From 413b0ee1f767d3d85d65f0431aff1f5e6343f23e Mon Sep 17 00:00:00 2001 From: Eva Maxfield Brown Date: Sun, 21 Jul 2024 09:23:47 -0700 Subject: [PATCH 1/6] newline + comma png --- bioio_imageio/reader_metadata.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bioio_imageio/reader_metadata.py b/bioio_imageio/reader_metadata.py index 8959167..bca2e80 100644 --- a/bioio_imageio/reader_metadata.py +++ b/bioio_imageio/reader_metadata.py @@ -77,7 +77,8 @@ def get_supported_extensions() -> List[str]: "mpo", "msp", "pdf", - "png" "ppm", + "png", + "ppm", "ps", "zif", ] From 26dbc98b2a75269e1758da4b6b924f7ef92a2560 Mon Sep 17 00:00:00 2001 From: Eva Maxfield Brown Date: Mon, 22 Jul 2024 21:32:58 -0700 Subject: [PATCH 2/6] Mirror base imageio version from aicsimageio --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index cf1321b..b1b0d0a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ dependencies = [ "bioio-base>=0.3.0", "dask[array]>=2021.4.1", "fsspec>=2022.8.0", - "imageio[ffmpeg]>=2.11.0,<2.28.0", + "imageio[ffmpeg]>=2.31.0", "numpy>=1.21.0", "Pillow>=9.3.0", "xarray>=2022.6.0", From b7bfecbfe07c49bcd3751015349652f05711cc69 Mon Sep 17 00:00:00 2001 From: Eva Maxfield Brown Date: Mon, 22 Jul 2024 21:33:27 -0700 Subject: [PATCH 3/6] Install ffmpeg on CI runners --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 123008a..d975db4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -60,6 +60,8 @@ jobs: - uses: extractions/setup-just@v2 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - name: Set up FFMPEG + uses: FedericoCarboni/setup-ffmpeg@v3 - name: Install Dependencies run: | python -m pip install --upgrade pip From 15d9930f94246b4859af731db4a479d49afa1eef Mon Sep 17 00:00:00 2001 From: Eva Maxfield Brown Date: Mon, 22 Jul 2024 21:37:20 -0700 Subject: [PATCH 4/6] Also mirror the RGB change associated with the version bump --- bioio_imageio/tests/test_reader.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bioio_imageio/tests/test_reader.py b/bioio_imageio/tests/test_reader.py index 322ee82..ced9c9b 100644 --- a/bioio_imageio/tests/test_reader.py +++ b/bioio_imageio/tests/test_reader.py @@ -15,10 +15,10 @@ @pytest.mark.parametrize( "filename, set_scene, expected_shape, expected_dims_order", [ - ("example.bmp", "Image:0", (480, 640, 4), "YXS"), + ("example.bmp", "Image:0", (480, 640, 3), "YXS"), ("example.png", "Image:0", (800, 537, 4), "YXS"), ("example.jpg", "Image:0", (452, 400, 3), "YXS"), - ("example.gif", "Image:0", (72, 268, 268, 4), "TYXS"), + ("example.gif", "Image:0", (72, 268, 268, 3), "TYXS"), ( "example_invalid_frame_count.mp4", "Image:0", From 2dd4029274961ca6320fc1e1fe0db4e2c76c70e9 Mon Sep 17 00:00:00 2001 From: BrianWhitneyAI Date: Wed, 11 Dec 2024 12:13:53 -0800 Subject: [PATCH 5/6] rerun tests --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5bcfe49..d23209b 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ A BioIO reader plugin for reading [all these formats](https://imageio.readthedocs.io/en/stable/formats/index.html) using `imageio` ---- +--- ## Documentation From 633188003aff8395a67e68a8d546f5a05e168a83 Mon Sep 17 00:00:00 2001 From: BrianWhitneyAI Date: Wed, 11 Dec 2024 12:14:19 -0800 Subject: [PATCH 6/6] rerun tests --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d23209b..5bcfe49 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ A BioIO reader plugin for reading [all these formats](https://imageio.readthedocs.io/en/stable/formats/index.html) using `imageio` ---- +--- ## Documentation