update pytz dep (#69)

* update pytz, nzshm-model, mkdocstrings-python dependencies
* handle tests and imports when optional dependencies not present

pyproject.toml

@@ -31,16 +31,16 @@ nshm-toshi-client = {version = "^1.0.0", optional = true}
 pyproj = "^3.3"
 python = ">=3.9,<4.0"
 python-dateutil = "^2.8.2"
-pytz = "2021.3"
 pyvista = {version = "^0.44.1", optional = true}
 geopandas = "^1.0.1"
 
 nzshm-common = "^0.8.1"
-nzshm-model = "^0.10.6"
 
 # see https://github.com/orgs/python-poetry/discussions/7937
 # urllib3 = "<2"
 pandera = {extras = ["mypy"], version = "^0.20.4"}
+pytz = "^2025.1"
+nzshm-model = {git = "https://github.com/GNS-Science/nzshm-model.git", rev = "pre-release"}
 
 
 
@@ -63,7 +63,7 @@ optional = true
 
 [tool.poetry.group.doc.dependencies]
 mkdocs = "^1.6.1"
-mkdocstrings = "^0.26.2"
+mkdocstrings = {version = "^0.26.2", extras = ["python"]}
 mkdocs-autorefs = "^1.0.1"
 mkdocs-include-markdown-plugin = "^6.0.6"
 mkdocs-material = "^9.5.21"

setup.cfg

@@ -35,6 +35,8 @@ exclude = .git,
 ignore_missing_imports = True
 # plugins = numpy.typing.mypy_plugin
 plugins = pandera.mypy
+exclude = solvis/fault_system_solution_helper.py
+
 
 [coverage:run]
 # exclude = */test_geometry_performance.py

solvis/dochelper/__init__.py

@@ -1,6 +1,5 @@
 """Package supporting dynamic dosstrings."""
 
-from .extension import DynamicDocstrings
 from .inherit_docstrings import inherit_docstrings
 
-__all__ = ["DynamicDocstrings", "inherit_docstrings"]
+__all__ = ["inherit_docstrings"]

solvis/solution/fault_system_solution/fault_system_solution.py

@@ -190,7 +190,7 @@ def get_branch_inversion_solution_id(branch: ModelLogicTreeBranch) -> str:
             This distinction may go away in future versions, simplifying this issue:
             https://github.com/GNS-Science/nzshm-model/issues/81
         """
-        if isinstance(branch, nm.logic_tree.source_logic_tree.version2.logic_tree.SourceBranch):
+        if isinstance(branch, nm.logic_tree.SourceBranch):
             # NZSHM Model 0.6: v2 branches take inversion ID from first InversionSource
             for source in branch.sources:
                 if source.type == "inversion":

test/geometry/test_geometry_distance.py

@@ -5,27 +5,28 @@
 import geopandas as gpd
 import numpy as np
 import pytest
-import pyvista as pv
 from nzshm_common.location.location import location_by_id
 from pyproj import Transformer
 from pytest import approx
 
 from solvis import InversionSolution, geometry
 
+pyvista = pytest.importorskip("pyvista")
+
 TEST_FOLDER = pathlib.PurePath(os.path.realpath(__file__)).parent.parent
 
 
 class TestPyvistaDistances(unittest.TestCase):
     def test_basic_0_rake_90(self):
 
-        mesh0 = pv.PolyData([[0, 0, 0]], force_float=False)
+        mesh0 = pyvista.PolyData([[0, 0, 0]], force_float=False)
 
         p0 = [0, 1, 0]  # 1st top-trace point
         p1 = [0, 2, 0]  # 2nd top-trace point
         p2 = [1, 1, 10]  # 1st botton trace point
         p3 = [1, 2, 10]  # 2nd bottom trace point
 
-        mesh1 = pv.PolyData([p0, p1, p2, p3], force_float=False)
+        mesh1 = pyvista.PolyData([p0, p1, p2, p3], force_float=False)
         closest_cells, closest_points = mesh1.find_closest_cell(mesh0.points, return_closest_point=True)
         d_exact = np.linalg.norm(mesh0.points - closest_points, axis=1)
 
@@ -36,14 +37,14 @@ def test_basic_0_rake_90(self):
         assert d_exact[0] == 1
 
     def test_basic_1_further_at_depth(self):
-        mesh0 = pv.PolyData([0, 0, 0], force_float=False)
+        mesh0 = pyvista.PolyData([0, 0, 0], force_float=False)
 
         p0 = [0, 2, 0]  # 1st top-trace point
         p1 = [0, 3, 0]  # 2nd top-trace point
         p2 = [2, 2, 10]  # 1st botton trace point
         p3 = [2, 3, 10]  # 2nd bottom trace point
 
-        mesh1 = pv.PolyData([p0, p1, p2, p3], force_float=False)
+        mesh1 = pyvista.PolyData([p0, p1, p2, p3], force_float=False)
 
         closest_cells, closest_points = mesh1.find_closest_cell(mesh0.points, return_closest_point=True)
         d_exact = np.linalg.norm(mesh0.points - closest_points, axis=1)
@@ -55,14 +56,14 @@ def test_basic_1_further_at_depth(self):
         assert d_exact[0] == 2.0
 
     def test_basic_2_closer_at_depth(self):
-        mesh0 = pv.PolyData([0, 0, 0], force_float=False)
+        mesh0 = pyvista.PolyData([0, 0, 0], force_float=False)
 
         p0 = [10, 2, 0]  # 1st top-trace point
         p1 = [10, 3, 0]  # 2nd top-trace point
         p2 = [0, 2, 5]  # 1st botton trace point
         p3 = [0, 3, 5]  # 2nd bottom trace point
 
-        mesh1 = pv.PolyData([p0, p1, p2, p3], force_float=False)
+        mesh1 = pyvista.PolyData([p0, p1, p2, p3], force_float=False)
         closest_cells, closest_points = mesh1.find_closest_cell(mesh0.points, return_closest_point=True)
         d_exact = np.linalg.norm(mesh0.points - closest_points, axis=1)
 
@@ -73,8 +74,8 @@ def test_basic_2_closer_at_depth(self):
         assert d_exact[0] > 5
 
     def test_calc_distance_345_line(self):
-        origin = pv.PolyData([0, 0, 0], force_float=False)
-        surface = pv.PolyData([[3, 0, 4], [3, 1, 4]], force_float=False)
+        origin = pyvista.PolyData([0, 0, 0], force_float=False)
+        surface = pyvista.PolyData([[3, 0, 4], [3, 1, 4]], force_float=False)
 
         closest_cells, closest_points = surface.find_closest_cell(origin.points, return_closest_point=True)
         d_exact = np.linalg.norm(origin.points - closest_points, axis=1)
@@ -84,8 +85,8 @@ def test_calc_distance_345_line(self):
         assert d_exact[0] == 5
 
     def test_calc_distance_345_surface(self):
-        origin = pv.PolyData([0, 0, 0], force_float=False)
-        surface = pv.PolyData([[3, 0, 4], [15, 0, 4], [15, 1, 10], [3, 1, 10]], force_float=False)
+        origin = pyvista.PolyData([0, 0, 0], force_float=False)
+        surface = pyvista.PolyData([[3, 0, 4], [15, 0, 4], [15, 1, 10], [3, 1, 10]], force_float=False)
         closest_cells, closest_points = surface.find_closest_cell(origin.points, return_closest_point=True)
         d_exact = np.linalg.norm(origin.points - closest_points, axis=1)