Staging

.github/workflows/pypi-publish.yml

@@ -0,0 +1,42 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Publish package to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/python-package.yml → .github/workflows/pytest.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
+name: pytest
 
 on:
   push:

.pre-commit-config.yaml

@@ -1,9 +1,9 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 22.8.0
     hooks:
       - id: black
-        language_version: python3.8
+        language_version: python3.10
   - repo: https://github.com/pycqa/pylint
     rev: pylint-2.6.0
     hooks:

Makefile

@@ -15,6 +15,12 @@ else
 HAS_CONDA=True
 endif
 
+ifeq (,$(shell which mamba))
+HAS_MAMBA=False
+else
+HAS_MAMBA=True
+endif
+
 #################################################################################
 # COMMANDS                                                                      #
 #################################################################################
@@ -30,6 +36,7 @@ lint:
 
 ## Format geograph directory using black
 format:
+	isort geograph
 	black geograph
 
 ## Set up pre-commit hooks
@@ -39,20 +46,22 @@ precommit:
 
 ## Set up python interpreter environment and install basic dependencies
 env:
-ifeq (True,$(HAS_CONDA))
-	@echo ">>> Detected conda, creating conda environment."
+ifeq (True, $(HAS_MAMBA))
+	@echo ">>> Detected mamba, creating conda environment via mamba."
+
+	# Create the conda environment
+	mamba env create --prefix=./env -f requirements/environment.yml
 
+	@echo ">>> New mamba env created. Activate from project directory with:\nconda activate ./env"
+else ifeq (True,$(HAS_CONDA))
+	@echo ">>> Detected conda, creating conda environment."
+
 	# Create the conda environment
 	conda env create --prefix=./env -f requirements/environment.yml
 
 	@echo ">>> New conda env created. Activate from project directory with:\nconda activate ./env"
 else
-	@echo ">>> No conda detected. Falling back to virtualenv instead. The python verison will be that of your python3 interpreter."
-	$(PYTHON_INTERPRETER) -m pip install -q virtualenv virtualenvwrapper
-	@echo ">>> Installing virtualenvwrapper if not already installed.\nMake sure the following lines are in shell startup file\n\
-	export WORKON_HOME=$$HOME/.virtualenvs\nexport PROJECT_HOME=$$HOME/Devel\nsource /usr/local/bin/virtualenvwrapper.sh\n"
-	@bash -c "source `which virtualenvwrapper.sh`;mkvirtualenv $(PROJECT_NAME) --python=$(PYTHON_INTERPRETER)"
-	@echo ">>> New virtualenv created. Activate with:\nworkon $(PROJECT_NAME)"
+	@echo ">>> No conda detected. Please install conda or manually install requirements in your preferred python version."
 endif
 
 #################################################################################

README.md

@@ -13,7 +13,6 @@
 
 ![GeoGraphViewer demo gif](docs/images/viewer_demo.gif)
 
-
 __Table of contents:__
 1. Description
 1. Installation

binder/environment.yml

@@ -1,8 +1,38 @@
+prefix: ./env
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.8
-  - pip
+  - python=3.10
+  - pip==21.2.4
+    # linear algebra and general data analysis
+  - numpy ==1.23.3            # arrays, linear algebra
+  - pandas ==1.5.0            # tabular data analysis
+
+  # plotting
+  - folium ==0.12.1.post1              # plotting maps
+  - ipyleaflet ==0.17.1        # plotting ipywidget maps
+
+  # interactive computing
+  - tqdm ==4.64.1               # progress bars
+
+  # geospatial analysis requirements
+  #  vector data
+  - geopandas ==0.11.1          # manipulating geospatial vector data
+  - shapely ==1.8.4            # working with vector shapes
+  - rtree ==1.0.0              # efficiently querying polygon data
+  #  raster data
+  - rasterio ==1.3.2           # opening and loading raster data
+  - xarray ==2022.6.0             # useful data structures
+
+  # graph requirements
+  - networkx ==2.8.6           # manipulating graph data
+
+  # For binder
+  - rioxarray ==0.12.2
+  - seaborn ==0.12.0
+  - netcdf4 ==1.6.1
+
   - pip:
-      - -r requirements.txt
+    - pylandstats ==2.4.2
+    - -e ..

docs/conf.py

@@ -76,7 +76,7 @@
 html_context = {
     "display_github": True,
     "github_user": "ai4er-cdt",
-    "github_repo": "gtc-biodiversity",
+    "github_repo": "geograph",
     "github_version": "main/docs/",
 }
 

docs/index.rst

@@ -57,6 +57,7 @@ Polygon Data Visualisation
    installation
    tutorials
    geograph
+   maintenance
    about
 
 

docs/maintenance.rst

@@ -0,0 +1,20 @@
+Maintenance
+===========
+
+Some tips for the maintainers of this project.
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy. Follow this checklist (inspired by `this checklist <https://gist.github.com/audreyfeldroy/5990987>`_ and `this packaging tutorial <https://packaging.python.org/en/latest/tutorials/packaging-projects/>`_):
+
+1. Update ``HISTORY.rst`` and commit with message like "aux: add changelog for upcoming release 0.1.0"
+2. Run
+
+    .. code-block:: console
+
+        bump2version patch # possible: major / minor / patch
+
+3. Push commits *and tags* (`see here how to do this in vscode <https://stackoverflow.com/a/66086007>`_)
+4. Merge pull request into ``main`` branch.
+5. Add release on GitHub (using existing tag)

geograph/binary_graph_operations.py

@@ -1,9 +1,12 @@
 """Contains tools for binary operations between GeoGraph objects."""
 from __future__ import annotations
+
 from typing import TYPE_CHECKING, Dict, List, Tuple
+
 import geopandas as gpd
 from shapely.geometry.base import BaseGeometry
 from shapely.geometry.polygon import Polygon
+
 import geograph.utils.geopandas_utils as gpd_utils
 from geograph.utils.polygon_utils import EMPTY_POLYGON, collapse_empty_polygon
 

geograph/demo/binder_constants.py

@@ -1,7 +1,6 @@
 """This file is for constants relevant to the binder demo."""
 from geograph.constants import PROJECT_PATH
 
-
 # Data directory on GWS
 DATA_DIR = PROJECT_PATH / "data"
 # Polygon data of Chernobyl Exclusion Zone (CEZ)

geograph/demo/plot_settings.py

@@ -42,6 +42,7 @@
 import itertools
 from distutils.spawn import find_executable
 from typing import Sequence, Tuple
+
 import matplotlib
 import matplotlib.style
 import numpy as np

geograph/geograph.py

@@ -4,6 +4,7 @@
 See https://networkx.org/documentation/stable/index.html for graph operations.
 """
 from __future__ import annotations
+
 import bz2
 import gzip
 import inspect
@@ -13,6 +14,7 @@
 from copy import deepcopy
 from itertools import zip_longest
 from typing import Any, Callable, Dict, Iterable, List, Optional, Sequence, Union
+
 import geopandas as gpd
 import networkx as nx
 import numpy as np
@@ -22,6 +24,7 @@
 import shapely
 from shapely.prepared import prep
 from tqdm import tqdm
+
 from geograph import binary_graph_operations, metrics
 from geograph.metrics import CLASS_METRICS_DICT, Metric
 from geograph.utils import rasterio_utils
@@ -107,6 +110,16 @@ def __init__(
             **apply_buffer (bool, optional): Apply shapely buffer function to
                 the polygons after polygonising. This can fix issues with the
                 polygonisation creating invalid geometries.
+
+        Example::
+            >>> import os
+            >>> from geograph.constants import WGS84
+            >>> from geograph.tests.create_data_test import TEST_DATA_FOLDER
+            >>> gg = GeoGraph(os.path.join(TEST_DATA_FOLDER, "adjacent", "full.gpkg"), WGS84, "savepath.gz")
+            Graph successfully loaded with 15 nodes and 40 edges.
+            >>> gg.crs == WGS84
+            True
+
         """
         super().__init__()
         self.graph = nx.Graph()

geograph/geotimeline.py

@@ -1,11 +1,14 @@
 """Module for analysing multiple GeoGraph objects."""
 from __future__ import annotations
+
 import datetime
 from bisect import bisect_left
 from typing import Callable, Dict, Iterable, List, Optional, Tuple, Union
+
 import numpy as np
 import pandas as pd
 import xarray as xr
+
 from geograph import GeoGraph
 from geograph.binary_graph_operations import NodeMap, identify_graphs