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Add testing for python 3.11, update reqs #1687

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merged 6 commits into from
Apr 12, 2023
Merged

Add testing for python 3.11, update reqs #1687

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fed6b0b
Add testing for python 3.11, update reqs
rly Apr 12, 2023
eb5c1db
Update changelog
rly Apr 12, 2023
0417f70
Update changelog
rly Apr 12, 2023
1397b27
Fix tox error
rly Apr 12, 2023
fe79499
Fix pandas2 int32 int64 win incompatibility
rly Apr 12, 2023
7ea13b7
Test windows-py3.11-upgraded on PR
rly Apr 12, 2023
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1 change: 1 addition & 0 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,7 @@ body:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
validations:
required: true
- type: textarea
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/check_external_links.yml
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Expand Up @@ -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: |
Expand Down
6 changes: 3 additions & 3 deletions .github/workflows/deploy_release.yml
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Expand Up @@ -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: |
Expand All @@ -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
Expand Down
52 changes: 28 additions & 24 deletions .github/workflows/run_all_tests.yml
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Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/run_coverage.yml
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Expand Up @@ -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]
Expand All @@ -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: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/run_flake8.yml
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Expand Up @@ -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: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/run_inspector_tests.yml
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Expand Up @@ -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
Expand Down
15 changes: 8 additions & 7 deletions .github/workflows/run_tests.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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
Expand Down
5 changes: 5 additions & 0 deletions CHANGELOG.md
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@@ -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
Expand Down
2 changes: 1 addition & 1 deletion docs/source/conf.py
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Expand Up @@ -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),
Expand Down
2 changes: 1 addition & 1 deletion docs/source/install_developers.rst
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Expand Up @@ -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


Expand Down
2 changes: 1 addition & 1 deletion docs/source/install_users.rst
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Expand Up @@ -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.
Expand Down
10 changes: 5 additions & 5 deletions environment-ros3.yml
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Expand Up @@ -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
6 changes: 3 additions & 3 deletions requirements.txt
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@@ -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
1 change: 1 addition & 0 deletions setup.py
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Expand Up @@ -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",
Expand Down
4 changes: 2 additions & 2 deletions tests/integration/hdf5/test_nwbfile.py
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Expand Up @@ -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')
Expand All @@ -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']))
Expand Down
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