From a7dcfca00673b16048b19efd60be6556343d10b9 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:07:15 -0700 Subject: [PATCH 01/14] Create gallery.yaml --- .github/workflows/gallery.yaml | 55 ++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 .github/workflows/gallery.yaml diff --git a/.github/workflows/gallery.yaml b/.github/workflows/gallery.yaml new file mode 100644 index 00000000..812d9cb2 --- /dev/null +++ b/.github/workflows/gallery.yaml @@ -0,0 +1,55 @@ +name: Run all tests +on: + schedule: + - cron: '0 5 * * *' # once per day at midnight ET + push: + tags: # run only on new tags that follow semver + - '/^[0-9]+(\.[0-9]+)?(\.[0-9]+)?$/' + workflow_dispatch: + +jobs: + run-all-gallery-tests: + name: ${{ matrix.name }} + runs-on: ${{ matrix.os }} + defaults: + run: + shell: bash + strategy: + fail-fast: false + matrix: + include: + - { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } + - { name: linux-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } + - { name: linux-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: ubuntu-latest } + # - { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest } + # - { name: windows-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: windows-latest } + # - { name: windows-gallery-python3.12-prerelease, test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: windows-latest } + # - { name: macos-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: macos-latest } + # - { name: macos-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: macos-latest } + # - { name: macos-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: macos-latest } + steps: + - name: Cancel non-latest runs + uses: styfle/cancel-workflow-action@0.11.0 + with: + all_but_latest: true + access_token: ${{ github.token }} + + - uses: actions/checkout@v4 + with: + submodules: 'recursive' + fetch-depth: 0 # tags are required for versioneer to determine the version + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-ver }} + + - name: Install build dependencies + run: | + python -m pip install --upgrade pip + python -m pip install tox + python -m pip list + + - name: Run tox tests + run: | + tox -e ${{ matrix.test-tox-env }} From 70c48f703aaa2a54ab916801ba5b5c4a8378964f Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:11:33 -0700 Subject: [PATCH 02/14] Update requirements.txt --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 338c96f2..6b7cb6aa 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR -hdmf==3.14.2 +hdmf==3.14.3 zarr==2.16.1 pynwb==2.5.0 numpy==2.0.0 From 797637ee369388271a357b5a3bfb779957de4832 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:17:48 -0700 Subject: [PATCH 03/14] Update requirements.txt --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 6b7cb6aa..a5ab3395 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR hdmf==3.14.3 zarr==2.16.1 -pynwb==2.5.0 +# pynwb==2.5.0 numpy==2.0.0 numcodecs==0.12.1 threadpoolctl==3.2.0 From 9e23997e1edbd99fe2dfc17cac074bc63db5461d Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:31:36 -0700 Subject: [PATCH 04/14] Delete .github/workflows/gallery.yaml --- .github/workflows/gallery.yaml | 55 ---------------------------------- 1 file changed, 55 deletions(-) delete mode 100644 .github/workflows/gallery.yaml diff --git a/.github/workflows/gallery.yaml b/.github/workflows/gallery.yaml deleted file mode 100644 index 812d9cb2..00000000 --- a/.github/workflows/gallery.yaml +++ /dev/null @@ -1,55 +0,0 @@ -name: Run all tests -on: - schedule: - - cron: '0 5 * * *' # once per day at midnight ET - push: - tags: # run only on new tags that follow semver - - '/^[0-9]+(\.[0-9]+)?(\.[0-9]+)?$/' - workflow_dispatch: - -jobs: - run-all-gallery-tests: - name: ${{ matrix.name }} - runs-on: ${{ matrix.os }} - defaults: - run: - shell: bash - strategy: - fail-fast: false - matrix: - include: - - { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } - - { name: linux-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } - - { name: linux-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: ubuntu-latest } - # - { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest } - # - { name: windows-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: windows-latest } - # - { name: windows-gallery-python3.12-prerelease, test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: windows-latest } - # - { name: macos-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: macos-latest } - # - { name: macos-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: macos-latest } - # - { name: macos-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: macos-latest } - steps: - - name: Cancel non-latest runs - uses: styfle/cancel-workflow-action@0.11.0 - with: - all_but_latest: true - access_token: ${{ github.token }} - - - uses: actions/checkout@v4 - with: - submodules: 'recursive' - fetch-depth: 0 # tags are required for versioneer to determine the version - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-ver }} - - - name: Install build dependencies - run: | - python -m pip install --upgrade pip - python -m pip install tox - python -m pip list - - - name: Run tox tests - run: | - tox -e ${{ matrix.test-tox-env }} From 9368f1223387a6a431ab6d3c4b3b13997a77c270 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:36:52 -0700 Subject: [PATCH 05/14] Update requirements.txt --- requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/requirements.txt b/requirements.txt index a5ab3395..72a58944 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR -hdmf==3.14.3 -zarr==2.16.1 +#hdmf==3.14.3 +#zarr==2.16.1 # pynwb==2.5.0 -numpy==2.0.0 -numcodecs==0.12.1 -threadpoolctl==3.2.0 +#numpy==2.0.0 +#numcodecs==0.12.1 +#threadpoolctl==3.2.0 From d21f6910e8d41fdcdb9fc5cbcd9529d9b1cd5c0e Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:40:22 -0700 Subject: [PATCH 06/14] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 199a0f56..ec8bab9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ classifiers = [ dependencies = [ 'hdmf>=3.14.3', 'zarr>=2.11.0, <3.0', # pin below 3.0 until HDMF-zarr supports zarr 3.0 - 'numpy>=1.24', + 'numpy>=1.26', 'numcodecs>=0.9.1', 'pynwb>=2.5.0', 'threadpoolctl>=3.1.0', From 2d52e034708f7203663d92144f9614d624fdd96f Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:44:33 -0700 Subject: [PATCH 07/14] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ec8bab9e..199a0f56 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ classifiers = [ dependencies = [ 'hdmf>=3.14.3', 'zarr>=2.11.0, <3.0', # pin below 3.0 until HDMF-zarr supports zarr 3.0 - 'numpy>=1.26', + 'numpy>=1.24', 'numcodecs>=0.9.1', 'pynwb>=2.5.0', 'threadpoolctl>=3.1.0', From f6b5fe014b545bb83c764f0062426e975c61f739 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:45:20 -0700 Subject: [PATCH 08/14] Update requirements.txt --- requirements.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/requirements.txt b/requirements.txt index 72a58944..6b7cb6aa 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR -#hdmf==3.14.3 -#zarr==2.16.1 -# pynwb==2.5.0 -#numpy==2.0.0 -#numcodecs==0.12.1 -#threadpoolctl==3.2.0 +hdmf==3.14.3 +zarr==2.16.1 +pynwb==2.5.0 +numpy==2.0.0 +numcodecs==0.12.1 +threadpoolctl==3.2.0 From e984ef0df55471a67dd8a1204eeae9b43c692f59 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:45:35 -0700 Subject: [PATCH 09/14] Update requirements-dev.txt --- requirements-dev.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index 0fd19af4..b9f3efc2 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -12,4 +12,5 @@ pytest==7.4.3 pytest-cov==4.1.0 python-dateutil==2.8.2 ruff==0.1.3 -tox==4.11.3 \ No newline at end of file +tox==4.11.3 +numpy==2.0.0 From 5bee95192e95242f97b18ff065f73bc427225fec Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:50:18 -0700 Subject: [PATCH 10/14] Update requirements-doc.txt --- requirements-doc.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements-doc.txt b/requirements-doc.txt index 4b921319..462e5822 100644 --- a/requirements-doc.txt +++ b/requirements-doc.txt @@ -4,3 +4,4 @@ sphinx>=4 # improved support for docutils>=0.17 sphinx_rtd_theme>=1 # <1 does not work with docutils>=0.17 sphinx-gallery sphinx-copybutton +numpy==2.0 From 8331a5aed29025bb6cce5afe89873c1a18609abe Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Wed, 21 Aug 2024 09:54:08 -0700 Subject: [PATCH 11/14] Update requirements-doc.txt --- requirements-doc.txt | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/requirements-doc.txt b/requirements-doc.txt index 462e5822..3f80ea45 100644 --- a/requirements-doc.txt +++ b/requirements-doc.txt @@ -1,7 +1,2 @@ # dependencies to generate the documentation for HDMF-Zarr -matplotlib -sphinx>=4 # improved support for docutils>=0.17 -sphinx_rtd_theme>=1 # <1 does not work with docutils>=0.17 -sphinx-gallery -sphinx-copybutton -numpy==2.0 + From d1b557b059ba2c386eef435eef376c57dc6e5f43 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 7 Nov 2024 16:31:33 -0500 Subject: [PATCH 12/14] Update all requirements except dev --- requirements-dev.txt | 1 - requirements-doc.txt | 6 +++++- requirements-opt.txt | 6 +++--- requirements.txt | 12 ++++++------ 4 files changed, 14 insertions(+), 11 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index b9f3efc2..047125eb 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -13,4 +13,3 @@ pytest-cov==4.1.0 python-dateutil==2.8.2 ruff==0.1.3 tox==4.11.3 -numpy==2.0.0 diff --git a/requirements-doc.txt b/requirements-doc.txt index 3f80ea45..4b921319 100644 --- a/requirements-doc.txt +++ b/requirements-doc.txt @@ -1,2 +1,6 @@ # dependencies to generate the documentation for HDMF-Zarr - +matplotlib +sphinx>=4 # improved support for docutils>=0.17 +sphinx_rtd_theme>=1 # <1 does not work with docutils>=0.17 +sphinx-gallery +sphinx-copybutton diff --git a/requirements-opt.txt b/requirements-opt.txt index 771f5d04..6fc3bcb0 100644 --- a/requirements-opt.txt +++ b/requirements-opt.txt @@ -1,3 +1,3 @@ -tqdm==4.66.4 -fsspec==2024.6.0 -s3fs==2024.6.0 +tqdm==4.67.0 +fsspec==2024.10.0 +s3fs==2024.10.0 diff --git a/requirements.txt b/requirements.txt index 6b7cb6aa..840b4815 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR -hdmf==3.14.3 -zarr==2.16.1 -pynwb==2.5.0 -numpy==2.0.0 -numcodecs==0.12.1 -threadpoolctl==3.2.0 +hdmf==3.14.5 +zarr==2.18.3 +pynwb==2.8.2 +numpy==2.1.3 +numcodecs==0.13.1 +threadpoolctl==3.5.0 From ebedf8b83770da564ad08f6ceeda7bc9a887b7e1 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 7 Nov 2024 16:38:16 -0500 Subject: [PATCH 13/14] Update rtd config --- .readthedocs.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f57db3ed..8d6ffb00 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,9 +6,9 @@ version: 2 build: - os: ubuntu-20.04 + os: ubuntu-22.04 tools: - python: '3.9' + python: '3.12' # Build documentation in the docs/ directory with Sphinx sphinx: From 82202bda72739ae909569292a8d009ed304e7750 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 7 Nov 2024 16:41:25 -0500 Subject: [PATCH 14/14] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 78b5742d..ecf61732 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,7 @@ ## 1.0.0 (Upcoming) ### Enhancements * Added support for Pathlib paths. @mavaylon1 [#212](https://github.com/hdmf-dev/hdmf-zarr/pull/212) +* Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly [#214](https://github.com/hdmf-dev/hdmf-zarr/pull/214) ## 0.9.0 (September 16, 2024) ### Enhancements