From 5a8e910dc95bf192ab6ebfeb59293a292fa668cf Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 19 Jun 2024 14:27:22 -0400 Subject: [PATCH] Bump numpy (#474) * bump numpy * Update assess-file-changes.yml * Update testing.yml to install h5py with ROS3 first (#475) * Update testing.yml * add zarr to minimal * adjust dev workflow * remove past versions --------- Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> --------- Co-authored-by: Ryan Ly --- .github/workflows/assess-file-changes.yml | 2 +- .github/workflows/deploy-tests.yml | 5 --- .github/workflows/dev-gallery.yml | 6 ++-- .github/workflows/testing.yml | 10 ++---- .github/workflows/version-gallery.yml | 37 ----------------------- requirements.txt | 3 +- 6 files changed, 7 insertions(+), 56 deletions(-) delete mode 100644 .github/workflows/version-gallery.yml diff --git a/.github/workflows/assess-file-changes.yml b/.github/workflows/assess-file-changes.yml index 402e7f99c..38fa258bb 100644 --- a/.github/workflows/assess-file-changes.yml +++ b/.github/workflows/assess-file-changes.yml @@ -36,7 +36,7 @@ jobs: echo "::set-output name=TESTING_CHANGED::false" for file in ${{ steps.changed-files.outputs.all_changed_files }}; do echo $file - if [[ $file == "src/nwbinspector/"* || $file == "requirements"* || $file == "setup.py" || $file == "tests/"* ]] + if [[ $file == "src/nwbinspector/"* || $file == "requirements.txt" || $file == "setup.py" || $file == "tests/"* ]] then echo "Source changed" echo "::set-output name=SOURCE_CHANGED::true" diff --git a/.github/workflows/deploy-tests.yml b/.github/workflows/deploy-tests.yml index 8f56cfab5..2a83be23e 100644 --- a/.github/workflows/deploy-tests.yml +++ b/.github/workflows/deploy-tests.yml @@ -41,11 +41,6 @@ jobs: if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }} uses: ./.github/workflows/streaming-tests.yml - run-past-gallery: - needs: assess-file-changes - if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }} - uses: ./.github/workflows/version-gallery.yml - run-dev-gallery: needs: assess-file-changes if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }} diff --git a/.github/workflows/dev-gallery.yml b/.github/workflows/dev-gallery.yml index c55d1c860..de828e651 100644 --- a/.github/workflows/dev-gallery.yml +++ b/.github/workflows/dev-gallery.yml @@ -16,6 +16,8 @@ jobs: - uses: actions/checkout@v3 - run: git fetch --prune --unshallow --tags + - name: Install ROS3 + run: conda install -c conda-forge h5py - name: Install pytest run: | pip install pytest @@ -28,10 +30,6 @@ jobs: run: | dandi download "https://gui-staging.dandiarchive.org/#/dandiset/204919" python -c "from nwbinspector.testing import update_testing_config; update_testing_config(key='LOCAL_PATH', value='./204919/testing_files/')" - - name: Uninstall h5py - run: pip uninstall -y h5py - - name: Install ROS3 - run: conda install -c conda-forge h5py - name: Run pytest with coverage run: pytest -rsx diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 27165cc61..73f9aaf7d 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -28,20 +28,14 @@ jobs: pip install pytest pip install pytest-cov + - name: Install ROS3 + run: conda install -c conda-forge h5py - name: Install package run: pip install ".[dandi]" - name: Download testing data and set config path run: | dandi download "https://gui-staging.dandiarchive.org/#/dandiset/204919" python -c "from nwbinspector.testing import update_testing_config; update_testing_config(key='LOCAL_PATH', value='./204919/testing_files/')" - - name: Uninstall h5py - run: pip uninstall -y h5py - - name: Install ROS3 - run: conda install -c conda-forge h5py - - name: Install HDMF-zarr # temporary - run: pip install hdmf-zarr - - name: Install latest HDMF # temporary - run: pip install -U hdmf - name: Run pytest with coverage run: | diff --git a/.github/workflows/version-gallery.yml b/.github/workflows/version-gallery.yml deleted file mode 100644 index d7a6213a2..000000000 --- a/.github/workflows/version-gallery.yml +++ /dev/null @@ -1,37 +0,0 @@ -name: Past PyNWB Version -on: - schedule: - - cron: "0 0 * * *" # daily - workflow_call: - -jobs: - build-and-test: - name: Testing against past PyNWB versions - runs-on: ubuntu-latest - strategy: - fail-fast: false - matrix: - pynwb-version: ["2.1.0", "2.0.0"] - steps: - - uses: s-weigand/setup-conda@v1 - with: - update-conda: true - python-version: 3.9 - conda-channels: conda-forge - - uses: actions/checkout@v3 - - run: git fetch --prune --unshallow --tags - - name: Install pytest - run: | - pip install pytest - pip install pytest-cov - - name: Install package - run: | - pip install -e ".[dandi]" - pip install pynwb==${{ matrix.pynwb-version }} - - name: Download testing data and set config path - run: | - dandi download "https://gui-staging.dandiarchive.org/#/dandiset/204919" - python -c "from nwbinspector.testing import update_testing_config; update_testing_config(key='LOCAL_PATH', value='./204919/testing_files/')" - - - name: Run pytest with coverage - run: pytest -rsx diff --git a/requirements.txt b/requirements.txt index 6a44b416e..53f62a427 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,5 @@ pynwb +hdmf-zarr fsspec s3fs requests @@ -11,4 +12,4 @@ click tqdm isodate numpy>=1.20.0,<1.21.0;python_version<'3.8' -numpy>=1.22.0;python_version>='3.8' # PyNWB usually has some upper bound here, though +numpy>=1.22.0,<2.0.0;python_version>='3.8'