General cleanup

.github/workflows/publish_pypi.yml

@@ -11,8 +11,8 @@ jobs:
       - uses: actions/setup-python@v2
       - name: Build a binary wheel and a source tarball
         run: |
-          python -mpip install setuptools versioneer wheel
-          python setup.py sdist bdist_wheel
+          python -mpip install setuptools build wheel
+          python -m build
       - name: Publish distribution to PyPI
         if: startsWith(github.ref, 'refs/tags')
         uses: pypa/[email protected]

.isort.cfg

@@ -1,2 +1,2 @@
 [settings]
-known_third_party = entrypoints,omero,omero_marshal,omero_rdf,rdflib,setuptools,versioneer,wikidataintegrator
+known_third_party = entrypoints,omero,omero_marshal,omero_rdf,rdflib,wikidataintegrator

.pre-commit-config.yaml

@@ -63,7 +63,7 @@ repos:
         ]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.971
+    rev: v1.7.1
     hooks:
       - id: mypy
         language_version: python3

pyproject.toml

@@ -0,0 +1,71 @@
+[build-system]
+requires = [
+    "setuptools>=60",
+    "setuptools-scm>=8.0",
+]
+
+[tools.setuptools.dynamic]
+version = {attr = "omero_rdf.__version__"}
+
+[project]
+name = "omero-rdf"
+readme = "README.rst"
+dynamic = ["version"]
+description="A plugin for exporting rdf from OMERO"
+
+requires-python = ">3.8"
+
+dependencies = [
+    "omero-py>=5.8",
+    "entrypoints",
+    "types-entrypoints",
+    "future",
+    "rdflib",
+    "omero-marshal",
+    "wikidataintegrator",
+]
+
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Environment :: Plugins",
+    "Intended Audience :: Developers",
+    "Intended Audience :: End Users/Desktop",
+    "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+
+keywords = [
+    "OMERO.cli", "plugin",
+]
+
+authors = [
+    {name = "The Open Microscopy Team"},
+]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+    "restview",
+    "mox3",
+]
+
+[project.urls]
+Repository = "https://github.com/German-BioImaging/omero-rdf"
+Changelog = "https://github.com/German-BioImaging/omero-rdf/blob/master/CHANGES.txt"
+
+[project.entry-points."omero_rdf.annotation_handler"]
+idr_annotations = "omero_rdf.idr_annotations:IDRAnnotationHandler"
+
+[tool.setuptools]
+package-dir = {""= "src"}
+
+[tools.mypy]
+check_untyped_defs = true
+disallow_incomplete_defs = true
+disallow_untyped_defs = true
+no_implicit_optional = true
+disallow_any_generics = false
+ignore_missing_imports = true

src/omero_rdf/__init__.py

@@ -154,9 +154,9 @@ def handle(self, data: Data) -> None:
             if output:
                 s, p, o = output
                 if None in (s, p, o):
-                    print(f""" skipping None value: {s} {p} {o}""")
+                    logging.debug("skipping None value: %s %s %s", s, p, o)
                 else:
-                    print(f"""{s.n3():50}\t{p.n3():60}\t{o.n3()} .""")
+                    print(f"""{s.n3()}\t{p.n3()}\t{o.n3()} .""")
 
     def rdf(
         self, data: Data, _id: Optional[Subj] = None
@@ -180,7 +180,7 @@ def rdf(
                 raise Exception(f"missing id: {data}")
             _id = self.get_identity(_type, str_id)
             if _id in self.cache:
-                logging.debug(f"# skipping previously seen {_id}")
+                logging.debug("# skipping previously seen %s", _id)
                 return
             else:
                 self.cache.add(_id)
@@ -344,6 +344,3 @@ def _lookup(
         if not obj:
             self.ctx.die(110, f"No such {_type}: {oid}")
         return obj
-
-from . import _version
-__version__ = _version.get_versions()['version']