revert to upstream main

Author: d-v-b

.github/workflows/needs_release_notes.yml

@@ -5,7 +5,6 @@ on:
 
 jobs:
   triage:
-    if: ${{ github.event.pull_request.user.login != 'dependabot[bot]' }} && ${{ github.event.pull_request.user.login != 'pre-commit-ci[bot]' }}
     runs-on: ubuntu-latest
     steps:
     - uses: actions/labeler@main

.github/workflows/releases.yml

@@ -64,7 +64,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.6.4
+      - uses: pypa/gh-action-pypi-publish@v1
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

docs/release.rst

@@ -14,88 +14,11 @@ Unreleased
     # .. warning::
     #    Pre-release! Use :command:`pip install --pre zarr` to evaluate this release.
 
-* Improve Zarr V3 support, adding partial store read/write and storage transformers.
-  Add two features of the [v3 spec](https://zarr-specs.readthedocs.io/en/latest/core/v3.0.html):
-  * storage transformers
-  * `get_partial_values` and `set_partial_values`
-  By :user:`Jonathan Striebel <jstriebel>`; :issue:`1096`.
-
-.. _release_2.13.6:
-
-2.13.6
-------
-
-Maintenance
-~~~~~~~~~~~
-
-* Bump gh-action-pypi-publish to 1.6.4.
-  By :user:`Josh Moore <joshmoore>` :issue:`1320`.
-
-.. _release_2.13.5:
-
-2.13.5
-------
-
-Bug fixes
-~~~~~~~~~
-
-* Ensure ``zarr.create`` uses writeable mode to fix issue with :issue:`1304`.
-  By :user:`James Bourbeau <jrbourbeau>` :issue:`1309`.
-
-.. _release_2.13.4:
-
-2.13.4
-------
-
-Appreciation
-~~~~~~~~~~~~~
-
-Special thanks to Outreachy participants for contributing to most of the
-maintenance PRs. Please read the blog post summarising the contribution phase
-and welcoming new Outreachy interns:
-https://zarr.dev/blog/welcoming-outreachy-2022-interns/
-
-
-Enhancements
-~~~~~~~~~~~~
-
-* Handle fsspec.FSMap using FSStore store.
-  By :user:`Rafal Wojdyla <ravwojdyla>` :issue:`1304`.
-
-Bug fixes
-~~~~~~~~~
-
-* Fix bug that caused double counting of groups in ``groups()`` and ``group_keys()`` methods with V3 stores.
-  By :user:`Ryan Abernathey <rabernat>` :issue:`1228`.
-
-* Remove unnecessary calling of `contains_array` for key that ended in `.array.json`.
-  By :user:`Joe Hamman <jhamman>` :issue:`1149`.
-
 * Fix bug that caused double counting of groups in ``groups()`` and ``group_keys()``
   methods with V3 stores.
   By :user:`Ryan Abernathey <rabernat>` :issue:`1228`.
 
-<<<<<<< HEAD
-* Add support for setting user-defined attributes at array / group creation time.
-  By :user: `Davis Bennett <d-v-b>` :issue:`538`.
-
 .. _release_2.13.2:
-=======
-Documentation
-~~~~~~~~~~~~~
-
-* Fix minor indexing errors in tutorial and specification examples of documentation. 
-  By :user:`Kola Babalola <sprynt001>` :issue:`1277`.
-
-* Add `requirements_rtfd.txt` in `contributing.rst`.
-  By :user:`AWA BRANDON AWA <DON-BRAN>` :issue:`1243`.
-
-* Add documentation for find/findall using visit.
-  By :user:`Weddy Gikunda <caviere>` :issue:`1241`.
-
-* Refresh of the main landing page.
-  By :user:`Josh Moore <joshmoore>` :issue:`1173`.
->>>>>>> 385b5d3635618e086eb4752f81c652379751a5ad
 
 Maintenance
 ~~~~~~~~~~~
@@ -130,77 +53,6 @@ Maintenance
 * Delete unused files.
   By :user:`John Kirkham <jakirkham>` :issue:`1251`.
 
-* Skip labeller for bot PRs.
-  By :user:`Saransh Chopra <Saransh-cpp>` :issue:`1271`.
-
-* Restore Flake8 configuration.
-  By :user:`John Kirkham <jakirkham>` :issue:`1249`.
-
-* Add missing newline at EOF.
-  By :user:`Dimitri Papadopoulos` :issue:`1253`.
-
-* Add `license_files` to `pyproject.toml`.
-  By :user:`John Kirkham <jakirkham>` :issue:`1247`.
-
-* Adding `pyupgrade` suggestions.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1225`.
-
-* Fixed some linting errors.
-  By :user:`Weddy Gikunda <caviere>` :issue:`1226`.
-
-* Added the link to main website in readthedocs sidebar.
-  By :user:`Stephanie_nkwatoh <steph237>` :issue:`1216`.
-
-* Remove redundant wheel dependency in `pyproject.toml`.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1233`.
-
-* Turned on `isloated_build` in `tox.ini` file.
-  By :user:`AWA BRANDON AWA <DON-BRAN>` :issue:`1210`.
-
-* Fixed `flake8` alert and avoid duplication of `Zarr Developers`.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1203`.
-
-* Bump to NumPy 1.20+ in `environment.yml`.
-  By :user:`John Kirkham <jakirkham>` :issue:`1201`.
-
-* Bump to NumPy 1.20 in `pyproject.toml`.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1192`.
-
-* Remove LGTM (`.lgtm.yml`) configuration file.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1191`.
-
-* Codespell will skip `fixture` in pre-commit.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1197`.
-
-* Add msgpack in `requirements_rtfd.txt`.
-  By :user:`Emmanuel Bolarinwa <GbotemiB>` :issue:`1188`.
-
-* Added license to docs fixed a typo from `_spec_v2` to `_spec_v3`.
-  By :user:`AWA BRANDON AWA <DON-BRAN>` :issue:`1182`.
-
-* Fixed installation link in `README.md`.
-  By :user:`AWA BRANDON AWA <DON-BRAN>` :issue:`1177`.
-
-* Fixed typos in `installation.rst` and `release.rst`.
-  By :user:`Chizoba Nweke <zobbs-git>` :issue:`1178`.
-
-* Set `docs/conf.py` language to `en`.
-  By :user:`AWA BRANDON AWA <DON-BRAN>` :issue:`1174`.
-
-* Added `installation.rst` to the docs.
-  By :user:`AWA BRANDON AWA <DON-BRAN>` :issue:`1170`.
-
-* Adjustment of year to `2015-2018` to `2015-2022` in the docs.
-  By :user:`Emmanuel Bolarinwa <GbotemiB>` :issue:`1165`.
-
-* Updated `Forking the repository` section in `contributing.rst`.
-  By :user:`AWA BRANDON AWA <DON-BRAN>` :issue:`1171`.
-
-* Updated GitHub actions.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1134`.
-
-* Uopdate web links: `http:// → https://`.
-  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1313`.
 
 .. _release_2.13.3:
 

docs/spec/v1.rst

@@ -144,9 +144,9 @@ are converted to strings and concatenated with the period character
 ('.') separating each index. For example, given an array with shape
 (10000, 10000) and chunk shape (1000, 1000) there will be 100 chunks
 laid out in a 10 by 10 grid. The chunk with indices (0, 0) provides
-data for rows 0-999 and columns 0-999 and is stored under the key
-'0.0'; the chunk with indices (2, 4) provides data for rows 2000-2999
-and columns 4000-4999 and is stored under the key '2.4'; etc.
+data for rows 0-1000 and columns 0-1000 and is stored under the key
+'0.0'; the chunk with indices (2, 4) provides data for rows 2000-3000
+and columns 4000-5000 and is stored under the key '2.4'; etc.
 
 There is no need for all chunks to be present within an array
 store. If a chunk is not present then it is considered to be in an

docs/spec/v2.rst

@@ -216,9 +216,9 @@ To form a string key for a chunk, the indices are converted to strings and
 concatenated with the period character (".") separating each index. For
 example, given an array with shape (10000, 10000) and chunk shape (1000, 1000)
 there will be 100 chunks laid out in a 10 by 10 grid. The chunk with indices
-(0, 0) provides data for rows 0-999 and columns 0-999 and is stored under the
-key "0.0"; the chunk with indices (2, 4) provides data for rows 2000-2999 and
-columns 4000-4999 and is stored under the key "2.4"; etc.
+(0, 0) provides data for rows 0-1000 and columns 0-1000 and is stored under the
+key "0.0"; the chunk with indices (2, 4) provides data for rows 2000-3000 and
+columns 4000-5000 and is stored under the key "2.4"; etc.
 
 There is no need for all chunks to be present within an array store. If a chunk
 is not present then it is considered to be in an uninitialized state.  An

docs/tutorial.rst

@@ -525,9 +525,9 @@ When the indexing arrays have different shapes, they are broadcast together.
 That is, the following two calls are equivalent::
 
     >>> z[1, [1, 3]]
-    array([6, 8])
+    array([5, 7])
     >>> z[[1, 1], [1, 3]]
-    array([6, 8])
+    array([5, 7])
 
 Indexing with a mask array
 ~~~~~~~~~~~~~~~~~~~~~~~~~~

notebooks/dask_copy.ipynb

@@ -33,7 +33,7 @@
       "text/html": [
        "\n",
        "    <div class=\"bk-root\">\n",
-       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
+       "        <a href=\"http://bokeh.pydata.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
        "        <span id=\"d4821cb3-378c-411d-a941-d0708c0c532b\">Loading BokehJS ...</span>\n",
        "    </div>"
       ]

notebooks/dask_count_alleles.ipynb

@@ -26,7 +26,7 @@
       "text/html": [
        "\n",
        "    <div class=\"bk-root\">\n",
-       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
+       "        <a href=\"http://bokeh.pydata.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
        "        <span id=\"b153ad5f-436a-4afb-945c-87790add89c8\">Loading BokehJS ...</span>\n",
        "    </div>"
       ]

requirements_dev_minimal.txt

@@ -1,8 +1,8 @@
 # library requirements
 asciitree==0.3.3
 fasteners==0.18
-numcodecs==0.11.0
+numcodecs==0.10.2
 msgpack-python==0.5.6
-setuptools-scm==7.1.0
+setuptools-scm==7.0.5
 # test requirements
-pytest==7.2.1
+pytest==7.2.0

requirements_dev_numpy.txt

@@ -1,4 +1,4 @@
 # Break this out into a separate file to allow testing against
 # different versions of numpy. This file should pin to the latest
 # numpy version.
-numpy==1.24.1
+numpy==1.23.5