Add testing for python 3.11, update reqs (#1687)

NeurodataWithoutBorders · Apr 12, 2023 · 1d1d142 · 1d1d142
1 parent de7f474
commit 1d1d142
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Showing 17 changed files with 96 additions and 75 deletions.
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -64,6 +64,7 @@ body:
         - "3.8"
         - "3.9"
         - "3.10"
+        - "3.11"
     validations:
       required: true
   - type: textarea

diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'  # allensdk requires 3.8
+          python-version: '3.11'
 
       - 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@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install build dependencies
         run: |
@@ -28,11 +28,11 @@ jobs:
 
       - name: Run tox tests
         run: |
-          tox -e py310-upgraded
+          tox -e py311-upgraded
 
       - name: Build wheel and source distribution
         run: |
-          tox -e build-py310-upgraded
+          tox -e build-py311-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
@@ -26,23 +26,26 @@ jobs:
           - { name: linux-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , 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-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.10-optional    , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.10-prerelease  , test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, 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: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: windows-latest }
           - { name: windows-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , 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-python3.10-optional  , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: windows-latest }
-          - { name: windows-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: windows-latest }
-          - { name: windows-python3.10-prerelease, test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, 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: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
           - { name: macos-python3.8              , test-tox-env: py38            , build-tox-env: build-py38            , 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-python3.10-optional    , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: macos-latest }
-          - { name: macos-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: macos-latest }
-          - { name: macos-python3.10-prerelease  , test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -90,14 +93,14 @@ jobs:
       matrix:
         include:
           - { name: linux-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.10-upgraded    , test-tox-env: gallery-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-gallery-python3.10-prerelease  , test-tox-env: gallery-py310-prerelease, python-ver: "3.10", 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: windows-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: windows-latest }
-          - { name: windows-gallery-python3.10-upgraded  , test-tox-env: gallery-py310-upgraded  , python-ver: "3.10", os: windows-latest }
-          - { name: windows-gallery-python3.10-prerelease, test-tox-env: gallery-py310-prerelease, python-ver: "3.10", 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: macos-gallery-python3.7-minimum      , test-tox-env: gallery-py37-minimum    , python-ver: "3.7" , os: macos-latest }
-          - { name: macos-gallery-python3.10-upgraded    , test-tox-env: gallery-py310-upgraded  , python-ver: "3.10", os: macos-latest }
-          - { name: macos-gallery-python3.10-prerelease  , test-tox-env: gallery-py310-prerelease, python-ver: "3.10", 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -138,9 +141,10 @@ jobs:
           - { name: conda-linux-python3.8            , test-tox-env: py38            , build-tox-env: build-py38            , 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-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
-          - { name: conda-linux-python3.10-optional  , test-tox-env: py310-optional  , build-tox-env: build-py310-optional  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: conda-linux-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: conda-linux-python3.10-prerelease, test-tox-env: py310-prerelease, build-tox-env: build-py310-prerelease, 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -195,9 +199,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.10-ros3  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: windows-python3.10-ros3, python-ver: "3.10", os: windows-latest }
-          - { name: macos-python3.10-ros3  , python-ver: "3.10", os: macos-latest }
+          - { name: linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: windows-python3.11-ros3, python-ver: "3.11", os: windows-latest }
+          - { name: macos-python3.11-ros3  , python-ver: "3.11", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -241,9 +245,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.10-ros3  , python-ver: "3.10", os: ubuntu-latest }
-          - { name: windows-gallery-python3.10-ros3, python-ver: "3.10", os: windows-latest }
-          - { name: macos-gallery-python3.10-ros3  , python-ver: "3.10", os: macos-latest }
+          - { name: linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
+          - { name: windows-gallery-python3.11-ros3, python-ver: "3.11", os: windows-latest }
+          - { name: macos-gallery-python3.11-ros3  , python-ver: "3.11", os: macos-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
@@ -24,7 +24,7 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
     env:
       OS: ${{ matrix.os }}
-      PYTHON: '3.10'
+      PYTHON: '3.11'
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -40,7 +40,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: ${{ env.PYTHON }}
 
       - name: Install dependencies
         run: |

diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml
@@ -19,7 +19,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install flake8
         run: |

diff --git a/.github/workflows/run_inspector_tests.yml b/.github/workflows/run_inspector_tests.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Update pip
         run: python -m pip install --upgrade pip

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -21,8 +21,9 @@ jobs:
         include:
           - { name: linux-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
-          - { name: linux-python3.10-upgraded    , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", os: ubuntu-latest , upload-wheels: true }
+          - { 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: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , 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: macos-python3.7-minimum      , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: macos-latest }
     steps:
       - name: Cancel non-latest runs
@@ -78,9 +79,9 @@ jobs:
       matrix:
         include:
           - { name: linux-gallery-python3.7-minimum    , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.10-upgraded  , test-tox-env: gallery-py310-upgraded, python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-gallery-python3.11-upgraded  , test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: ubuntu-latest }
           - { name: windows-gallery-python3.7-minimum  , test-tox-env: gallery-py37-minimum  , python-ver: "3.7" , os: windows-latest }
-          - { name: windows-gallery-python3.10-upgraded, test-tox-env: gallery-py310-upgraded, python-ver: "3.10", os: windows-latest }
+          - { name: windows-gallery-python3.11-upgraded, test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: windows-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -118,7 +119,7 @@ jobs:
       matrix:
         include:
           - { name: conda-linux-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: conda-linux-python3.10-upgraded  , test-tox-env: py310-upgraded  , build-tox-env: build-py310-upgraded  , python-ver: "3.10", 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 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -173,7 +174,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.10-ros3  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -217,7 +218,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-gallery-python3.10-ros3  , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-gallery-python3.11-ros3  , python-ver: "3.11", os: ubuntu-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -275,7 +276,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Download wheel and source distributions from artifact
         uses: actions/download-artifact@v3

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # PyNWB Changelog
 
+## PyNWB 2.3.3 (Upcoming)
+
+### Enhancements and minor changes
+- Add testing support for Python 3.11. @rly [#1687](https://github.com/NeurodataWithoutBorders/pynwb/pull/1687)
+
 ## PyNWB 2.3.2 (April 10, 2023)
 
 ### Enhancements and minor changes

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -137,7 +137,7 @@ def __call__(self, filename):
 }
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3.10', None),
+    'python': ('https://docs.python.org/3.11', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
     'matplotlib': ('https://matplotlib.org/stable/', None),
     'h5py': ('https://docs.h5py.org/en/latest/', None),

diff --git a/docs/source/install_developers.rst b/docs/source/install_developers.rst
@@ -6,7 +6,7 @@ Installing PyNWB for Developers
 
 PyNWB has the following minimum requirements, which must be installed before you can get started using PyNWB.
 
-#. Python 3.7, 3.8, 3.9, or 3.10
+#. Python 3.7, 3.8, 3.9, 3.10, or 3.11
 #. pip
 
 

diff --git a/docs/source/install_users.rst b/docs/source/install_users.rst
@@ -6,7 +6,7 @@ Installing PyNWB
 
 PyNWB has the following minimum requirements, which must be installed before you can get started using PyNWB.
 
-#. Python 3.7, 3.8, 3.9, or 3.10
+#. Python 3.7, 3.8, 3.9, 3.10, or 3.11
 #. pip
 
 .. note:: If you are a developer then please see the :ref:`install_developers` installation instructions instead.

diff --git a/environment-ros3.yml b/environment-ros3.yml
@@ -4,12 +4,12 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python==3.10
+  - python==3.11
   - h5py==3.8.0
-  - hdmf==3.5.1
+  - hdmf==3.5.4
   - matplotlib==3.7.1
-  - numpy==1.23.3
-  - pandas==1.5.0
+  - numpy==1.24.2
+  - pandas==2.0.0
   - python-dateutil==2.8.2
   - setuptools
-  - dandi==0.51.0  # NOTE: dandi does not support osx-arm64
+  - dandi==0.52.0  # NOTE: dandi does not support osx-arm64
diff --git a/requirements.txt b/requirements.txt
@@ -1,9 +1,9 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
-h5py==3.7.0
+h5py==3.8.0
 hdmf==3.5.4
-numpy==1.23.3; python_version >= "3.8"
+numpy==1.24.2; python_version >= "3.8"
 numpy==1.21.5; python_version < "3.8"  # note that numpy 1.22 dropped python 3.7 support
-pandas==1.5.0; python_version >= "3.8"
+pandas==2.0.0; python_version >= "3.8"
 pandas==1.3.5; python_version < "3.8"  # note that pandas 1.4 dropped python 3.7 support
 python-dateutil==2.8.2
 setuptools==65.5.1
diff --git a/setup.py b/setup.py
@@ -51,6 +51,7 @@
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "License :: OSI Approved :: BSD License",
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",

diff --git a/tests/integration/hdf5/test_nwbfile.py b/tests/integration/hdf5/test_nwbfile.py
@@ -340,7 +340,7 @@ def test_df_comparison(self):
                                [(4, 1, tsa)]],
                 'tags': [[''], [''], ['fizz', 'buzz'], ['qaz']]
             },
-            index=pd.Index(np.arange(4), name='id')
+            index=pd.Index(np.arange(4, dtype=np.int64), name='id')
         )
         # pop the timeseries column out because ts_obt has rows of lists of tuples and ts_exp has rows of lists of lists
         ts_obt = df_obt.pop('timeseries')
@@ -367,7 +367,7 @@ def test_df_comparison_no_ts(self):
                 'stop_time': [0.25, 0.30, 0.40, 0.45],
                 'tags': [[''], [''], ['fizz', 'buzz'], ['qaz']]
             },
-            index=pd.Index(np.arange(4), name='id')
+            index=pd.Index(np.arange(4, dtype=np.int64), name='id')
         )
 
         df_obt = self.read_container.to_dataframe(exclude=set(['timeseries', 'timeseries_index']))