Merge pull request #9 from jburel/add_badges

Add flake8 and updates of the readme

.github/workflows/publish_pypi.yml

@@ -7,9 +7,15 @@ 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/setup-node@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      - uses: actions/setup-node@v4
+      - name: Run flake8
+        run: |
+          python -mpip install flake8
+          flake8 .
       - name: Build a binary wheel and a source tarball
         run: |
           python -mpip install wheel

README.rst

@@ -1,5 +1,13 @@
+.. image:: https://github.com/German-BioImaging/omero-autotag/workflows/PyPI/badge.svg
+   :target: https://github.com/German-BioImaging/omero-autotag/actions
+
+.. image:: https://badge.fury.io/py/omero-autotag.svg
+    :target: https://badge.fury.io/py/omero-autotag
+
+
 OMERO.autotag
-================
+=============
+
 OMERO.autotag is a plugin for `OMERO.web <https://github.com/ome/omero-web>`_ that automates the application of tags to images based on the
 original filename, path, and extensions of the images.
 
@@ -12,9 +20,9 @@ As Python 2 has now reached end-of-life, OMERO 5.6 now
 requires Python 3. With release 3.1.0 of autotag, the following are now required. To use autotag on older OMERO systems (running Python 2),
 please use versions older than 3.1.0.
 
-* Python 3.5 or later
+* Python 3.8 or later
 * omero-web 5.6 or later
-* django 1.11 or later
+* django 4.2 or later
 
 User Documentation
 ==================
@@ -122,14 +130,14 @@ Harvard Medical School, then later extended by DPWR
 Consulting Ltd.
 
 These plugins were developed originally with the
-support of [Micron Advanced Bioimaging Unit](https://micronoxford.com/)
+support of `Micron Advanced Bioimaging Unit <https://micronoxford.com/>`_
 funded by the Wellcome Trust Strategic Award 091911,
-and [Open Microscopy](https://www.openmicroscopy.org/).
+and `Open Microscopy <https://www.openmicroscopy.org/>`_.
 
-Continued development was supported by [The Laboratory
-of Systems Pharmacology, Harvard Medical School](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/research-program/) and
-[Research Computing, Harvard Medical School](https://it.hms.harvard.edu/our-services/research-computing).
+Continued development was supported by `The Laboratory
+of Systems Pharmacology, Harvard Medical School <https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/research-program/>`_ and
+`Research Computing, Harvard Medical School <https://it.hms.harvard.edu/our-services/research-computing>`_.
 
 Continued development was sponsored by
-[Micron Advanced Bioimaging Unit](https://micronoxford.com/)
+`Micron Advanced Bioimaging Unit <https://micronoxford.com/>`_
 funded by the Wellcome Trust Strategic Award 107457.

omero_autotag/utils.py

@@ -3,47 +3,48 @@
 from omero.rtypes import rlong
 
 
-def createTagAnnotationsLinks(conn, additions=[], removals=[]):
+def create_tag_annotations_links(conn, additions=[], removals=[]):
     """
     Links or unlinks existing Images with existing Tag annotations
 
     @param additions:       List of tags to add to images
     @param additions:       List of tags to remove from images
     """
 
-    newLinks = []
+    new_links = []
     # Create a list of links to apply
     for addition in additions:
         link = omero.model.ImageAnnotationLinkI()
         link.parent = omero.model.ImageI(addition[0], False)
         link.child = omero.model.TagAnnotationI(addition[1], False)
-        newLinks.append(link)
+        new_links.append(link)
 
     # Apply the links
     failed = 0
-    savedLinks = []
+    saved_links = []
+    svc = conn.getUpdateService()
     try:
         # will fail if any of the links already exist
-        savedLinks = conn.getUpdateService().saveAndReturnArray(
-            newLinks, conn.SERVICE_OPTS
+        saved_links = svc.saveAndReturnArray(
+            new_links, conn.SERVICE_OPTS
         )
     except omero.ValidationException:
         # This will occur if the user has modified the tag landscape outside
         # of the auto-tagger while using the auto-tagger. Not likely to often
         # happen, but very possible.
 
-        for link in newLinks:
+        for link in new_links:
             try:
-                savedLinks.append(
-                    conn.getUpdateService().saveAndReturnObject(link, conn.SERVICE_OPTS)
+                saved_links.append(
+                    svc.saveAndReturnObject(link, conn.SERVICE_OPTS)
                 )
             except omero.ValidationException:
                 failed += 1
 
     if len(removals) > 0:
         # Get existing links belonging to current user (all at once to save
         # on queries)
-        allImageIds, allTagIds = list(zip(*removals))
+        all_image_ids, all_tag_ids = list(zip(*removals))
 
         params = omero.sys.Parameters()
         params.theFilter = omero.sys.Filter()
@@ -52,8 +53,8 @@ def createTagAnnotationsLinks(conn, additions=[], removals=[]):
         # tags, otherwise we'd have to get them individually.
         links = conn.getAnnotationLinks(
             "Image",
-            parent_ids=list(allImageIds),
-            ann_ids=list(allTagIds),
+            parent_ids=list(all_image_ids),
+            ann_ids=list(all_tag_ids),
             params=params,
         )
 

omero_autotag/views.py

@@ -13,7 +13,7 @@
 import omero
 from omero.rtypes import rstring, unwrap
 from omeroweb.webclient import tree
-from .utils import createTagAnnotationsLinks
+from .utils import create_tag_annotations_links
 
 logger = logging.getLogger(__name__)
 
@@ -30,19 +30,19 @@ def process_update(request, conn=None, **kwargs):
     removals = []
 
     for image in images:
-        image_id = image["imageId"]
+        iid = image["imageId"]
 
         additions.extend(
-            [(int(image_id), int(addition),) for addition in image["additions"]]
+            [(int(iid), int(addition),) for addition in image["additions"]]
         )
 
         removals.extend(
-            [(int(image_id), int(removal),) for removal in image["removals"]]
+            [(int(iid), int(removal),) for removal in image["removals"]]
         )
 
-    # TODO Interface for createTagAnnotationsLinks is a bit nasty, but go
+    # TODO Interface for create_tag_annotations_links is a bit nasty, but go
     # along with it for now
-    createTagAnnotationsLinks(conn, additions, removals)
+    create_tag_annotations_links(conn, additions, removals)
 
     return HttpResponse("")
 

setup.py

@@ -60,22 +60,23 @@ def run(self):
     description=DESCRIPTION,
     long_description=read_file("README.rst"),
     classifiers=[
-        "Development Status :: 5 - Production/Stable",
-        "Environment :: Web Environment",
-        "Framework :: Django",
-        "Intended Audience :: End Users/Desktop",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: GNU Affero General Public License v3",
-        "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",
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Web Environment',
+        'Framework :: Django',
+        'Intended Audience :: End Users/Desktop',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: GNU Affero General Public License v3',
+        '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'
     ],
     author=AUTHOR,
     author_email="[email protected]",