From dcce26e6d4cdecdf7192ae1943127f381b16557c Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Thu, 12 Jan 2023 14:00:51 +0100 Subject: [PATCH 1/6] =?UTF-8?q?http://=20=E2=86=92=20https://=20(#1313)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/release.rst | 6 ++++-- notebooks/dask_copy.ipynb | 2 +- notebooks/dask_count_alleles.ipynb | 2 +- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/release.rst b/docs/release.rst index 50eb8316bf..e63e7f8c22 100644 --- a/docs/release.rst +++ b/docs/release.rst @@ -17,11 +17,10 @@ Unreleased * Fix bug that caused double counting of groups in ``groups()`` and ``group_keys()`` methods with V3 stores. By :user:`Ryan Abernathey ` :issue:`1228`. + * Handle fsspec.FSMap using FSStore store By :user:`Rafal Wojdyla ` :issue:`1304`. -.. _release_2.13.2: - Maintenance ~~~~~~~~~~~ @@ -55,6 +54,9 @@ Maintenance * Delete unused files. By :user:`John Kirkham ` :issue:`1251`. +* Uopdate web links: http:// → https:// + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1313`. + .. _release_2.13.3: diff --git a/notebooks/dask_copy.ipynb b/notebooks/dask_copy.ipynb index 5cb712508c..ba4391737a 100644 --- a/notebooks/dask_copy.ipynb +++ b/notebooks/dask_copy.ipynb @@ -33,7 +33,7 @@ "text/html": [ "\n", "
\n", - " \n", + " \n", " Loading BokehJS ...\n", "
" ] diff --git a/notebooks/dask_count_alleles.ipynb b/notebooks/dask_count_alleles.ipynb index 8ca462b232..8b9b7cec6e 100644 --- a/notebooks/dask_count_alleles.ipynb +++ b/notebooks/dask_count_alleles.ipynb @@ -26,7 +26,7 @@ "text/html": [ "\n", "
\n", - " \n", + " \n", " Loading BokehJS ...\n", "
" ] From af2600297d506778c7480b52df6d8efb9ac0bc4b Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Mon, 16 Jan 2023 14:37:22 +0100 Subject: [PATCH 2/6] 2.13.4/2.14.0 draft release notes (#1316) * 2.13.4/2.14.0 draft release notes * Correct typo * Fix headings * Fix issue markup * Fix bullet points * Re-arrange some PRs * Update docs/release.rst Co-authored-by: Sanket Verma * Update docs/release.rst Co-authored-by: Sanket Verma * Apply suggestions from code review Co-authored-by: Sanket Verma * Update docs/release.rst Co-authored-by: Sanket Verma Co-authored-by: Sanket Verma --- docs/release.rst | 120 ++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 113 insertions(+), 7 deletions(-) diff --git a/docs/release.rst b/docs/release.rst index e63e7f8c22..7ffd751696 100644 --- a/docs/release.rst +++ b/docs/release.rst @@ -6,20 +6,58 @@ Release notes # to document your changes. On releases it will be # re-indented so that it does not show up in the notes. -.. _unreleased: + .. _unreleased: -Unreleased ----------- + Unreleased + ---------- .. # .. warning:: # Pre-release! Use :command:`pip install --pre zarr` to evaluate this release. +.. _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 ` :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 ` :issue:`1228`. + +* Remove unnecessary calling of `contains_array` for key that ended in `.array.json`. + By :user:`Joe Hamman ` :issue:`1149`. + * Fix bug that caused double counting of groups in ``groups()`` and ``group_keys()`` methods with V3 stores. By :user:`Ryan Abernathey ` :issue:`1228`. -* Handle fsspec.FSMap using FSStore store - By :user:`Rafal Wojdyla ` :issue:`1304`. +Documentation +~~~~~~~~~~~~~ + +* Fix minor indexing errors in tutorial and specification examples of documentation. + By :user:`Kola Babalola ` :issue:`1277`. + +* Add `requirements_rtfd.txt` in `contributing.rst`. + By :user:`AWA BRANDON AWA ` :issue:`1243`. + +* Add documentation for find/findall using visit. + By :user:`Weddy Gikunda ` :issue:`1241`. + +* Refresh of the main landing page. + By :user:`Josh Moore ` :issue:`1173`. Maintenance ~~~~~~~~~~~ @@ -54,9 +92,77 @@ Maintenance * Delete unused files. By :user:`John Kirkham ` :issue:`1251`. -* Uopdate web links: http:// → https:// - By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1313`. +* Skip labeller for bot PRs. + By :user:`Saransh Chopra ` :issue:`1271`. + +* Restore Flake8 configuration. + By :user:`John Kirkham ` :issue:`1249`. + +* Add missing newline at EOF. + By :user:`Dimitri Papadopoulos` :issue:`1253`. + +* Add `license_files` to `pyproject.toml`. + By :user:`John Kirkham ` :issue:`1247`. + +* Adding `pyupgrade` suggestions. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1225`. + +* Fixed some linting errors. + By :user:`Weddy Gikunda ` :issue:`1226`. + +* Added the link to main website in readthedocs sidebar. + By :user:`Stephanie_nkwatoh ` :issue:`1216`. + +* Remove redundant wheel dependency in `pyproject.toml`. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1233`. + +* Turned on `isloated_build` in `tox.ini` file. + By :user:`AWA BRANDON AWA ` :issue:`1210`. + +* Fixed `flake8` alert and avoid duplication of `Zarr Developers`. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1203`. + +* Bump to NumPy 1.20+ in `environment.yml`. + By :user:`John Kirkham ` :issue:`1201`. + +* Bump to NumPy 1.20 in `pyproject.toml`. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1192`. +* Remove LGTM (`.lgtm.yml`) configuration file. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1191`. + +* Codespell will skip `fixture` in pre-commit. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1197`. + +* Add msgpack in `requirements_rtfd.txt`. + By :user:`Emmanuel Bolarinwa ` :issue:`1188`. + +* Added license to docs fixed a typo from `_spec_v2` to `_spec_v3`. + By :user:`AWA BRANDON AWA ` :issue:`1182`. + +* Fixed installation link in `README.md`. + By :user:`AWA BRANDON AWA ` :issue:`1177`. + +* Fixed typos in `installation.rst` and `release.rst`. + By :user:`Chizoba Nweke ` :issue:`1178`. + +* Set `docs/conf.py` language to `en`. + By :user:`AWA BRANDON AWA ` :issue:`1174`. + +* Added `installation.rst` to the docs. + By :user:`AWA BRANDON AWA ` :issue:`1170`. + +* Adjustment of year to `2015-2018` to `2015-2022` in the docs. + By :user:`Emmanuel Bolarinwa ` :issue:`1165`. + +* Updated `Forking the repository` section in `contributing.rst`. + By :user:`AWA BRANDON AWA ` :issue:`1171`. + +* Updated GitHub actions. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1134`. + +* Uopdate web links: `http:// → https://`. + By :user:`Dimitri Papadopoulos Orfanos ` :issue:`1313`. .. _release_2.13.3: From f0beb454f58331e50e7c34e7320e77ae89dd674e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Jan 2023 14:42:50 +0100 Subject: [PATCH 3/6] Bump pytest from 7.2.0 to 7.2.1 (#1317) Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.2.0 to 7.2.1. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/7.2.0...7.2.1) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_dev_minimal.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_minimal.txt b/requirements_dev_minimal.txt index d5e0798e86..34d7d98e7e 100644 --- a/requirements_dev_minimal.txt +++ b/requirements_dev_minimal.txt @@ -5,4 +5,4 @@ numcodecs==0.11.0 msgpack-python==0.5.6 setuptools-scm==7.1.0 # test requirements -pytest==7.2.0 +pytest==7.2.1 From bf1d37293044535d32cb6655d06cc078e66b6a37 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Jan 2023 14:43:03 +0100 Subject: [PATCH 4/6] Bump redis from 4.4.0 to 4.4.2 (#1315) Bumps [redis](https://github.com/redis/redis-py) from 4.4.0 to 4.4.2. - [Release notes](https://github.com/redis/redis-py/releases) - [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES) - [Commits](https://github.com/redis/redis-py/compare/v4.4.0...v4.4.2) --- updated-dependencies: - dependency-name: redis dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index 05cc2b8730..e44c60e9c9 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -8,7 +8,7 @@ ipywidgets==8.0.3 # don't let pyup change pinning for azure-storage-blob, need to pin to older # version to get compatibility with azure storage emulator on appveyor (FIXME) azure-storage-blob==12.14.1 # pyup: ignore -redis==4.4.0 +redis==4.4.2 types-redis types-setuptools pymongo==4.3.3 From c9fe26273511395e9b295f17d17224f2cde52f3b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Jan 2023 14:43:25 +0100 Subject: [PATCH 5/6] Bump numpy from 1.24.0 to 1.24.1 (#1311) Bumps [numpy](https://github.com/numpy/numpy) from 1.24.0 to 1.24.1. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.24.0...v1.24.1) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_dev_numpy.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_numpy.txt b/requirements_dev_numpy.txt index 6b5b91b6c8..7d373a254d 100644 --- a/requirements_dev_numpy.txt +++ b/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==1.24.0 +numpy==1.24.1 From 876ccf2cd66135d53b3962dc6120c98624ba9d3c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Jan 2023 14:43:38 +0100 Subject: [PATCH 6/6] Bump ipywidgets from 8.0.3 to 8.0.4 (#1307) Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.0.3 to 8.0.4. - [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases) - [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.0.3...8.0.4) --- updated-dependencies: - dependency-name: ipywidgets dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_dev_optional.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt index e44c60e9c9..5d7dc3398c 100644 --- a/requirements_dev_optional.txt +++ b/requirements_dev_optional.txt @@ -3,7 +3,7 @@ lmdb==1.4.0; sys_platform != 'win32' # optional library requirements for Jupyter ipytree==0.2.2 -ipywidgets==8.0.3 +ipywidgets==8.0.4 # optional library requirements for services # don't let pyup change pinning for azure-storage-blob, need to pin to older # version to get compatibility with azure storage emulator on appveyor (FIXME)