Update configuration, metadata and tests

- Update pyproject.toml to sync with Mesa approach (e.g. use of Hatch) - Remove setup files - Update README badging - fix ruff failures with updates - minimize pytests failures - update build_lint - update .gitignore
projectmesa · Jun 25, 2024 · 7fbd751 · 7fbd751
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diff --git a/.github/workflows/build_lint.yml b/.github/workflows/build_lint.yml
@@ -12,10 +12,23 @@ on:
     paths-ignore:
       - '**.md'
       - '**.rst'
+  workflow_dispatch:
+  schedule:
+    - cron: '0 6 * * 1'
+
+# This will cancel previous run if a newer job that obsoletes the said previous
+# run, is started.
+# Based on https://github.com/zulip/zulip/commit/4a11642cee3c8aec976d305d51a86e60e5d70522
+concurrency:
+  group: "${{ github.workflow }}-${{ github.head_ref || github.run_id }}"
+  cancel-in-progress: true
 
 jobs:
   build:
     runs-on: ${{ matrix.os }}-latest
+    # We need an explicit timeout because sometimes the batch_runner test never
+    # completes.
+    timeout-minutes: 6
     strategy:
       fail-fast: False
       matrix:
@@ -26,8 +39,6 @@ jobs:
             python-version: "3.11"
           - os: ubuntu
             python-version: "3.10"
-          - os: ubuntu
-            python-version: "3.9"
           # Disabled for now. See https://github.com/projectmesa/mesa/issues/1253
           #- os: ubuntu
           #  python-version: 'pypy-3.8'
@@ -38,14 +49,14 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v4
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('Pipfile.lock') }}
-    - name: Install dependencies
-      run: pip install wheel && pip install .[dev]
+        cache: 'pip'
+    - name: Install uv
+      run: pip install uv
+    - name: Install Mesa-Geo
+      # See https://github.com/astral-sh/uv/issues/1945
+      run: uv pip install --system .[dev]
     - name: Test with pytest
-      run: pytest --cov=mesa_geo tests/ --cov-report=xml
+      run: pytest --durations=10 --cov=mesa_geo tests/ --cov-report=xml
     - if: matrix.os == 'ubuntu'
       name: Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
@@ -268,6 +268,7 @@ target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
+.virtual_documents
 
 # pyenv
 .python-version

diff --git a/README.md b/README.md
@@ -1,14 +1,11 @@
 # Mesa-Geo: GIS Extension for Mesa Agent-Based Modeling
 
-[![GitHub CI](https://github.com/projectmesa/mesa-geo/workflows/build/badge.svg)](https://github.com/projectmesa/mesa-geo/actions)
-[![Read the Docs](https://readthedocs.org/projects/mesa-geo/badge/?version=main)](https://mesa-geo.readthedocs.io/en/main)
-[![Codecov](https://codecov.io/gh/projectmesa/mesa-geo/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa-geo)
-[![Code Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![PyPI](https://img.shields.io/pypi/v/mesa-geo.svg)](https://pypi.org/project/mesa-geo)
-[![PyPI - License](https://img.shields.io/pypi/l/mesa-geo)](https://pypi.org/project/mesa-geo/)
-[![PyPI - Downloads](https://img.shields.io/pypi/dw/mesa-geo)](https://pypistats.org/packages/mesa-geo)
-[![Matrix Chat](https://img.shields.io/matrix/mesa-geo:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#mesa-geo:matrix.org)
-[![DOI](https://zenodo.org/badge/DOI/10.1145/3557989.3566157.svg)](https://doi.org/10.1145/3557989.3566157)
+| | |
+| --- | --- |
+| CI/CD | ![GitHub CI](https://github.com/projectmesa/mesa-geo/workflows/build/badge.svg)](https://github.com/projectmesa/mesa-geo/actions) [![Read the Docs](https://readthedocs.org/projects/mesa-geo/badge/?version=main)](https://mesa-geo.readthedocs.io/en/main) [![Codecov](https://codecov.io/gh/projectmesa/mesa-geo/branch/main/graph/badge.svg)](https://codecov.io/gh/projectmesa/mesa-geo) |
+| Package | [![PyPI](https://img.shields.io/pypi/v/mesa-geo.svg)](https://pypi.org/project/mesa-geo) [![PyPI - License](https://img.shields.io/pypi/l/mesa-geo)](https://pypi.org/project/mesa-geo/) [![PyPI - Downloads](https://img.shields.io/pypi/dw/mesa-geo)](https://pypistats.org/packages/mesa-geo) |
+| Meta | [![linting - Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch) [![PyPI - Downloads](https://img.shields.io/pypi/dw/mesa-geo)](https://pypistats.org/packages/mesa-geo) |
+| Chat | [![chat](https://img.shields.io/matrix/project-mesa:matrix.org?label=chat&logo=Matrix)](https://matrix.to/#/#project-mesa:matrix.org) [![DOI](https://zenodo.org/badge/DOI/10.1145/3557989.3566157.svg)](https://doi.org/10.1145/3557989.3566157) |
 
 Mesa-Geo implements a `GeoSpace` that can host GIS-based `GeoAgents`, which are like normal Agents, except they have a `geometry` attribute that is a [Shapely object](https://shapely.readthedocs.io/en/latest/manual.html) and a `crs` attribute for its Coordinate Reference System. You can use `Shapely` directly to create arbitrary geometries, but in most cases you will want to import your geometries from a file. Mesa-Geo allows you to create GeoAgents from any vector data file (e.g. shapefiles), valid GeoJSON objects or a GeoPandas GeoDataFrame.
 

diff --git a/docs/tutorials/intro_tutorial.ipynb b/docs/tutorials/intro_tutorial.ipynb
@@ -22,13 +22,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "6c026625",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2022-10-17T18:18:56.247846Z",
      "start_time": "2022-10-17T18:18:29.927694Z"
-    }
+    },
+    "has_explanation": false
    },
    "outputs": [],
    "source": [
@@ -61,13 +62,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "c07e7a9a",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2022-10-17T18:18:56.256884Z",
      "start_time": "2022-10-17T18:18:56.251192Z"
-    }
+    },
+    "has_explanation": false
    },
    "outputs": [],
    "source": [
@@ -98,36 +100,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "ebee624a",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2022-10-17T18:18:56.466576Z",
      "start_time": "2022-10-17T18:18:56.260255Z"
-    }
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Arizona\n"
-     ]
     },
-    {
-     "data": {
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-      ],
-      "text/plain": [
-       "<shapely.geometry.polygon.Polygon at 0x1345e2c70>"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+    "has_explanation": false
+   },
+   "outputs": [],
    "source": [
     "m = GeoModel()\n",
     "\n",
@@ -148,26 +130,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "0f7c0ee6",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2022-10-17T18:18:56.473375Z",
      "start_time": "2022-10-17T18:18:56.469477Z"
-    }
+    },
+    "has_explanation": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "113594.084"
-      ]
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "agent.CENSUSAREA"
    ]
@@ -182,23 +154,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "154e56b2",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2022-10-17T18:18:56.759515Z",
      "start_time": "2022-10-17T18:18:56.475418Z"
-    }
+    },
+    "has_explanation": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['California', 'Colorado', 'Utah', 'Nevada', 'New Mexico']\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "neighbors = m.space.get_neighbors(agent)\n",
     "print([a.unique_id for a in neighbors])"
@@ -214,33 +179,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "63b36a85",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2022-10-17T18:18:56.769281Z",
      "start_time": "2022-10-17T18:18:56.761925Z"
-    }
+    },
+    "has_explanation": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['California',\n",
-       " 'Nevada',\n",
-       " 'Arizona',\n",
-       " 'Utah',\n",
-       " 'Wyoming',\n",
-       " 'New Mexico',\n",
-       " 'Colorado',\n",
-       " 'Texas']"
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "[a.unique_id for a in m.space.get_neighbors_within_distance(agent, 600000)]"
    ]
@@ -282,7 +230,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.12.3"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/mesa_geo/tile_layers.py b/mesa_geo/tile_layers.py
@@ -7,11 +7,10 @@
 
 import dataclasses
 from dataclasses import dataclass
-from typing import Union
 
 import xyzservices
 
-LeafletOption = Union[str, bool, int, float]
+LeafletOption = str | bool | int | float
 
 
 @dataclass