Update CI to fix deprecation issues, update dev install instructions (#…

…1594)
NeurodataWithoutBorders · Nov 30, 2022 · a1af42d · a1af42d
1 parent c1afdc1
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Showing 13 changed files with 90 additions and 66 deletions.
diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
@@ -9,8 +9,8 @@ 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 }}
@@ -21,7 +21,7 @@ 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: '3.8'  # allensdk requires 3.8
 

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'
 

diff --git a/.github/workflows/generate_test_files.yml b/.github/workflows/generate_test_files.yml
@@ -23,7 +23,7 @@ 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-version }}
 

diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -44,13 +44,19 @@ jobs:
           - { 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 }}
 
@@ -100,17 +106,18 @@ 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'
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-ver }}
 
@@ -142,9 +149,10 @@ jobs:
           - { 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
@@ -194,9 +202,10 @@ jobs:
           - { name: windows-python3.9-ros3, python-ver: "3.9", os: windows-latest }
           - { name: macos-python3.9-ros3  , python-ver: "3.9", 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
@@ -239,9 +248,10 @@ jobs:
           - { name: windows-gallery-python3.9-ros3, python-ver: "3.9", os: windows-latest }
           - { name: macos-gallery-python3.9-ros3  , python-ver: "3.9", 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

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -26,8 +26,8 @@ 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 }}
@@ -38,9 +38,9 @@ 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: '3.9'
+          python-version: '3.10'
 
       - name: Install dependencies
         run: |

diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml
@@ -5,27 +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'
-        fetch-depth: 0  # tags are required for versioneer to determine the version
+      - 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_inspector_tests.yml b/.github/workflows/run_inspector_tests.yml
@@ -9,8 +9,8 @@ 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 }}
@@ -21,9 +21,9 @@ 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: '3.9'
+          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
@@ -25,8 +25,8 @@ jobs:
           - { name: windows-python3.7-minimum    , test-tox-env: py37-minimum    , build-tox-env: build-py37-minimum    , python-ver: "3.7" , 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 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 }}
@@ -37,7 +37,7 @@ 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 }}
 
@@ -85,17 +85,18 @@ jobs:
           - { name: windows-gallery-python3.8-upgraded , test-tox-env: gallery-py38-upgraded , python-ver: "3.8" , 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 }}
 
@@ -122,9 +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
@@ -172,9 +174,10 @@ jobs:
         include:
           - { name: linux-python3.9-ros3  , python-ver: "3.9", 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
@@ -215,9 +218,10 @@ jobs:
         include:
           - { name: linux-gallery-python3.9-ros3  , python-ver: "3.9", 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
@@ -252,9 +256,10 @@ 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
@@ -263,7 +268,7 @@ 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/.readthedocs.yaml b/.readthedocs.yaml
@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-20.04
+  tools:
+    python: '3.8'
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
@@ -18,7 +23,6 @@ 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
@@ -5,6 +5,7 @@
 ### Enhancements and minor changes
 - `Subject.age` can be input as a `timedelta`. @bendichter [#1590](https://github.com/NeurodataWithoutBorders/pynwb/pull/1590)
 - Remove redundant object mapper code. @rly [#1600](https://github.com/NeurodataWithoutBorders/pynwb/pull/1600)
+- Fix pending deprecations and issues in CI. @rly [#1594](https://github.com/NeurodataWithoutBorders/pynwb/pull/1594)
 
 ### Documentation and tutorial enhancements:
 - Adjusted [ecephys tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/domain/ecephys.html) to create fake data with proper dimensions @bendichter [#1581](https://github.com/NeurodataWithoutBorders/pynwb/pull/1581)

diff --git a/docs/source/install_developers.rst b/docs/source/install_developers.rst
@@ -76,11 +76,12 @@ Install from Git repository
 ---------------------------
 
 After you have created and activated a virtual environment, clone the PyNWB git repository from GitHub, install the
-package requirements using the `pip <https://pip.pypa.io/en/stable/>`_ Python package manager, and install PyNWB in editable mode.
+package requirements using the `pip <https://pip.pypa.io/en/stable/>`_ Python package manager, and install PyNWB in
+editable mode.
 
 .. code::
 
-   $ git clone --recurse-submodules git@github.com:NeurodataWithoutBorders/pynwb.git
+   $ git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git
    $ cd pynwb
    $ pip install -r requirements.txt
    $ pip install -e .
@@ -94,7 +95,7 @@ virtualenv or conda environment.
 
 .. code::
 
-   $ git clone --recurse-submodules git@github.com:NeurodataWithoutBorders/pynwb.git
+   $ git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git
    $ cd pynwb
    $ pip install -r requirements.txt -r requirements-dev.txt
    $ pip install -e .
@@ -123,12 +124,15 @@ FAQ
 1.  I am using a git cloned copy of PyNWB and getting the error:
     ``RuntimeError: Unable to load a TypeMap - no namespace file found``
 
+    or the error:
+    ``RuntimeError: 'core' is not a registered namespace.``
+
     - The PyNWB repo uses git submodules that have to be checked out when cloning the repos. Please make sure you
       are using the ``--recurse-submodules`` flag when running ``git clone``:
 
       .. code-block:: bash
 
-          git clone --recurse-submodules git@github.com:NeurodataWithoutBorders/pynwb.git
+          git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git
 
       You can also run the following on your existing cloned repo.
 

diff --git a/setup.cfg b/setup.cfg
@@ -1,4 +1,3 @@
-
 [versioneer]
 VCS = git
 versionfile_source = src/pynwb/_version.py