Finally fix validation bug

GeoscienceAustralia · Aug 2, 2024 · e5936c9 · e5936c9
1 parent 748297c
commit e5936c9
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Showing 3 changed files with 49 additions and 54 deletions.
diff --git a/.github/workflows/dea-coastlines-image.yaml b/.github/workflows/dea-coastlines-image.yaml
@@ -98,31 +98,26 @@ jobs:
             --volume ${GITHUB_WORKSPACE}/tide_models:/var/share/tide_models \
             dea_coastlines pytest -v --cov=coastlines --cov-report=xml tests
 
-          ls -l .
-          ls -l ./data/validation/processed/
-          ls -l ./tests/
-          git status
-
-      # # Commit validation results produced by integration tests back into repo
-      # - name: Commit validation results into repository
-      #   uses: stefanzweifel/git-auto-commit-action@v4
-      #   if: github.event_name == 'pull_request'
-      #   continue-on-error: true
-      #   with:
-      #     commit_message: Automatically update integration test validation results
-      #     file_pattern: 'tests/stats_tests.png tests/stats_tests.csv tests/README.md'
+      # Commit validation results produced by integration tests back into repo
+      - name: Commit validation results into repository
+        uses: stefanzweifel/git-auto-commit-action@v4
+        if: github.event_name == 'pull_request'
+        continue-on-error: true
+        with:
+          commit_message: Automatically update integration test validation results
+          file_pattern: 'tests/stats_tests.png tests/stats_tests.csv tests/README.md'
 
-      # # Post validation tesults as comment on PR
-      # - name: Post validation results as comment
-      #   uses: mshick/add-pr-comment@v2
-      #   if: github.event_name == 'pull_request'
-      #   with:
-      #     message: |
-      #       ![](https://github.com/GeoscienceAustralia/dea-coastlines/blob/${{ github.head_ref }}/tests/stats_tests.png?raw=true")
+      # Post validation tesults as comment on PR
+      - name: Post validation results as comment
+        uses: mshick/add-pr-comment@v2
+        if: github.event_name == 'pull_request'
+        with:
+          message: |
+            ![](https://github.com/GeoscienceAustralia/dea-coastlines/blob/${{ github.head_ref }}/tests/stats_tests.png?raw=true")
             
-      #       For full integration test results, refer to the [Tests directory README](https://github.com/GeoscienceAustralia/dea-coastlines/tree/${{ github.head_ref }}/tests).
+            For full integration test results, refer to the [Tests directory README](https://github.com/GeoscienceAustralia/dea-coastlines/tree/${{ github.head_ref }}/tests).
 
-      # - name: Upload coverage reports to Codecov
-      #   uses: codecov/codecov-action@v3
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/coastlines/validation.py b/coastlines/validation.py
@@ -2295,7 +2295,7 @@ def deacl_validation(
                 lambda x: pd.Series.mode(x).iloc[0]
             )
             count_vals = val_df.groupby(["year", "id"]).year.count().rename("n")
-            median_vals = val_df.groupby(["year", "id"]).median()
+            median_vals = val_df.groupby(["year", "id"]).median(numeric_only=True)
 
             # Combine all aggregated stats into one dataframe
             val_df = pd.concat(

diff --git a/tests/test_coastline.py b/tests/test_coastline.py
@@ -76,34 +76,34 @@ def test_generate_continental_cli():
     # assert result.output == '' # for debugging
     assert result.exit_code == 0
 
-# @pytest.mark.dependency(depends=["test_generate_continental_cli"])
-# def test_validation_cli(capsys):
-#     runner = CliRunner()
-#     result = runner.invoke(
-#         validation_cli,
-#         [
-#             "--inputs_path",
-#             "data/validation/interim/wrl_narrabeen",
-#             "--deacl_path",
-#             "data/processed/tests/coastlines_tests.gpkg",
-#             "--prefix",
-#             "tests",
-#             "--append_stats",
-#             "True",
-#             "--markdown_report",
-#             "True",
-#         ],
-#     )
+@pytest.mark.dependency(depends=["test_generate_continental_cli"])
+def test_validation_cli(capsys):
+    runner = CliRunner()
+    result = runner.invoke(
+        validation_cli,
+        [
+            "--inputs_path",
+            "data/validation/interim/wrl_narrabeen",
+            "--deacl_path",
+            "data/processed/tests/coastlines_tests.gpkg",
+            "--prefix",
+            "tests",
+            "--append_stats",
+            "True",
+            "--markdown_report",
+            "True",
+        ],
+    )
 
-#     # Prepare detailed error information
-#     error_info = {
-#         "exit_code": result.exit_code,
-#         "output": result.output,
-#         "exception": str(result.exception) if result.exception else None,
-#     }
+    # Prepare detailed error information
+    error_info = {
+        "exit_code": result.exit_code,
+        "output": result.output,
+        "exception": str(result.exception) if result.exception else None,
+    }
 
-#     # Convert error_info to a formatted string
-#     error_details = json.dumps(error_info, indent=2)
+    # Convert error_info to a formatted string
+    error_details = json.dumps(error_info, indent=2)
 
-#     # Use the detailed error information in the assertion message
-#     assert result.exit_code == 0, f"Command failed. Error details:\n{error_details}"  
+    # Use the detailed error information in the assertion message
+    assert result.exit_code == 0, f"Command failed. Error details:\n{error_details}"