Migrate to pyproject.toml

.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/release_and_publish.yml

@@ -1,10 +1,4 @@
-# Release package on GitHub and publish to PyPI
-# IMPORTANT -- 1 MANUAL STEP
-#   * FOLLOWING TAGGED RELEASE
-#       - update CHANGELOG.md
-#--------------------------------------------------
-
-name: Build, Release, and publish
+name: Release Package
 
 on:
   push:
@@ -20,69 +14,32 @@ on:
 
 jobs:
   build:
-    name: Create release & publish to PyPI
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout repo
-        uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+
+    - name: Build source and wheel distributions
+      run: |
+        python -m pip install --upgrade build twine
+        python -m build
+        twine check --strict dist/*
 
-      - name: Set up python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
+    - 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: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine jupyter urllib3 pandas pyyaml
-          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: 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: Create Release
-#        id: create_release
-#        uses: actions/create-release@v1
-#        env:
-#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # token is provided by GHA, DO NOT create
-#        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: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_PASSWORD }}
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/unittests.yml → .github/workflows/tests.yml

@@ -18,8 +18,6 @@ on:
 
 jobs:
   unittests:
-    env:
-      RUN_TEST: pytest giddy --cov giddy -v -n auto -r a --cov-config .coveragerc --cov-report xml --color yes --cov-append --cov-report term-missing
     name: ${{ matrix.os }}, ${{ matrix.environment-file }}
     runs-on: ${{ matrix.os }}
     defaults:
@@ -30,7 +28,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         environment-file:
-          - ci/39.yaml
+          - ci/39-MIN.yaml
           - ci/310.yaml
           - ci/311.yaml
           - ci/311-DEV.yaml
@@ -72,7 +70,7 @@ jobs:
         if: contains(matrix.environment-file, 'DEV')
 
       - name: run tests
-        run: ${{ env.RUN_TEST }}
+        run: pytest giddy --cov giddy -v -n auto -r a --doctest-modules --color yes --cov-report term-missing --cov-report xml
 
       - name: codecov
         uses: codecov/codecov-action@v3

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
       - id: black
         language_version: python3
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.0.292"
+    rev: "v0.1.0"
     hooks:
       - id: ruff
 

README.md

@@ -1,32 +1,29 @@
 PySAL-giddy for exploratory spatiotemporal data analysis
-========================================================
+============================================
 
-[![Continuous Integration](https://github.com/pysal/giddy/actions/workflows/unittests.yml/badge.svg)](https://github.com/pysal/giddy/actions/workflows/unittests.yml)
-[![codecov](https://codecov.io/gh/pysal/giddy/branch/master/graph/badge.svg)](https://codecov.io/gh/pysal/giddy)
+[![Continuous Integration](https://github.com/pysal/giddy/actions/workflows/testing.yml/badge.svg)](https://github.com/pysal/giddy/actions/workflows/testing.yml)
+[![codecov](https://codecov.io/gh/pysal/giddy/branch/main/graph/badge.svg)](https://codecov.io/gh/pysal/giddy)
 [![Gitter room](https://badges.gitter.im/pysal/giddy.svg)](https://gitter.im/pysal/giddy)
 [![PyPI version](https://badge.fury.io/py/giddy.svg)](https://badge.fury.io/py/giddy)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7693957.svg)](https://doi.org/10.5281/zenodo.7693957)
-[![badge](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pysal/giddy/master)
+[![badge](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pysal/giddy/main)
 [![Downloads](https://static.pepy.tech/badge/giddy)](https://pepy.tech/project/giddy)
 
-Giddy is an open-source python library for exploratory spatiotemporal data analysis and the analysis of 
-geospatial distribution dynamics. 
-It is under active development
-for the inclusion of newly proposed analytics that consider the
-role of space in the evolution of distributions over time.
+Giddy is an open-source python library for exploratory spatiotemporal data analysis and the analysis of geospatial distribution dynamics. It is under active development for the inclusion of newly proposed analytics that consider the role of space in the evolution of distributions over time.
 
 *Below are six choropleth maps of U.S. state per-capita incomes from 1929 to 2004 at a fifteen-year interval.*
 
 ![us_qunitile_maps](figs/us_qunitile_maps.png)
 
 Documentation
--------------
+--------------------
 
 Online documentation is available [here](http://pysal.org/giddy/).
 
 
 Features
---------
+------------
+
 - Directional LISA, inference and visualization as rose diagram
 
 [![rose_conditional](figs/rose_conditional.png)](notebooks/DirectionalLISA.ipynb)
@@ -50,7 +47,7 @@ Features
 
 
 Examples
---------
+-------------
 
 * [Directional LISA](notebooks/DirectionalLISA.ipynb)
 * [Markov based methods](notebooks/MarkovBasedMethods.ipynb)
@@ -60,7 +57,7 @@ Examples
 * [Sequence methods (Optimal matching)](notebooks/Sequence.ipynb)
 
 Installation
-------------
+--------------
 
 Install the stable version released on the [Python Package Index](https://pypi.org/project/giddy/) from the command line:
 
@@ -71,7 +68,7 @@ pip install giddy
 Install the development version on [pysal/giddy](https://github.com/pysal/giddy):
 
 ```
-pip install https://github.com/pysal/giddy/archive/main.zip
+pip install git+https://github.com/pysal/giddy
 ```
 
 #### Requirements
@@ -83,25 +80,25 @@ pip install https://github.com/pysal/giddy/archive/main.zip
 - quantecon>=0.4.7
 
 Contribute
-----------
+--------------
 
 PySAL-giddy is under active development and contributors are welcome.
 
 If you have any suggestion, feature request, or bug report, please open a new [issue](https://github.com/pysal/giddy/issues) on GitHub. To submit patches, please follow the PySAL development [guidelines](https://github.com/pysal/pysal/wiki) and open a [pull request](https://github.com/pysal/giddy). Once your changes get merged, you’ll automatically be added to the [Contributors List](https://github.com/pysal/giddy/graphs/contributors).
 
 Support
--------
+-----------
 
 If you are having issues, please talk to us in the [gitter room](https://gitter.im/pysal/giddy).
 
 License
--------
+----------
 
-The project is licensed under the [BSD license](https://github.com/pysal/giddy/blob/master/LICENSE.txt).
+The project is licensed under the [BSD license](https://github.com/pysal/giddy/blob/main/LICENSE.txt).
 
 
 BibTeX Citation
----------------
+---------------------
 
 ```
 @software{wei_kang_2023_7693957,
@@ -126,6 +123,6 @@ BibTeX Citation
 ```
 
 Funding
--------
+-----------
 
 <img src="figs/nsf_logo.jpg" width="50"> Award #1421935 [New Approaches to Spatial Distribution Dynamics](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1421935)

codecov.yml

@@ -1,6 +1,6 @@
 codecov:
   notify:
-    after_n_builds: 16
+    after_n_builds: 5
 coverage:
   range: 50..95
   round: nearest
@@ -18,5 +18,5 @@ coverage:
 comment:
   layout: "reach, diff, files"
   behavior: once
-  after_n_builds: 16
+  after_n_builds: 5
   require_changes: true

giddy/__init__.py

@@ -1,16 +1,13 @@
-__version__ = "2.3.4"
-# __version__ has to be defined in the first line
-
 """
 :mod:`giddy` --- Spatial Dynamics and Mobility
 ==============================================
 
 """
 
-from . import directional
-from . import ergodic
-from . import markov
-from . import mobility
-from . import rank
-from . import util
-from . import sequence
+import contextlib
+from importlib.metadata import PackageNotFoundError, version
+
+from . import directional, ergodic, markov, mobility, rank, sequence, util
+
+with contextlib.suppress(PackageNotFoundError):
+    __version__ = version("giddy")

giddy/components.py

@@ -32,7 +32,7 @@ def is_component(w, ids):
     """
 
     components = 0
-    marks = dict([(node, 0) for node in ids])
+    marks = {node: 0 for node in ids}
     q = []
     for node in ids:
         if marks[node] == 0:
@@ -103,7 +103,7 @@ def check_contiguity(w, neighbors, leaver):
     return is_component(w, ids)
 
 
-class Graph(object):
+class Graph:
     def __init__(self, undirected=True):
         self.nodes = set()
         self.edges = {}

giddy/directional.py

@@ -17,7 +17,7 @@
 _NEG4 = 1 - _POS4
 
 
-class Rose(object):
+class Rose:
     """
     Rose diagram based inference for directional LISAs.
 
@@ -200,7 +200,12 @@ def __init__(self, Y, w, k=8):
         rose diagram conditional on the starting relative income:
 
         >>> fig1, _ = r8.plot(attribute=Y[:,0])
-        >>> plt.show()
+        >>> plt.show(block=False)
+
+        Close plot when finished viewing.
+
+        >>> plt.close("all")
+
         """
 
         self.Y = Y
@@ -292,7 +297,7 @@ def permute(self, permutations=99, alternative="two.sided"):
             P = NEG * L + (1 - NEG) * S
             self.p = P
         else:
-            print(("Bad option for alternative: %s." % alternative))
+            print("Bad option for alternative: %s." % alternative)
 
     def _calc(self, Y, w, k):
         wY = weights.lag_spatial(w, Y)