Overhaul repo infrastructure

.ci/310.yaml

@@ -13,7 +13,7 @@ dependencies:
   - scipy>=1.3.2
   - shapely
   - spaghetti
-  - tqdm=>4.27.0
+  - tqdm>=4.27.0
   # testing
   - codecov
   - coverage

.ci/311-DEV.yaml

@@ -3,19 +3,21 @@ channels:
   - conda-forge
 dependencies:
   - python=3.11
-  - geopandas>=0.10.0
   - matplotlib
-  - networkx
   - numpy>=1.21
   - pandas>=1.0.5
   - pip
   - scikit-learn>=0.22
   - scipy>=1.3.2
-  - spaghetti
   - tqdm>=4.27.0
   # testing
   - codecov
   - coverage
   - pytest
   - pytest-cov
   - pytest-xdist
+  - pip:
+    - git+https://github.com/geopandas/geopandas.git
+    - git+https://github.com/networkx/networkx.git
+    - git+https://github.com/pysal/libpysal.git
+    - git+https://github.com/pysal/spaghetti.git

.ci/311.yaml

@@ -3,15 +3,14 @@ channels:
   - conda-forge
 dependencies:
   - python=3.11
-  - geopandas>=0.10.0
+  - geopandas
   - libpysal
   - matplotlib
   - networkx
   - numpy>=1.21
   - pandas>=1.0.5
   - scikit-learn>=0.22
   - scipy>=1.3.2
-  - shapely
   - spaghetti
   - tqdm=>4.27.0
   # testing

.ci/39.yaml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python=3.9
-  - geopandas>=0.10.0
+  - geopandas
   - libpysal
   - matplotlib
   - networkx

.github/workflows/testing.yml

@@ -16,7 +16,7 @@
      runs-on: ${{ matrix.os }}
      timeout-minutes: 30
      env:
-       RUN_TEST: pytest spopt -v -r a -n auto --cov spopt --cov-config .coveragerc --cov-report xml --color yes --cov-append --cov-report term-missing
+       RUN_TEST: pytest spopt -v -r a -n auto --cov spopt --color yes --cov-report term-missing --cov-append --cov-report xml .
      strategy:
        matrix:
          os: [ubuntu-latest]
@@ -26,7 +26,6 @@
             .ci/310.yaml,
             .ci/311.yaml,
             .ci/311-DEV.yaml,
-            .ci/311-DEV_shapely_dev.yaml,
          ]
          include:
            - environment-file: .ci/311.yaml
@@ -48,12 +47,7 @@
 
        - name: install pulp via pip
          shell: bash -l {0}
-         run: pip install pulp 
-
-       - name: install bleeding edge libpysal (only Ubuntu w/ latest Python)
-         shell: bash -l {0}
-         run: pip install git+https://github.com/pysal/libpysal.git@master
-         if: matrix.os == 'ubuntu-latest' && contains(matrix.environment-file, 'DEV')
+         run: pip install pulp
 
        - name: environment info
          shell: bash -l {0}
@@ -80,4 +74,14 @@
          with:
            token: ${{ secrets.CODECOV_TOKEN }}
            file: ./coverage.xml
-           name: spot-codecov
+           name: spopt-codecov
+
+       - name: Generate and publish the report
+         if: |
+           failure()
+           && steps.status.outcome == 'failure'
+           && github.event_name == 'schedule'
+           && github.repository_owner == 'pysal'
+         uses: xarray-contrib/issue-from-pytest-log@v1
+         with:
+           log-path: pytest-log.jsonl

.gitignore

@@ -25,4 +25,7 @@ lib
 lib64
 __pycache__
 
-.coverage
+.coverage
+
+.ruff_cache
+.pytest_cache

.pre-commit-config.yaml

@@ -1,6 +1,14 @@
+files: 'spopt\/'
 repos:
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:
-    - id: black
-      language_version: python3
+      - id: black
+        language_version: python3
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.0.252"
+    hooks:
+      - id: ruff
+
+ci:
+  autofix_prs: false

codecov.yml

@@ -1,6 +1,6 @@
 codecov:
   notify:
-    after_n_builds: 8
+    after_n_builds: 7
 coverage:
   range: 50..95
   round: nearest
@@ -18,5 +18,5 @@ coverage:
 comment:
   layout: "reach, diff, files"
   behavior: once
-  after_n_builds: 8
+  after_n_builds: 7
   require_changes: true

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies: 
   - python=3.10
-  - geopandas>=0.10.0
+  - geopandas>=0.12.0
   - jupyterlab
   - libpysal
   - mapclassify
@@ -14,6 +14,7 @@ dependencies:
   - pulp
   - scikit-learn>=0.22
   - scipy>=1.3.2
+  - shapely>=2.0
   - tqdm>=4.27.0
 
   # notebook/binder specific

pyproject.toml

@@ -0,0 +1,106 @@
+[build-system]
+requires = ["setuptools>=61.0", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+
+[project]
+name = "spopt"
+dynamic = ["version"]
+authors = [
+    { name = "James D. Gaboardi", email = "[email protected]" },
+    { name = "Xin Feng", email = "[email protected]" },
+]
+
+maintainers = [{ name = "spopt contributors" }]
+license = { text = "BSD 3-Clause" }
+description = "Spatial Optimization in PySAL"
+keywords = ["spatial optimization"]
+readme = { text = """\
+Spopt is an open-source Python library for solving optimization problems with spatial data. Originating from the `region` module in `PySAL`_ (Python Spatial Analysis Library), it is under active development for the inclusion of newly proposed models and methods for regionalization, facility location, and transportation-oriented solutions.
+
+.. _PySAL: http://pysal.org
+""", content-type = "text/x-rst" }
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: GIS",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "geopandas>=0.10.0",
+    "libpysal",
+    "mapclassify",
+    "networkx",
+    "numpy>=1.21",
+    "pandas>=1.0.5",
+    "pulp",
+    "scikit-learn>=0.22",
+    "scipy>=1.3.2",
+    "spaghetti",
+    "tqdm>=4.27.0",
+]
+
+
+[project.urls]
+Home = "https://pysal.org/spopt/"
+Repository = "https://github.com/pysal/spopt"
+
+[project.optional-dependencies]
+tests = [
+    "codecov",
+    "coverage",
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+]
+dev = ["pre-commit"]
+docs = [
+    "nbsphinx",
+    "numpydoc",
+    "pandoc",
+    "sphinx",
+    "sphinxcontrib-bibtex",
+    "sphinx_bootstrap_theme",
+]
+notebooks = [
+    "folium",
+    "glpk",
+    "inequality",
+    "matplotlib",
+    "matplotlib-scalebar",
+    "overpy",
+    "routingpy",
+    "seaborn",
+    "watermark",
+]
+
+
+[tool.setuptools.packages.find]
+include = ["spopt", "spopt.*"]
+
+[tool.black]
+line-length = 88
+
+[tool.ruff]
+line-length = 88
+select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
+target-version = "py311"
+ignore = ["B006", "F401", "F403"]
+exclude = ["spopt/tests/*", "docs/*"]
+
+[tool.coverage.run]
+source = ["spopt"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "if self.debug:",
+    "pragma: no cover",
+    "raise NotImplementedError",
+    "except ModuleNotFoundError:",
+    "except ImportError",
+]
+ignore_errors = true
+omit = ["spopt/tests/*", "docs/conf.py"]