diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml index 731f3968d..95b32f068 100644 --- a/.github/workflows/testing_dev.yml +++ b/.github/workflows/testing_dev.yml @@ -74,6 +74,12 @@ jobs: - name: Install GUIDE run: npm ci --verbose + - name: Install testing dependencies + run: pip install pytest pytest-cov + + - name: Manually remove matplotlib + run: pip uninstall matplotlib --yes + - if: matrix.os != 'ubuntu-latest' name: Run tests run: npm run test:coverage diff --git a/.github/workflows/testing_dev_with_live_services.yml b/.github/workflows/testing_dev_with_live_services.yml index b44c90c8d..1e2e90042 100644 --- a/.github/workflows/testing_dev_with_live_services.yml +++ b/.github/workflows/testing_dev_with_live_services.yml @@ -76,6 +76,12 @@ jobs: - name: Install GUIDE run: npm ci --verbose + - name: Install testing dependencies + run: pip install pytest pytest-cov + + - name: Manually remove matplotlib + run: pip uninstall matplotlib --yes + - name: Create env file run: | touch .env diff --git a/.github/workflows/testing_flask_build_and_dist.yml b/.github/workflows/testing_flask_build_and_dist.yml index 83f483cf5..401a7470e 100644 --- a/.github/workflows/testing_flask_build_and_dist.yml +++ b/.github/workflows/testing_flask_build_and_dist.yml @@ -79,7 +79,14 @@ jobs: with: node-version: "20" - - run: npm ci --verbose + - name: Install GUIDE + run: npm ci --verbose + + - name: Install testing dependencies + run: pip install pytest pytest-cov + + - name: Manually remove matplotlib + run: pip uninstall matplotlib --yes # Fix for macos build - remove bad sonpy file - if: matrix.os == 'macos-latest' || matrix.os == 'macos-13' diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml index f8e5022e9..c39f258d5 100644 --- a/.github/workflows/testing_pipelines.yml +++ b/.github/workflows/testing_pipelines.yml @@ -72,6 +72,12 @@ jobs: - name: Install GUIDE run: npm ci --verbose + - name: Install testing dependencies + run: pip install pytest pytest-cov + + - name: Manually remove matplotlib + run: pip uninstall matplotlib --yes + # Load example data caches - name: Get ephy_testing_data current head hash id: ephys diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml index ea486f110..91e201373 100644 --- a/environments/environment-Linux.yml +++ b/environments/environment-Linux.yml @@ -15,10 +15,7 @@ dependencies: - flask == 2.3.2 - flask-cors == 4.0.0 - flask_restx == 1.1.0 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - dandi >= 0.60.0 - - pytest == 7.4.0 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling diff --git a/environments/environment-MAC-apple-silicon.yml b/environments/environment-MAC-apple-silicon.yml index 39daf9452..99eb52dcd 100644 --- a/environments/environment-MAC-apple-silicon.yml +++ b/environments/environment-MAC-apple-silicon.yml @@ -5,13 +5,13 @@ channels: dependencies: - python = 3.9.18 - nodejs = 18.16.1 + # Install these from conda-forge so that dependent packages get included in the distributable - numcodecs = 0.11.0 - - lxml = 4.9.3 # pypi build fails due to x64/arm64 mismatch so install from conda-forge - - pyedflib = 0.1.32 # pypi build fails due to x64/arm64 mismatch so install from conda-forge - - numpy # may have x64/arm64 mismatch issues so install from conda-forge - - pytables = 3.8 # pypi build fails on arm64 so install from conda-forge (used by neuroconv deps) - # install these from conda-forge so that dependent packages get included in the distributable - - jsonschema = 4.18.0 # installs jsonschema-specifications + - lxml = 4.9.3 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge + - pyedflib = 0.1.32 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge + - numpy # May have x64/arm64 mismatch issues so install from conda-forge + - pytables = 3.8 # PyPI build fails on arm64 so install from conda-forge (used by neuroconv deps) + - jsonschema = 4.18.0 # Also installs jsonschema-specifications - pip - pip: - setuptools==70.0.0 @@ -21,12 +21,9 @@ dependencies: - flask == 2.3.2 - flask-cors == 4.0.0 - flask_restx == 1.1.0 - # NOTE: the neuroconv wheel on pypi includes sonpy which is not compatible with arm64, so build and install - # neuroconv from github, which will remove the sonpy dependency when building from mac arm64 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - dandi >= 0.60.0 - - pytest == 7.4.0 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + # NOTE: the NeuroConv wheel on PyPI includes sonpy which is not compatible with arm64, so build and install + # NeuroConv from GitHub, which will remove the sonpy dependency when building from Mac arm64 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling diff --git a/environments/environment-MAC-intel.yml b/environments/environment-MAC-intel.yml index 3cb937767..75d060825 100644 --- a/environments/environment-MAC-intel.yml +++ b/environments/environment-MAC-intel.yml @@ -18,10 +18,7 @@ dependencies: - flask == 2.3.2 - flask-cors == 4.0.0 - flask_restx == 1.1.0 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - dandi >= 0.60.0 - - pytest == 7.4.0 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml index 1cb6f2e23..e26b38e9a 100644 --- a/environments/environment-Windows.yml +++ b/environments/environment-Windows.yml @@ -18,10 +18,7 @@ dependencies: - flask == 2.3.2 - flask-cors === 3.0.10 - flask_restx == 1.1.0 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - dandi >= 0.60.0 - - pytest == 7.2.2 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling