Overhaul repo infrastructure

.ci/310.yaml

@@ -13,10 +13,14 @@ dependencies:
   - scipy>=1.3.2
   - shapely
   - spaghetti
-  - tqdm=>4.27.0
+  - tqdm>=4.27.0
   # testing
   - codecov
   - coverage
   - pytest
   - pytest-cov
   - pytest-xdist
+  # with pip
+  - pip
+  - pip:
+    - pulp

.ci/311-DEV.yaml

@@ -3,12 +3,12 @@ channels:
   - conda-forge
 dependencies:
   - python=3.11
-  - geopandas>=0.10.0
+  - geopandas
+  - libpysal
   - matplotlib
   - networkx
   - numpy>=1.21
   - pandas>=1.0.5
-  - pip
   - scikit-learn>=0.22
   - scipy>=1.3.2
   - spaghetti
@@ -19,3 +19,12 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-xdist
+  # with pip
+  - pip
+  - pip:
+    - pulp
+    - 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/mapclassify.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
@@ -26,3 +25,8 @@ dependencies:
   - sphinx
   - sphinxcontrib-bibtex
   - sphinx_bootstrap_theme
+  # with pip
+  - pip
+  - pip:
+    - pulp
+

.ci/38-MIN.yaml

@@ -19,3 +19,7 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-xdist
+  # with pip
+  - pip
+  - pip:
+    - pulp

.ci/39.yaml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python=3.9
-  - geopandas>=0.10.0
+  - geopandas
   - libpysal
   - matplotlib
   - networkx
@@ -20,3 +20,7 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-xdist
+  # with pip
+  - pip
+  - pip:
+    - pulp

.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
@@ -45,15 +44,12 @@
            environment-file: ${{ matrix.environment-file }}
            micromamba-version: 'latest'
            channel-priority: 'flexible'
-
-       - 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')
+
+       ##############################################################################
+       #- name: install pulp via pip
+       #  shell: bash -l {0}
+       #  run: pip install pulp
+       ##############################################################################
 
        - name: environment info
          shell: bash -l {0}
@@ -80,4 +76,14 @@
          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