✏️ Fix reST syntax and links

Author: veit

README.rst

@@ -15,11 +15,11 @@ Status
    :target: https://github.com/cusyio/python4datascience/graphs/contributors
 .. image:: https://img.shields.io/github/license/cusyio/Python4DataScience.svg
    :alt: License
-   :target: https://github.com/cusyio/python4datascience/blob/main/LICENSE
+   :target: https://github.com/cusyio/Python4DataScience/blob/main/LICENSES/BSD-3-Clause.txt
 .. 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
+.. image:: https://app.readthedocs.org/projects/python4datascience/badge/?version=latest
    :alt: Docs
    :target: https://www.python4data.science/en/latest/
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo..14031392.svg

docs/clean-prep/dask-pipeline.ipynb

@@ -15,7 +15,7 @@
     "\n",
     "In this notebook we will use two APIs:\n",
     "\n",
-    "1. [Google Maps Geocoder](https://developers.google.com/maps/documentation/geocoding/overview)\n",
+    "1. [Google Maps Geocoder](https://developers.google.com/maps/documentation/geocoding/guides-v3/overview)\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/index.rst

@@ -18,7 +18,7 @@ Expectations <https://greatexpectations.io/>`_ or `MobyDQ
 
 .. tip::
    `cusy seminar: Cleanse and validate data with Python
-   <https://cusy.io/en/our-training-courses/cleanse-and-validate-data-with-python>`_
+   <https://cusy.io/en/our-training-courses/cleanse-and-validate-data-with-python.html>`_
 
 Overview
 --------
@@ -27,7 +27,7 @@ Overview
     :header: "Name", "Stars", "Mitwirkende", "Commit-Aktivität", "Lizenz"
 
     "`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"
-    "`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"
+    "`fg-data-profiling <https://github.com/Data-Centric-AI-Community/fg-data-profiling>`_",".. image:: https://raster.shields.io/github/stars/Data-Centric-AI-Community/fg-data-profiling",".. image:: https://raster.shields.io/github/contributors/Data-Centric-AI-Community/fg-data-profiling",".. image:: https://raster.shields.io/github/commit-activity/y/Data-Centric-AI-Community/fg-data-profiling",".. image:: https://raster.shields.io/github/license/Data-Centric-AI-Community/fg-data-profiling"
     "`fuzzywuzzy <https://github.com/seatgeek/fuzzywuzzy>`_",".. image:: https://raster.shields.io/github/stars/seatgeek/fuzzywuzzy",".. image:: https://raster.shields.io/github/contributors/seatgeek/fuzzywuzzy",".. image:: https://raster.shields.io/github/commit-activity/y/seatgeek/fuzzywuzzy",".. image:: https://raster.shields.io/github/license/seatgeek/fuzzywuzzy"
     "`Hypothesis <https://github.com/HypothesisWorks/hypothesis>`_",".. image:: https://raster.shields.io/github/stars/HypothesisWorks/hypothesis",".. image:: https://raster.shields.io/github/contributors/HypothesisWorks/hypothesis",".. image:: https://raster.shields.io/github/commit-activity/y/HypothesisWorks/hypothesis",".. image:: https://raster.shields.io/github/license/HypothesisWorks/hypothesis"
     "`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"

docs/clean-prep/nulls.ipynb

@@ -1316,7 +1316,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We then use [pandas.DataFrame.groupby](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.groupby.html) to group the records by `username` and then fill in the missing data using the backfill method from [pandas.core.groupby.DataFrameGroupBy.fillna](https://pandas.pydata.org/docs/reference/api/pandas.core.groupby.DataFrameGroupBy.fillna.html). `limit` defines the maximum number of consecutive `NaN` values:"
+    "We then use [pandas.DataFrame.groupby](https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.groupby.html) to group the records by `username` and then fill in the missing data using the backfill method from [pandas.api.typing.DataFrameGroupBy.bfill](https://pandas.pydata.org/docs/reference/api/pandas.api.typing.DataFrameGroupBy.bfill.html). `limit` defines the maximum number of consecutive `NaN` values:"
    ]
   },
   {

docs/clean-prep/string-matching.ipynb

@@ -505,7 +505,7 @@
     "* C#: [FuzzySharp](https://github.com/BoomTownRoi/BoomTown.FuzzySharp)\n",
     "* Go: [go-fuzzywuzzy](https://github.com/paul-mannino/go-fuzzywuzzy)\n",
     "* Pascal: [FuzzyWuzzy.pas](https://github.com/DavidMoraisFerreira/FuzzyWuzzy.pas)\n",
-    "* Kotlin: [FuzzyWuzzy-Kotlin](https://github.com/willowtreeapps/fuzzywuzzy-kotlin)\n",
+    "* Kotlin: [FuzzyWuzzy-Kotlin](https://github.com/jens-muenker/fuzzywuzzy-kotlin)\n",
     "* R: [fuzzywuzzyR](https://github.com/mlampros/fuzzywuzzyR)"
    ]
   }

docs/conf.py

@@ -190,12 +190,11 @@
     r"https://doi.org/10.5281/zenodo.14031392": r"https://zenodo.org/records/14031392",
     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://repository.uantwerpen.be/desktop/irua": r"https://repository.uantwerpen.be/desktop/irua",
     r"https://sqlalchemy-imageattach.readthedocs.io/": r"https://sqlalchemy-imageattach.readthedocs.io/en/1.1.0/",
+    r"https://www.monetdb.org/Documentation": r"https://www.monetdb.org/documentation-Aug2024/",
 }
 
 linkcheck_ignore = [
@@ -211,27 +210,47 @@
     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",
+    r"https://zenodo.org/records/7540792#.Y-QQGK3MKUn",
     # 403 Client Error: Forbidden for url
+    r"https://academic.oup.com/*",
+    r"https://besjournals.onlinelibrary.wiley.com/journal/*",
     r"https://codebeautify.org/yaml-validator",
     r"https://collections.plos.org/collection/software/",
     r"https://currentprotocols.onlinelibrary.wiley.com/journal/1934340x",
+    r"https://data.mendeley.com/datasets/wg4bpm33hj/2",
+    r"https://data.stackexchange.com/",
     r"https://data.unicef.org/",
+    r"https://dataverse.org/",
     r"https://direct.mit.edu/artl",
-    r"https://besjournals.onlinelibrary.wiley.com/journal/*",
-    r"https://journals.sagepub.com/home/*",
+    r"https://dl.acm.org/journal/toms",
     r"https://doi.org/10.1002/asi.23538",
+    r"https://exiftool.sourceforge.net/install.html",
+    r"https://journals.iucr.org/j/",
+    r"https://journals.sagepub.com/home/*",
     r"https://linux.die.net/man/",
     r"https://onlinelibrary.wiley.com/",
     r"https://opensource.org/",
+    r"https://peerj.com/articles/cs-86/",
+    r"https://pubmed.ncbi.nlm.nih.gov/11726920/",
     r"https://pubs.acs.org/journal/",
+    r"https://sourceforge.net/",
+    r"https://wordnet.princeton.edu/*",
+    r"https://www.canlii.org/",
     r"https://www.cell.com/",
+    r"https://www.gesis.org/cews/daten-und-informationen/statistiken/datenzugang",
+    r"https://www.ipums.org/",
     r"https://www.journals.elsevier.com/",
+    r"https://www.lpi.usra.edu/meteor/",
+    r"https://www.nhtsa.gov/research-data/fatality-analysis-reporting-system-fars",
+    r"https://www.npmjs.com/*",
+    r"https://www.oecd.org/en/data.html",
     r"https://www.psychonomic.org/",
     r"https://www.reddit.com/r/datasets/",
     r"https://www.sciencedirect.com/journal/",
+    r"https://www.sec.gov/submit-filings/about-edgar",
     r"https://www.siam.org/publications/journals/",
-    r"https://sourceforge.net/",
     r"https://www.tandfonline.com/",
+    r"https://zsh.sourceforge.io/",
 ]
 
 

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

@@ -8,7 +8,7 @@ Extensions
 Administration
 --------------
 
-`SQLAlchemy Admin for Starlette/FastAPI <https://github.com/aminalaee/sqladmin>`_
+`SQLAlchemy Admin for Starlette/FastAPI <https://github.com/smithyhq/sqladmin>`_
     Flexible admin interface for :doc:`/data-processing/postgresql/sqlalchemy`
     models.
 
@@ -130,22 +130,23 @@ ORMs
     .. image:: https://raster.shields.io/github/license/tortoise/tortoise-orm
        :alt: License
 
-`ormar <https://github.com/collerek/ormar/>`_
+`ormar <https://github.com/ormar-orm/ormar>`_
     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/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>`_
+    <https://ormar-orm.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
-    .. image:: https://raster.shields.io/github/contributors/collerek/ormar
+    .. image:: https://raster.shields.io/github/contributors/ormar-orm/ormar
        :alt: Contributors
-    .. image:: https://raster.shields.io/github/commit-activity/y/collerek/ormar
+    .. image:: https://raster.shields.io/github/commit-activity/y/ormar-orm/ormar
        :alt: Commit activity
-    .. image:: https://raster.shields.io/github/license/collerek/ormar
+    .. image:: https://raster.shields.io/github/license/ormar-orm/ormar
        :alt: License
 
 `Prisma Client Python <https://github.com/RobertCraigie/prisma-client-py>`_
@@ -227,7 +228,7 @@ ODMs
 `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://docs.pydantic.dev/latest/>`__
+    <https://pydantic.dev/docs/validation/latest/get-started/>`__
 
     .. image:: https://raster.shields.io/pypi/dm/beanie
        :alt: Downloads
@@ -240,7 +241,7 @@ ODMs
 
 `ODMantic <https://github.com/art049/odmantic/>`_
     Asynchronous ODM (Object Document Mapper) for MongoDB based on Python type
-    hints and `pydantic <https://docs.pydantic.dev/latest/>`__
+    hints and `pydantic <https://pydantic.dev/docs/validation/latest/get-started/>`__
 
     .. image:: https://raster.shields.io/pypi/dm/odmantic
        :alt: Downloads
@@ -670,17 +671,17 @@ Dormant projects
     .. image:: https://raster.shields.io/github/license/perdy/starlette-prometheus
        :alt: Licence
 
-`FastAPI Utilities <https://github.com/dmontagu/fastapi-utils>`_
+`FastAPI Utilities <https://github.com/fastapiutils/fastapi-utils>`_
     Utilities to reduce boilerplate and reuse common functionality across
     projects.
 
     .. image:: https://raster.shields.io/pypi/dm/fastapi-utils
        :alt: Downloads
-    .. image:: https://raster.shields.io/github/contributors/dmontagu/fastapi-utils
+    .. image:: https://raster.shields.io/github/contributors/fastapiutils/fastapi-utils
        :alt: Contributors
-    .. image:: https://raster.shields.io/github/commit-activity/y/dmontagu/fastapi-utils
+    .. image:: https://raster.shields.io/github/commit-activity/y/fastapiutils/fastapi-utils
        :alt: Commit activity
-    .. image:: https://raster.shields.io/github/license/dmontagu/fastapi-utils
+    .. image:: https://raster.shields.io/github/license/fastapiutils/fastapi-utils
        :alt: Licence
 
 `Fastapi Camelcase <https://github.com/nf1s/fastapi-camelcase>`_

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

@@ -10,8 +10,8 @@ FastAPI is a web framework for building APIs with Python 3.6+ based type hints.
 Key features are:
 
 * very high performance thanks to `pydantic
-  <https://docs.pydantic.dev/latest/>`_ for the data part and `Starlette
-  <https://www.starlette.io/>`_ for the web part.
+  <https://pydantic.dev/docs/validation/latest/get-started/>`_ for the data part
+  and `Starlette <https://www.starlette.io/>`_ for the web part.
 
 * fast and easy to code
 * validation for most Python data types, including

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

@@ -23,7 +23,7 @@ Optional requirements
 ~~~~~~~~~~~~~~~~~~~~~
 
 For production you also need an `ASGI <https://asgi.readthedocs.io/en/latest/>`_
-server, such as `uvicorn <http://www.uvicorn.org/>`_:
+server, such as `uvicorn <https://uvicorn.dev/>`_:
 
 .. code-block:: console
 

docs/data-processing/file-systems.rst

@@ -23,29 +23,32 @@ High-level APIs
 
     Integrated file systems:
 
-    * `AppFS <https://www.pyfilesystem.org/page/appfs/>`_ for predefined storage
-      locations in operating systems where applications can store data
-    * `FTPFS <https://www.pyfilesystem.org/page/ftpfs/>`_ for working with FTP
-      servers
-    * `MemoryFS <https://www.pyfilesystem.org/page/memoryfs/>`_ for caches, temporary data storage, unit tests, :abbr:`etc. (et cetera)` that exist in the
-      working memory
-    * `MountFS <https://www.pyfilesystem.org/page/mountfs/>`_ for a virtual file
-      system that can mount other file systems
-    * `MultiFS <https://www.pyfilesystem.org/page/multifs/>`_ for a virtual file
-      system that combines other file systems
-    * `OSFS <https://www.pyfilesystem.org/page/osfs/>`_ for the OS file system
-    * `TarFS <https://www.pyfilesystem.org/page/tarfs/>`_ reads and writes
-      compressed tar archives
-    * `TempFS <https://www.pyfilesystem.org/page/tempfs/>`_ contains temporary
-      data
-    * `ZipFS <https://www.pyfilesystem.org/page/zipfs/>`_ reads and writes Zip
-      files
+    * `AppFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/appfs.html>`_
+      for predefined storage locations in operating systems where applications
+      can store data
+    * `FTPFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/ftpfs.html>`_
+      for working with FTP servers
+    * `MemoryFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/memoryfs.html>`_
+      for caches, temporary data storage, unit tests, :abbr:`etc. (et cetera)`
+      that exist in the working memory
+    * `MountFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/mountfs.html>`_
+      for a virtual file system that can mount other file systems
+    * `MultiFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/multifs.html>`_
+      for a virtual file system that combines other file systems
+    * `OSFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/osfs.html>`_
+      for the OS file system
+    * `TarFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/zipfs.html>`_
+      reads and writes compressed tar archives
+    * `TempFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/tempfs.html?highlight=tempfs#module-fs.tempfs>`_
+      contains temporary data
+    * `ZipFS <https://pyfilesystem2.readthedocs.io/en/latest/reference/zipfs.html>`_
+      reads and writes Zip files
 
     File systems of the PyFilesystem organization on GitHub:
 
-    * `DropBoxFS <https://www.pyfilesystem.org/page/dropboxfs/>`_
-    * `S3FS <https://www.pyfilesystem.org/page/s3fs/>`_
-    * `WebDavFS <https://www.pyfilesystem.org/page/index-of-filesystems/>`_
+    * `DropBoxFS <https://github.com/PyFilesystem/fs.dropboxfs>`_
+    * `S3FS <https://github.com/PyFilesystem/s3fs>`_
+    * `WebDavFS <https://github.com/PyFilesystem/webdavfs>`_
 
     File systems from third-party developers:
 
@@ -59,8 +62,6 @@ High-level APIs
     * `fs.smbfs <https://github.com/althonos/fs.smbfs>`_ for Samba
     * `fs.sshfs <https://github.com/althonos/fs.sshfs>`_ for  SSH with
       :ref:`paramiko`
-    * `mp-fs-wsgidav <https://github.com/mikespub-org/mp-fs-wsgidav>`_ for
-      WsgiDAV
 
 .. _fsspec:
 
@@ -91,11 +92,11 @@ High-level APIs
     * `boxfs <https://github.com/IBM/boxfs>`_ for access to Box file storage
     * `dropbox <https://github.com/fsspec/dropboxdrivefs>`_ for access to
       Dropbox shares
-    * `dvc <https://github.com/iterative/dvc>`_ for accessing a DVC repository
+    * `dvc <https://github.com/treeverse/dvc>`_ for accessing a DVC repository
       as a file system
     * `gcsfs <https://github.com/fsspec/gcsfs>`_ for Google Cloud Storage
-    * `gdrive <https://github.com/fsspec/gdrivefs>`_ for access to Google Drive
-      and shares
+    * `gdrive <https://github.com/fsspec/gdrive-fsspec>`_ for access to Google
+      Drive and shares
     * `huggingface_hub
       <https://huggingface.co/docs/huggingface_hub/main/en/guides/hf_file_system>`_
       for access to the Hugging Face Hub file system
@@ -192,7 +193,7 @@ Specialised libraries
     .. image::
        https://raster.shields.io/github/license/aliyun/aliyun-oss-python-sdk
 
-`minio <https://min.io/docs/minio/linux/developers/python/minio-py.html>`_
+`minio <https://docs.min.io/aistor/developers/sdk/python/>`_
     MinIO Python Client SDK for Amazon S3 compatible cloud storage.
 
     .. image::