Fix broken CI (#1566)

NeurodataWithoutBorders · Oct 11, 2022 · 083b950 · 083b950
1 parent 6e1f131
commit 083b950
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diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -18,6 +18,7 @@ jobs:
       - 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
@@ -27,7 +28,7 @@ jobs:
       - 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/generate_test_files.yml b/.github/workflows/generate_test_files.yml
@@ -19,6 +19,7 @@ jobs:
       - 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

diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -23,23 +23,20 @@ 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 }
@@ -50,6 +47,7 @@ jobs:
       - 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
@@ -137,7 +135,6 @@ 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 }

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -35,6 +35,7 @@ jobs:
       - 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

diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml
@@ -14,6 +14,7 @@ jobs:
     - 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

diff --git a/.github/workflows/run_inspector_tests.yml b/.github/workflows/run_inspector_tests.yml
@@ -18,6 +18,7 @@ jobs:
       - 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

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 }

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -18,6 +18,7 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
+  version: "3.8"
   install:
     - requirements: requirements-doc.txt
     - requirements: requirements.txt

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,9 +1,10 @@
 # PyNWB Changelog
 
-## PyNWB 2.2.0 (October 3, 2022)
+## PyNWB 2.2.0 (October 11, 2022)
 
 ### Internal enhancements:
-- Moved CI to GitHub Actions. @rly [#1560](https://github.com/NeurodataWithoutBorders/pynwb/pull/1560)
+- Moved CI to GitHub Actions. @rly [#1560](https://github.com/NeurodataWithoutBorders/pynwb/pull/1560),
+  [#1566](https://github.com/NeurodataWithoutBorders/pynwb/pull/1566)
 
 ### Bug fixes
 - Fixed bug in ``pynwb.testing.mock.file.mock_NWBFile`` to identifier UUID to string. @oruebel

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -2,10 +2,9 @@
 # compute coverage, and create test environments
 codecov==2.1.12
 coverage==6.4.2
-flake8==5.0.4
+flake8==5.0.4;
 flake8-debugger==4.1.2
 flake8-print==5.0.0
-importlib-metadata==4.2.0
 pytest==7.1.2
 pytest-cov==3.0.0
 tox==3.25.1
diff --git a/requirements-doc.txt b/requirements-doc.txt
@@ -4,7 +4,7 @@ sphinx>=4  # improved support for docutils>=0.17
 sphinx_rtd_theme>=1  # <1 does not work with docutils>=0.17
 matplotlib
 sphinx-gallery
-allensdk>=2.11.0  # python 3.8 is not supported in allensdk<2.11
+allensdk>=2.13.2  # allensdk <=2.13.1 requires pynwb<2
 MarkupSafe==2.0.1  # resolve incompatibility between jinja2 and markupsafe: https://github.com/AllenInstitute/AllenSDK/issues/2308
 Pillow
 sphinx-copybutton

diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,9 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
 h5py==3.7.0
-hdmf==3.4.2
-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
+hdmf==3.4.6
+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
 python-dateutil==2.8.2
-setuptools==63.4.1
+setuptools==65.4.1
diff --git a/setup.cfg b/setup.cfg
@@ -5,8 +5,7 @@ universal = 1
 VCS = git
 versionfile_source = src/pynwb/_version.py
 versionfile_build = pynwb/_version.py
-style = pep440-pre
-tag_prefix = *.*.*
+tag_prefix = ''
 
 [flake8]
 max-line-length = 120
@@ -38,4 +37,4 @@ per-file-ignores =
 extend-ignore = E203
 
 [metadata]
-description-file = README.rst
+description_file = README.rst
diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py
@@ -310,9 +310,8 @@ def export(self, **kwargs):
 from hdmf.data_utils import DataChunkIterator  # noqa: F401,E402
 from hdmf.backends.hdf5 import H5DataIO  # noqa: F401,E402
 
-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
 due.cite(BibTeX("""