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Merge pull request #1056 from NeurodataWithoutBorders/support-neuroconv-latest
Support NeuroConv 0.9.1
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‎.github/workflows/build_and_deploy_mac.yml‎

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jobs:
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deploy-on-mac:
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runs-on: macos-13
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runs-on: macos-15-intel
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# NOTE: macos-latest is an arm64 mac, and the dependency sonpy (Spike2RecordingInterface) has a .so file that
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# works only on mac x64. This causes issues building and deploying on mac arm64. So we use macos-13 (x64)
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# to build and deploy both the x64 and arm64 versions of the app.

‎.github/workflows/example_data_cache.yml‎

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fail-fast: false
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matrix:
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python-version: ["3.12"]
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os: [ubuntu-latest, windows-latest, macos-latest, macos-13]
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os: [ubuntu-latest, windows-latest, macos-latest, macos-15-intel]
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steps:
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id: cache-ephys-datasets
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with:
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path: ./ephy_testing_data
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key: ephys-datasets-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
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key: ephys-datasets-v2-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
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- name: Get ophys_testing_data current head hash
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id: ophys
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run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"

‎.github/workflows/testing_dev.yml‎

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- os: macos-latest # Mac arm64 runner
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label: environments/environment-MAC-apple-silicon.yml
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- os: macos-13 # Mac x64 runner
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- os: macos-15-intel # Mac x64 runner
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label: environments/environment-MAC-intel.yml
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- os: windows-latest

‎.github/workflows/testing_dev_e2e_with_live_services.yml‎

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- os: macos-latest # Mac arm64 runner
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label: environments/environment-MAC-apple-silicon.yml
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- os: macos-13 # Mac x64 runner
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- os: macos-15-intel # Mac x64 runner
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label: environments/environment-MAC-intel.yml
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- os: windows-latest

‎.github/workflows/testing_dev_with_live_services.yml‎

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- os: macos-latest # Mac arm64 runner
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label: environments/environment-MAC-apple-silicon.yml
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- os: macos-13 # Mac x64 runner
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- os: macos-15-intel # Mac x64 runner
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label: environments/environment-MAC-intel.yml
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- os: windows-latest
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label: environments/environment-Windows.yml
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‎.github/workflows/testing_flask_build_and_dist.yml‎

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- os: macos-latest # Mac arm64 runner
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label: environments/environment-MAC-apple-silicon.yml
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- os: macos-13 # Mac x64 runner
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- os: macos-15-intel # Mac x64 runner
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label: environments/environment-MAC-intel.yml
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- os: windows-latest
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label: environments/environment-Windows.yml
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run: pip uninstall matplotlib --yes
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# Fix for macos build - remove bad sonpy file
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- if: matrix.os == 'macos-latest' || matrix.os == 'macos-13'
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- if: matrix.os == 'macos-latest'
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run: rm -f "$CONDA_PREFIX/lib/python3.9/site-packages/sonpy/linux/sonpy.so"
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- name: Build PyFlask distribution

‎.github/workflows/testing_pipelines.yml‎

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- os: macos-latest # Mac arm64 runner
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label: environments/environment-MAC-apple-silicon.yml
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- os: macos-13 # Mac x64 runner
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- os: macos-15-intel # Mac x64 runner
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label: environments/environment-MAC-intel.yml
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- os: windows-latest
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id: cache-ephys-datasets
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with:
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path: ./ephy_testing_data
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key: ephys-datasets-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
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key: ephys-datasets-v2-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
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- name: Get ophys_testing_data current head hash
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id: ophys

‎.gitignore‎

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# PyCharm
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.idea/
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# Auto-generated storybook schemas (regenerate with: python generateInterfaceSchema.py)
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stories/inputs/interface_schemas/
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stories/pages/SourceData.stories.js
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ophys_testing_data/

‎environments/environment-Linux.yml‎

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- flask-cors == 4.0.0
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- flask_restx == 1.1.0
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- werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
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- neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.1
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- pandas < 3.0 # pandas 3.0 returns read-only arrays, breaking spikeinterface Phy extractor
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- neo == 0.14.1 # 0.14.2 is not compatible with neuroconv < 0.7.5
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- scikit-learn == 1.4.0 # Tutorial data generation
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- tqdm_publisher >= 0.0.1 # Progress bars
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- tzlocal >= 5.2 # Frontend timezone handling
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- ndx-pose == 0.1.1
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- nwbinspector == 0.6.2
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- neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.9.3
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- scikit-learn == 1.6.1 # Tutorial data generation
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- tqdm_publisher == 0.1.1 # Progress bars
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- tzlocal == 5.3.1 # Frontend timezone handling
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- ndx-pose == 0.2.2
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- nwbinspector == 0.6.5
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- tables
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- numcodecs < 0.16.0 # numcodecs 0.16.0 is not compatible with zarr 2.18.5
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- numcodecs == 0.15.1 # numcodecs 0.16.0 is not compatible with zarr 2.18.5

‎environments/environment-MAC-apple-silicon.yml‎

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- lxml = 4.9.3 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
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- pyedflib = 0.1.38 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
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- numpy # May have x64/arm64 mismatch issues so install from conda-forge
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- pytables = 3.9.1 # PyPI build fails on arm64; must be <3.9.2 per neuroconv 0.6.1 constraint
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- pytables = 3.10.2 # PyPI build fails on arm64 so install from conda-forge (used by neuroconv deps)
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- jsonschema = 4.18.0 # Also installs jsonschema-specifications
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- pip
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- pip:
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- werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
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# NOTE: the NeuroConv wheel on PyPI includes sonpy which is not compatible with arm64, so build and install
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# NeuroConv from GitHub, which will remove the sonpy dependency when building from Mac arm64
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- neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.1
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- pandas < 3.0 # pandas 3.0 returns read-only arrays, breaking spikeinterface Phy extractor
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- neo == 0.14.1 # 0.14.2 is not compatible with neuroconv < 0.7.5
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- scikit-learn == 1.4.0 # Tutorial data generation
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- tqdm_publisher >= 0.0.1 # Progress bars
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- tzlocal >= 5.2 # Frontend timezone handling
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- ndx-pose == 0.1.1
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- nwbinspector == 0.6.2
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- numcodecs < 0.16.0 # numcodecs 0.16.0 is not compatible with zarr 2.18.5
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- h5py < 3.13 # 3.13+ uses HDF5 1.14.4 features not in pytables 3.10.2's bundled HDF5 1.14.2
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- neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.9.3
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- scikit-learn == 1.6.1 # Tutorial data generation
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- tqdm_publisher == 0.1.1 # Progress bars
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- tzlocal == 5.3.1 # Frontend timezone handling
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- ndx-pose == 0.2.2
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- nwbinspector == 0.6.5
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- numcodecs == 0.15.1 # numcodecs 0.16.0 is not compatible with zarr 2.18.5

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