Overhaul repo infrastructure (#721)

* update pre-commit

* update infrastructure

* ruff [1]

* ruffen repo [2]

* update infra [2]

* update extract_comp() stacklevel

* noqa ARG001 for geom_col for now

.github/workflows/release_and_publish.yml

@@ -34,8 +34,9 @@ jobs:
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine jupyter urllib3 pandas pyyaml
-          python setup.py sdist bdist_wheel
+          python -m pip install --upgrade build twine
+          python -m build
+          twine check --strict dist/*
       
       - name: Create Release Notes
         uses: actions/github-script@v6

.github/workflows/testing.yml

@@ -27,7 +27,7 @@
    testing:
      needs: linting
      env:
-       RUN_TEST: pytest spaghetti -v -r a -n auto --cov spaghetti --doctest-modules --cov-config .coveragerc --cov-report xml --color yes --cov-append --cov-report term-missing --timeout 60
+       RUN_TEST: pytest spaghetti -v -r a -n auto --cov spaghetti --doctest-modules --cov-report xml --color yes --cov-append --cov-report term-missing --timeout 60
      name: ${{ matrix.os }}, ${{ matrix.environment-file }}
      runs-on: ${{ matrix.os }}
      timeout-minutes: 30

.pre-commit-config.yaml

@@ -1,18 +1,14 @@
+files: 'spaghetti\/'
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    language_version: python3
-- repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
-    entry: pflake8
-    additional_dependencies: [pyproject-flake8]
-    language_version: python3
-- repo: https://github.com/psf/black
-  rev: 23.3.0
-  hooks:
-  - id: black
-    language_version: python3
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        language_version: python3
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.0.265"
+    hooks:
+      - id: ruff
+
+ci:
+  autofix_prs: false

environment.yml

@@ -2,7 +2,7 @@ name: notebooks-environment
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.11
   - esda
   - geopandas>=0.12.0
   - libspatialindex

pyproject.toml

@@ -1,14 +1,9 @@
 [build-system]
-requires = [
-    "black",
-    "isort",
-    "pyproject-flake8",
-    "setuptools>=61.0.0",
-    "versioneer[toml]",
-
-]
+requires = ["setuptools>=61.0", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools_scm]
+
 [project]
 name = "spaghetti"
 dynamic = ["version"]
@@ -55,10 +50,8 @@ Repository = "https://github.com/pysal/spaghetti"
 [project.optional-dependencies]
 dev = [
     "black",
-    "flake8",
-    "isort",
+    "ruff",
     "pre-commit",
-    "pyproject-flake8",
 ]
 docs = [
     "nbsphinx",
@@ -100,40 +93,44 @@ include = [
     "spaghetti.*",
 ]
 
-[tool.versioneer]
-VCS = "git"
-style = "pep440"
-versionfile_source = "spaghetti/_version.py"
-versionfile_build = "spaghetti/_version.py"
-tag_prefix = "v"
-parentdir_prefix = "spaghetti-"
-
-[tool.isort]
-profile = "black"
-src_paths = ["spaghetti"]
-skip = [
-    "docs/conf.py",
-    "versioneer.py",
-    "spaghetti/_version.py"
-]
-
-[tool.flake8]
-max_line_length = 88
-per-file-ignores = [
-    "*__init__.py:F401",
-]
-exclude = [
-    "docs/conf.py",
-    "versioneer.py",
-    "spaghetti/_version.py"
-]
-
 [tool.black]
 line-length = 88
 extend-exclude = '''
 (
   docs/conf.py
-  "versioneer.py",
-  "spaghetti/_version.py"
 )
-'''
+#'''
+
+[tool.ruff]
+line-length = 88
+select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
+target-version = "py38"
+ignore = [
+    "B006",
+    "B008",
+    "B009",
+    "B010",
+    "C408",
+    "E731",
+    "F401",
+    "F403",
+    "N803",
+    "N806",
+    "N999",
+    "UP007"
+]
+exclude = ["spaghetti/tests/*", "docs/*"]
+
+[tool.coverage.run]
+source = ["./spaghetti"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "if self.debug:",
+    "pragma: no cover",
+    "raise NotImplementedError",
+    "except ModuleNotFoundError:",
+    "except ImportError",
+]
+ignore_errors = true
+omit = ["spaghetti/tests/*", "docs/conf.py"]

spaghetti/__init__.py

@@ -2,7 +2,9 @@
 # `spaghetti` --- Spatial Graphs: Networks, Topology, & Inference
 """
 
-from . import _version
+import contextlib
+from importlib.metadata import PackageNotFoundError, version
+
 from .network import (
     Network,
     PointPattern,
@@ -13,4 +15,5 @@
     spanning_tree,
 )
 
-__version__ = _version.get_versions()["version"]
+with contextlib.suppress(PackageNotFoundError):
+    __version__ = version("spaghetti")