Fix URLs (#1074)

DimitriPapadopoulos · web-flow · commit 7bf7998056f9 · 2022-08-06T02:58:48.000+02:00
* Fix invalid extension documentation URL * Fix invalid numpydoc URL First I tried removing the spurious .txt file extension in HOWTO_DOCUMENT.rst.txt. Then the current contents of HOWTO_DOCUMENT.rst are: This document has been replaced, see https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard * The Python issue tracker has moved to GitHub * Fix PyMongo URL Prefer the link to the PyMongo documentation. * Fix URL to Blosc file Change the default Git branch: master ⤑ main * Fix tox URL It is not hosted by codespeak.net any more. * Fix URL: HTTP ⤑ HTTPS
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,5 +1,5 @@
 Contributing
 ============
 
-Please see the [project documentation](http://zarr.readthedocs.io/en/stable/contributing.html) for information about contributing to Zarr.
+Please see the [project documentation](https://zarr.readthedocs.io/en/stable/contributing.html) for information about contributing to Zarr.
 
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -40,7 +40,7 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://www.contributor-covenant.org/version/1/4][version]
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://www.contributor-covenant.org
+[version]: https://www.contributor-covenant.org/version/1/4
diff --git a/build.cmd b/build.cmd
@@ -13,10 +13,10 @@
 ::
 :: More details at:
 :: https://github.com/cython/cython/wiki/64BitCythonExtensionsOnWindows
-:: http://stackoverflow.com/a/13751649/163740
+:: https://stackoverflow.com/a/13751649/163740
 ::
 :: Author: Olivier Grisel
-:: License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+:: License: CC0 1.0 Universal: https://creativecommons.org/publicdomain/zero/1.0/
 @ECHO OFF
 
 SET COMMAND_TO_RUN=%*
diff --git a/docs/Makefile b/docs/Makefile
@@ -9,7 +9,7 @@ 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/)
+	$(error The '$(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 https://www.sphinx-doc.org/)
 endif
 
 # Internal variables.
diff --git a/docs/api/codecs.rst b/docs/api/codecs.rst
@@ -16,8 +16,8 @@ Codec classes can also be used as filters. See the tutorial section on :ref:`tut
 for more information.
 
 Please note that it is also relatively straightforward to define and register custom codec
-classes. See the Numcodecs `codec API <http://numcodecs.readthedocs.io/en/latest/abc.html>`_ and
-`codec registry <http://numcodecs.readthedocs.io/en/latest/registry.html>`_ documentation for more
+classes. See the Numcodecs `codec API <https://numcodecs.readthedocs.io/en/latest/abc.html>`_ and
+`codec registry <https://numcodecs.readthedocs.io/en/latest/registry.html>`_ documentation for more
 information.
 
-.. _Numcodecs: http://numcodecs.readthedocs.io/
+.. _Numcodecs: https://numcodecs.readthedocs.io/
diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -206,7 +206,7 @@ Documentation
 
 Docstrings for user-facing classes and functions should follow the
 `numpydoc
-<https://github.com/numpy/numpy/blob/main/doc/HOWTO_DOCUMENT.rst.txt>`_
+<https://numpydoc.readthedocs.io/en/stable/format.html#docstring-standard>`_
 standard, including sections for Parameters and Examples. All examples
 should run and pass as doctests under Python 3.8. To run doctests,
 activate your development environment, install optional requirements,
diff --git a/docs/index.rst b/docs/index.rst
@@ -93,10 +93,10 @@ documentation, code reviews, comments and/or ideas:
 * :user:`Prakhar Goel <newt0311>`
 
 Zarr is inspired by `HDF5 <https://www.hdfgroup.org/HDF5/>`_, `h5py
-<http://www.h5py.org/>`_ and `bcolz <http://bcolz.blosc.org/>`_.
+<https://www.h5py.org/>`_ and `bcolz <https://bcolz.readthedocs.io/>`_.
 
 Development of Zarr is supported by the
-`MRC Centre for Genomics and Global Health <http://www.cggh.org>`_.
+`MRC Centre for Genomics and Global Health <https://www.cggh.org>`_.
 
 Indices and tables
 ------------------
@@ -105,4 +105,4 @@ Indices and tables
 * :ref:`modindex`
 * :ref:`search`
 
-.. _NumCodecs: http://numcodecs.readthedocs.io/
+.. _NumCodecs: https://numcodecs.readthedocs.io/
diff --git a/docs/release.rst b/docs/release.rst
@@ -1333,4 +1333,4 @@ See `v0.4.0 release notes on GitHub
 See `v0.3.0 release notes on GitHub
 <https://github.com/zarr-developers/zarr-python/releases/tag/v0.3.0>`_.
 
-.. _Numcodecs: http://numcodecs.readthedocs.io/
+.. _Numcodecs: https://numcodecs.readthedocs.io/
diff --git a/docs/spec/v1.rst b/docs/spec/v1.rst
@@ -133,7 +133,7 @@ of bytes comprising the compressed chunk data. No header is added to
 the compressed bytes or any other modification made. The internal
 structure of the compressed bytes will depend on which primary
 compressor was used. For example, the `Blosc compressor
-<https://github.com/Blosc/c-blosc/blob/master/README_HEADER.rst>`_
+<https://github.com/Blosc/c-blosc/blob/main/README_HEADER.rst>`_
 produces a sequence of bytes that begins with a 16-byte header
 followed by compressed data.
 
diff --git a/docs/spec/v2.rst b/docs/spec/v2.rst
@@ -206,7 +206,7 @@ through the primary compression library to obtain a new sequence of bytes
 comprising the compressed chunk data. No header is added to the compressed
 bytes or any other modification made. The internal structure of the compressed
 bytes will depend on which primary compressor was used. For example, the `Blosc
-compressor <https://github.com/Blosc/c-blosc/blob/master/README_CHUNK_FORMAT.rst>`_
+compressor <https://github.com/Blosc/c-blosc/blob/main/README_CHUNK_FORMAT.rst>`_
 produces a sequence of bytes that begins with a 16-byte header followed by
 compressed data.
 
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -275,7 +275,7 @@ Here is an example using a delta filter with the Blosc compressor::
     Chunks initialized : 100/100
 
 For more information about available filter codecs, see the `Numcodecs
-<http://numcodecs.readthedocs.io/>`_ documentation.
+<https://numcodecs.readthedocs.io/>`_ documentation.
 
 .. _tutorial_groups:
 
@@ -293,7 +293,7 @@ To create a group, use the :func:`zarr.group` function::
     <zarr.hierarchy.Group '/'>
 
 Groups have a similar API to the Group class from `h5py
-<http://www.h5py.org/>`_.  For example, groups can contain other groups::
+<https://www.h5py.org/>`_.  For example, groups can contain other groups::
 
     >>> foo = root.create_group('foo')
     >>> bar = foo.create_group('bar')
@@ -427,7 +427,7 @@ Groups also have the :func:`zarr.hierarchy.Group.tree` method, e.g.::
 If you're using Zarr within a Jupyter notebook (requires
 `ipytree <https://github.com/QuantStack/ipytree>`_), calling ``tree()`` will generate an
 interactive tree representation, see the `repr_tree.ipynb notebook
-<http://nbviewer.jupyter.org/github/zarr-developers/zarr-python/blob/main/notebooks/repr_tree.ipynb>`_
+<https://nbviewer.org/github/zarr-developers/zarr-python/blob/main/notebooks/repr_tree.ipynb>`_
 for more examples.
 
 .. _tutorial_attrs:
@@ -735,7 +735,7 @@ database for storage (requires `bsddb3
 
 Also added in Zarr version 2.2 is the :class:`zarr.storage.LMDBStore` class which
 enables the lightning memory-mapped database (LMDB) to be used for storing an array or
-group (requires `lmdb <http://lmdb.readthedocs.io/>`_ to be installed)::
+group (requires `lmdb <https://lmdb.readthedocs.io/>`_ to be installed)::
 
     >>> store = zarr.LMDBStore('data/example.lmdb')
     >>> root = zarr.group(store=store, overwrite=True)
@@ -779,9 +779,9 @@ Distributed/cloud storage
 
 It is also possible to use distributed storage systems. The Dask project has
 implementations of the ``MutableMapping`` interface for Amazon S3 (`S3Map
-<http://s3fs.readthedocs.io/en/latest/api.html#s3fs.mapping.S3Map>`_), Hadoop
+<https://s3fs.readthedocs.io/en/latest/api.html#s3fs.mapping.S3Map>`_), Hadoop
 Distributed File System (`HDFSMap
-<http://hdfs3.readthedocs.io/en/latest/api.html#hdfs3.mapping.HDFSMap>`_) and
+<https://hdfs3.readthedocs.io/en/latest/api.html#hdfs3.mapping.HDFSMap>`_) and
 Google Cloud Storage (`GCSMap
 <http://gcsfs.readthedocs.io/en/latest/api.html#gcsfs.mapping.GCSMap>`_), which
 can be used with Zarr.
diff --git a/tox.ini b/tox.ini
@@ -1,4 +1,4 @@
-# Tox (http://tox.testrun.org/) is a tool for running tests
+# Tox (https://tox.wiki/) is a tool for running tests
 # in multiple virtualenvs. This configuration file will run the
 # test suite on all supported python versions. To use it, "pip install tox"
 # and then run "tox" from this directory.
diff --git a/zarr/meta.py b/zarr/meta.py
@@ -76,7 +76,7 @@ def get_extended_dtype_info(dtype) -> dict:
         )
     elif dtype.str in _v3_datetime_types:
         return dict(
-            extension="https://zarr-specs.readthedocs.io/en/core-protocol-v3.0-dev/protocol/extensions/datetime-dtypes/v1.0.html",  # noqa
+            extension="https://zarr-specs.readthedocs.io/en/latest/extensions/data-types/datetime/v1.0.html",  # noqa
             type=dtype.str,
             fallback=None,
         )
diff --git a/zarr/storage.py b/zarr/storage.py
@@ -2097,7 +2097,7 @@ def rmdir(self, path: str = "") -> None:
 
 
 class LMDBStore(Store):
-    """Storage class using LMDB. Requires the `lmdb <http://lmdb.readthedocs.io/>`_
+    """Storage class using LMDB. Requires the `lmdb <https://lmdb.readthedocs.io/>`_
     package to be installed.
 
 
@@ -2503,7 +2503,7 @@ def __init__(self, path, dimension_separator=None, **kwargs):
         # allow threading if SQLite connections are thread-safe
         #
         # ref: https://www.sqlite.org/releaselog/3_3_1.html
-        # ref: https://bugs.python.org/issue27190
+        # ref: https://github.com/python/cpython/issues/71377
         check_same_thread = True
         if sqlite3.sqlite_version_info >= (3, 3, 1):
             check_same_thread = False
@@ -2663,7 +2663,7 @@ class MongoDBStore(Store):
 
     .. note:: This is an experimental feature.
 
-    Requires the `pymongo <https://api.mongodb.com/python/current/>`_
+    Requires the `pymongo <https://pymongo.readthedocs.io/en/stable/>`_
     package to be installed.
 
     Parameters
diff --git a/zarr/sync.py b/zarr/sync.py
@@ -26,7 +26,7 @@ def __setstate__(self, *args):
 
 class ProcessSynchronizer:
     """Provides synchronization using file locks via the
-    `fasteners <http://fasteners.readthedocs.io/en/latest/api/process_lock.html>`_
+    `fasteners <https://fasteners.readthedocs.io/en/latest/api/inter_process/>`_
     package.
 
     Parameters
