add tests + github action

.github/workflows/dataset_checks.yml

@@ -0,0 +1,35 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: dataset checks
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main", "essd_review" ]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pandas geopandas delayed-assert gitpython
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Run Dataset Checks
+      run: |
+        pytest 

essd/environment.yml → environment.yml

@@ -10,3 +10,6 @@ dependencies:
   - squarify
   - geoutils
   - cartopy
+  - pytest
+  - gitpython
+  - delayed-assert

scripts/test_submission.py

@@ -0,0 +1,112 @@
+from pathlib import Path
+from glob import glob
+from delayed_assert import expect, assert_expectations
+from git import Repo
+import pandas as pd
+import geopandas as gpd
+
+
+rgi_regions = ['RGI2000-v7.0-G-01_alaska',
+    'RGI2000-v7.0-G-02_western_canada_usa',
+    'RGI2000-v7.0-G-03_arctic_canada_north',
+    'RGI2000-v7.0-G-04_arctic_canada_south',
+    'RGI2000-v7.0-G-05_greenland_periphery',
+    'RGI2000-v7.0-G-06_iceland',
+    'RGI2000-v7.0-G-07_svalbard_jan_mayen',
+    'RGI2000-v7.0-G-08_scandinavia',
+    'RGI2000-v7.0-G-09_russian_arctic',
+    'RGI2000-v7.0-G-10_north_asia',
+    'RGI2000-v7.0-G-11_central_europe',
+    'RGI2000-v7.0-G-12_caucasus_middle_east',
+    'RGI2000-v7.0-G-13_central_asia',
+    'RGI2000-v7.0-G-14_south_asia_west',
+    'RGI2000-v7.0-G-15_south_asia_east',
+    'RGI2000-v7.0-G-16_low_latitudes',
+    'RGI2000-v7.0-G-17_southern_andes',
+    'RGI2000-v7.0-G-18_new_zealand',
+    'RGI2000-v7.0-G-19_subantarctic_antarctic_islands'
+]
+
+def test_columns():
+    """
+    Checks that each new/updated file in dataset/csv and dataset/contributor_files has the correct columns, based on
+    what is found in lake_term_data_template.csv:
+
+    rgi_id,lake_cat,image_id,image_date,inventory_doi,contributor
+
+    Raises an AssertionError if one or more files is missing one or more columns.
+
+    """
+    # check all files in dataset/contributor_files/
+    contribs = [f"dataset/csv/{fn}" for fn in glob('**/*.csv',
+                                                   root_dir='dataset/csv',
+                                                   recursive=True)] \
+               + [f"dataset/contributor_files/{fn}" for fn in glob('**/*.csv',
+                                                                   root_dir='dataset/contributor_files',
+                                                                   recursive=True)]
+
+    # get a list of "new" or changed files from the current branch
+    repo = Repo('.')
+    diff = [item.a_path for item in repo.index.diff('origin/main')]
+
+    new_contribs = list(set(contribs) & set(diff))
+
+    print(f"Found {len(new_contribs)} new or changed submissions: ")
+    for fn in new_contribs:
+        print(fn)
+
+    # required columns
+    req_cols = pd.read_csv('lake_term_data_template.csv').columns
+
+    for fn_csv in new_contribs:
+        csv = pd.read_csv(fn_csv)
+        # first, check that columns are all there.
+        for col in req_cols:
+            expect(col in csv.columns, f"{col} not found in {fn_csv}: \n{list(csv.columns)}")
+
+    assert_expectations()
+
+
+def test_geopackage():
+    """
+    Tests whether all geopackage files (a) exist for each region, and (b) have the correct column names.
+    """
+    req_cols = pd.read_csv('lake_term_data_template.csv').columns
+
+    for reg in rgi_regions:
+        expect(Path('dataset', 'lakeflags', f"{reg}_lakeflag.gpkg").exists(),
+               f"geopackage file not found in dataset/lakeflags/ for {reg}")
+        expect(Path('dataset', 'outlines', f"{reg}_laketerminating.gpkg").exists(),
+               f"geopackage file not found in dataset/outlines/ for {reg}")
+
+        lakeflag = gpd.read_file(Path('dataset', 'lakeflags', f"{reg}_lakeflag.gpkg"))
+        outlines = gpd.read_file(Path('dataset', 'outlines', f"{reg}_laketerminating.gpkg"))
+
+        for col in req_cols:
+            expect(col in lakeflag.columns, f"{col} not found in {reg} lakeflag file: \n{list(lakeflag.columns)}")
+            expect(col in outlines.columns, f"{col} not found in {reg} outlines file: \n{list(outlines.columns)}")
+
+    assert_expectations()
+
+
+def test_lake_cat():
+    """
+    Tests whether the lake_cat value is the same in the csv tables and the geopackage files for all regions.
+    """
+
+    for reg in rgi_regions:
+        attributes = pd.read_csv(Path('dataset', 'csv', f"{reg}_lakeflag.csv")).set_index('rgi_id')
+
+        lakeflag = gpd.read_file(Path('dataset', 'lakeflags', f"{reg}_lakeflag.gpkg")).set_index('rgi_id')
+        outlines = gpd.read_file(Path('dataset', 'outlines', f"{reg}_laketerminating.gpkg")).set_index('rgi_id')
+
+        # can compare these directly, as they should be identically indexed (and if not, it's an error)
+        expect((attributes['lake_cat'] == lakeflag['lake_cat']).all(),
+               f"lake_cat doesn't match for {reg} points file.")
+
+        # have to first select from attributes where index is also in outlines
+        same_index = attributes.index[attributes.index.isin(outlines.index)]
+        expect((attributes.loc[same_index, 'lake_cat'] == outlines['lake_cat']).all(),
+               f"lake_cat doesn't match for {reg} outlines.")
+
+    assert_expectations()