Update versioneer and CI (#786)

hdmf-dev · Nov 10, 2022 · ccc5c25 · ccc5c25
1 parent 35dab0f
commit ccc5c25
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diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -9,25 +9,26 @@ jobs:
  check-external-links:
  runs-on: ubuntu-latest
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - 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@v3
  with:
  submodules: 'recursive'
+ fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: '3.10'
 
  - name: Install Sphinx dependencies and package
  run: |
  python -m pip install --upgrade pip
- python -m pip install -r requirements-doc.txt -r requirements.txt
+ python -m pip install -r requirements-doc.txt
  python -m pip install .
 
  - name: Check Sphinx external links

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -16,7 +16,7 @@ jobs:
  fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: '3.10'
 
@@ -43,7 +43,7 @@ jobs:
  run: |
  python -m pip install twine
  ls -1 dist
- # twine upload --repository testpypi -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
+ # twine upload --repository-url https://test.pypi.org/legacy/ -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
  twine upload -u ${{ secrets.BOT_PYPI_USER }} -p ${{ secrets.BOT_PYPI_PASSWORD }} --skip-existing dist/*
 
  - name: Publish wheel and source distributions as a GitHub release

diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -23,36 +23,40 @@ jobs:
  matrix:
  include:
  - { name: linux-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- - { name: linux-python3.7 , test-tox-env: py37 , build-tox-env: build-py37 , python-ver: "3.7" , os: ubuntu-latest }
  - { 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: windows-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: windows-latest }
- - { name: windows-python3.7 , test-tox-env: py37 , build-tox-env: build-py37 , 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: macos-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: macos-latest }
- - { name: macos-python3.7 , test-tox-env: py37 , build-tox-env: build-py37 , 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 }
  steps:
+ - name: Cancel non-latest runs
+ uses: styfle/[email protected]
+ with:
+ all_but_latest: true
+ access_token: ${{ github.token }}
+
  - uses: actions/checkout@v3
  with:
  submodules: 'recursive'
+ fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-ver }}
 
@@ -95,17 +99,19 @@ jobs:
  - { 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 }
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - 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@v3
  with:
  submodules: 'recursive'
+ fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-ver }}
 
@@ -130,22 +136,23 @@ 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-python3.7 , test-tox-env: py37 , build-tox-env: build-py37 , python-ver: "3.7" , os: ubuntu-latest }
  - { 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 }
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - 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@v3
  with:
  submodules: 'recursive'
+ fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Conda
  uses: conda-incubator/setup-miniconda@v2

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -30,18 +30,19 @@ jobs:
  OS: ${{ matrix.os }}
  PYTHON: '3.10'
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - 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@v3
  with:
  submodules: 'recursive'
+ fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: '3.10'
 

diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml
@@ -5,26 +5,27 @@ jobs:
  run-flake8:
  runs-on: ubuntu-latest
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
- with:
- all_but_latest: true
- access_token: ${{ github.token }}
+  - 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@v3
- with:
- submodules: 'recursive'
+ - uses: actions/checkout@v3
+ with:
+ submodules: 'recursive'
+ fetch-depth: 0 # tags are required for versioneer to determine the version
 
- - name: Set up Python
- uses: actions/setup-python@v3
- with:
- python-version: '3.10'
+  - name: Set up Python
+  uses: actions/setup-python@v4
+  with:
+  python-version: '3.10'
 
- - name: Install flake8
- run: |
- python -m pip install --upgrade pip
- python -m pip install flake8
- python -m pip list
+  - name: Install flake8
+  run: |
+  python -m pip install --upgrade pip
+  python -m pip install flake8
+  python -m pip list
 
- - name: Run flake8
- run: flake8
+  - name: Run flake8
+  run: flake8
diff --git a/.github/workflows/run_pynwb_tests.yml b/.github/workflows/run_pynwb_tests.yml
@@ -9,20 +9,21 @@ jobs:
  run-tests:
  runs-on: ubuntu-latest
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - 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@v3
  with:
  submodules: 'recursive'
+ fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
- python-version: '3.9'
+ python-version: '3.10'
 
  - name: Update pip
  run: python -m pip install --upgrade pip

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -20,7 +20,6 @@ jobs:
  matrix:
  include:
  - { name: linux-python3.7-minimum , test-tox-env: py37-minimum , build-tox-env: build-py37-minimum , python-ver: "3.7" , os: ubuntu-latest }
- - { name: linux-python3.7 , test-tox-env: py37 , build-tox-env: build-py37 , python-ver: "3.7" , os: ubuntu-latest }
  - { name: linux-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", 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 }
@@ -29,8 +28,8 @@ jobs:
  - { 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-python3.10-upgraded , test-tox-env: py310-upgraded , build-tox-env: build-py310-upgraded , python-ver: "3.10", os: macos-latest }
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - name: Cancel non-latest runs
+ uses: styfle/cancel-workflow-action@0.11.0
  with:
  all_but_latest: true
  access_token: ${{ github.token }}
@@ -41,7 +40,7 @@ jobs:
  fetch-depth: 0 # tags are required for versioneer to determine the version
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-ver }}
 
@@ -86,17 +85,18 @@ jobs:
  - { 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 }
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - 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@v3
  with:
  submodules: 'recursive'
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-ver }}
 
@@ -123,9 +123,10 @@ jobs:
  - { 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 }
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - 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@v3
@@ -167,9 +168,10 @@ jobs:
  if: ${{ github.event_name == 'push' }}
  runs-on: ubuntu-latest
  steps:
- - name: Cancel any previous incomplete runs
- uses: styfle/cancel-workflow-action@0.9.1
+ - name: Cancel non-latest runs
+ uses: styfle/cancel-workflow-action@0.11.0
  with:
+ all_but_latest: true
  access_token: ${{ github.token }}
 
  - name: Checkout repo with submodules
@@ -178,7 +180,7 @@ jobs:
  submodules: 'recursive'
 
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: '3.10'
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,9 @@
 
 ## HDMF 3.4.7 (November 9, 2022)
 
+### Minor improvements
+- Update CI, versioneer, and some requirements. @rly ([#786](https://github.com/hdmf-dev/hdmf/pull/786))
+
 ### Bug fixes
 - Fix an issue where not providing an optional argument to `__init__` of an auto-generated `MultiContainerInterface`
  class raised an error. @rly ([#779](https://github.com/hdmf-dev/hdmf/pull/779))

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -5,7 +5,6 @@ coverage==6.4.2
 flake8==5.0.4
 flake8-debugger==4.1.2
 flake8-print==5.0.0
-importlib-metadata==4.2.0 # there may be compatibility issues with newer versions
 pytest==7.1.2
 pytest-cov==3.0.0
 python-dateutil==2.8.2

diff --git a/requirements.txt b/requirements.txt
@@ -2,8 +2,11 @@
 # note that python 3.7 end of life is 27 Jun 2023
 h5py==3.7.0
 jsonschema==4.9.1
-numpy==1.21.5 # note that numpy 1.22 dropped python 3.7 support
-pandas==1.3.5 # note that pandas 1.4 dropped python 3.7 support
+numpy==1.23.3;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==1.3.5;python_version<'3.8' # note that pandas 1.4 dropped python 3.7 support
 ruamel.yaml==0.17.21
-scipy==1.7.3 # note that scipy 1.8 dropped python 3.7 support
-setuptools==63.4.1
+scipy==1.9.3;python_version>='3.8'
+scipy==1.7.3;python_version<'3.8' # note that scipy 1.8 dropped python 3.7 support
+setuptools==65.4.1
diff --git a/setup.cfg b/setup.cfg
@@ -2,8 +2,7 @@
 VCS = git
 versionfile_source = src/hdmf/_version.py
 versionfile_build = hdmf/_version.py
-style = pep440-pre
-tag_prefix = *.*.*
+tag_prefix = ''
 
 [flake8]
 max-line-length = 120

diff --git a/src/hdmf/__init__.py b/src/hdmf/__init__.py
@@ -20,9 +20,8 @@ def get_region_slicer(**kwargs):
  return None
 
 
-from ._version import get_versions # noqa: E402
-__version__ = get_versions()['version']
-del get_versions
+from . import _version # noqa: F401,E402
+__version__ = _version.get_versions()['version']
 
 
 from ._due import due, BibTeX # noqa: E402