patchworks 0.3.0__tar.gz → 0.4.0__tar.gz

{patchworks-0.3.0 → patchworks-0.4.0}/.github/workflows/release.yml

@@ -22,6 +22,9 @@ jobs:
         with:
           config: cliff.toml
           args: --latest --strip header
+        env:
+          # Lets git-cliff resolve commit authors to GitHub handles/avatars.
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Create GitHub release
         uses: softprops/action-gh-release@v2

{patchworks-0.3.0 → patchworks-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 0.3.0
+Version: 0.4.0
 Summary: Tiled processing of arbitrarily large images with globally consistent labels
 Project-URL: Homepage, https://github.com/imcf/patchworks
 Project-URL: Issues, https://github.com/imcf/patchworks/issues
@@ -24,6 +24,11 @@ Requires-Dist: zarr>=2.14
 Provides-Extra: all
 Requires-Dist: bioio; extra == 'all'
 Requires-Dist: bioio-bioformats; extra == 'all'
+Requires-Dist: bioio-czi; extra == 'all'
+Requires-Dist: bioio-lif; extra == 'all'
+Requires-Dist: bioio-nd2; extra == 'all'
+Requires-Dist: bioio-ome-tiff; extra == 'all'
+Requires-Dist: bioio-tifffile; extra == 'all'
 Requires-Dist: nvidia-ml-py; extra == 'all'
 Requires-Dist: psutil; extra == 'all'
 Requires-Dist: scikit-image; extra == 'all'
@@ -31,6 +36,11 @@ Requires-Dist: tqdm; extra == 'all'
 Provides-Extra: bioio
 Requires-Dist: bioio; extra == 'bioio'
 Requires-Dist: bioio-bioformats; extra == 'bioio'
+Requires-Dist: bioio-czi; extra == 'bioio'
+Requires-Dist: bioio-lif; extra == 'bioio'
+Requires-Dist: bioio-nd2; extra == 'bioio'
+Requires-Dist: bioio-ome-tiff; extra == 'bioio'
+Requires-Dist: bioio-tifffile; extra == 'bioio'
 Provides-Extra: cellpose
 Requires-Dist: cellpose>=3.0; extra == 'cellpose'
 Provides-Extra: dev
@@ -92,9 +102,9 @@ pip install "patchworks[napari]"   # interactive napari viewer plugin
 pip install "patchworks[all]"      # Everything (except napari GUI)
 ```
 
-> `bioio` reads CZI/LIF/ND2/OME-TIFF/… — it ships with `bioio-bioformats`, the
-> Bio-Formats catch-all reader (needs a JVM). Add faster native readers where
-> you want them (e.g. `bioio-ome-tiff`, `bioio-czi`, `bioio-lif`, `bioio-nd2`).
+> `bioio` reads CZI/LIF/ND2/OME-TIFF/… The `[bioio]` extra bundles the common
+> native readers (`bioio-nd2`, `bioio-ome-tiff`, `bioio-czi`, `bioio-tifffile`,
+> `bioio-lif`) plus `bioio-bioformats`, the Bio-Formats catch-all reader (JVM).
 
 ---
 

{patchworks-0.3.0 → patchworks-0.4.0}/README.md

@@ -39,9 +39,9 @@ pip install "patchworks[napari]"   # interactive napari viewer plugin
 pip install "patchworks[all]"      # Everything (except napari GUI)
 ```
 
-> `bioio` reads CZI/LIF/ND2/OME-TIFF/… — it ships with `bioio-bioformats`, the
-> Bio-Formats catch-all reader (needs a JVM). Add faster native readers where
-> you want them (e.g. `bioio-ome-tiff`, `bioio-czi`, `bioio-lif`, `bioio-nd2`).
+> `bioio` reads CZI/LIF/ND2/OME-TIFF/… The `[bioio]` extra bundles the common
+> native readers (`bioio-nd2`, `bioio-ome-tiff`, `bioio-czi`, `bioio-tifffile`,
+> `bioio-lif`) plus `bioio-bioformats`, the Bio-Formats catch-all reader (JVM).
 
 ---
 

{patchworks-0.3.0 → patchworks-0.4.0}/cliff.toml

@@ -8,12 +8,11 @@ body = """
 - {% if commit.scope %}**{{ commit.scope }}**: {% endif %}{{ commit.message | split(pat="\n") | first }}
 {% endfor %}
 {% endfor %}\
-{% set contributors = commits | map(attribute="author.name") | unique | sort -%}
-{% if contributors | length > 0 %}
+{% if github.contributors | length > 0 %}
 ### 👥 Contributors
 
-{% for name in contributors %}\
-- {{ name }}
+{% for contributor in github.contributors | sort(attribute="username") %}\
+* @{{ contributor.username }}
 {% endfor %}
 {% endif %}\
 """
@@ -47,3 +46,7 @@ commit_parsers = [
 filter_commits = true
 tag_pattern = "v[0-9].*"
 sort_commits = "oldest"
+
+[remote.github]
+owner = "imcf"
+repo = "patchworks"

{patchworks-0.3.0 → patchworks-0.4.0}/pyproject.toml

@@ -43,10 +43,17 @@ io = ["psutil", "tqdm"]
 cellpose = ["cellpose>=3.0"]
 gpu = ["nvidia-ml-py"]
 # bioio enables converting any image format (CZI, LIF, ND2, OME-TIFF, …) to
-# OME-ZARR. bioio-bioformats is the Bio-Formats catch-all reader (needs a JVM);
-# add narrower native readers too where you want them (bioio-ome-tiff,
-# bioio-czi, bioio-lif, bioio-nd2) as they are faster than going through Java.
-bioio = ["bioio", "bioio-bioformats"]
+# OME-ZARR. Ships the common native readers (faster than going through Java)
+# plus bioio-bioformats, the Bio-Formats catch-all reader (needs a JVM).
+bioio = [
+    "bioio",
+    "bioio-bioformats",
+    "bioio-nd2",
+    "bioio-ome-tiff",
+    "bioio-czi",
+    "bioio-tifffile",
+    "bioio-lif",
+]
 # napari enables the interactive viewer plugin (GUI-heavy, kept out of [all]).
 napari = ["napari[all]"]
 dev = ["pytest", "pytest-cov", "scikit-image", "psutil", "tqdm"]