Create .flake8

.flake8

@@ -0,0 +1,5 @@
+# .flake8
+[flake8]
+exclude = docs/
+ignore = E501, W503, E203, E266, E402
+max-line-length = 88

.github/workflows/build-main.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Test with pytest
       run: |
         pytest --cov-report xml --cov=vessel_analysis_3d vessel_analysis_3d/tests/
@@ -50,9 +50,9 @@ jobs:
     - name: Lint with flake8
       run: |
         flake8 vessel_analysis_3d --count --verbose --show-source --statistics
-    - name: Check with black
-      run: |
-        black --check vessel_analysis_3d
+    #- name: Check with black
+    #  run: |
+    #    black --check vessel_analysis_3d
 
   publish:
     if: "contains(github.event.head_commit.message, 'Bump version')"
@@ -68,12 +68,11 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel
+        pip install build
     - name: Build Package
-      run: |
-        python setup.py sdist bdist_wheel
+      run: python -m build
     - name: Publish to PyPI
       uses: pypa/gh-action-pypi-publish@master
       with:
-        user: MMV-Lab
+        user: __token__
         password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test-and-lint.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Test with pytest
       run: |
         pytest vessel_analysis_3d/tests/
@@ -38,10 +38,10 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .[test]
+        pip install .[test] --verbose
     - name: Lint with flake8
       run: |
         flake8 vessel_analysis_3d --count --verbose --show-source --statistics
-    - name: Check with black
-      run: |
-        black --check vessel_analysis_3d
+    # - name: Check with black
+    #  run: |
+    #    black --check vessel_analysis_3d

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61.0"]
+requires = ["setuptools>=64", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -12,14 +12,13 @@ license = {file = "LICENSE"}
 authors = [
     {name = "Jianxu Chen", email = "jianxuchen.ai@gmail.com"},
 ]
-keywords = ["vessel_analysis_3d"]
+keywords = ["vessel analysis", "morphology", "topology"]
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Developers",
-    "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
 ]
 dependencies = [
     "bioio==1.6.1",
@@ -69,16 +68,51 @@ dev = [
     "wheel>=0.34.2",
 ]
 
+all = [
+    "vessel_analysis_3d[dev]",
+    "vessel_analysis_3d[test]",
+    "vessel_analysis_3d[setup]",
+]
+
 [project.urls]
 Homepage = "https://github.com/MMV-Lab/vessel_analysis_3d"
 
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.packages.find]
+include = ["vessel_analysis_3d"]
+
 [project.scripts]
 run_vessel_analysis = "vessel_analysis_3d.bin.run_analysis:main"
 
 [tool.pytest.ini_options]
-collect_ignore = ["setup.py"]
+addopts = "--cov=vessel_analysis_3d --no-cov-on-fail --cov-report=term-missing --cov-report=xml --cov-branch --durations=10"
+testpaths = [
+    "vessel_analysis_3d/tests",
+]
+python_files = "test_*.py"
+
 
 [tool.flake8]
-exclude = ["docs/"]
-ignore = ["E203", "E402", "W291", "W503", "E501"]
-max-line-length = 88
+exclude = [
+    "docs/",
+    ".git/",
+    "__pycache__/",
+    "build/",
+    "dist/",
+    ".venv/",
+    ".tox/",
+    "*.egg-info/",
+]
+ignore = [
+	"E203",
+	"E402",
+	"W291",
+	"W503",
+	"W293",
+	"W292",
+	"E501",
+] 
+max-line-length = 88

setup.cfg

@@ -3,13 +3,13 @@ current_version = 0.0.1
 commit = True
 tag = True
 
-[bumpversion:file:setup.py]
-search = version="{current_version}"
-replace = version="{new_version}"
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
 
 [bumpversion:file:vessel_analysis_3d/__init__.py]
-search = {current_version}
-replace = {new_version}
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
 
 ignore = E203, E402, W291, W503, W293, W292, E501
 max-line-length = 88

vessel_analysis_3d/__init__.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 """Top-level package for 3D Vascular Structure Analysis."""
+from .processing_pipeline import Pipeline3D  # noqa: F401
 
 __author__ = "Jianxu Chen"
 __email__ = "jianxuchen.ai@gmail.com"
@@ -11,6 +12,3 @@
 
 def get_module_version():
     return __version__
-
-
-from .processing_pipeline import Pipeline3D  # noqa: F401

vessel_analysis_3d/graph/core.py

@@ -217,15 +217,15 @@ def prune_and_analyze(self, return_final_skel: bool = True):
                     # fill dictionaries containing all filament, segment and branch
                     # point statistics
                     self.segStatsDict[ithDisjointGraph] = filament.segmentStats
-                    self.filStatsDict[ithDisjointGraph][
-                        "TerminalPoints"
-                    ] = self.countEndPointsDict[ithDisjointGraph]
-                    self.filStatsDict[ithDisjointGraph][
-                        "BranchPoints"
-                    ] = self.countBranchPointsDict[ithDisjointGraph]
-                    self.filStatsDict[ithDisjointGraph][
-                        "Segments"
-                    ] = self.countSegmentsDict[ithDisjointGraph]
+                    self.filStatsDict[ithDisjointGraph]["TerminalPoints"] = (
+                        self.countEndPointsDict[ithDisjointGraph]
+                    )
+                    self.filStatsDict[ithDisjointGraph]["BranchPoints"] = (
+                        self.countBranchPointsDict[ithDisjointGraph]
+                    )
+                    self.filStatsDict[ithDisjointGraph]["Segments"] = (
+                        self.countSegmentsDict[ithDisjointGraph]
+                    )
                     self.branchesBrPtDict[ithDisjointGraph] = filament.brPtsDict
                 else:
                     self.infoDict["filaments"] -= 1

vessel_analysis_3d/graph/filament.py

@@ -97,13 +97,13 @@ def dfs_iterative(self):
                     ):  # cycle found
                         if len(self.graph[neighbor]) > 2:  # neighbor is branch point
                             oldPred = self._predDict[neighbor]
-                            self._predDict[
-                                neighbor
-                            ] = vertex  # change predecessor to get segment of cycle
+                            self._predDict[neighbor] = (
+                                vertex  # change predecessor to get segment of cycle
+                            )
                             segment = self._getSegment(neighbor)
-                            self._predDict[
-                                neighbor
-                            ] = oldPred  # change back to old predecessor
+                            self._predDict[neighbor] = (
+                                oldPred  # change back to old predecessor
+                            )
                             self._setSegStats(segment, interpolate=self.interpolate)
                 if len(self.graph[vertex]) == 1:  # end point found
                     self.endPtsList.append(vertex)

vessel_analysis_3d/graph/stats_reporting.py

@@ -66,7 +66,7 @@ def getAllStats(dictionary: Dict, imgName: str) -> List:
         for segment in dictionary[filament]:
             final = []
             for element in segment:
-                element= tuple(int(x) for x in element)
+                element = tuple(int(x) for x in element)
                 final.append(element)
             segment = tuple(final)
             list_item = [imgName, filament, segment]