refactor sim code

.ci/310.yml

@@ -9,14 +9,11 @@ dependencies:
   - cenpy
   - geopandas  >=0.9
   - hdbscan
-  - matplotlib <=3.3.4
+  - matplotlib 
   - scikit-learn
   - seaborn
   - pyarrow >=0.14.1
   - platformdirs
-  - dash
-  - dash-bootstrap-components
-  - palettable
   - pip
   - tqdm
   - quilt3 >=3.6
@@ -26,7 +23,6 @@ dependencies:
   - fsspec
   - s3fs
   - segregation >=2.0
-  - versioneer
   - pyproj >=3
   - pandana
   - pooch
@@ -39,7 +35,6 @@ dependencies:
   - coverage
   - coveralls
   - python-wget
-  - proplot
   - contextily
   - scikit-plot
   - python-graphviz

.ci/38.yml → .ci/311.yml

@@ -2,21 +2,18 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python =3.8
+  - python =3.11
   - pandas
   - giddy >=2.2.1
   - libpysal
   - cenpy
   - geopandas >=0.9
   - hdbscan
-  - matplotlib <=3.3.4
+  - matplotlib 
   - scikit-learn
   - seaborn
   - pyarrow >=0.14.1
   - platformdirs
-  - dash
-  - dash-bootstrap-components
-  - palettable
   - pip
   - tqdm
   - quilt3 >=3.6
@@ -26,7 +23,6 @@ dependencies:
   - fsspec
   - s3fs
   - segregation >=2.0
-  - versioneer
   - pyproj >=3
   - pandana
   - pooch
@@ -39,7 +35,6 @@ dependencies:
   - coverage
   - coveralls
   - python-wget
-  - proplot
   - contextily
   - scikit-plot
   - python-graphviz

.ci/39.yml

@@ -8,15 +8,12 @@ dependencies:
   - libpysal
   - cenpy
   - geopandas  >=0.9
-  - matplotlib <=3.3.4
+  - matplotlib 
   - scikit-learn
   - seaborn
   - hdbscan
   - pyarrow >=0.14.1
   - platformdirs
-  - dash
-  - dash-bootstrap-components
-  - palettable
   - pip
   - tqdm
   - quilt3 >=3.6
@@ -26,7 +23,6 @@ dependencies:
   - fsspec
   - s3fs
   - segregation >=2.0
-  - versioneer
   - pyproj >=3
   - pandana
   - pooch
@@ -39,7 +35,6 @@ dependencies:
   - coverage
   - coveralls
   - python-wget
-  - proplot
   - contextily
   - scikit-plot
   - python-graphviz

.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:
+        - "*"

.github/workflows/build_docs.yml

@@ -8,33 +8,42 @@
    docs:
      name: CI (${{ matrix.os }}-${{ matrix.environment-file }})
      runs-on: ${{ matrix.os }}
+     continue-on-error: ${{ matrix.experimental }}
+     timeout-minutes: 20
      strategy:
        matrix:
          os: ['ubuntu-latest']
          environment-file: [.ci/39.yml]
-
+         experimental: [false]
+     defaults:
+       run:
+         shell: bash -l {0}
      steps:
-       - name: checkout repo
-         uses: actions/checkout@v2
-
-       - name: setup micromamba
-         uses: mamba-org/provision-with-micromamba@main
+       - uses: actions/checkout@v2
+       - uses: actions/cache@v2
+         env:
+           CACHE_NUMBER: 0
          with:
-           environment-file: ${{ matrix.environment-file }}
-           micromamba-version: 'latest'
-           mamba-version: "*"
-           channels: conda-forge
-           channel-priority: true
-
-       - name: install geosnap - bash
-         shell: bash -l {0}
-         run: pip install -e . --no-deps --force-reinstall
-         if: matrix.os != 'windows-latest'
-
-       - name: build docs
-         shell: bash -l {0}
-         run: cd docs; make html
-
+           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
@@ -46,7 +55,6 @@
            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 changes
          uses: ad-m/github-push-action@master
          with:

.github/workflows/unittests.yml

@@ -19,7 +19,7 @@
      strategy:
        matrix:
          os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-         environment-file: [.ci/38.yml, .ci/39.yml, .ci/310.yml]
+         environment-file: [.ci/39.yml, .ci/310.yml, .ci/311.yml]
 
      steps:
        - name: checkout repo

.github/workflows/upload_package.yml

@@ -1,64 +1,50 @@
-
-name: Release Package
+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
+      - "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:
-    - uses: actions/checkout@v1
-    - name: Set up Python
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine jupyter urllib3 pandas pyyaml
-        python setup.py develop --no-deps
-        python setup.py sdist bdist_wheel
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        password: ${{ secrets.pypi_password }}
-    - 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: Create Release
-      id: create_release
-      uses: actions/create-release@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
-      with:
-        tag_name: ${{ github.ref }}
-        release_name: Release ${{ github.ref }}
-        body: ${{ steps.changetxt.outputs.text }}
-        draft: false
-        prerelease: false
-    - name: Get Asset name
-      run: |
-        export PKG=$(ls dist/)
-        set -- $PKG
-        echo "name=$1" >> $GITHUB_ENV
-    - name: Upload Release Asset
-      id: upload-release-asset 
-      uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-        upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
-        asset_path: dist/${{ env.name }}
-        asset_name: ${{ env.name }}
-        asset_content_type: application/zip
+      - 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
+          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 }}

README.md

@@ -68,10 +68,10 @@ The package supports social scientists examining questions such as:
 ## Installation
 
 The recommended method for installing geosnap is with
-[anaconda](https://www.anaconda.com/download/).
+[anaconda](https://www.anaconda.com/download/). In particular, we recommend the [mambaforge distribution](https://github.com/conda-forge/miniforge#mambaforge)
 
 ```bash
-conda install -c conda-forge geosnap
+mamba install -c conda-forge geosnap
 ```
 
 `geosnap` is alaso available on PyPI and can be install with pip via
@@ -100,7 +100,7 @@ following commands:
 ```bash
 conda env create -f environment.yml
 conda activate geosnap 
-python setup.py develop
+pip install -e . --no-deps
 ```
 
 This will download the appropriate dependencies and install geosnap in its own conda environment.

docs/conf.py

@@ -38,9 +38,25 @@
     "sphinx.ext.intersphinx",
     "numpydoc",
     "matplotlib.sphinxext.plot_directive",
+    "myst-parser"
 ]
 
-
+myst_enable_extensions = [
+    "amsmath",
+    "attrs_inline",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "strikethrough",
+    "substitution",
+    "tasklist",
+]
 
 # sphinx_gallery_conf = {
 #      # path to your examples scripts

environment.yml

@@ -8,7 +8,7 @@ dependencies:
   - libpysal
   - cenpy
   - geopandas  >=0.9
-  - matplotlib <=3.3.4  # workaround for proplot missing pin upstream
+  - matplotlib
   - scikit-learn
   - seaborn
   - pyarrow >=0.14.1
@@ -18,14 +18,12 @@ dependencies:
   - quilt3 >=3.6
   - xlrd
   - tobler >=0.8.2
-  - proplot >=0.9
   - contextily
   - scikit-plot
   - mapclassify
   - spopt >=0.3.0
   - s3fs
   - segregation >=2.0
-  - versioneer
   - pyproj >=3
   - pandana
   - pooch