Update Workflows (#317)

* downgrade mac-os to 13 * downgrade to macos-12 * removed setup-conda * added macos-13 to update testing data * removed conda * added 3.12 * added quotes to version numbers * added macos-latest * removed macos-latest * added dev testing * unpin xdist * condense tests into 1 line for better output * downgrade python setup for wheel support * added macos-latest with scanimage skips * continue on collection errors * added platform check for scanimage import * added platform check for scanimage import * switched to try-except * fixed ignores * fixed ignores * updated dev install * fixed ignores * added formatting * added macos-latest to update-testing-data * switched back to if-else import * updated changelog
catalystneuro · May 1, 2024 · d078f60 · d078f60
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diff --git a/.github/workflows/dev-testing.yaml b/.github/workflows/dev-testing.yaml
@@ -0,0 +1,57 @@
+name: Dev Testing
+on:
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  run:
+    name: Ubuntu tests with Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v2
+      - run: git fetch --prune --unshallow --tags
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Global Setup
+        run: |
+            pip install -U pip
+            pip install pytest-xdist
+            git config --global user.email "[email protected]"
+            git config --global user.name "CI Almighty"
+            pip install wheel==0.41.2  # needed for scanimage
+
+      - name: Install full requirements
+        run: |
+            pip install .[test]
+            pip install .[full]
+
+      - name: Clone and Install NeuroConv
+        run: |
+            git clone https://github.com/catalystneuro/neuroconv.git
+            cd neuroconv
+            pip install --no-cache-dir .[full,test]
+            cd ../
+      - name: Get ophys_testing_data current head hash
+        id: ophys
+        run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
+      - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
+        uses: actions/cache@v2
+        id: cache-ophys-datasets
+        with:
+          path: ./ophys_testing_data
+          key: ophys-datasets-042023-ubuntu-latest-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
+
+      - name: Run NeuroConv tests
+        run: |
+            pytest -n auto --dist loadscope neuroconv/tests/test_ophys neuroconv/tests/test_on_data/test_imaging_interfaces.py neuroconv/tests/test_on_data/test_segmentation_interfaces.py
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -6,6 +6,10 @@ on:
     workflows: [update-testing-data]
     types: [completed]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   on-failure:
     name: Notify on failure
@@ -37,10 +41,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, "3.10", 3.11]
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, windows-latest, macos-latest, macos-13] # macos-13 is the latest version of macOS with Intel chip
     steps:
-      - uses: s-weigand/setup-conda@v1
       - uses: actions/checkout@v2
       - run: git fetch --prune --unshallow --tags
       - name: Setup Python ${{ matrix.python-version }}
@@ -79,7 +82,7 @@ jobs:
         run: pytest -n auto --dist loadscope --cov=./ --cov-report xml:./codecov.xml
       - if: ${{ matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'}}
         name: Upload full coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./codecov.xml

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ### Features
 
+* Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: [PR #317](https://github.com/catalystneuro/roiextractors/pull/317)
+
 ### Fixes
 
 * Remove unecessary scipy import error handling [#315]((https://github.com/catalystneuro/roiextractors/pull/315)

diff --git a/tests/test_io.py b/tests/test_io.py
@@ -25,6 +25,11 @@
 
 from .setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
 
+import platform
+
+# Remove this check once scanimage tiff reader is available on ARM -- see https://gitlab.com/vidriotech/scanimagetiffreader-python/-/issues/31
+is_m_series_mac = platform.system() == "Darwin" and platform.machine() == "arm64"
+
 
 def custom_name_func(testcase_func, param_num, param):
     return (
@@ -68,6 +73,9 @@ class TestExtractors(TestCase):
 
     @parameterized.expand(imaging_extractor_list, name_func=custom_name_func)
     def test_imaging_extractors(self, extractor_class, extractor_kwargs):
+        if extractor_class == ScanImageTiffImagingExtractor and is_m_series_mac:
+            return
+
         extractor = extractor_class(**extractor_kwargs)
         check_imaging_return_types(extractor)
 
@@ -88,6 +96,9 @@ def test_imaging_extractors(self, extractor_class, extractor_kwargs):
     @parameterized.expand(imaging_extractor_list, name_func=custom_name_func)
     def test_imaging_extractors_canonical_shape(self, extractor_class, extractor_kwargs):
         """Test that get_video and get_frame methods for their shapes and types under different indexing scenarios"""
+        if extractor_class == ScanImageTiffImagingExtractor and is_m_series_mac:
+            return
+
         extractor = extractor_class(**extractor_kwargs)
         image_size = extractor.get_image_size()
         num_channels = extractor.get_num_channels()

diff --git a/tests/test_scan_image_tiff.py b/tests/test_scan_image_tiff.py
@@ -2,22 +2,30 @@
 from pathlib import Path
 from tempfile import mkdtemp
 from shutil import rmtree, copy
-
 from hdmf.testing import TestCase
 from numpy.testing import assert_array_equal
-from ScanImageTiffReader import ScanImageTiffReader
+import pytest
 
 from roiextractors import TiffImagingExtractor, ScanImageTiffImagingExtractor
-
+from roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils import _get_scanimage_reader
 from .setup_paths import OPHYS_DATA_PATH
 
+import platform
+
+is_m_series_mac = platform.system() == "Darwin" and platform.machine() == "arm64"
+if (
+    is_m_series_mac
+):  # Remove this check once scanimage tiff reader is available on ARM -- see https://gitlab.com/vidriotech/scanimagetiffreader-python/-/issues/31
+    pytest.skip("ScanImageTiffReader does not support M-series Macs", allow_module_level=True)
+
 
 class TestScanImageTiffExtractor(TestCase):
     @classmethod
     def setUpClass(cls):
         cls.file_path = OPHYS_DATA_PATH / "imaging_datasets" / "Tif" / "sample_scanimage.tiff"
         cls.tmpdir = Path(mkdtemp())
         cls.imaging_extractor = ScanImageTiffImagingExtractor(file_path=cls.file_path, sampling_frequency=30.0)
+        ScanImageTiffReader = _get_scanimage_reader()
         with ScanImageTiffReader(filename=str(cls.imaging_extractor.file_path)) as io:
             cls.data = io.data()
 

diff --git a/tests/test_scanimage_utils.py b/tests/test_scanimage_utils.py
@@ -11,6 +11,14 @@
 
 from .setup_paths import OPHYS_DATA_PATH
 
+import platform
+
+is_m_series_mac = platform.system() == "Darwin" and platform.machine() == "arm64"
+if (
+    is_m_series_mac
+):  # Remove this check once scanimage tiff reader is available on ARM -- see https://gitlab.com/vidriotech/scanimagetiffreader-python/-/issues/31
+    pytest.skip("ScanImageTiffReader does not support M-series Macs", allow_module_level=True)
+
 
 def test_get_scanimage_reader():
     ScanImageTiffReader = _get_scanimage_reader()

diff --git a/tests/test_scanimagetiffimagingextractor.py b/tests/test_scanimagetiffimagingextractor.py
@@ -1,16 +1,27 @@
 import pytest
 from numpy.testing import assert_array_equal
-from ScanImageTiffReader import ScanImageTiffReader
+
 from roiextractors import (
     ScanImageTiffSinglePlaneImagingExtractor,
     ScanImageTiffMultiPlaneImagingExtractor,
     ScanImageTiffSinglePlaneMultiFileImagingExtractor,
     ScanImageTiffMultiPlaneMultiFileImagingExtractor,
 )
-from roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils import extract_extra_metadata, parse_metadata
-
+from roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils import (
+    extract_extra_metadata,
+    parse_metadata,
+    _get_scanimage_reader,
+)
 from .setup_paths import OPHYS_DATA_PATH
 
+import platform
+
+is_m_series_mac = platform.system() == "Darwin" and platform.machine() == "arm64"
+if (
+    is_m_series_mac
+):  # Remove this check once scanimage tiff reader is available on ARM -- see https://gitlab.com/vidriotech/scanimagetiffreader-python/-/issues/31
+    pytest.skip("ScanImageTiffReader does not support M-series Macs", allow_module_level=True)
+
 
 @pytest.fixture(scope="module")
 def file_path():
@@ -91,6 +102,8 @@ def test_ScanImageTiffSinglePlaneImagingExtractor__init__parsed_metadata_not_pro
 
 @pytest.mark.parametrize("frame_idxs", (0, [0, 1, 2], [0, 2, 5]))
 def test_get_frames(scan_image_tiff_single_plane_imaging_extractor, frame_idxs, expected_properties):
+    ScanImageTiffReader = _get_scanimage_reader()
+
     frames = scan_image_tiff_single_plane_imaging_extractor.get_frames(frame_idxs=frame_idxs)
     file_path = str(scan_image_tiff_single_plane_imaging_extractor.file_path)
     plane = scan_image_tiff_single_plane_imaging_extractor.plane
@@ -100,6 +113,7 @@ def test_get_frames(scan_image_tiff_single_plane_imaging_extractor, frame_idxs,
     frames_per_slice = expected_properties["frames_per_slice"]
     if isinstance(frame_idxs, int):
         frame_idxs = [frame_idxs]
+
     raw_idxs = []
     for idx in frame_idxs:
         cycle = idx // frames_per_slice
@@ -111,6 +125,7 @@ def test_get_frames(scan_image_tiff_single_plane_imaging_extractor, frame_idxs,
             + channel
         )
         raw_idxs.append(raw_idx)
+
     with ScanImageTiffReader(file_path) as io:
         assert_array_equal(frames, io.data()[raw_idxs])
 
@@ -123,6 +138,8 @@ def test_get_frames_invalid(scan_image_tiff_single_plane_imaging_extractor, fram
 
 @pytest.mark.parametrize("frame_idx", (1, 3, 5))
 def test_get_single_frame(scan_image_tiff_single_plane_imaging_extractor, expected_properties, frame_idx):
+    ScanImageTiffReader = _get_scanimage_reader()
+
     frame = scan_image_tiff_single_plane_imaging_extractor._get_single_frame(frame=frame_idx)
     file_path = str(scan_image_tiff_single_plane_imaging_extractor.file_path)
     plane = scan_image_tiff_single_plane_imaging_extractor.plane
@@ -155,6 +172,8 @@ def test_get_video(
     start_frame,
     end_frame,
 ):
+    ScanImageTiffReader = _get_scanimage_reader()
+
     video = scan_image_tiff_single_plane_imaging_extractor.get_video(start_frame=start_frame, end_frame=end_frame)
     if start_frame is None:
         start_frame = 0
@@ -166,6 +185,7 @@ def test_get_video(
     num_planes = expected_properties["num_planes"]
     num_channels = expected_properties["num_channels"]
     frames_per_slice = expected_properties["frames_per_slice"]
+
     raw_idxs = []
     for idx in range(start_frame, end_frame):
         cycle = idx // frames_per_slice
@@ -177,6 +197,7 @@ def test_get_video(
             + channel
         )
         raw_idxs.append(raw_idx)
+
     with ScanImageTiffReader(file_path) as io:
         assert_array_equal(video, io.data()[raw_idxs])