Build

.github/workflows/omero_plugin.yml

@@ -23,7 +23,7 @@ jobs:
     env:
       STAGE: app
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:

.github/workflows/publish_pypi.yml

@@ -7,14 +7,16 @@ jobs:
     name: Build and publish Python distribution to PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
       - name: Build a binary wheel and a source tarball
         run: |
-          python -mpip install wheel
-          python setup.py sdist bdist_wheel
+          python -m pip install build
+          python -m build
       - name: Publish distribution to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@v1.3.0
+        uses: pypa/gh-action-pypi-publish@v1.8.14
         with:
           password: ${{ secrets.PYPI_PASSWORD }}

.omeroci/app-deps

@@ -0,0 +1,12 @@
+#!/bin/bash
+source /infra/utils
+
+set -u
+set -x
+
+TARGET=${TARGET:-..}
+
+dir=$(cd -P -- "$(dirname -- "$0")" && pwd -P)
+cd $TARGET
+
+pip install --upgrade ome_zarr

omero_web_zarr/utils.py

@@ -87,12 +87,12 @@ def marshal_axes(image, version):
 
 def generate_coordinate_transformations(shapes):
 
-        data_shape = shapes[0]
-        transformations = []
-        # calculate minimal 'scale' transform based on pyramid dims
-        for shape in shapes:
-            assert len(shape) == len(data_shape)
-            scale = [full / level for full, level in zip(data_shape, shape)]
-            transformations.append([{"type": "scale", "scale": scale}])
-
-        return transformations
+    data_shape = shapes[0]
+    transformations = []
+    # calculate minimal 'scale' transform based on pyramid dims
+    for shape in shapes:
+        assert len(shape) == len(data_shape)
+        scale = [full / level for full, level in zip(data_shape, shape)]
+        transformations.append([{"type": "scale", "scale": scale}])
+
+    return transformations

setup.py

@@ -69,25 +69,25 @@ def read(fname):
     version=VERSION,
     description=DESCRIPTION,
     long_description=read('README.rst'),
-          classifiers=[
-          'Development Status :: 3 - Alpha',
-          'Environment :: Web Environment',
-          'Framework :: Django',
-          'Intended Audience :: End Users/Desktop',
-          'Intended Audience :: Science/Research',
-          'Natural Language :: English',
-          'Operating System :: OS Independent',
-          'Programming Language :: JavaScript',
-          'Programming Language :: Python :: 3',
-          'Topic :: Internet :: WWW/HTTP',
-          'Topic :: Internet :: WWW/HTTP :: Dynamic Content',
-          'Topic :: Internet :: WWW/HTTP :: WSGI',
-          'Topic :: Scientific/Engineering :: Visualization',
-          'Topic :: Software Development :: Libraries :: '
-          'Application Frameworks',
-          'Topic :: Text Processing :: Markup :: HTML'
-      ],  # Get strings from
-          # http://pypi.python.org/pypi?%3Aaction=list_classifiers
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Environment :: Web Environment',
+        'Framework :: Django',
+        'Intended Audience :: End Users/Desktop',
+        'Intended Audience :: Science/Research',
+        'Natural Language :: English',
+        'Operating System :: OS Independent',
+        'Programming Language :: JavaScript',
+        'Programming Language :: Python :: 3',
+        'Topic :: Internet :: WWW/HTTP',
+        'Topic :: Internet :: WWW/HTTP :: Dynamic Content',
+        'Topic :: Internet :: WWW/HTTP :: WSGI',
+        'Topic :: Scientific/Engineering :: Visualization',
+        'Topic :: Software Development :: Libraries :: '
+        'Application Frameworks',
+        'Topic :: Text Processing :: Markup :: HTML'
+    ],  # Get strings from
+    # http://pypi.python.org/pypi?%3Aaction=list_classifiers
     author=AUTHOR,
     author_email='[email protected]',
     license=LICENSE,

test/integration/test_ngff.py

@@ -83,7 +83,7 @@ def test_image_zarr(self, user1, tmpdir, version):
         kwargs = {"iid": image_id, "version": version}
         zattrs_url = reverse('zarr_image_zattrs', kwargs=kwargs)
         zattrs_json = get_json(django_client, zattrs_url)
-        assert(len(zattrs_json["multiscales"]) == 1)
+        assert len(zattrs_json["multiscales"]) == 1
 
         zgroup_url = reverse('zarr_image_zgroup', kwargs=kwargs)
         zgroup_json = get_json(django_client, zgroup_url)