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| Original file line number | Diff line number | Diff line change |
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| @@ -1,35 +1,19 @@ | ||
| name: Add Issue or PR to Dashboard | ||
| name: Add Issue or Pull Request to Dashboard | ||
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| on: | ||
| issues: | ||
| types: opened | ||
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| types: | ||
| - opened | ||
| pull_request: | ||
| types: | ||
| - opened | ||
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| jobs: | ||
| issue_opened: | ||
| name: Add Issue to Dashboard | ||
| runs-on: ubuntu-latest | ||
| if: github.event_name == 'issues' | ||
| steps: | ||
| - name: Add Issue to Dashboard | ||
| uses: leonsteinhaeuser/project-beta-automations@v1.2.1 | ||
| with: | ||
| gh_token: ${{ secrets.MY_GITHUB_TOKEN }} | ||
| organization: catalystneuro | ||
| project_id: 3 | ||
| resource_node_id: ${{ github.event.issue.node_id }} | ||
| pr_opened: | ||
| name: Add PR to Dashboard | ||
| add-to-project: | ||
| name: Add issue or pull request to project | ||
| runs-on: ubuntu-latest | ||
| if: github.event_name == 'pull_request' && github.event.action == 'opened' | ||
| steps: | ||
| - name: Add PR to Dashboard | ||
| uses: leonsteinhaeuser/project-beta-automations@v1.2.1 | ||
| - uses: actions/add-to-project@v0.5.0 | ||
| with: | ||
| gh_token: ${{ secrets.MY_GITHUB_TOKEN }} | ||
| organization: catalystneuro | ||
| project_id: 3 | ||
| resource_node_id: ${{ github.event.pull_request.node_id }} | ||
| project-url: https://github.com/orgs/catalystneuro/projects/3 | ||
| github-token: ${{ secrets.PROJECT_TOKEN }} |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,12 @@ | ||
| name: Check Docstrings | ||
| on: | ||
| workflow_dispatch: | ||
| pull_request: | ||
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| jobs: | ||
| check-docstrings: | ||
| uses: catalystneuro/.github/.github/workflows/check_docstrings.yaml@main | ||
| with: | ||
| python-version: '3.10' | ||
| repository: 'catalystneuro/roiextractors' | ||
| package-name: 'roiextractors' |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,48 @@ | ||
| name: update-testing-data | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * *" # daily | ||
| workflow_dispatch: | ||
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| jobs: | ||
| run: | ||
| name: Update testing data on ${{ matrix.os }} | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: [ubuntu-latest, windows-latest, macos-latest] | ||
| steps: | ||
| - uses: s-weigand/setup-conda@v1 | ||
| - uses: actions/checkout@v2 | ||
| - run: git fetch --prune --unshallow --tags | ||
| - name: Setup Python 3.11 | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: 3.11 | ||
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| - name: Global Setup | ||
| run: | | ||
| pip install -U pip | ||
| git config --global user.email "CI@example.com" | ||
| git config --global user.name "CI Almighty" | ||
| pip install wheel==0.41.2 # needed for scanimage | ||
| - name: Get ophys_testing_data current head hash | ||
| id: ophys | ||
| run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)" | ||
| - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | ||
| uses: actions/cache@v2 | ||
| id: cache-ophys-datasets | ||
| with: | ||
| path: ./ophys_testing_data | ||
| key: ophys-datasets-042023-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | ||
| - if: steps.cache-ophys-datasets.outputs.cache-hit == false | ||
| name: Install and configure AWS CLI | ||
| run: | | ||
| pip install awscli==1.29.56 | ||
| aws configure set aws_access_key_id ${{ secrets.AWS_ACCESS_KEY_ID }} | ||
| aws configure set aws_secret_access_key ${{ secrets.AWS_SECRET_ACCESS_KEY }} | ||
| - if: steps.cache-ophys-datasets.outputs.cache-hit == false | ||
| name: Download data from S3 | ||
| run: aws s3 cp --recursive s3://${{ secrets.S3_GIN_BUCKET }}//ophys_testing_data ./ophys_testing_data |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,12 +1,19 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.3.0 | ||
| rev: v4.5.0 | ||
| hooks: | ||
| - id: check-yaml | ||
| - id: end-of-file-fixer | ||
| - id: trailing-whitespace | ||
| - repo: https://github.com/psf/black | ||
| rev: 22.6.0 | ||
| rev: 24.1.1 | ||
| hooks: | ||
| - id: black | ||
| exclude: ^docs/ | ||
| - repo: https://github.com/pycqa/pydocstyle | ||
| rev: 6.3.0 | ||
| hooks: | ||
| - id: pydocstyle | ||
| args: | ||
| - --convention=numpy | ||
| - --add-ignore=D1 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,124 @@ | ||
| # Upcoming | ||
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| ### Improvements | ||
| * Improved xml parsing with Bruker [PR #267](https://github.com/catalystneuro/roiextractors/pull/267) | ||
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| # v0.5.5 | ||
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| ### Features | ||
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| * Updated `Suite2pSegmentationExtractor` to support multi channel and multi plane data. [PR #242](https://github.com/catalystneuro/roiextractors/pull/242) | ||
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| ### Fixes | ||
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| * Fixed `MicroManagerTiffImagingExtractor` private extractor's dtype to not override the parent's dtype. [PR #257](https://github.com/catalystneuro/roiextractors/pull/257) | ||
| * Fixed override of `channel_name` in `Suite2pSegmentationExtractor`. [PR #263](https://github.com/catalystneuro/roiextractors/pull/263) | ||
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| # v0.5.4 | ||
|
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| ### Features | ||
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| * Added volumetric and multi-channel support for Bruker format. [PR #230](https://github.com/catalystneuro/roiextractors/pull/230) | ||
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| # v0.5.3 | ||
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| ### Features | ||
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| * Added support for Miniscope AVI files with the `MiniscopeImagingExtractor`. [PR #225](https://github.com/catalystneuro/roiextractors/pull/225) | ||
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| # v0.5.2 | ||
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| ### Features | ||
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| * Added support for MicroManager TIFF files with the `MicroManagerTiffImagingExtractor`. [PR #222](https://github.com/catalystneuro/roiextractors/pull/222) | ||
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| * Added support for Bruker TIFF files with the `BrukerTiffImagingExtractor`. [PR #220](https://github.com/catalystneuro/roiextractors/pull/220) | ||
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| # v0.5.1 | ||
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| ### Features | ||
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| * Added a `has_time_vector` function for ImagingExtractors and SegmentationExtractors, similar to the SpikeInterface API for detecting if timestamps have been set. [PR #216](https://github.com/catalystneuro/roiextractors/pull/216) | ||
|
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| ### Fixes | ||
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| * Fixed two issues with the `SubFrameSegementation` class: (i) attempting to set the private attribute `_image_masks` even when this was not present in the parent, and (ii) not calling the parent function for `get_pixel_masks` and instead using the base method even in cases where this had been overridden by the parent. [PR #215](https://github.com/catalystneuro/roiextractors/pull/215) | ||
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| # v0.5.0 | ||
|
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| ### Back-compatability break | ||
| * The orientation of traces in all `SegmentationExtractor`s has been standardized to have time (frames) as the first axis, and ROIs as the final axis. [PR #200](https://github.com/catalystneuro/roiextractors/pull/200) | ||
|
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| ### Features | ||
| * Add support for newer versions of EXTRACT output files. [PR #170](https://github.com/catalystneuro/roiextractors/pull/170) | ||
| The `ExtractSegmentationExtractor` class is now abstract and redirects to the newer or older | ||
| extractor depending on the version of the file. [PR #170](https://github.com/catalystneuro/roiextractors/pull/170) | ||
| * The `ExtractSegmentationExtractor.write_segmentation` method has now been deprecated. [PR #170](https://github.com/catalystneuro/roiextractors/pull/170) | ||
|
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| ### Improvements | ||
| * Add `frame_to_time` to `SegmentationExtractor`, `get_roi_ids` is now a class method. [PR #187](https://github.com/catalystneuro/roiextractors/pull/187) | ||
| * Add `set_times` to `SegmentationExtractor`. [PR #188](https://github.com/catalystneuro/roiextractors/pull/188) | ||
| * Updated the test for segmentation images to check all images for the given segmentation extractors. [PR #190](https://github.com/catalystneuro/roiextractors/pull/190) | ||
| * Refactored the `NwbSegmentationExtractor` to be more flexible with segmentation images and keep up | ||
| with the change in [catalystneuro/neuoroconv#41](https://github.com/catalystneuro/neuroconv/pull/41) | ||
| of trace names. [PR #191](https://github.com/catalystneuro/roiextractors/pull/191) | ||
| * Implemented a more efficient case of the base `ImagingExtractor.get_frames` through `get_video` when the indices are contiguous. [PR #195](https://github.com/catalystneuro/neuroconv/pull/195) | ||
| * Removed `max_frame` check on `MultiImagingExtractor.get_video()` to adhere to upper-bound slicing semantics. [PR #195](https://github.com/catalystneuro/neuroconv/pull/195) | ||
| * Improved the `MultiImagingExtractor.get_video()` to no longer rely on `get_frames`. [PR #195](https://github.com/catalystneuro/neuroconv/pull/195) | ||
| * Added `dtype` consistency check across `MultiImaging` components as well as a direct override method. [PR #195](https://github.com/catalystneuro/neuroconv/pull/195) | ||
| * Added the `FrameSliceSegmentationExtractor` class and corresponding `Segmentation.frame_slice(...)` method. [PR #201](https://github.com/catalystneuro/neuroconv/pull/201) | ||
| * Changed the `output_struct_name` argument to optional in `ExtractSegmentationExtractor`. | ||
| to allow more flexible usage for the user and better error message when it cannot be found in the file. | ||
| For consistency, `output_struct_name` argument has been also added to the legacy extractor. | ||
| The orientation of segmentation images are transposed for consistency in image orientation (height x width). [PR #210](https://github.com/catalystneuro/roiextractors/pull/210) | ||
| * Relaxed rounding of `ImagingExtractor.frame_to_time(...)` and `SegmentationExtractor.frame_to_time(...)` to be more consistent with SpikeInterface. [PR #212](https://github.com/catalystneuro/roiextractors/pull/212) | ||
|
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| ### Fixes | ||
| * Fixed the reference to the proper `mov_field` in `Hdf5ImagingExtractor`. [PR #195](https://github.com/catalystneuro/neuroconv/pull/195) | ||
| * Updated the name of the ROICentroids column for the `NwbSegmentationExtractor` to be up-to-date with NeuroConv v0.2.0 `write_segmentation`. [PR #208](https://github.com/catalystneuro/roiextractors/pull/208) | ||
| * Updated the trace orientation for the `NwbSegmentationExtractor`. [PR #208](https://github.com/catalystneuro/roiextractors/pull/208) | ||
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| # v0.4.18 | ||
|
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| ### Improvements | ||
| * `get_video` is now an abstract method in `ImagingExtractor` [PR #180](https://github.com/catalystneuro/roiextractors/pull/180) | ||
|
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| ### Features | ||
| * Add dummy segmentation extractor [PR #176](https://github.com/catalystneuro/roiextractors/pull/176) | ||
|
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| ### Testing | ||
| * Added unittests to the `get_frames` method from `ImagingExtractors` to assert that they are consistent with numpy | ||
| indexing behavior. [PR #154](https://github.com/catalystneuro/roiextractors/pull/154) | ||
| * Tests for spikeinterface like-behavior for the `get_video` funtiction [PR #181](https://github.com/catalystneuro/roiextractors/pull/181) | ||
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| # v0.4.17 | ||
|
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| ### Depreceations | ||
| - Suite2P argument has become `folder_path` instead of `file_path`, `file_path` deprecation scheduled for august or later. | ||
|
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| ### Documentation | ||
| - Improved docstrings across many extractors. | ||
|
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| ### Features | ||
| - Adds MultiImagingExtractor for combining multiple imaging extractors. | ||
| - Adds ScanImageTiffExtractor for reading .tiff files output from ScanImage | ||
| - Adds NumpyImagingExtractor for extracting raw video data as memmaps. | ||
| - Added frame slicing capabilities for imaging extractors. | ||
|
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| ### Testing | ||
| - Added checks and debugs that all sampling frequencies returns are floats | ||
| - Round trip testing working for all extractors that have a working write method. |
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