Setup testing (#67)

* fix tutorials paths in gitignore

* fix step-1 resolve deprecation warnings

* run step_2, remove deprecations including dict structure for CRS

* get Step 3 working

* fix examples notebooks

* fix crs in doc-strings and as defaults to str

* reduce number of paths for example speed

* lengthen timeout for docs to run

* text, formatting for step-1 tutorial

* formatting step-2 tutorial

* formatting for step-3 notebook

* update example_finding notebook

* fix doc-strings ex-fixing

* update ex gravity notebook

* start testing

* placeholder tests

* add tests

* one more test, coverage to 9%

* try miniconda ci

* non-interactive conda install

* try to fix ci job

* specify coverage rcfile

* dont report coverage for now

* remove flag

* add tests

* add tests

* core funcs and tests

* finish tests for calculate_od_raw

* more tests

* add integrated test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* more tests and edits for new networkx versions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add tests

* stop building on macos

* add test

* updates

* fix and test for length of multilinesegment

* more tests, use sample data in tests

* more tests and fixes to core fcts

* add test

* cleanup tests, test isochrone function

* more tests and edits to core functions

* more testing of core functions

* add more tests

* more tests, up to 70% test coverage

* add more tests

* minor edits

* clean up tests a bit, add pooch for some data

* remove cov report

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/build.yml

@@ -26,8 +26,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8"]
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10"]
     steps:
       - name: Checkout code
         uses: actions/checkout@v4

.github/workflows/test.yml

@@ -0,0 +1,31 @@
+name: tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  ubuntu-build:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+    env:
+      OS: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          activate-environment: test-env
+          auto-activate-base: false
+      - name: Install dependencies then test
+        run: |
+          conda install -c conda-forge gdal
+          conda install -c conda-forge pip
+          pip install .[dev]
+          coverage run -m pytest

pyproject.toml

@@ -37,15 +37,15 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = ["pre-commit", "pytest", "pytest-cov", "tomli", "GOStnets[docs,osm,opt]"]
+dev = ["pre-commit", "pytest", "pytest-cov", "tomli", "coverage[toml]", "GOStnets[docs,osm,opt]", "pooch"]
 docs = [
 	"docutils==0.17.1",
 	"jupyter-book>=1,<2",
 	"sphinxcontrib-apidoc>=0.4.0,<1",
 	"jupyter-cache>=0.6.0",
 	"nbconvert",
 ]
-osm = ["gdal", "geopy", "boltons"]
+osm = ["gdal"]
 opt = ["pulp"]
 
 [project.urls]
@@ -66,3 +66,12 @@ convention = "numpy"
 
 [tool.ruff]
 exclude = ["__init__.py"]
+
+[tool.coverage.run]
+omit = [
+	"tests/*",
+	"docs/*",
+	"Tutorials/*",
+	"src/GOSTnets/_version.py",
+	"src/GOSTnets/__init__.py",
+]

src/GOSTnets/calculate_od_raw.py

@@ -51,7 +51,7 @@ def calculateOD_gdf(
     destinations["OD_D"] = destinations["NN"].apply(
         lambda x: np.where(dNodes == x)[0][0]
     )
-    outputMatrix = od[origins["OD_O"].values, :][:, destinations["OD_D"].values]
+    outputMatrix = od[origins["OD_O"].values][destinations["OD_D"].values]
     if calculate_snap:
         originsUTM = pandana_snap(G, origins, target_crs="epsg:3857")
         destinationsUTM = pandana_snap(G, destinations, target_crs="epsg:3857")

src/GOSTnets/conversion_utils.py

@@ -20,6 +20,8 @@ def rasterize_od_results(inD, outFile, field, template=None):
         path to save output raster
     field : string
         field to rasterize
+    template : string, optional
+        path to raster template file, by default None
 
     Returns
     -------