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V3 main sync merge #2340

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Oct 11, 2024
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ea90564
Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
dependabot[bot] Dec 4, 2023
79e80b3
Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
dependabot[bot] Dec 4, 2023
25dbeed
* Cache result of FSStore._fsspec_installed (#1581)
ph03 Dec 5, 2023
8579e21
Bump version of black in pre-commit (#1559)
dstansby Dec 7, 2023
54e31e9
Use list comprehension where applicable (#1555)
DimitriPapadopoulos Dec 7, 2023
7d2c9bf
Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
dependabot[bot] Dec 7, 2023
10dee6b
Use format specification mini-language to format string (#1558)
DimitriPapadopoulos Dec 7, 2023
40a6e81
Single startswith() call instead of multiple ones (#1556)
DimitriPapadopoulos Dec 7, 2023
5954ff9
Bump pymongo from 4.5.0 to 4.6.1 (#1585)
dependabot[bot] Dec 7, 2023
6ad7b0e
Move codespell options around (#1196)
DimitriPapadopoulos Dec 7, 2023
cf32382
Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
dependabot[bot] Dec 8, 2023
4d79cfc
Add type hints to zarr.create (#1536)
dstansby Dec 8, 2023
12abd4e
Remove unused mypy ignore comments (#1602)
dstansby Dec 18, 2023
c2f5f00
Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
dependabot[bot] Dec 20, 2023
490e0fe
Bump github/codeql-action from 2 to 3 (#1609)
dependabot[bot] Dec 20, 2023
b5f79dd
chore: update pre-commit hooks (#1448)
pre-commit-ci[bot] Dec 20, 2023
e09ee14
chore: update pre-commit hooks (#1618)
pre-commit-ci[bot] Dec 26, 2023
cd13989
Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
dependabot[bot] Dec 26, 2023
5fb420f
Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
dependabot[bot] Dec 27, 2023
435a7ca
Bump pytest from 7.4.3 to 7.4.4 (#1622)
dependabot[bot] Jan 1, 2024
6961fa9
chore: update pre-commit hooks (#1626)
pre-commit-ci[bot] Jan 9, 2024
ee51835
Create TEAM.md (#1628)
jhamman Jan 10, 2024
c7d66b4
Drop python 3.8 and numpy 1.20 (#1557)
joshmoore Jan 10, 2024
6ad464b
Add Norman Rzepka to core-dev team (#1630)
jhamman Jan 10, 2024
a292dc4
chore: update pre-commit hooks (#1633)
pre-commit-ci[bot] Jan 15, 2024
68c87bb
Bump actions/download-artifact from 3 to 4 (#1611)
dependabot[bot] Jan 15, 2024
1d56da0
Update tutorial.rst to include section about accessing Zip Files on S…
jeffpeck10x Jan 16, 2024
8ac8553
doc(v3): add v3 roadmap and design document (#1583)
jhamman Jan 16, 2024
a81db07
chore: update pre-commit hooks (#1636)
pre-commit-ci[bot] Jan 22, 2024
4f2ace4
Fix zarr sync (#1663)
hoodmane Feb 14, 2024
0b0ac88
Update release.rst (#1621)
MSanKeys963 Feb 14, 2024
e50b471
Bump numpy from 1.24.3 to 1.26.1 (#1543)
dependabot[bot] Feb 14, 2024
81bbb2e
chore: update pre-commit hooks (#1642)
pre-commit-ci[bot] Feb 14, 2024
3678488
Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
dependabot[bot] Feb 14, 2024
720bea6
Proper argument for numpy.reshape (#1425)
DimitriPapadopoulos Feb 14, 2024
7449853
Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
dependabot[bot] Feb 15, 2024
3db4176
docs: ZIP-related tweaks (#1641)
d-v-b Feb 15, 2024
d23683d
Bump numpy from 1.26.1 to 1.26.4 (#1669)
dependabot[bot] Feb 16, 2024
003ff33
Change occurrences of % and format() to f-strings (#1423)
DimitriPapadopoulos Feb 16, 2024
f80f697
chore: update pre-commit hooks (#1672)
pre-commit-ci[bot] Feb 20, 2024
54bc90c
Bump pymongo from 4.6.1 to 4.6.2 (#1674)
dependabot[bot] Feb 26, 2024
70a15bb
Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
dependabot[bot] Feb 26, 2024
ec4d216
Update config.yml with Zulip
joshmoore Feb 27, 2024
a0e5559
Type dimension separator (#1620)
dstansby Feb 27, 2024
99e03c6
Replace Gitter with new Zulip Chat link (#1685)
MSanKeys963 Feb 28, 2024
67d5d82
Bump redis from 5.0.1 to 5.0.2 (#1688)
dependabot[bot] Mar 1, 2024
9c2a412
Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
dependabot[bot] Mar 4, 2024
237f934
Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
dependabot[bot] Mar 5, 2024
240bb82
Fix RTD build (#1694)
MSanKeys963 Mar 6, 2024
a1fbedb
Update release.rst for v2.17.1 (#1673)
MSanKeys963 Mar 6, 2024
d986f89
Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
dependabot[bot] Mar 9, 2024
d642da6
Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
dependabot[bot] Mar 10, 2024
029cff7
docs(tutorial.rst): fix link to GCSMap (#1689)
DahnJ Mar 10, 2024
9fc4981
Update installation.rst stating version support policy (#1665)
MSanKeys963 Mar 10, 2024
f58065b
Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
dependabot[bot] Mar 11, 2024
bbac254
Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
dependabot[bot] Mar 13, 2024
6fe553d
Bump redis from 5.0.2 to 5.0.3 (#1698)
dependabot[bot] Mar 13, 2024
f4f0b42
Add Python 3.12 to CI (#1719)
jhamman Mar 25, 2024
04e862c
Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
dependabot[bot] Mar 25, 2024
0e58b79
chore: update pre-commit hooks (#1708)
pre-commit-ci[bot] Mar 25, 2024
8d0d910
chore: update pre-commit hooks (#1723)
pre-commit-ci[bot] Mar 25, 2024
2534413
Fix release notes (following #1719) (#1725)
jhamman Mar 27, 2024
bad8dd0
Override ipython repr methods. (#1724)
dcherian Mar 27, 2024
37e0a1a
Bump pymongo from 4.6.2 to 4.6.3 (#1729)
dependabot[bot] Mar 28, 2024
cb5b77a
Remove v1 and v2 specification (#1582)
MSanKeys963 Mar 29, 2024
97cb3a7
chore: update pre-commit hooks (#1738)
pre-commit-ci[bot] Apr 1, 2024
6ef6714
Optimize Array.info and Group.info (#1733)
dcherian Apr 2, 2024
9864b40
Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
dependabot[bot] Apr 2, 2024
aa9a0d5
Couple fixes (#1737)
DimitriPapadopoulos Apr 2, 2024
d0fb875
Fix tests with Pytest 8 (#1714)
dstansby Apr 3, 2024
bcb7684
Avoid redundant __contains__ (#1739)
dcherian Apr 4, 2024
0cfd2be
Array & Group: Use already loaded attributes to populate cache. (#1734)
dcherian Apr 5, 2024
62910bc
Optimize attribute setting (#1741)
dcherian Apr 5, 2024
5fde3a2
Make sure fs exceptions are raised if not MissingFs exceptions (clone…
itcarroll Apr 5, 2024
1631c10
chore(release): update changelog for 2.17.2 (#1775)
jhamman Apr 5, 2024
6105ef2
chore(docs): reset release notes as unreleased (#1776)
jhamman Apr 6, 2024
5d566eb
Bump codecov/codecov-action from 3 to 4 (#1647)
dependabot[bot] Apr 22, 2024
b98f694
Update release.rst for v2.17.2 (#1778)
MSanKeys963 Apr 22, 2024
dd3dd96
Deprecate the experimental v3 implementation (#1802)
jhamman Apr 22, 2024
0a29fb3
chore: update pre-commit hooks (#1779)
pre-commit-ci[bot] Apr 22, 2024
9d046ea
Fix `is_total_slice` for size-1 dimensions (#1800)
dcherian Apr 22, 2024
60b53b0
add note to the top of the release page noting the plan for 2.18.* an…
jhamman Apr 25, 2024
f4f6e86
Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
dependabot[bot] Apr 29, 2024
29b4acc
dep(docs): deprecate experimental v3 support in docs (#1807)
jhamman Apr 30, 2024
7fa17b8
Bump h5py from 3.10.0 to 3.11.0 (#1786)
dependabot[bot] May 2, 2024
9331430
Bump redis from 5.0.3 to 5.0.4 (#1810)
dependabot[bot] May 2, 2024
2f29144
deprecate(stores): add deprecation warnings to stores that we plan to…
jhamman May 6, 2024
863c3c0
use np.inf instead of PINF/NINF (#1842)
jhamman May 7, 2024
360eb53
chore: update pre-commit hooks (#1825)
pre-commit-ci[bot] May 7, 2024
270aff1
Enable ruff/bugbear rules (B) and fix issues (#1702)
DimitriPapadopoulos May 7, 2024
056657c
Release notes for 2.18.0 (#1843)
jhamman May 7, 2024
cb4230d
Update release.rst (#1850)
jhamman May 8, 2024
8979205
Group dependabot updates (#1854)
jhamman May 13, 2024
8264ace
chore: update pre-commit hooks (#1876)
pre-commit-ci[bot] May 14, 2024
908e920
Fix a regression with scalar indexing due to #1800 (#1875)
dcherian May 16, 2024
4bd9764
release notes for 2.18.1 (#1885)
jhamman May 17, 2024
bf89533
reset release notes (#1886)
jhamman May 17, 2024
3e98c3b
Add zstd to old V3 supported codecs (#1914)
rabernat May 26, 2024
0855bd6
doc: update release notes for 2.18.2 (#1915)
jhamman May 26, 2024
a054afb
Drop support for Python 3.9
dstansby Aug 10, 2024
5437386
Revert "Drop support for Python 3.9"
dstansby Aug 10, 2024
6888c59
Update TEAM.md (#2071)
jhamman Aug 11, 2024
c72d0e2
[v2] Fix doctests with numpy 2.0 (#2073)
dstansby Aug 14, 2024
f231bb2
Fix version number in built docs (#2044)
dstansby Aug 14, 2024
11fd8db
Fix orthogonal indexing with scalar. (#1947)
dcherian Aug 14, 2024
ee43bb8
Bump the requirements group across 1 directory with 7 updates (#2092)
dependabot[bot] Aug 16, 2024
addc39d
Bump the actions group with 2 updates (#2087)
dependabot[bot] Aug 16, 2024
c5c4698
[v2] Drop support for Python 3.9 (#2074)
dstansby Aug 17, 2024
35e8106
Fix Array.__array__ for numpy 2.1 (#2106)
dstansby Aug 23, 2024
025e103
Bump test version of numcodecs (#2114)
dstansby Aug 26, 2024
d1b92b5
fix: numpy 1.24 compat for Array.__array__ (#2123)
jhamman Aug 26, 2024
2e928b1
Deprecate N5Store (#2103)
jhamman Aug 26, 2024
5bf57bd
Run tests on numpy 1.23 (#2124)
dstansby Aug 26, 2024
9e0b5e8
Bump the requirements group across 1 directory with 3 updates (#2129)
dependabot[bot] Aug 27, 2024
cc2cdee
chore: bump minimum numpy version to 1.24 (#2127)
jhamman Aug 27, 2024
cb2c669
Remove un-needed package installs in CI (#2095)
dstansby Aug 29, 2024
6656d1a
Bump the actions group with 2 updates (#2146)
dependabot[bot] Sep 2, 2024
f1978dd
Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
dependabot[bot] Sep 4, 2024
88b2100
chore(docs): update release notes ahead of 2.18.4 (#2152)
jhamman Sep 5, 2024
aa9da2b
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions…
dependabot[bot] Sep 9, 2024
774f5b1
[docs] remove primary sidebar from tutorial (#2142)
sneakers-the-rat Sep 10, 2024
e1d98cd
Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
dependabot[bot] Sep 11, 2024
a011079
Bump pypa/gh-action-pypi-publish in the actions group (#2220)
dependabot[bot] Sep 24, 2024
53f600b
Update TEAM.md (#2227)
jhamman Sep 24, 2024
a9abbe7
Bump the requirements group across 1 directory with 3 updates (#2284)
dependabot[bot] Oct 1, 2024
559c2e3
Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
dependabot[bot] Oct 2, 2024
6b9ab9e
Fix low contrast box titles (#2287) (#2292)
dstansby Oct 2, 2024
f175de4
Bump pypa/gh-action-pypi-publish in the actions group (#2304)
dependabot[bot] Oct 7, 2024
a1dfd01
Bump the requirements group with 2 updates (#2303)
dependabot[bot] Oct 7, 2024
eaf5d7a
Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
dependabot[bot] Oct 10, 2024
0e52e52
Merge branch 'main' of https://github.com/zarr-developers/zarr-python…
jhamman Oct 11, 2024
7bcb92b
remove zarr.types from v2
jhamman Oct 11, 2024
437234a
Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…
jhamman Oct 11, 2024
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ body:
attributes:
label: Python Version
description: Version of Python interpreter
placeholder: 3.8.5, 3.9, 3.10, etc.
placeholder: 3.10, 3.11, 3.12 etc.
validations:
required: true
- type: input
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2 changes: 1 addition & 1 deletion .github/workflows/releases.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ jobs:
submodules: true
fetch-depth: 0

- uses: actions/setup-python@v5
- uses: actions/setup-python@v5.2.0
name: Install Python
with:
python-version: '3.11'
Expand Down
2 changes: 1 addition & 1 deletion LICENSE.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
The MIT License (MIT)

Copyright (c) 2015-2023 Zarr Developers <https://github.com/zarr-developers>
Copyright (c) 2015-2024 Zarr Developers <https://github.com/zarr-developers>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
Expand Down
6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -70,10 +70,10 @@
</td>
</tr>
<tr>
<td>Gitter</td>
<td>Zulip</td>
<td>
<a href="https://gitter.im/zarr-developers/community">
<img src="https://badges.gitter.im/zarr-developers/community.svg" />
<a href="https://ossci.zulipchat.com/">
<img src="https://img.shields.io/badge/zulip-join_chat-brightgreen.svg" />
</a>
</td>
</tr>
Expand Down
29 changes: 29 additions & 0 deletions TEAM.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
## Active core-developers
- @joshmoore (Josh Moore)
- @jni (Juan Nunez-Iglesias)
- @rabernat (Ryan Abernathey)
- @jhamman (Joe Hamman)
- @d-v-b (Davis Bennett)
- @jakirkham (jakirkham)
- @martindurant (Martin Durant)
- @normanrz (Norman Rzepka)
- @dstansby (David Stansby)
- @dcherian (Deepak Cherian)
- @TomAugspurger (Tom Augspurger)

## Emeritus core-developers
- @alimanfoo (Alistair Miles)
- @shoyer (Stephan Hoyer)
- @ryan-williams (Ryan Williams)
- @jrbourbeau (James Bourbeau)
- @mzjp2 (Zain Patel)
- @grlee77 (Gregory Lee)

## Former core-developers
- @jeromekelleher (Jerome Kelleher)
- @tjcrone (Tim Crone)
- @funkey (Jan Funke)
- @shikharsg
- @Carreau (Matthias Bussonnier)
- @dazzag24
- @WardF (Ward Fisher)
16 changes: 6 additions & 10 deletions docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,8 @@

import sphinx.application

# 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.
from importlib.metadata import version as get_version

import zarr
import sphinx

Expand Down Expand Up @@ -79,12 +76,11 @@

# General information about the project.
project = "zarr"
copyright = "2023, Zarr Developers"
copyright = "2024, Zarr Developers"
author = "Zarr Developers"

version = zarr.__version__
# The full version, including alpha/beta/rc tags.
release = zarr.__version__
version = get_version("zarr")
release = get_version("zarr")

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
Expand Down Expand Up @@ -205,7 +201,7 @@ def setup(app: sphinx.application.Sphinx) -> None:
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
# html_sidebars = {}
html_sidebars = {"tutorial": []}

# Additional templates that should be rendered to pages, maps page names to
# template names.
Expand Down
4 changes: 2 additions & 2 deletions docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,13 @@ Zarr-Python

**Version**: |version|

**Download documentation**: `PDF/Zipped HTML/EPUB <https://readthedocs.org/projects/zarr/downloads/>`_
**Download documentation**: `PDF/Zipped HTML <https://readthedocs.org/projects/zarr/downloads/>`_

**Useful links**:
`Installation <installation.html>`_ |
`Source Repository <https://github.com/zarr-developers/zarr-python>`_ |
`Issue Tracker <https://github.com/zarr-developers/zarr-python/issues>`_ |
`Gitter <https://gitter.im/zarr-developers/community>`_
`Zulip Chat <https://ossci.zulipchat.com/>`_

Zarr is a file storage format for chunked, compressed, N-dimensional arrays based on an open-source specification.

Expand Down
5 changes: 5 additions & 0 deletions docs/installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,11 @@ Zarr depends on NumPy. It is generally best to `install NumPy
appropriate for your operating system and Python distribution. Other dependencies should be
installed automatically if using one of the installation methods below.

Note: Zarr has endorsed `Scientific-Python SPEC 0 <https://scientific-python.org/specs/spec-0000/>`_ and now follows the version support window as outlined below:

- Python: 36 months after initial release
- Core package dependencies (e.g. NumPy): 24 months after initial release

Install Zarr from PyPI::

$ pip install zarr
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33 changes: 33 additions & 0 deletions docs/release.rst
Original file line number Diff line number Diff line change
Expand Up @@ -303,6 +303,39 @@ Documentation
* doc: update release notes for 3.0.0.alpha.
By :user:`Joe Hamman <jhamman>` :issue:`1959`.

.. _release_2.18.3:

2.18.3
------

Enhancements
~~~~~~~~~~~~
* Added support for creating a copy of data when converting a `zarr.Array`
to a numpy array.
By :user:`David Stansby <dstansby>` (:issue:`2106`) and
:user:`Joe Hamman <jhamman>` (:issue:`2123`).

Maintenance
~~~~~~~~~~~
* Removed support for Python 3.9.
By :user:`David Stansby <dstansby>` (:issue:`2074`).

* Fix a regression when using orthogonal indexing with a scalar.
By :user:`Deepak Cherian <dcherian>` :issue:`1931`

* Added compatibility with NumPy 2.1.
By :user:`David Stansby <dstansby>`

* Bump minimum NumPy version to 1.24.
:user:`Joe Hamman <jhamman>` (:issue:`2127`).

Deprecations
~~~~~~~~~~~~

* Deprecate :class:`zarr.n5.N5Store` and :class:`zarr.n5.N5FSStore`. These
stores are slated to be removed in Zarr Python 3.0.
By :user:`Joe Hamman <jhamman>` :issue:`2085`.

.. _release_2.18.2:

2.18.2
Expand Down
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