Deepinterpolation revived: training, transfer, and inference with more flexibility

.github/workflows/deepinterpolation.yml

@@ -0,0 +1,37 @@
+name: Testing deepinterpolation
+
+on:
+  pull_request:
+    types: [synchronize, opened, reopened]
+    branches:
+      - main
+
+concurrency:  # Cancel previous workflows on the same pull request
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-and-test:
+    name: Test on ${{ matrix.os }} OS
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip  # Official recommended way
+          # install deepinteprolation
+          pip install tensorflow==2.7.0
+          pip install deepinterpolation@git+https://github.com/AllenInstitute/deepinterpolation.git
+          pip install protobuf==3.20.*
+          pip install -e .[full,test_core]
+      - name: Test core with pytest
+        run: |
+          pytest -v src/spikeinterface/preprocessing/deepinterpolation
+        shell: bash  # Necessary for pipeline to work on windows

.github/workflows/full-test.yml

@@ -129,7 +129,7 @@ jobs:
         run: ./.github/run_tests.sh "extractors and not streaming_extractors"
       - name: Test preprocessing
         if: ${{ steps.modules-changed.outputs.PREPROCESSING_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }}
-        run: ./.github/run_tests.sh preprocessing
+        run: ./.github/run_tests.sh "preprocessing and not deepinterpolation"
       - name: Test postprocessing
         if: ${{ steps.modules-changed.outputs.POSTPROCESSING_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }}
         run: ./.github/run_tests.sh postprocessing

conftest.py

@@ -11,7 +11,7 @@
 mark_names = ["core", "extractors", "preprocessing", "postprocessing",
               "sorters_external", "sorters_internal", "sorters",
               "qualitymetrics", "comparison", "curation",
-              "widgets", "exporters", "sortingcomponents"]
+              "widgets", "exporters", "sortingcomponents", "deepinterpolation"]
 
 
 # define global test folder

pyproject.toml

@@ -175,6 +175,7 @@ markers = [
     "exporters",
     "widgets",
     "sortingcomponents",
+    "deepinterpolation",
     "streaming_extractors: extractors that require streaming such as ross and fsspec",
 ]
 filterwarnings =[

src/spikeinterface/preprocessing/deepinterpolation/__init__.py

@@ -1 +1,2 @@
 from .deepinterpolation import DeepInterpolatedRecording, deepinterpolate
+from .train import train_deepinterpolation