Replace basic itzi GRASS-based tests by in-memory tests (#218)

* add memory test for number of outputs

* add memory test for flow symmetry

* add in-memory tests for max_values, stats, boundaries and wse

* remove obsolete grass-based tests

* move fixtures to conftest. Disable boundary test because of flakiness

* split boundary test in two because corners are flaky

* split test_5by5 into separate files

* move core tests in their own dir. Tag tests needing forking

* only fork essential functions in TestBMI

* remove forced --forked from CI tests. This is handled by in-file tag for each test needing it.

* CI: set correct subdir for post-wheel tests. Run all fast, non-grass tests

* update the way tests are run

* CI build wheel: install extra dependencies before tests

* test_csv_vector: replace deprecated positional indexing on Pandas Series objects.

* use windows-compatible paths

* CSV vector: use Path internally and get posix path to obstore for Windows compat.

* mark tests depending using cloud dependencies. Do not run them in wheel CI.

* skip tests if import fail

* csv vector output: fix relative path

Author: lrntct

.github/workflows/build_wheels.yml

@@ -31,12 +31,12 @@ jobs:
           CIBW_ENVIRONMENT: "ITZI_BDIST_WHEEL=1 NO_STABLE_ABI=1"  # Trigger generic compiler flags
           CIBW_ENVIRONMENT_MACOS: >
             MACOSX_DEPLOYMENT_TARGET=14.0
-            ITZI_BDIST_WHEEL=1 
+            ITZI_BDIST_WHEEL=1
             NO_STABLE_ABI=1
-          CIBW_BEFORE_TEST: "pip install pytest pytest-benchmark pandas"
+          CIBW_BEFORE_TEST: "pip install pytest pytest-benchmark pandas scipy"
           CIBW_TEST_SOURCES: tests
           CIBW_TEST_COMMAND: >  # Fast tests which do not require GRASS
-            pytest tests/test_flow.py tests/test_analytic.py tests/test_rastermetrics.py
+            pytest -m "not slow and not cloud" tests/core/
 
       - uses: actions/upload-artifact@v4
         with:

.github/workflows/tests.yml

@@ -29,7 +29,10 @@ jobs:
 
     - name: Pytest
       run: |
-        $HOME/.local/bin/uv run --all-extras --python ${{ matrix.python-version }} pytest --cov=src --forked --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html tests/
+        $HOME/.local/bin/uv run --all-extras --python ${{ matrix.python-version }} pytest --cov=src --junitxml=junit/test-core-results.xml --cov-report=xml --cov-report=html tests/core
+        $HOME/.local/bin/uv run --all-extras --python ${{ matrix.python-version }} pytest --cov=src --junitxml=junit/test-itzi-results.xml --cov-report=xml --cov-report=html tests/grass/test_itzi.py
+        $HOME/.local/bin/uv run --all-extras --python ${{ matrix.python-version }} pytest --cov=src --junitxml=junit/test-bmi-results.xml --cov-report=xml --cov-report=html tests/grass/test_bmi.py
+        $HOME/.local/bin/uv run --all-extras --python ${{ matrix.python-version }} pytest --cov=src --junitxml=junit/test-tutorial-results.xml --cov-report=xml --cov-report=html tests/grass/test_tutorial.py
 
     - name: Upload coverage
       uses: actions/upload-artifact@v4

docs/prog_manual.rst

@@ -55,7 +55,7 @@ Testing
 -------
 
 Testing is done with pytest.
-Due to global variables in GRASS (`see issue <https://github.com/OSGeo/grass/issues/629>`__),
+Due to mapset switching issues in GRASS (`see issue <https://github.com/OSGeo/grass/issues/629>`__),
 the tests must be run in separate processes using *pytest-forked*.
 
 .. code:: sh
@@ -68,6 +68,18 @@ To estimate the test coverage:
 
     uv run pytest --cov=itzi --forked -v tests/
 
+The GRASS-specific tests could be sped up a bit by running them separately:
+
+.. code:: sh
+    uv run pytest tests/grass/test_itzi.py && uv run pytest tests/grass/test_bmi.py && uv run pytest tests/grass/test_tutorial.py
+
+
+The tests not relying on GRASS can be run directly:
+
+.. code:: sh
+    uv run pytest tests/core
+
+
 Select the python version to test against with the *--python* option.
 For example *uv run --python 3.12 pytest tests/* for python 3.12.
 This will automatically install the correct python version.

pyproject.toml

@@ -82,6 +82,7 @@ pythonpath = ["src", "."]
 addopts = ["--import-mode=importlib", "--benchmark-min-rounds=7"]
 markers = [
     "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "cloud: marks tests using cloud functions (deselect with '-m \"not cloud\"')",
 ]
 
 [tool.ruff]

src/itzi/massbalance.py

@@ -1,5 +1,5 @@
 """
-Copyright (C) 2016-2025 Laurent Courty
+Copyright (C) 2016-2026 Laurent Courty
 
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License
@@ -34,7 +34,7 @@ def __init__(
     def _set_file_name(self, file_name: str) -> str:
         """Generate output file name"""
         if not file_name:
-            file_name = "{}_stats.csv".format(str(datetime.now().strftime("%Y-%m-%dT%H:%M:%S")))
+            file_name = "{}_stats.csv".format(str(datetime.now().strftime("%Y-%m-%dT%H-%M-%S")))
         return file_name
 
     def _create_file(self) -> None:

src/itzi/providers/csv_output.py

@@ -1,5 +1,5 @@
 """
-Copyright (C) 2025 Laurent Courty
+Copyright (C) 2025-2026 Laurent Courty
 
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License
@@ -17,6 +17,7 @@
 from datetime import datetime, timedelta
 from typing import TypedDict, TYPE_CHECKING, Tuple, List
 from io import StringIO
+from pathlib import Path
 import csv
 
 import pandas as pd
@@ -61,7 +62,13 @@ def __init__(self, config: CSVVectorOutputConfig) -> None:
         except AttributeError:
             self.srid = 0
         self.store = config["store"]
-        results_prefix = config["results_prefix"]
+        # Normalize path for obstore (requires forward slashes)
+        # Use resolve() to handle relative paths like "./out", but skip for empty strings
+        prefix_str = config["results_prefix"]
+        if prefix_str:
+            results_prefix = Path(prefix_str).resolve().as_posix()
+        else:
+            results_prefix = ""
 
         self.existing_ids = {"link": None, "node": None}  # Objects ids already in the file
         self.existing_max_time = {"link": None, "node": None}  # Max of sim_time in existing_file
@@ -77,7 +84,7 @@ def __init__(self, config: CSVVectorOutputConfig) -> None:
             self.headers[geom_type] = ["sim_time"] + base_headers + ["srid", "geometry"]
 
             results_name = f"{config['drainage_results_name']}_{geom_type}s.csv"
-            self.file_paths[geom_type] = results_prefix + "/" + results_name
+            self.file_paths[geom_type] = f"{results_prefix}/{results_name}"
             # No need to check if we overwrite
             if not config["overwrite"]:
                 self._check_existing_csv(geom_type)

tests/conftest.py

@@ -5,6 +5,8 @@
 import pytest
 import numpy as np
 
+from itzi.array_definitions import ARRAY_DEFINITIONS, ArrayCategory
+
 
 class Helpers:
     @staticmethod
@@ -50,6 +52,32 @@ def md5(file_path):
                 hash_md5.update(chunk)
         return hash_md5.hexdigest()
 
+    @staticmethod
+    def make_input_map_names(**overrides) -> dict[str, str | None]:
+        """Generate default input_map_names dict from ARRAY_DEFINITIONS.
+
+        Keys set to None are inactive; keys set to a truthy string activate features.
+        """
+        names = {ad.key: None for ad in ARRAY_DEFINITIONS if ArrayCategory.INPUT in ad.category}
+        names.update(overrides)
+        return names
+
+    @staticmethod
+    def make_output_map_names(prefix: str, keys: list[str]) -> dict[str, str | None]:
+        """Generate output_map_names dict from ARRAY_DEFINITIONS.
+
+        Args:
+            prefix: Prefix for output map names (e.g., "out_5by5")
+            keys: List of output keys to activate
+
+        Returns:
+            Dict with all OUTPUT-category keys, activated ones set to "prefix_keyname"
+        """
+        names = {ad.key: None for ad in ARRAY_DEFINITIONS if ArrayCategory.OUTPUT in ad.category}
+        for k in keys:
+            names[k] = f"{prefix}_{k}"
+        return names
+
 
 @pytest.fixture(scope="session")
 def helpers():

tests/core/conftest.py

@@ -0,0 +1,98 @@
+from collections import namedtuple
+
+
+import pytest
+import numpy as np
+
+from itzi.providers.domain_data import DomainData
+
+
+Domain5by5Data = namedtuple(
+    "Domain5by5Data",
+    [
+        "domain_data",  # DomainData instance
+        "arr_dem_flat",  # DEM with z=0
+        "arr_dem_high",  # DEM with z=132
+        "arr_n",  # Manning's n = 0.05
+        "arr_start_h",  # Initial depth: 0.2 at center [2,2]
+        "arr_start_wse",  # Initial WSE: 132.2 at center [2,2]
+        "arr_mask",  # All False (no mask)
+        "arr_bctype",  # Boundary condition type for open boundaries
+        "arr_rain",  # Rainfall in m/s
+        "arr_inf",  # Infiltration in m/s
+        "arr_loss",  # Losses in m/s
+        "arr_inflow",  # Inflow in m/s
+    ],
+)
+
+
+@pytest.fixture(scope="module")
+def domain_5by5() -> Domain5by5Data:
+    """Create a 5x5 domain with all base arrays.
+
+    This fixture provides the foundational data for all 5x5 tests:
+    - 5x5 grid at 10m resolution
+    - Domain extends: north=50, south=0, east=50, west=0
+    - Total area: 2500 m²
+    """
+    # Domain dimensions
+    rows, cols = 5, 5
+    north, south, east, west = 50.0, 0.0, 50.0, 0.0
+
+    # Create DomainData
+    domain_data = DomainData(
+        north=north, south=south, east=east, west=west, rows=rows, cols=cols, crs_wkt=""
+    )
+
+    # DEM arrays
+    arr_dem_flat = np.zeros(domain_data.shape, dtype=np.float32)
+    arr_dem_high = np.full(domain_data.shape, 132.0, dtype=np.float32)
+
+    # Manning's n
+    arr_n = np.full(domain_data.shape, 0.05, dtype=np.float32)
+
+    # Initial water depth: 0.2m at center cell [2, 2], 0 elsewhere
+    arr_start_h = np.zeros(domain_data.shape, dtype=np.float32)
+    arr_start_h[2, 2] = 0.2
+
+    # Initial water surface elevation: 132.2m at center cell [2, 2]
+    # (high DEM + 0.2m depth)
+    arr_start_wse = np.zeros(domain_data.shape, dtype=np.float32)
+    arr_start_wse[2, 2] = 132.2
+
+    # No mask - whole domain active
+    arr_mask = np.full(domain_data.shape, False, dtype=np.bool_)
+
+    # Boundary condition type: 2 (open) at all 16 edge cells
+    arr_bctype = np.zeros(domain_data.shape, dtype=np.float32)
+    # Top and bottom rows
+    arr_bctype[0, :] = 2
+    arr_bctype[4, :] = 2
+    # Left and right columns (excluding corners already set)
+    arr_bctype[:, 0] = 2
+    arr_bctype[:, 4] = 2
+
+    # Rate arrays in m/s
+    # Rainfall: 10 mm/h = 10/(1000*3600) m/s
+    arr_rain = np.full(domain_data.shape, 10.0 / (1000 * 3600), dtype=np.float32)
+    # Infiltration: 2 mm/h = 2/(1000*3600) m/s
+    arr_inf = np.full(domain_data.shape, 2.0 / (1000 * 3600), dtype=np.float32)
+    # Losses: 1.5 mm/h = 1.5/(1000*3600) m/s
+    arr_loss = np.full(domain_data.shape, 1.5 / (1000 * 3600), dtype=np.float32)
+    # Inflow: 0.1 m/s (already in m/s)
+    arr_inflow = np.full(domain_data.shape, 0.1, dtype=np.float32)
+
+    return Domain5by5Data(
+        domain_data=domain_data,
+        arr_dem_flat=arr_dem_flat,
+        arr_dem_high=arr_dem_high,
+        arr_n=arr_n,
+        arr_start_h=arr_start_h,
+        arr_start_wse=arr_start_wse,
+        arr_mask=arr_mask,
+        arr_bctype=arr_bctype,
+        arr_rain=arr_rain,
+        arr_inf=arr_inf,
+        arr_loss=arr_loss,
+        arr_inflow=arr_inflow,
+    )