Update to support python 3.12 (#172)

* Update tox.ini * Update pyproject.toml * Update HDMF_dev.yaml * Update check_external_links.yml * Update black.yml * Update deploy_release.yml * Update run_all_tests.yml * Update run_coverage.yml * Update run_tests.yml * Update conf.py * Update bug_report.yml * Update test_gallery.py * Update requirements-min.txt * Update pyproject.toml * Update test_gallery.py * Update pyproject.toml * Update tox.ini * Update CHANGELOG.md
hdmf-dev · Mar 11, 2024 · 897d3b9 · 897d3b9
1 parent 556ed12
commit 897d3b9
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Showing 14 changed files with 102 additions and 76 deletions.
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -66,6 +66,7 @@ body:
         - "3.9"
         - "3.10"
         - "3.11"
+        - "3.12"
     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 3.11
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install HDMF_Zarr Requirements
         run: |

diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -6,8 +6,8 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3.2.0
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
     - uses: pre-commit/[email protected]
       with:
         extra_args: black
diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -15,14 +15,14 @@ jobs:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install Sphinx dependencies and package
         run: |

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install build dependencies
         run: |
@@ -28,11 +28,11 @@ jobs:
 
       - name: Run tox tests
         run: |
-          tox -e py311-upgraded
+          tox -e py312-upgraded
 
       - name: Build wheel and source distribution
         run: |
-          tox -e build-py311-upgraded
+          tox -e build-py312-upgraded
           ls -1 dist
 
       - name: Test installation from a wheel

diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -26,37 +26,40 @@ jobs:
           - { name: linux-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , 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-python3.11-optional    , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-python3.11-prerelease  , test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, 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: 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-python3.11-optional  , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: windows-latest }
-          - { name: windows-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: windows-latest }
-          - { name: windows-python3.11-prerelease, test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, 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: 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-python3.11-optional    , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: macos-latest }
-          - { name: macos-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: macos-latest }
-          - { name: macos-python3.11-prerelease  , test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - 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@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -86,28 +89,28 @@ jobs:
       matrix:
         include:
           - { name: linux-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.11-upgraded    , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: linux-gallery-python3.11-prerelease  , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", 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-python3.11-upgraded  , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: windows-latest }
-          - { name: windows-gallery-python3.11-prerelease, test-tox-env: gallery-py311-prerelease, python-ver: "3.11", 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-python3.11-upgraded    , test-tox-env: gallery-py311-upgraded  , python-ver: "3.11", os: macos-latest }
-          - { name: macos-gallery-python3.11-prerelease  , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", 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/[email protected]
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - 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@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -133,17 +136,18 @@ jobs:
           - { name: conda-linux-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
           - { name: conda-linux-python3.10           , 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-python3.11-optional  , test-tox-env: py311-optional  , build-tox-env: build-py311-optional  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.11-prerelease, test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required for versioneer to determine the version

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -28,20 +28,20 @@ jobs:
           - { os: macos-latest  , opt_req: false }
     env:
       OS: ${{ matrix.os }}
-      PYTHON: '3.11'
+      PYTHON: '3.12'
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PYTHON }}
 

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -20,27 +20,27 @@ jobs:
       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-python3.11             , 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 }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
-          - { name: linux-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", os: ubuntu-latest , upload-wheels: true }
+          - { 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-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", 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-python3.11-upgraded    , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - 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@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -77,22 +77,22 @@ jobs:
       matrix:
         include:
           - { name: linux-gallery-python3.8-minimum    , test-tox-env: gallery-py38-minimum  , python-ver: "3.8" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.11-upgraded  , test-tox-env: gallery-py311-upgraded, python-ver: "3.11", 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-python3.11-upgraded, test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: windows-latest }
+          - { name: windows-gallery-python3.12-upgraded, test-tox-env: gallery-py312-upgraded, python-ver: "3.12", os: windows-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -115,15 +115,15 @@ jobs:
       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-python3.11-upgraded  , test-tox-env: py311-upgraded  , build-tox-env: build-py311-upgraded  , python-ver: "3.11", 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
         with:
           all_but_latest: true
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required for versioneer to determine the version
@@ -165,12 +165,12 @@ jobs:
           access_token: ${{ github.token }}
 
       - name: Checkout repo with submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # HDMF-ZARR Changelog
 
+## 0.7.0 (Upcoming)
+### Enhancements
+* Added support for python 3.12. @mavaylon1 [#172](https://github.com/hdmf-dev/hdmf-zarr/pull/172)
+
 ## 0.6.0 (February 21, 2024)
 
 ### Enhancements

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -75,7 +75,7 @@
 }
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3.11', None),
+    'python': ('https://docs.python.org/3.12', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/', None),
     'matplotlib': ('https://matplotlib.org/stable/', None),

diff --git a/pyproject.toml b/pyproject.toml
@@ -18,6 +18,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: BSD License",
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",

diff --git a/requirements-min.txt b/requirements-min.txt
@@ -1,4 +1,4 @@
-hdmf==3.9.0
+hdmf==3.12.0
 zarr==2.11.0
 numcodecs==0.9.1
 pynwb==2.5.0

diff --git a/test_gallery.py b/test_gallery.py
@@ -73,6 +73,9 @@ def _import_from_file(script):
     r"\nPyarrow will become a required dependency of pandas.*"
 )
 
+_deprecation_warning_datetime = (
+    r"datetime.datetime.utcfromtimestamp() *"
+)
 
 def run_gallery_tests():
     global TOTAL, FAILURES, ERRORS
@@ -135,6 +138,10 @@ def run_gallery_tests():
                     # this warning is triggered from pandas
                     "ignore", message=_deprecation_warning_pandas_pyarrow_re, category=DeprecationWarning
                 )
+                warnings.filterwarnings(
+                    # this is triggered from datetime
+                    "ignore", message=_deprecation_warning_datetime, category=DeprecationWarning
+                )
                 _import_from_file(script_abs)
         except Exception:
             print(traceback.format_exc())