merge upstream/main

pysal · Oct 7, 2023 · 9644f56 · 9644f56
2 parents 8a5a8a1 + c0ead26
commit 9644f56
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diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/release.yml b/.github/release.yml
@@ -0,0 +1,16 @@
+changelog:
+  exclude:
+    labels:
+      - ignore-for-release
+    authors:
+      - dependabot
+  categories:
+    - title: Bug Fixes
+      labels:
+        - bug
+    - title: Enhancements
+      labels:
+        - enhancement
+    - title: Other Changes
+      labels:
+        - "*"
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
@@ -1,44 +1,48 @@
  name: Build Docs
-
  on:
    push:
-     # Sequence of patterns matched against refs/tags
-     tags:
-       - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
-   workflow_dispatch:
-     inputs:
-       version:
-         description: Manual Doc Build Reason
-         default: test
-         required: false
+     branches:
+     - master
+     - main
  jobs:
    docs:
-     name: build & push docs
+     name: CI (${{ matrix.os }}-${{ matrix.environment-file }})
      runs-on: ${{ matrix.os }}
-     timeout-minutes: 90
+     continue-on-error: ${{ matrix.experimental }}
+     timeout-minutes: 20
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [ci/310.yaml]
+         environment-file: [ci/39.yaml]
          experimental: [false]
      defaults:
        run:
          shell: bash -l {0}
-
      steps:
-       - name: checkout repo
-         uses: actions/checkout@v3
-
-       - name: setup micromamba
-         uses: mamba-org/provision-with-micromamba@main
+       - uses: actions/checkout@v4
+       - uses: actions/cache@v3
+         env:
+           CACHE_NUMBER: 0
          with:
-           environment-file: ${{ matrix.environment-file }}
-           micromamba-version: 'latest'
-
-       - name: make docs
-         run: cd docs; make html
-
-       - name: commit docs
+           path: ~/conda_pkgs_dir
+           key: ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(matrix.environment-file) }}
+       - uses: conda-incubator/setup-miniconda@v2
+         with:
+            miniconda-version: 'latest'
+            channels: conda-forge
+            channel-priority: true
+            auto-update-conda: true
+            auto-activate-base: false
+            environment-file: ${{ matrix.environment-file }}
+            activate-environment: test
+            use-only-tar-bz2: true
+       - run: conda info --all
+       - run: conda list
+       - run: conda config --show-sources
+       - run: conda config --show
+       - run: pip install -e . --no-deps --force-reinstall
+       - run: cd docs; make html
+       - name: Commit documentation changes
          run: |
            git clone https://github.com/ammaraskar/sphinx-action-test.git --branch gh-pages --single-branch gh-pages
            cp -r docs/_build/html/* gh-pages/
@@ -47,10 +51,9 @@
            git config --local user.name "GitHub Action"
            git add .
            git commit -m "Update documentation" -a || true
-           # The above command will fail if no changes were present,
-           # so we ignore the return code.
-       
-       - name: push to gh-pages
+           # The above command will fail if no changes were present, so we ignore
+           # the return code.
+       - name: Push changes
          uses: ad-m/github-push-action@master
          with:
             branch: gh-pages

diff --git a/.github/workflows/release_and_publish.yml b/.github/workflows/release_and_publish.yml
@@ -7,59 +7,52 @@
  # under the user's name, not the organzation.
 
  #--------------------------------------------------
- name: Release & Publish
+name: Release & Publish
 
- on:
-   push:
-     # Sequence of patterns matched against refs/tags
-     tags:
-       - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
-
- jobs:
-   build:
-     name: Create release & publish to PyPI
-     runs-on: ubuntu-latest
-     steps:
-       - name: Checkout repo
-         uses: actions/checkout@v3
-
-       - name: Set up python
-         uses: actions/setup-python@v4
-         with:
-           python-version: "3.x"
-
-       - name: Install Dependencies
-         run: |
-           python -m pip install --upgrade pip
-           pip install setuptools wheel twine jupyter urllib3 pandas pyyaml versioneer
-           python setup.py sdist bdist_wheel
- 
-       - name: run Changelog
-         run: |
-           jupyter nbconvert --to notebook --execute --inplace  --ExecutePreprocessor.timeout=-1  --ExecutePreprocessor.kernel_name=python3 tools/gitcount.ipynb
- 
-       - name: cat Changelog
-         uses: pCYSl5EDgo/cat@master
-         id: changetxt
-         with:
-           path: ./tools/changelog.md
-         env:
-           TEXT: ${{ steps.changetxt.outputs.text }}
-
-       - name: Get the tag name
-         run: echo "TAG=${GITHUB_REF/refs\/tags\//}" >> $GITHUB_ENV
-
-       - name: Release
-         uses: softprops/action-gh-release@v1
-         with:
-           body: ${{ steps.changetxt.outputs.text }}
-           body_path: ${{ steps.changetxt.outputs.path }}
-           name: Release ${{ env.TAG }}
-         env:
-           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-       - name: Publish distribution 📦 to PyPI
-         uses: pypa/gh-action-pypi-publish@master
-         with:
-           user: __token__
-           password: ${{ secrets.PYPI_PASSWORD }}
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  workflow_dispatch:
+    inputs:
+      version:
+        description: Manual Release
+        default: test
+        required: false
+
+jobs:
+  build:
+    name: Create release & publish to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade build twine
+          python -m build
+          twine check --strict dist/*
+      
+      - name: Create Release Notes
+        uses: actions/github-script@v6
+        with:
+          github-token: ${{secrets.GITHUB_TOKEN}}
+          script: |
+            await github.request(`POST /repos/${{ github.repository }}/releases`, {
+              tag_name: "${{ github.ref }}",
+              generate_release_notes: true
+            });
+      
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
@@ -21,11 +21,11 @@
        matrix:
          os: [ubuntu-latest]
          environment-file:
-           - ci/38.yaml
            - ci/39.yaml
            - ci/310.yaml
            - ci/310-BASE.yaml
            - ci/310-DEV.yaml
+           - ci/311.yaml
          include:
            - environment-file: ci/310.yaml
              os: macos-latest
@@ -34,7 +34,7 @@
 
      steps:
        - name: checkout repo
-         uses: actions/checkout@v3
+         uses: actions/checkout@v4
 
        - name: setup micromamba
          uses: mamba-org/provision-with-micromamba@main
@@ -44,7 +44,7 @@
 
        - name: install bleeding edge libpysal (only Ubuntu / Python 3.9)
          shell: bash -l {0}
-         run: pip install git+https://github.com/pysal/libpysal.git@master
+         run: pip install git+https://github.com/pysal/libpysal.git@main
          if: matrix.os == 'ubuntu-latest' && contains(matrix.environment-file, 'DEV')
 
        - name: run tests - bash

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/Makefile b/Makefile
diff --git a/ci/38.yaml → ci/311.yaml b/ci/38.yaml → ci/311.yaml
@@ -2,7 +2,7 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.11
   # required
   - libpysal
   - numpy>=1.3

diff --git a/docs/api.rst b/docs/api.rst
@@ -47,6 +47,7 @@ Regimes models are variants of spatial regression models which allow for structu
     :toctree: generated/
 
     spreg.OLS_Regimes
+    spreg.TSLS_Regimes
     spreg.ML_Lag_Regimes
     spreg.ML_Error_Regimes
     spreg.GM_Lag_Regimes
@@ -59,6 +60,7 @@ Regimes models are variants of spatial regression models which allow for structu
     spreg.GM_Endog_Error_Regimes
     spreg.GM_Endog_Error_Hom_Regimes
     spreg.GM_Endog_Error_Het_Regimes
+    spreg.Skater_reg
 
 Seemingly-Unrelated Regressions
 --------------------------------
@@ -74,17 +76,6 @@ Seemingly-unrelated regression models are a generalization of linear regression.
     spreg.SURlagIV
     spreg.ThreeSLS
 
-Panel Models
-------------
-
-.. autosummary::
-    :toctree: generated/
-
-    spreg.Panel_FE_Lag
-    spreg.Panel_FE_Error
-    spreg.Panel_RE_Lag
-    spreg.Panel_RE_Error
-
 Spatial Panel Models
 --------------------
 
@@ -93,6 +84,10 @@ Spatial panel models allow for evaluating correlation in both spatial and time d
 .. autosummary::
    :toctree: generated/
 
+    spreg.Panel_FE_Lag
+    spreg.Panel_FE_Error
+    spreg.Panel_RE_Lag
+    spreg.Panel_RE_Error
     spreg.GM_KKP
 
 Diagnostics
@@ -128,3 +123,8 @@ Diagnostic tests are useful for identifying model fit, sufficiency, and specific
     spreg.surLMe
     spreg.surLMlag
     spreg.constant_check
+    spreg.panel_LMlag
+    spreg.panel_LMerror
+    spreg.panel_rLMlag
+    spreg.panel_rLMerror
+    spreg.panel_Hausman
diff --git a/docs/conf.py b/docs/conf.py
@@ -16,12 +16,8 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import sys, os
 import sphinx_bootstrap_theme
 
-
-sys.path.insert(0, os.path.abspath("../"))
-
 # import your package to obtain the version info to display on the docs website
 import spreg
 

diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -15,3 +15,9 @@ Tutorials
     :caption: Spatial Panel Models with Fixed Effects
 
     notebooks/Panel_FE_example.ipynb
+
+.. toctree::
+    :maxdepth: 1
+    :caption: Skater_reg: Endogenous Spatial Regimes
+
+    notebooks/skater_reg.ipynb
diff --git a/environment.yml b/environment.yml
@@ -1,8 +1,8 @@
-name: notebooks-environment
+name: spreg
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python>=3.10
   - bokeh
   - folium
   - geojson