Fix new test warnings (issue #971)

.github/workflows/ci.yml

@@ -20,6 +20,8 @@ jobs:
       # ubuntu-latest runner home is /home/runner; matches $HOME/hera_unittest_data
       # which is both bootstrap_unittest_data.sh's default and conftest's default.
       TEST_HERA: /home/runner/hera_unittest_data
+      # Silence jupyter_client's platformdirs migration DeprecationWarning in test output
+      JUPYTER_PLATFORM_DIRS: "1"
 
     services:
       mongodb:

hera/measurements/GIS/raster/topography.py

@@ -37,6 +37,7 @@ def _open_raster(fheight):
 import xarray as xr
 import geopandas as gpd
 from shapely.geometry import Point
+from pyproj import Transformer
 
 
 WSG84 = 4326
@@ -253,25 +254,36 @@ def convertPointsCRS(self, points, inputCRS, outputCRS, **kwargs):
 
         if isinstance(points, np.ndarray):
             if points.ndim == 1:
-                gdf = gpd.GeoDataFrame(geometry=gpd.points_from_xy([points[0]], [points[1]]))
+                x_vals, y_vals = [points[0]], [points[1]]
             else:
-                gdf = gpd.GeoDataFrame(geometry=gpd.points_from_xy(points[:, 0], points[:, 1]))
+                x_vals, y_vals = points[:, 0], points[:, 1]
 
         elif isinstance(points, pd.DataFrame):
             x_col = kwargs.get("x", "x")
             y_col = kwargs.get("y", "y")
-            gdf = gpd.GeoDataFrame(geometry=gpd.points_from_xy(points[x_col], points[y_col]))
+            x_vals, y_vals = points[x_col], points[y_col]
 
         elif isinstance(points, list):
             if len(points) == 1:
-                gdf = gpd.GeoDataFrame(geometry=gpd.points_from_xy([points[0][0]], [points[0][1]]))
+                x_vals, y_vals = [points[0][0]], [points[0][1]]
             else:
-                gdf = gpd.GeoDataFrame(geometry=gpd.points_from_xy([x[0] for x in points], [x[1] for x in points]))
+                x_vals, y_vals = [x[0] for x in points], [x[1] for x in points]
 
         else:
             raise ValueError(f"Unsupported type: {type(points)}")
 
+        gdf = gpd.GeoDataFrame(geometry=gpd.points_from_xy(x_vals, y_vals))
         gdf.set_crs(inputCRS, inplace=True)
+
+        # A single-point GeoDataFrame.to_crs() triggers a spurious pyproj
+        # "ndim > 0 to a scalar" DeprecationWarning on the pinned geopandas/pyproj
+        # versions (the array-transform path mishandles length-1 arrays), so route
+        # the single-point case through a scalar pyproj transform instead.
+        if len(gdf) == 1:
+            transformer = Transformer.from_crs(inputCRS, outputCRS, always_xy=True)
+            x_out, y_out = transformer.transform(list(x_vals)[0], list(y_vals)[0])
+            return gpd.GeoDataFrame(geometry=[Point(x_out, y_out)], crs=outputCRS)
+
         return gdf.to_crs(outputCRS)
 
     def create_xarray(self, minx, miny, maxx, maxy, dxdy=30, inputCRS=WSG84):

hera/riskassessment/agents/effects/Calculator.py

@@ -128,7 +128,7 @@ def __init__(self,tenbergeCoefficient,breathingRate=10*ureg.L/ureg.min,**kwargs)
 		self.n 	   = tenbergeCoefficient
 
 	def calculate(self,concentrationField,field,breathingRate=10*ureg.L/ureg.min,time="datetime",inUnits=None):
-		"""
+		r"""
             Calculates the toxic load  from a concentration field.
             \begin{equation}
             		D(T) = \int_0^T C^n dt

hera/riskassessment/agents/effects/InjuryLevel.py

@@ -98,7 +98,8 @@ def calculateContours(self, toxicLoads, time="datetime", x="x", y="y"):
 			The data returns in km because itm is in km. 
 
 		"""
-		curBackend = plt.get_backend()	
+		curBackend = plt.get_backend()
+		plt.close('all')
 		plt.switch_backend("pdf")
 
 		if time in toxicLoads.dims:
@@ -138,6 +139,7 @@ def calculateContours(self, toxicLoads, time="datetime", x="x", y="y"):
 				retList.append(ret)
 
 		ret = None if ret.empty else pandas.concat(retList,ignore_index=True)
+		plt.close('all')
 		plt.switch_backend(curBackend)
 
 		return ret

hera/simulations/gaussian/Meteorology.py

@@ -194,7 +194,7 @@ def getAirTemperature(self, height):
                 default unit m
         :return:
             air temperature at C.
-        """
+        r"""
         return self._temperature - 6.5e-3 * tonumber(height, ureg.m) * ureg.K
 
     def getAirDensity(self, height):
@@ -213,7 +213,7 @@ def getAirDensity(self, height):
                default m
         :return:
                air density in kg/m**3
-        """
+        r"""
         P = unumToPint(self.getAirPressure(height)).m_as(ureg.mmHg)
         T = unumToPint(self.getAirTemperature(height)).m_as(ureg.degC)
 
@@ -243,7 +243,7 @@ def _setPvalues(self):
 
         :return:
             The coefficient (dimensionless).
-        """
+        r"""
         if (self.z0 is None or self.stability is None):
             return
         pstab = self._pvalues[self.stability]
@@ -262,7 +262,7 @@ def getWindVelocity(self, height):
                 default units [m]
         :return:
             The wind velocity at the requested height.
-        """
+        r"""
         height = tonumber(height, ureg.m)
         refHeight = tonumber(self.refHeight, ureg.m)
         height = numpy.min([numpy.max([height, 0]), 300])

hera/simulations/gaussian/gasCloud.py

@@ -672,7 +672,7 @@ class Continuous(object):
     _FullKernel = None
 
     def __init__(self,dt,kernelsize,timetofinish=10*ureg.min):
-        """
+        r"""
         Time to finish.
         the time (min) it take to reach 0.1.
 

hera/simulations/hydrodynamics/nearWallFlow.py

@@ -10,7 +10,7 @@
 import numpy
 
 class functionG:
-    """
+    r"""
         The G(Lambda,D) is defined implicitly (Eqn. 17.60, page 537):
 
         \begin{equation}

hera/simulations/openFoam/CLI.py

@@ -490,11 +490,11 @@ def stochasticLagrangian_source_makeEscapedMassFile(args):
         data = data.interpolate()
     newstr = "/*--------------------------------*- C++ -*----------------------------------*\n" \
              "| =========                 |                                                 |\n" \
-             "| \      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |\n" \
-             "|  \    /   O peration     | Version:  dev                                   |\n" \
-             "|   \  /    A nd           | Web:      www.OpenFOAM.org                      |\n" \
-             "|    \/     M anipulation  |                                                 |\n" \
-             "\*---------------------------------------------------------------------------*/\n" \
+             "| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |\n" \
+             "|  \\    /   O peration     | Version:  dev                                   |\n" \
+             "|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |\n" \
+             "|    \\/     M anipulation  |                                                 |\n" \
+             "\\*---------------------------------------------------------------------------*/\n" \
              "FoamFile\n{    version     2.0;\n    format      ascii;\n    class       scalarField;\n    object      kinematicCloudPositions;\n}\n" \
              f"// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n\n{len(data)}\n(\n"
     for time in timesteps:

hera/simulations/openFoam/eulerian/NavierStokes.old/postprocess/gui/morphology.py

@@ -13001,15 +13001,15 @@ def areastatistics():
     plt.plot(x1,y1,'*r')
     plt.plot(x2,y2,'or')
     plt.plot(x3,y3,'+r')
-    plt.title('$\lambda_f$')
+    plt.title(r'$\lambda_f$')
     plt.subplot(1,3,2)
     plt.imshow(zilp, origin='lower', interpolation='nearest',extent=[xmin,xmax,ymin,ymax])  # jet, Paired
     plt.colorbar()
     plt.grid()
     plt.plot(x1,y1,'*r')
     plt.plot(x2,y2,'or')
     plt.plot(x3,y3,'+r')
-    plt.title('$\lambda_p$')
+    plt.title(r'$\lambda_p$')
     plt.subplot(1,3,3)
     plt.imshow(zilh, origin='lower', interpolation='nearest',extent=[xmin,xmax,ymin,ymax], norm=matplotlib.colors.LogNorm())  # jet, Paired
     plt.colorbar()

hera/simulations/openFoam/lagrangian/LSM/toolkit.py

@@ -402,11 +402,11 @@ def makeSource(self, x, y, z, nParticles, type="Point", fileName="kinematicCloud
         """
         string = "/*--------------------------------*- C++ -*----------------------------------*\n " \
                  "| =========                 |                                                 |\n" \
-                 "| \      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |\n" \
-                 "|  \    /   O peration     | Version:  dev                                   |\n" \
-                 "|   \  /    A nd           | Web:      www.OpenFOAM.org                      |\n" \
-                 "|    \/     M anipulation  |                                                 |\n" \
-                 "\*---------------------------------------------------------------------------*/\n" \
+                 "| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |\n" \
+                 "|  \\    /   O peration     | Version:  dev                                   |\n" \
+                 "|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |\n" \
+                 "|    \\/     M anipulation  |                                                 |\n" \
+                 "\\*---------------------------------------------------------------------------*/\n" \
                  "FoamFile\n{    version     2.0;\n    format      ascii;\n    class       vectorField;\n" \
                  "    object      kinematicCloudPositions;\n}\n" \
                  "// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n\n" \

hera/simulations/openFoam/lagrangian/abstractLagrangianSolver.py

@@ -679,11 +679,11 @@ def writeParticlePositionFile(self, x, y, z, nParticles, dispersionName, type="P
         """
         string = "/*--------------------------------*- C++ -*----------------------------------*\n " \
                  "| =========                 |                                                 |\n" \
-                 "| \      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |\n" \
-                 "|  \    /   O peration     | Version:  dev                                   |\n" \
-                 "|   \  /    A nd           | Web:      www.OpenFOAM.org                      |\n" \
-                 "|    \/     M anipulation  |                                                 |\n" \
-                 "\*---------------------------------------------------------------------------*/\n" \
+                 "| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |\n" \
+                 "|  \\    /   O peration     | Version:  dev                                   |\n" \
+                 "|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |\n" \
+                 "|    \\/     M anipulation  |                                                 |\n" \
+                 "\\*---------------------------------------------------------------------------*/\n" \
                  "FoamFile\n{    version     2.0;\n    format      ascii;\n    class       vectorField;\n" \
                  "    object      kinematicCloudPositions;\n}\n" \
                  "// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n\n" \

hera/simulations/openFoam/toberewritten/wrf2of.py

@@ -284,11 +284,11 @@ def regrid3(data, factorxy, factorz):
 lines.append('// built with wrf2of.py for '+outputdir)
 lines.append("/*--------------------------------*- C++ -*----------------------------------*\'")
 lines.append('| =========                |                                                  |')
-lines.append('| \      /  F ield         | OpenFOAM: The Open Source CFD Toolbox            |')
-lines.append('|  \    /   O peration     | Version:  10.0                                   |')
-lines.append('|   \  /    A nd           | Web:      www.OpenFOAM.org                       |')
-lines.append('|    \/     M anipulation  |                                                  |')
-lines.append('\*---------------------------------------------------------------------------*/')
+lines.append('| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox            |')
+lines.append('|  \\    /   O peration     | Version:  10.0                                   |')
+lines.append('|   \\  /    A nd           | Web:      www.OpenFOAM.org                       |')
+lines.append('|    \\/     M anipulation  |                                                  |')
+lines.append('\\*---------------------------------------------------------------------------*/')
 lines.append('FoamFile')
 lines.append('{')
 lines.append('    version     10.0;')

hera/tests/test_logging_helpers.py

@@ -0,0 +1,18 @@
+import warnings
+
+from hera.utils.logging import helpers
+
+
+class TestGetDefaultLoggingConfig:
+    def test_no_deprecation_warning_when_creating_default_config(self, tmp_path, monkeypatch):
+        """Loading the packaged default config must not use deprecated importlib.resources APIs."""
+        log_dir = tmp_path / "log"
+        log_dir.mkdir()
+        monkeypatch.setattr(helpers, "HERA_DEFAULT_LOG_DIR", log_dir)
+
+        with warnings.catch_warnings():
+            warnings.simplefilter("error", DeprecationWarning)
+            config = helpers.get_default_logging_config()
+
+        assert isinstance(config, dict)
+        assert (log_dir / "heraLogging.config").is_file()

hera/tests/test_no_invalid_escapes.py

@@ -0,0 +1,27 @@
+import pathlib
+import warnings
+
+import pytest
+
+HERA_ROOT = pathlib.Path(__file__).resolve().parents[1]
+
+
+def _python_sources():
+    return sorted(HERA_ROOT.rglob("*.py"))
+
+
+@pytest.mark.parametrize("path", _python_sources(), ids=lambda p: str(p.relative_to(HERA_ROOT)))
+def test_no_invalid_escape_sequences(path):
+    """Compiling every hera source file must not emit invalid-escape warnings.
+
+    Python <=3.11 emits DeprecationWarning, >=3.12 emits SyntaxWarning."""
+    source = path.read_text(encoding="utf-8", errors="replace")
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", SyntaxWarning)
+        warnings.simplefilter("error", DeprecationWarning)
+        try:
+            compile(source, str(path), "exec")
+        except SyntaxError as err:
+            # Legacy files that never compiled (dead code) are out of scope here;
+            # they cannot emit escape warnings because they cannot be imported at all.
+            pytest.skip(f"pre-existing SyntaxError, file is not importable: {err.msg} (line {err.lineno})")

hera/tests/test_topography.py

@@ -256,6 +256,27 @@ def test_basic(self, topo_toolkit):
         converted = topo_toolkit.convertPointsCRS(points, inputCRS=4326, outputCRS=2039)
         assert converted.shape[0] == 2
 
+    def test_single_point_no_deprecation_warning(self, topo_toolkit):
+        """A single-point conversion must not trigger pyproj's array-to-scalar
+        DeprecationWarning (issue971) — geopandas.to_crs() on a 1-row
+        GeoDataFrame mishandles length-1 arrays on the pinned pyproj/geopandas."""
+        import warnings
+
+        with warnings.catch_warnings():
+            warnings.simplefilter("error", DeprecationWarning)
+            converted = topo_toolkit.convertPointsCRS([(35.1, 33.85)], inputCRS=4326, outputCRS=2039)
+
+        assert converted.shape[0] == 1
+
+    def test_single_point_matches_multi_point_conversion(self, topo_toolkit):
+        """The single-point fast path must produce the same result as the
+        general (multi-point) to_crs path for the same coordinate."""
+        single = topo_toolkit.convertPointsCRS([(35.1, 33.85)], inputCRS=4326, outputCRS=2039)
+        multi = topo_toolkit.convertPointsCRS([(35.1, 33.85), (36.05, 33.9)], inputCRS=4326, outputCRS=2039)
+
+        assert single.geometry.iloc[0].x == pytest.approx(multi.geometry.iloc[0].x)
+        assert single.geometry.iloc[0].y == pytest.approx(multi.geometry.iloc[0].y)
+
 
 class TestCreateElevationSTL:
     def test_basic(self, topo_toolkit):

hera/utils/latex.py

@@ -8,7 +8,7 @@
 
 
 class bibItem:
-    """
+    r"""
         Represents a single bib item.
 
         \bibitem{paper2}

hera/utils/logging/helpers.py

@@ -3,7 +3,7 @@
 import logging.config
 import os.path
 import pathlib
-from importlib.resources import read_text
+from importlib.resources import files
 
 
 HERA_DEFAULT_LOG_DIR = pathlib.Path.home() / ".pyhera" / "log"
@@ -31,7 +31,7 @@ def get_default_logging_config(*, disable_existing_loggers: bool = False) -> dic
     """Load the default Hera logging configuration, creating it on first use."""
     defaultLocalConfig = os.path.join(HERA_DEFAULT_LOG_DIR,'heraLogging.config')
     if not os.path.isfile(defaultLocalConfig):
-        defaultConfig = read_text('hera.utils.logging', 'heraLogging.config')
+        defaultConfig = files('hera.utils.logging').joinpath('heraLogging.config').read_text()
         with open(defaultLocalConfig,'w') as localConfig:
             localConfig.write(defaultConfig)