From 1c9a0a708bf9f9c8cecebf985dd80b55552e7550 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 26 Jun 2025 00:26:16 -0400 Subject: [PATCH 1/3] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/codespell.yml diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..c59e047 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,25 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Annotate locations with typos + uses: codespell-project/codespell-problem-matcher@v1 + - name: Codespell + uses: codespell-project/actions-codespell@v2 From 3a2da9672f90875d44116d35895a0ca40f7341a9 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 26 Jun 2025 00:26:16 -0400 Subject: [PATCH 2/3] Add rudimentary codespell config --- .codespellrc | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..4f546d5 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,.codespellrc +check-hidden = true +ignore-regex = ^\s*"image/\S+": ".* +# ignore-words-list = From f89981b8c5fcbaaa9236e0dd6fcf2803f03e0de1 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 26 Jun 2025 00:26:20 -0400 Subject: [PATCH 3/3] [DATALAD RUNCMD] chore: run codespell throughout fixing few left typos automagically === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- README.md | 2 +- write_kyoda_wormdata.ipynb | 2 +- wt-N2-081015-01.ome.zarr/omero.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 998b126..6d975c7 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ However, if, for example, the nuclear contour is represented as a set of vertice Knowing that there is a framework of AnnData, we think of using OME-Zarr Mask to describe the ROI based on pixels associated with the image, and storing the representative position for biological object in each row of X in AnnData. We think that the features for each biological object such as area, volume, mean value of GFP signal, etc., can be stored in obs. We think the same issue arises in spatial transcriptome data when describing data for a cell that are detected across multiple pixels. -We think it would be hard to understand without some exmaples, so we would like to create some examples. +We think it would be hard to understand without some examples, so we would like to create some examples. We have already developed several data formats based on XML and HDF5, but we want to make a new format highly compatible(?) with OME-NGFF. diff --git a/write_kyoda_wormdata.ipynb b/write_kyoda_wormdata.ipynb index d8e801d..e4834a4 100644 --- a/write_kyoda_wormdata.ipynb +++ b/write_kyoda_wormdata.ipynb @@ -182,7 +182,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/tmp/ipykernel_10974/2054089064.py:1: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.\n", + "/tmp/ipykernel_10974/2054089064.py:1: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behaviour.\n", " adata = ad.AnnData(X = dfa, obs = obs_meta)\n", "/home/kyoda/ngff/lib/python3.10/site-packages/anndata/_core/anndata.py:121: ImplicitModificationWarning: Transforming to str index.\n", " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n" diff --git a/wt-N2-081015-01.ome.zarr/omero.json b/wt-N2-081015-01.ome.zarr/omero.json index 142e7b9..a499421 100644 --- a/wt-N2-081015-01.ome.zarr/omero.json +++ b/wt-N2-081015-01.ome.zarr/omero.json @@ -41,7 +41,7 @@ "color": "FFFFFF", "inverted": false, "reverseIntensity": false, - "famly": "linear", + "family": "linear", "coefficient": 1.0 "window": { "min": 0.0,