Bump version to v0.2.1 for release

closes #9

.github/actions/setup-venv/action.yml

@@ -0,0 +1,53 @@
+name: Python virtualenv
+description: Set up a Python virtual environment with caching
+inputs:
+  python-version:
+    description: The Python version to use
+    required: true
+  cache-prefix:
+    description: Update this to invalidate the cache
+    required: true
+    default: v0
+runs:
+  using: composite
+  steps:
+    - name: Setup Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - shell: bash
+      run: |
+        # Install prerequisites.
+        pip install --upgrade pip setuptools wheel virtualenv
+
+    - shell: bash
+      run: |
+        # Get the exact Python version to use in the cache key.
+        echo "PYTHON_VERSION=$(python --version)" >> $GITHUB_ENV
+
+    - uses: actions/cache@v2
+      id: virtualenv-cache
+      with:
+        path: .venv
+        key: ${{ inputs.cache-prefix }}-${{ runner.os }}-${{ env.PYTHON_VERSION }}-${{ hashFiles('Pipfile.lock') }}
+    - if: steps.virtualenv-cache.outputs.cache-hit != 'true'
+      shell: bash
+      run: |
+        # Set up virtual environment without cache hit.
+        test -d .venv || virtualenv -p $(which python) --copies --reset-app-data .venv
+        . .venv/bin/activate
+        pip install -e .[dev]
+
+    - if: steps.virtualenv-cache.outputs.cache-hit == 'true'
+      shell: bash
+      run: |
+        # Set up virtual environment from cache hit.
+        . .venv/bin/activate
+        pip install --no-deps -e .[dev]
+
+    - shell: bash
+      run: |
+        # Show environment info.
+        . .venv/bin/activate
+        echo "✓ Installed $(python --version) virtual environment to $(which python)"

.github/workflows/lint.yml

@@ -1,10 +0,0 @@
-name: Lint
-
-on: [push]
-
-jobs:
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: psf/black@stable

.github/workflows/main.yml

@@ -0,0 +1,113 @@
+name: Main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+# on: [push]
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+    tags:
+      - "v*.*.*"
+
+env:
+  # Change this to invalidate existing cache.
+  CACHE_PREFIX: v0
+  PYTHONPATH: ./
+
+jobs:
+  checks:
+    name: Python ${{ matrix.python }} - ${{ matrix.task.name }}
+    runs-on: [ubuntu-latest]
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - python: "3.10"
+            task:
+              name: "Build"
+              run: |
+                python setup.py check
+                python setup.py bdist_wheel sdist
+
+          - python: "3.10"
+            task:
+              name: "Style"
+              run: |
+                black --check .
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python environment
+        uses: ./.github/actions/setup-venv
+        with:
+          python-version: ${{ matrix.python }}
+          cache-prefix: ${{ env.CACHE_PREFIX }}
+
+      - name: ${{ matrix.task.name }}
+        run: |
+          . .venv/bin/activate
+          ${{ matrix.task.run }}
+
+      - name: Upload package distribution files
+        if: matrix.task.name == 'Build'
+        uses: actions/upload-artifact@v3
+        with:
+          name: package
+          path: dist
+
+      - name: Clean up
+        if: always()
+        run: |
+          . .venv/bin/activate
+          pip uninstall -y geoclustering
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    needs: [checks]
+    if: startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install requirements
+        run: |
+          pip install --upgrade pip setuptools wheel "twine>=1.11.0"
+
+      - name: Prepare environment
+        run: |
+          echo "RELEASE_VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV
+          echo "TAG=${GITHUB_REF#refs/tags/}" >> $GITHUB_ENV
+
+      - name: Download package distribution files
+        uses: actions/download-artifact@v3
+        with:
+          name: package
+          path: dist
+
+      - name: Publish package to PyPI
+        run: |
+          twine upload -u '${{ secrets.PYPI_USERNAME }}' -p '${{ secrets.PYPI_PASSWORD }}' dist/*
+
+      - name: Publish GitHub release
+        uses: softprops/action-gh-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          # body_path: ${{ github.workspace }}-RELEASE_NOTES.md
+          prerelease: ${{ contains(env.TAG, 'rc') }}
+          files: |
+            dist/*

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022, Felix Spöttel
+Copyright (c) 2022, Stichting Bellingcat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Pipfile

@@ -0,0 +1,19 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+click = "*"
+geojson = "*"
+keplergl = "*"
+numpy = "*"
+pandas = "*"
+scikit-learn = "*"
+
+[dev-packages]
+black = "*"
+wheel = "*"
+
+[requires]
+python_version = "3.9"

README.md

@@ -1,4 +1,4 @@
-# geocluster
+# geoclustering
 
 > 📍 command-line tool for clustering geolocations.
 
@@ -18,8 +18,8 @@ A cluster is created when a certain number of points (=> `--size`) each are with
 Clone the repository:
 
 ```sh
-git clone https://github.com/fspoettel/geocluster
+git clone https://github.com/bellingcat/geoclustering
-cd geocluster
+cd geoclustering
 ```
 
 Install keplergl build dependencies:
@@ -37,7 +37,13 @@ pip install .
 ## Usage
 
 ```
-Usage: geocluster [OPTIONS] FILENAME
+Usage: geoclustering [OPTIONS] FILENAME
+
+  Tool to cluster geolocations. A cluster is created when a certain number of
+  points (--size) each are within a given distance (--distance) of at least
+  one other point in the cluster. Input is supplied as a csv file. At a
+  minimum, each row needs to have a 'lat' and a 'lon' column. Other rows are
+  reflected to the output.
 
 Options:
   -d, --distance FLOAT            (in km) Max. distance between two points in
@@ -50,6 +56,9 @@ Options:
                                   Clustering algorithm to be used. `optics`
                                   produces tighter clusters but is slower.
                                   Default: dbscan
+  --open                          Open the generated visualization in the
+                                  default browser automatically.
+  --debug                         Print debug output.
   --help                          Show this message and exit.
 ```
 

geoclustering/__main__.py

@@ -1,12 +1,16 @@
+from pathlib import Path
 import click
+import os
 import webbrowser
 
-import geocluster.clustering as clustering
+import geoclustering.clustering as clustering
-import geocluster.encoding as encoding
+import geoclustering.encoding as encoding
-import geocluster.io as io
+import geoclustering.io as io
 
 
-@click.command()
+@click.command(
+    help="Tool to cluster geolocations. A cluster is created when a certain number of points (--size) each are within a given distance (--distance) of at least one other point in the cluster. Input is supplied as a csv file. At a minimum, each row needs to have a 'lat' and a 'lon' column. Other rows are reflected to the output."
+)
 @click.option(
     "--distance",
     "-d",
@@ -38,26 +42,44 @@ import geocluster.io as io
     default="dbscan",
     help="Clustering algorithm to be used. `optics` produces tighter clusters but is slower. Default: dbscan",
 )
+@click.option(
+    "--open",
+    is_flag=True,
+    help="Open the generated visualization in the default browser automatically.",
+)
+@click.option("--debug", is_flag=True, help="Print debug output.")
 @click.argument("filename", type=click.Path(exists=True))
-def main(distance, size, output, filename, algorithm):
+def main(distance, size, output, filename, algorithm, open, debug):
+    def print_debug(s):
+        if debug:
+            click.secho(s, fg="bright_black")
+
     df = io.read_csv_file(filename)
+    print_debug(f"Read {len(df)} valid coordinates from {Path(filename).absolute()}")
 
     clusters = clustering.cluster_locations(
         df=df, algorithm=algorithm, radius_km=distance, min_cluster_size=size
     )
 
     if not bool(clusters):
-        click.echo("Did not find clusters matching input parameters.")
+        click.secho("Did not find clusters matching input parameters.", fg="yellow")
         return
 
+    print_debug(f"Found {len(clusters)} valid clusters using {algorithm}")
+
     encoded = encoding.encode_clusters(clusters)
 
     io.write_output_file(output, "result.txt", encoded["string"])
     io.write_output_file(output, "result.json", encoded["json"])
     io.write_output_file(output, "result.geojson", encoded["geojson"])
     vis = io.write_visualization(output, "result.html", encoded["geojson"])
+    click.echo(f"Output files saved to {Path(output).absolute()}")
 
-    webbrowser.open_new_tab("file://" + str(vis.absolute()))
+    if open:
+        print_debug(f"Opening visualization in default browser")
+        webbrowser.open_new_tab("file://" + str(vis.absolute()))
+
+    click.secho("Clustering completed.", fg="green")
 
 
 if __name__ == "__main__":

geoclustering/clustering.py

@@ -14,8 +14,6 @@ def to_cluster_dict(df, clustering):
     """
     clusters_by_id = {}
 
-    print(clustering.labels_)
-
     for idx, cluster_id in enumerate(clustering.labels_):
         # ignore "noise" locations that don't belong to any cluster.
         if cluster_id > -1:

geoclustering/io.py

@@ -2,9 +2,22 @@ from keplergl import KeplerGl
 from pathlib import Path
 from pkg_resources import resource_filename
 import json
-import json
 import pandas as pd
 import numpy as np
+import os
+import sys
+
+
+class HiddenPrints:
+    """Disables stdout prints for a block of code."""
+
+    def __enter__(self):
+        self._original_stdout = sys.stdout
+        sys.stdout = open(os.devnull, "w")
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        sys.stdout.close()
+        sys.stdout = self._original_stdout
 
 
 def is_valid_lat(val: str) -> bool:
@@ -64,15 +77,21 @@ def write_output_file(dirname, filename, data):
 
 def write_visualization(dirname, filename, data):
     """Write a visualization, ensuring parent directories."""
-    map = KeplerGl()
+    # Hide kepler stdout output.
+    with HiddenPrints():
+        map = KeplerGl()
+
     map.add_data(data=data, name="clusters")
 
     # config configures a default color scheme for our clusters layer.
-    config_file = resource_filename("geocluster", "kepler_config.json")
+    config_file = resource_filename("geoclustering", "kepler_config.json")
     with open(config_file) as f:
         map.config = json.loads(f.read())
 
     filepath = ensure_file_path(dirname, filename)
-    map.save_to_html(file_name=str(filepath), center_map=True)
+
+    # Hide kepler stdout output.
+    with HiddenPrints():
+        map.save_to_html(file_name=str(filepath), center_map=True)
 
     return filepath

geoclustering/kepler_config.json

@@ -9,7 +9,7 @@
           "config": {
             "dataId": "clusters",
             "label": "clusters",
-            "color": [179, 173, 158],
+            "color": [248, 149, 112],
             "highlightColor": [252, 242, 26, 255],
             "columns": { "geojson": "_geojson" },
             "isVisible": true,
@@ -19,16 +19,30 @@
               "thickness": 0.5,
               "strokeColor": null,
               "colorRange": {
-                "name": "Global Warming",
+                "name": "Uber Viz Qualitative 4",
-                "type": "sequential",
+                "type": "qualitative",
                 "category": "Uber",
                 "colors": [
-                  "#5A1846",
+                  "#12939A",
-                  "#900C3F",
+                  "#DDB27C",
-                  "#C70039",
+                  "#88572C",
-                  "#E3611C",
+                  "#FF991F",
-                  "#F1920E",
+                  "#F15C17",
-                  "#FFC300"
+                  "#223F9A",
+                  "#DA70BF",
+                  "#125C77",
+                  "#4DC19C",
+                  "#776E57",
+                  "#17B8BE",
+                  "#F6D18A",
+                  "#B7885E",
+                  "#FFCB99",
+                  "#F89570",
+                  "#829AE3",
+                  "#E79FD5",
+                  "#1E96BE",
+                  "#89DAC1",
+                  "#B3AD9E"
                 ]
               },
               "strokeColorRange": {

geoclustering/version.py

@@ -0,0 +1,11 @@
+_MAJOR = "0"
+_MINOR = "2"
+# On main and in a nightly release the patch should be one ahead of the last
+# released build.
+_PATCH = "1"
+# This is mainly for nightly builds which have the suffix ".dev$DATE". See
+# https://semver.org/#is-v123-a-semantic-version for the semantics.
+_SUFFIX = ""
+
+VERSION_SHORT = "{0}.{1}".format(_MAJOR, _MINOR)
+VERSION = "{0}.{1}.{2}{3}".format(_MAJOR, _MINOR, _PATCH, _SUFFIX)

scripts/release.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -e
+
+TAG=$(python -c 'from geoclustering.version import VERSION; print("v" + VERSION)')
+
+read -p "Creating new release for $TAG. Do you want to continue? [Y/n] " prompt
+
+if [[ $prompt == "y" || $prompt == "Y" || $prompt == "yes" || $prompt == "Yes" ]]; then
+    git add -A
+    git commit -m "Bump version to $TAG for release" || true && git push
+    echo "Creating new git tag $TAG"
+    git tag "$TAG" -m "$TAG"
+    git push --tags
+else
+    echo "Cancelled"
+    exit 1
+fi

setup.py

@@ -1,12 +1,30 @@
 from setuptools import setup
 
+# version.py defines the VERSION and VERSION_SHORT variables.
+# We use exec here so we don't import cached_path whilst setting up.
+VERSION = {}  # type: ignore
+with open("geoclustering/version.py", "r") as version_file:
+    exec(version_file.read(), VERSION)
+
 setup(
-    name="geocluster",
+    name="geoclustering",
-    version="0.1",
+    version=VERSION["VERSION"],
-    description="",
+    description="📍 command-line tool for clustering geolocations.",
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
+    classifiers=[
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: MIT License",
+        "Programming Language :: Python :: 3",
+    ],
     author="Bellingcat",
-    packages=["geocluster"],
+    author_email="tech@bellingcat.com",
-    entry_points={"console_scripts": ["geocluster = geocluster.__main__:main"]},
+    license="MIT",
+    packages=["geoclustering"],
+    package_data={"geoclustering": ["kepler_config.json"]},
+    keywords=["cluster", "gis", "pattern-analysis"],
+    entry_points={"console_scripts": ["geoclustering = geoclustering.__main__:main"]},
     install_requires=[
         "click",
         "geojson",

tests/fixtures/mock50.csv

@@ -1,51 +1,51 @@
-id,name,lat,lon
+id,name,lat,lon
-1,Bonnibelle Mathwen,40.1324085,64.4911086
+1,Bonnibelle Mathwen,40.1324085,64.4911086
-2,Fayette Elt,49.6235379,6.2379992
+2,Fayette Elt,49.6235379,6.2379992
-3,Jandy Cooch,-7.5874497,110.7420464
+3,Jandy Cooch,-7.5874497,110.7420464
-4,Robb Gerbel,22.2455315,-80.3936994
+4,Robb Gerbel,22.2455315,-80.3936994
-5,Silvie Clipson,40.3418956,21.5118754
+5,Silvie Clipson,40.3418956,21.5118754
-6,Kristina Izakoff,30.741991,121.341969
+6,Kristina Izakoff,30.741991,121.341969
-7,Ricky Sweeting,11.2666664,122.5333328
+7,Ricky Sweeting,11.2666664,122.5333328
-8,Quintin Hazart,35.119385,109.167435
+8,Quintin Hazart,35.119385,109.167435
-9,Sholom Kilmister,55.7393377,37.6642542
+9,Sholom Kilmister,55.7393377,37.6642542
-10,Misty Dooher,49.9776657,20.9421091
+10,Misty Dooher,49.9776657,20.9421091
-11,Knox Phython,-8.4985,123.5226
+11,Knox Phython,-8.4985,123.5226
-12,Shay Davidy,14.4142191,120.9495257
+12,Shay Davidy,14.4142191,120.9495257
-13,Dre Benoey,-31.4561755,-64.2111608
+13,Dre Benoey,-31.4561755,-64.2111608
-14,Prudi Tomek,40.692169,117.163821
+14,Prudi Tomek,40.692169,117.163821
-15,Evey Ealam,31.123586,114.893666
+15,Evey Ealam,31.123586,114.893666
-16,Norry Urch,45.8022541,17.497172
+16,Norry Urch,45.8022541,17.497172
-17,Valerye Dumberell,50.4438122,48.1450932
+17,Valerye Dumberell,50.4438122,48.1450932
-18,Freddy Furtado,58.3767785,11.6764538
+18,Freddy Furtado,58.3767785,11.6764538
-19,Catarina Samett,50.4034992,26.141892
+19,Catarina Samett,50.4034992,26.141892
-20,Lidia Muckian,-38.7359018,-72.5903739
+20,Lidia Muckian,-38.7359018,-72.5903739
-21,Stacey Dockrey,29.741986,106.273576
+21,Stacey Dockrey,29.741986,106.273576
-22,Norri Bonhill,60.6184239,16.7769535
+22,Norri Bonhill,60.6184239,16.7769535
-23,Florence Pretsel,55.96667,25.15
+23,Florence Pretsel,55.96667,25.15
-24,Marten Matantsev,50.9603536,14.3596743
+24,Marten Matantsev,50.9603536,14.3596743
-25,Claiborn Everall,43.884893,-0.5046003
+25,Claiborn Everall,43.884893,-0.5046003
-26,Randolf Hailey,49.4679131,18.2282007
+26,Randolf Hailey,49.4679131,18.2282007
-27,Meggi Kirkebye,57.6888453,11.9943311
+27,Meggi Kirkebye,57.6888453,11.9943311
-28,Denna Le Grove,16.7124054,98.5746649
+28,Denna Le Grove,16.7124054,98.5746649
-29,Randy Verheijden,40.4722617,-7.9751886
+29,Randy Verheijden,40.4722617,-7.9751886
-30,Caterina Blancowe,35.422892,103.352654
+30,Caterina Blancowe,35.422892,103.352654
-31,Joanne Adamovitch,55.9251242,39.4489055
+31,Joanne Adamovitch,55.9251242,39.4489055
-32,Orazio Coppins,,111.6556388
+32,Orazio Coppins,,111.6556388
-33,Anastassia Bennedsen,45.212088,130.478187
+33,Anastassia Bennedsen,45.212088,130.478187
-34,Linoel Ruggier,22.066171,107.781956
+34,Linoel Ruggier,22.066171,107.781956
-35,Paulina Moralis,-11.806679,-77.1657716
+35,Paulina Moralis,-11.806679,-77.1657716
-36,Ambur Outhwaite,59.4033695,17.9443213
+36,Ambur Outhwaite,59.4033695,17.9443213
-37,Laetitia Aspland,37.6086169,138.9089988
+37,Laetitia Aspland,37.6086169,138.9089988
-38,Dew Moxstead,6.1317011,-75.6382657
+38,Dew Moxstead,6.1317011,-75.6382657
-39,Berna Klaiser,40.1394691,-8.3092933
+39,Berna Klaiser,40.1394691,-8.3092933
-40,Krystle Ingold,7.1518505,0.4738293
+40,Krystle Ingold,7.1518505,0.4738293
-41,Cassaundra Cuffin,56.6342788,36.885813
+41,Cassaundra Cuffin,56.6342788,36.885813
-42,Malanie Harpin,46.9,109.75
+42,Malanie Harpin,46.9,109.75
-43,Laurence Stothart,39.912765,116.18362
+43,Laurence Stothart,39.912765,116.18362
-44,Luz O'Siaghail,40.4476834,25.5917918
+44,Luz O'Siaghail,40.4476834,25.5917918
-45,Brittni Garrod,59.0836123,16.18741
+45,Brittni Garrod,59.0836123,16.18741
-46,Karlie Semrad,-8.793392,121.9330894
+46,Karlie Semrad,-8.793392,121.9330894
-47,Leigh Allderidge,45.768045,15.947739
+47,Leigh Allderidge,45.768045,15.947739
-48,Ashlin Gogerty,50.3250139,34.9100068
+48,Ashlin Gogerty,50.3250139,34.9100068
-49,Mozelle De Launde,53.31611,40.70806
+49,Mozelle De Launde,53.31611,40.70806
-50,Ema le Keux,41.6315023,19.9310781
+50,Ema le Keux,41.6315023,19.9310781