 
 If you have suggestions for improvements and additions, I recommend that you
-create a `Fork <https://github.com/veit/python4datascience/fork>`_ of my `GitHub
-Repository <https://github.com/veit/python4datascience/>`_ and make your changes
-there. . You are also welcome to make a *pull request*. If the changes
-contained therein are small and atomic, I’ll be happy to look at your
+create a `Fork <https://github.com/cusyio/python4datascience/fork>`_ of my
+`GitHub Repository <https://github.com/cusyio/python4datascience/>`_ and make
+your changes there. You are also welcome to make a *pull request*. If the
+changes contained therein are small and atomic, I’ll be happy to look at your
 suggestions.
 
-The following guidelines help us to maintain the German translation of the tutorial:
+The following guidelines help us to maintain the German translation of the
+tutorial:
 
 * Write commit messages in Englisch
 * Start commit messages with a `Gitmoji <https://gitmoji.dev/>`__

docs/clean-prep/bulwark.ipynb

@@ -17,7 +17,7 @@
    "source": [
     "## 1. Installation\n",
     "\n",
-    "``` bash\n",
+    "``` console\n",
     "$ pipenv install bulwark\n",
     "Installing bulwark…\n",
     "Adding bulwark to Pipfile's [packages]…\n",

docs/clean-prep/dask-pipeline.ipynb

@@ -16,7 +16,7 @@
     "In this notebook we will use two APIs:\n",
     "\n",
     "1. [Google Maps Geocoder](https://developers.google.com/maps/documentation/geocoding/overview)\n",
-    "2. [Open Notify API for ISS location](http://api.open-notify.org/)\n",
+    "2. [Open Notify API for ISS location](http://api.open-notify.org)\n",
     "\n",
     "We will use them to track ISS location and next transit time with respect to a list of cities. To create our charts and parallelise data intelligently, we will use Dask, specifically [Dask Delayed](../performance/dask.ipynb)."
    ]

docs/clean-prep/deduplicate.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Deduplicating data\n",
     "\n",
-    "In this notebook, we deduplicate data using the [Dedupe](https://docs.dedupe.io/) library, which uses a flat neural network to learn from a little training.\n",
+    "In this notebook, we deduplicate data using the [Dedupe](https://docs.dedupe.io/en/latest/) library, which uses a flat neural network to learn from a little training.\n",
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
@@ -961,7 +961,7 @@
    "source": [
     "## 3. dedupe\n",
     "\n",
-    "Alternatively, we can detect the duplicated data with the [Dedupe](https://docs.dedupe.io/) library, which uses a flat neural network to learn from a small training.\n",
+    "Alternatively, we can detect the duplicated data with the [Dedupe](https://docs.dedupe.io/en/latest/) library, which uses a flat neural network to learn from a small training.\n",
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",

docs/clean-prep/index.rst

@@ -32,13 +32,13 @@ Overview
     "`TDDA <https://github.com/tdda/tdda>`_",".. image:: https://raster.shields.io/github/stars/tdda/tdda",".. image:: https://raster.shields.io/github/contributors/tdda/tdda",".. image:: https://raster.shields.io/github/commit-activity/y/tdda/tdda",".. image:: https://raster.shields.io/github/license/tdda/tdda"
     "`Voluptuous <https://github.com/alecthomas/voluptuous>`_",".. image:: https://raster.shields.io/github/stars/alecthomas/voluptuous",".. image:: https://raster.shields.io/github/contributors/alecthomas/voluptuous",".. image:: https://raster.shields.io/github/commit-activity/y/alecthomas/voluptuous",".. image:: https://raster.shields.io/github/license/alecthomas/voluptuous"
     "`scikit-learn <https://github.com/scikit-learn/scikit-learn>`_",".. image:: https://raster.shields.io/github/stars/scikit-learn/scikit-learn",".. image:: https://raster.shields.io/github/contributors/scikit-learn/scikit-learn",".. image:: https://raster.shields.io/github/commit-activity/y/scikit-learn/scikit-learn",".. image:: https://raster.shields.io/github/license/scikit-learn/scikit-learn"
-    "`pandera <https://github.com/pandera-dev/pandera>`_",".. image:: https://raster.shields.io/github/stars/pandera-dev/pandera",".. image:: https://raster.shields.io/github/contributors/pandera-dev/pandera",".. image:: https://raster.shields.io/github/commit-activity/y/pandera-dev/pandera",".. image:: https://raster.shields.io/github/license/pandera-dev/pandera"
+    "`pandera <https://github.com/unionai-oss/pandera>`_",".. image:: https://raster.shields.io/github/stars/unionai-oss/pandera",".. image:: https://raster.shields.io/github/contributors/unionai-oss/pandera",".. image:: https://raster.shields.io/github/commit-activity/y/unionai-oss/pandera",".. image:: https://raster.shields.io/github/license/unionai-oss/pandera"
     "`Validr <https://github.com/guyskk/validr>`_",".. image:: https://raster.shields.io/github/stars/guyskk/validr",".. image:: https://raster.shields.io/github/contributors/guyskk/validr",".. image:: https://raster.shields.io/github/commit-activity/y/guyskk/validr",".. image:: https://raster.shields.io/github/license/guyskk/validr"
     "`marshmallow <https://github.com/marshmallow-code/marshmallow>`_",".. image:: https://raster.shields.io/github/stars/marshmallow-code/marshmallow",".. image:: https://raster.shields.io/github/contributors/marshmallow-code/marshmallow",".. image:: https://raster.shields.io/github/commit-activity/y/marshmallow-code/marshmallow",".. image:: https://raster.shields.io/github/license/marshmallow-code/marshmallow"
     "`datacleaner <https://github.com/rhiever/datacleaner>`_",".. image:: https://raster.shields.io/github/stars/rhiever/datacleaner",".. image:: https://raster.shields.io/github/contributors/rhiever/datacleaner",".. image:: https://raster.shields.io/github/commit-activity/y/rhiever/datacleaner",".. image:: https://raster.shields.io/github/license/rhiever/datacleaner"
     "`Probatus <https://github.com/ing-bank/probatus>`_",".. image:: https://raster.shields.io/github/stars/ing-bank/probatus",".. image:: https://raster.shields.io/github/contributors/ing-bank/probatus",".. image:: https://raster.shields.io/github/commit-activity/y/ing-bank/probatus",".. image:: https://raster.shields.io/github/license/ing-bank/probatus"
     "`popmon <https://github.com/ing-bank/popmon>`_",".. image:: https://raster.shields.io/github/stars/ing-bank/popmon",".. image:: https://raster.shields.io/github/contributors/ing-bank/popmon",".. image:: https://raster.shields.io/github/commit-activity/y/ing-bank/popmon",".. image:: https://raster.shields.io/github/license/ing-bank/popmon"
-    "`Pandas Profiling <https://github.com/ydataai/pandas-profiling>`_",".. image:: https://raster.shields.io/github/stars/ydataai/pandas-profiling",".. image:: https://raster.shields.io/github/contributors/ydataai/pandas-profiling",".. image:: https://raster.shields.io/github/commit-activity/y/ydataai/pandas-profiling",".. image:: https://raster.shields.io/github/license/ydataai/pandas-profiling"
+    "ydata-profiling <https://github.com/ydataai/ydata-profiling>`_",".. image:: https://raster.shields.io/github/stars/ydataai/ydata-profiling",".. image:: https://raster.shields.io/github/contributors/ydataai/ydata-profiling",".. image:: https://raster.shields.io/github/commit-activity/y/ydataai/ydata-profiling",".. image:: https://raster.shields.io/github/license/ydataai/ydata-profiling"
     "`pandas-validation <https://github.com/jmenglund/pandas-validation>`_",".. image:: https://raster.shields.io/github/stars/jmenglund/pandas-validation",".. image:: https://raster.shields.io/github/contributors/jmenglund/pandas-validation",".. image:: https://raster.shields.io/github/commit-activity/y/jmenglund/pandas-validation",".. image:: https://raster.shields.io/github/license/jmenglund/pandas-validation"
     "`PandasSchema <https://github.com/multimeric/PandasSchema>`_",".. image:: https://raster.shields.io/github/stars/multimeric/PandasSchema",".. image:: https://raster.shields.io/github/contributors/multimeric/PandasSchema",".. image:: https://raster.shields.io/github/commit-activity/y/multimeric/PandasSchema",".. image:: https://raster.shields.io/github/license/multimeric/PandasSchema"
     "`Opulent-Pandas <https://github.com/danielvdende/opulent-pandas>`_",".. image:: https://raster.shields.io/github/stars/danielvdende/opulent-pandas",".. image:: https://raster.shields.io/github/contributors/danielvdende/opulent-pandas",".. image:: https://raster.shields.io/github/commit-activity/y/danielvdende/opulent-pandas",".. image:: https://raster.shields.io/github/license/danielvdende/opulent-pandas"

docs/clean-prep/scikit-learn-reprocessing.ipynb

@@ -258,7 +258,7 @@
    "source": [
     "### 3. Attribute the mean value to missing values\n",
     "\n",
-    "For this we use the `mean` strategy of [sklearn.impute.SimpleImputer](https://scikit-learn.org/stable/modules/generated/sklearn.impute.SimpleImputer.html#sklearn-impute-simpleimputer):"
+    "For this we use the `mean` strategy of [sklearn.impute.SimpleImputer](https://scikit-learn.org/stable/modules/generated/sklearn.impute.SimpleImputer.html#simpleimputer):"
    ]
   },
   {

docs/conf.py

@@ -150,37 +150,86 @@
 
 intersphinx_mapping = {
     "jupyter-tutorial": (
-        "https://jupyter-tutorial.readthedocs.io/en/latest/",
+        "https://jupyter-tutorial.readthedocs.io/en/latest",
         None,
     ),
     "python": ("https://docs.python.org/3", None),
-    "ipython": ("https://ipython.readthedocs.io/en/latest/", None),
-    "pytest": ("https://docs.pytest.org/en/latest/", None),
+    "ipython": ("https://ipython.readthedocs.io/en/latest", None),
+    "pytest": ("https://docs.pytest.org/en/latest", None),
     "jupyter-notebook": (
-        "https://jupyter-notebook.readthedocs.io/en/stable/",
+        "https://jupyter-notebook.readthedocs.io/en/stable",
         None,
     ),
-    "jupyterhub": ("https://jupyterhub.readthedocs.io/en/stable/", None),
-    "nbconvert": ("https://nbconvert.readthedocs.io/en/latest/", None),
+    "jupyterhub": ("https://jupyterhub.readthedocs.io/en/stable", None),
+    "nbconvert": ("https://nbconvert.readthedocs.io/en/latest", None),
     "jupyter-contrib-nbextensions": (
-        "https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/",
+        "https://jupyter-contrib-nbextensions.readthedocs.io/en/latest",
         None,
     ),
-    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
-    "nbsphinx": ("https://nbsphinx.readthedocs.io/en/0.4.2/", None),
-    "pipenv": ("https://pipenv.pypa.io/en/latest/", None),
-    "spack": ("https://spack-tutorial.readthedocs.io/en/latest/", None),
-    "ipyparallel": ("https://ipyparallel.readthedocs.io/en/latest/", None),
-    "bokeh": ("https://docs.bokeh.org/en/latest/", None),
-    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
-    "pyviz": ("https://pyviz-tutorial.readthedocs.io/de/latest/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master", None),
+    "nbsphinx": ("https://nbsphinx.readthedocs.io/en/0.4.2", None),
+    "pipenv": ("https://pipenv.pypa.io/en/latest", None),
+    "spack": ("https://spack-tutorial.readthedocs.io/en/latest", None),
+    "ipyparallel": ("https://ipyparallel.readthedocs.io/en/latest", None),
+    "bokeh": ("https://docs.bokeh.org/en/latest", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    "pyviz": ("https://pyviz-tutorial.readthedocs.io/de/latest", None),
     "python-basics": (
-        "https://python-basics-tutorial.readthedocs.io/en/latest/",
+        "https://python-basics-tutorial.readthedocs.io/en/latest",
         None,
     ),
 }
 
 
+# All HTTP redirections from the source URI to the canonical URI will be treated# as "working".
+linkcheck_allowed_redirects = {
+    r"https://app.pganalyze.com/": r"https://app.pganalyze.com/users/sign_in",
+    r"https://doi.org/10.5281/zenodo.12593850": r"https://zenodo.org/records/12593850",
+    r"https://itsdangerous.palletsprojects.com/": r"https://itsdangerous.palletsprojects.com/en/2.2.x/",
+    r"https://jinja.palletsprojects.com/": r"https://jinja.palletsprojects.com/en/3.1.x/",
+    r"https://www.monetdb.org/Documentation": r"https://www.monetdb.org/documentation-Aug2024/",
+    r"https://ohwr.org/cern_ohl_p_v2.txt": r"https://ohwr.org/project/cernohl/-/wikis/uploads/3eff4154d05e7a0459f3ddbf0674cae4/cern_ohl_p_v2.txt",
+    r"https://ohwr.org/cern_ohl_s_v2.txt": r"https://ohwr.org/project/cernohl/-/wikis/uploads/819d71bea3458f71fba6cf4fb0f2de6b/cern_ohl_s_v2.txt",
+    r"https://ohwr.org/cern_ohl_w_v2.txt": r"https://ohwr.org/project/cernohl/-/wikis/uploads/82b567f43ce515395f7ddbfbad7a8806/cern_ohl_w_v2.txt",
+    r"https://proj.org/": r"https://proj.org/en/9.5/",
+    r"https://sqlalchemy-imageattach.readthedocs.io/": r"https://sqlalchemy-imageattach.readthedocs.io/en/1.1.0/",
+}
+
+linkcheck_ignore = [
+    r".*/_sources/.*/*.txt",
+    r"http://127.0.0.1:8000/",
+    r"https://docs.arangodb.com/",
+    r"https://github.com/cusyio/python4datascience/fork",
+    r"https://iopscience.iop.org/journal/*",
+    r"https://sandbox.zenodo.org/account/settings/applications/tokens/new/",
+    # Anchor not found
+    r"https://github.com/facebook/sapp/blob/main/README.md#command-line-interface",
+    r"https://github.com/github/codeql-action/blob/main/README.md#usage",
+    r"https://github.com/ohmyzsh/ohmyzsh/blob/master/plugins/git/README.md#aliases",
+    r"https://github.com/spring-projects/spring-framework/blob/30bce7/CONTRIBUTING.md#format-commit-messages",
+    r"https://github.com/torvalds/subsurface-for-dirk/blob/master/README.md#contributing",
+    # 403 Client Error: Forbidden for url
+    r"https://codebeautify.org/yaml-validator",
+    r"https://collections.plos.org/collection/software/",
+    r"https://currentprotocols.onlinelibrary.wiley.com/journal/1934340x",
+    r"https://data.unicef.org/",
+    r"https://direct.mit.edu/artl",
+    r"https://besjournals.onlinelibrary.wiley.com/journal/*",
+    r"https://journals.sagepub.com/home/*",
+    r"https://doi.org/10.1002/asi.23538",
+    r"https://linux.die.net/man/",
+    r"https://onlinelibrary.wiley.com/",
+    r"https://pubs.acs.org/journal/",
+    r"https://www.cell.com/",
+    r"https://www.journals.elsevier.com/",
+    r"https://www.psychonomic.org/",
+    r"https://www.reddit.com/r/datasets/",
+    r"https://www.sciencedirect.com/journal/",
+    r"https://www.siam.org/publications/journals/",
+    r"https://www.tandfonline.com/",
+]
+
+
 def setup(app):
     # from sphinx.ext.autodoc import cut_lines
     # app.connect('autodoc-process-docstring', cut_lines(4, what=['module']))

docs/data-processing/apis/fastapi/extensions.rst

@@ -100,7 +100,7 @@ Authentication
 ORMs
 ----
 
-`SQLModel <https://github.com/tiangolo/sqlmodel>`_
+`SQLModel <https://github.com/fastapi/sqlmodel>`_
     Library for the interaction of SQL databases with Python objects
 
     .. image:: https://raster.shields.io/pypi/dm/sqlmodel
@@ -144,11 +144,11 @@ ORMs
 `ormar <https://collerek.github.io/ormar/latest/fastapi/>`_
     Asynchronous mini-ORM, with which you only need to maintain one set of
     models and migrate them with :doc:`/data-processing/postgresql/alembic` if
-    necessary (→ `example <https://collerek.github.io/ormar/fastapi/>`__); it is
-    also supported by `fastapi-users
-    <https://github.com/fastapi-users/fastapi-users>`_, `fastapi-crudrouter
-    <https://github.com/awtkns/fastapi-crudrouter>`_ and `fastapi-pagination
-    <https://github.com/uriyyo/fastapi-pagination>`_
+    necessary (→ `example
+    <https://collerek.github.io/ormar/latest/fastapi/>`__); it is also supported
+    by `fastapi-users <https://github.com/fastapi-users/fastapi-users>`_,
+    `fastapi-crudrouter <https://github.com/awtkns/fastapi-crudrouter>`_ and
+    `fastapi-pagination <https://github.com/uriyyo/fastapi-pagination>`_
 
     .. image:: https://raster.shields.io/pypi/dm/ormar
        :alt: Downloads
@@ -252,10 +252,10 @@ ODMs
     .. image:: https://raster.shields.io/github/license/MongoEngine/mongoengine
        :alt: License
 
-`Beanie <https://github.com/roman-right/beanie>`_
+`Beanie <https://github.com/BeanieODM/beanie>`_
     Asynchronous Python object document mapper (ODM) for MongoDB, based on
     `Motor <https://motor.readthedocs.io/en/stable/>`_ and `Pydantic
-    <https://pydantic-docs.helpmanual.io/>`__
+    <https://docs.pydantic.dev/latest/>`__
 
     .. image:: https://raster.shields.io/pypi/dm/beanie
        :alt: Downloads
@@ -268,7 +268,7 @@ ODMs
 
 `ODMantic <https://github.com/art049/odmantic/>`_
     Asynchronous ODM (Object Document Mapper) for MongoDB based on Python type
-    hints and `pydantic <https://pydantic-docs.helpmanual.io/>`__
+    hints and `pydantic <https://docs.pydantic.dev/latest/>`__
 
     .. image:: https://raster.shields.io/pypi/dm/odmantic
        :alt: Downloads