Remove Python 3.8 and add Python 3.13 (#240)

* Update tox.ini * Update requirements-min.txt * Update HDMF_dev.yaml * Update check_external_links.yml * Update run_all_tests.yml * Update run_coverage.yml * Update run_tests.yml * Update bug_report.yml * Update requirements-min.txt * Update requirements-min.txt * Update requirements-min.txt * Update requirements-min.txt * Update pyproject.toml * Update HDMF_dev.yaml * Update HDMF_dev.yaml * Update pyproject.toml * Update requirements-min.txt * Update requirements-min.txt * Update requirements.txt * Update requirements-min.txt * Update pyproject.toml * Update CHANGELOG.md * Update requirements.txt * Update pyproject.toml * Update CHANGELOG.md * Update pyproject.toml * Update requirements-dev.txt * Update requirements-dev.txt --------- Co-authored-by: Ryan Ly <[email protected]>
hdmf-dev · Nov 23, 2024 · 3d08b60 · 3d08b60
1 parent 6fd9d53
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -62,11 +62,11 @@ body:
     attributes:
       label: Python Version
       options:
-        - "3.8"
         - "3.9"
         - "3.10"
         - "3.11"
         - "3.12"
+        - "3.13"
     validations:
       required: true
   - type: textarea

diff --git a/.github/workflows/HDMF_dev.yaml b/.github/workflows/HDMF_dev.yaml
@@ -16,10 +16,10 @@ jobs:
         with:
             fetch-depth: 0  # tags are required for versioneer to determine the version
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install HDMF_Zarr Requirements
         run: |

diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install Sphinx dependencies and package
         run: |

diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -22,30 +22,30 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
           - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           - { name: linux-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-optional    , test-tox-env: py312-optional  , build-tox-env: build-py312-optional  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.12-prerelease  , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: ubuntu-latest }
-          - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: windows-latest }
-          - { name: windows-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: windows-latest }
+          - { name: linux-python3.13             , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-optional    , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-prerelease  , test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: windows-latest }
           - { name: windows-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: windows-latest }
           - { name: windows-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
           - { name: windows-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: windows-latest } 
-          - { name: windows-python3.12-optional  , test-tox-env: py312-optional  , build-tox-env: build-py312-optional  , python-ver: "3.12", os: windows-latest }
-          - { name: windows-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: windows-latest }
-          - { name: windows-python3.12-prerelease, test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: windows-latest }
-          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: macos-latest }
-          - { name: macos-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-latest }
+          - { name: windows-python3.13           , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: windows-latest } 
+          - { name: windows-python3.13-optional  , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-prerelease, test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: macos-latest }
           - { name: macos-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: macos-latest }
           - { name: macos-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
           - { name: macos-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.12-optional    , test-tox-env: py312-optional  , build-tox-env: build-py312-optional  , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.12-prerelease  , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.13             , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-optional    , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-prerelease  , test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -88,15 +88,15 @@ jobs:
       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 }
+          - { name: linux-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-gallery-python3.9-minimum    , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-gallery-python3.13-upgraded  , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: windows-latest }
+          - { name: windows-gallery-python3.13-prerelease, test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: windows-latest }
+          - { name: macos-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: macos-latest }
+          - { name: macos-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -132,14 +132,14 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: conda-linux-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.8" , os: ubuntu-latest }
           - { name: conda-linux-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           - { name: conda-linux-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }          
-          - { name: conda-linux-python3.12-optional  , test-tox-env: py312-optional  , build-tox-env: build-py312-optional  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-linux-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
-          - { name: conda-linux-python3.12-prerelease, test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }  
+          - { name: conda-linux-python3.13           , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }          
+          - { name: conda-linux-python3.13-optional  , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-prerelease, test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -28,7 +28,7 @@ jobs:
           - { os: macos-latest  , opt_req: false }
     env:
       OS: ${{ matrix.os }}
-      PYTHON: '3.12'
+      PYTHON: '3.13'
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -19,14 +19,14 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.13             , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
-          - { name: linux-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest , upload-wheels: true }
-          - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: windows-latest }
-          - { name: windows-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: windows-latest }
-          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: macos-latest }
-          - { name: macos-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: macos-latest }
+          - { name: linux-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest , upload-wheels: true }
+          - { name: windows-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -76,10 +76,10 @@ jobs:
       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: 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: linux-gallery-python3.9-minimum    , test-tox-env: gallery-py39-minimum  , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-gallery-python3.13-upgraded  , test-tox-env: gallery-py313-upgraded, python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-gallery-python3.9-minimum  , test-tox-env: gallery-py39-minimum  , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-gallery-python3.13-upgraded, test-tox-env: gallery-py313-upgraded, python-ver: "3.13", os: windows-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -114,8 +114,8 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: conda-linux-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -172,7 +172,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.13'
 
       - name: Download wheel and source distributions from artifact
         uses: actions/download-artifact@v4

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@
 * Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly [#214](https://github.com/hdmf-dev/hdmf-zarr/pull/214)
 * Add `force_overwite` parameter for `ZarrIO.__init__` to allow overwriting an existing file or directory. @oruebel [#229](https://github.com/hdmf-dev/hdmf-zarr/pull/229)
 * Remove allowance of `hdmf.Array` in `__init__` of `AbstractZarrTableDataset` and `ZarrDataset` to be compatible with HDMF 4.0. @rly [#236](https://github.com/hdmf-dev/hdmf-zarr/pull/236)
+* Remove support for python 3.8. @mavaylon1 [#240](https://github.com/hdmf-dev/hdmf-zarr/pull/240)
 
 ### Bug Fixes
 * Fix reading of cached specs and caching of specs during export. @rly [#232](https://github.com/hdmf-dev/hdmf-zarr/pull/232)

diff --git a/pyproject.toml b/pyproject.toml
@@ -10,11 +10,10 @@ authors = [
 ]
 description = "A package defining a Zarr I/O backend for HDMF"
 readme = "README.rst"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {text = "BSD"}
 classifiers = [
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -30,9 +29,9 @@ classifiers = [
 ]
 dependencies = [
     'hdmf>=3.14.5',
-    'zarr>=2.11.0, <3.0', # pin below 3.0 until HDMF-zarr supports zarr 3.0
+    'zarr>=2.18.0, <3.0', # pin below 3.0 until HDMF-zarr supports zarr 3.0
     'numpy>=1.24',
-    'numcodecs>=0.9.1',
+    'numcodecs>=0.10.0',
     'pynwb>=2.8.3',
     'threadpoolctl>=3.1.0',
 ]

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -5,11 +5,11 @@
 #
 black==24.3.0
 codespell==2.2.6
-coverage==7.3.2
+coverage==7.6.7
 hdf5plugin==4.3.0  # hdf5plugin is used to test conversion of plugin filters
 pre-commit==3.5.0
-pytest==7.4.3
-pytest-cov==4.1.0
+pytest==8.3.3
+pytest-cov==6.0.0
 python-dateutil==2.8.2
 ruff==0.1.3
 tox==4.11.3
diff --git a/requirements-min.txt b/requirements-min.txt
@@ -1,7 +1,6 @@
-hdmf==3.14.2
-zarr==2.11.0
-numcodecs==0.9.1
-pynwb==2.5.0
+hdmf==3.14.5
+zarr==2.13.0
+numcodecs==0.10.0
+pynwb==2.8.3
 setuptools
-importlib_resources;python_version<'3.9' # Remove when python 3.9 becomes the new minimum
 threadpoolctl==3.1.0