resqpy 4.18.11__tar.gz → 5.0.0__tar.gz

{resqpy-4.18.11 → resqpy-5.0.0}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: resqpy
-Version: 4.18.11
+Version: 5.0.0
 Summary: Python API for working with RESQML models
 Home-page: https://github.com/bp/resqpy
 License: MIT
 Keywords: RESQML
 Author: BP
-Requires-Python: >=3.8.1,<3.12
+Requires-Python: >=3.9,<3.13
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
@@ -14,17 +14,17 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Topic :: System :: Filesystems
 Requires-Dist: h5py (>=3.7,<4.0)
 Requires-Dist: joblib (>=1.2,<2.0)
 Requires-Dist: lasio (>=0.31,<0.32)
-Requires-Dist: lxml (>=4.9,<5.0)
-Requires-Dist: numba (>=0.56,<1.0)
-Requires-Dist: numpy (>=1.23,<2.0)
-Requires-Dist: pandas (>=1.4,<2.0)
+Requires-Dist: lxml (>=5.1,<6.0)
+Requires-Dist: numba (>=0.59,<1.0)
+Requires-Dist: numpy (>=1.26,<2.0)
+Requires-Dist: pandas (>=2.2,<3.0)
 Requires-Dist: scipy (>=1.9,<2.0)
 Project-URL: Documentation, https://resqpy.readthedocs.io/en/latest/
 Project-URL: Repository, https://github.com/bp/resqpy

{resqpy-4.18.11 → resqpy-5.0.0}/pyproject.toml

@@ -9,7 +9,7 @@ build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "resqpy"
-version = "4.18.11" # Set at build time
+version = "5.0.0" # Set at build time
 description = "Python API for working with RESQML models"
 authors = ["BP"]
 license = "MIT"
@@ -20,10 +20,10 @@ keywords = ["RESQML"]
 classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Development Status :: 5 - Production/Stable",
     "Topic :: Scientific/Engineering",
     "Topic :: System :: Filesystems",
@@ -40,14 +40,14 @@ include = ["data/*.json"]
 #   - https://semver.org/
 # See here for "caret" style dependency specifications:
 #   - https://python-poetry.org/docs/dependency-specification/
-python = ">= 3.8.1, < 3.12"
-numpy = "^1.23"
-pandas = "^1.4"
+python = ">= 3.9, < 3.13"
+numpy = "^1.26"
+pandas = "^2.2"
 h5py = "^3.7"
-lxml = "^4.9"
+lxml = "^5.1"
 lasio = "^0.31"
 scipy = "^1.9"
-numba = ">=0.56, < 1.0"
+numba = ">=0.59, < 1.0"
 joblib = "^1.2"
 
 [tool.poetry.group.dev.dependencies]
@@ -117,4 +117,4 @@ filterwarnings = [
     "ignore:.*importing the ABCs from 'collections'.*:DeprecationWarning:.*pyreadline.*",
     "ignore:.*the imp module is deprecated in favour of importlib.*:DeprecationWarning:.*pywintypes.*",
     "ignore:.*distutils package is deprecated.*:DeprecationWarning:.*joblib.*",
-    ]
+    ]

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/__init__.py

@@ -28,6 +28,6 @@
 
 import logging
 
-__version__ = "4.18.11"  # Set at build time
+__version__ = "5.0.0"  # Set at build time
 log = logging.getLogger(__name__)
 log.info(f"Imported resqpy version {__version__}")

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/grid/__init__.py

@@ -1,14 +1,13 @@
 """The Grid Module."""
 
 __all__ = [
-    'Grid', 'RegularGrid', 'extract_grid_parent', 'establish_zone_property_kind', 'find_cell_for_x_sect_xz',
-    'grid_flavour', 'is_regular_grid', 'any_grid'
+    'Grid', 'RegularGrid', 'extract_grid_parent', 'find_cell_for_x_sect_xz', 'grid_flavour', 'is_regular_grid',
+    'any_grid'
 ]
 
 from ._grid import Grid
 from ._regular_grid import RegularGrid
 from ._grid_types import grid_flavour, is_regular_grid, any_grid
-from ._moved_functions import establish_zone_property_kind
 from ._extract_functions import extract_grid_parent, extent_kji_from_root
 from ._points_functions import find_cell_for_x_sect_xz
 

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/grid/_grid.py

@@ -680,13 +680,7 @@ class Grid(BaseResqpy):
         return _create_grid_xml(self, ijk, ext_uuid, add_as_part, add_relationships, write_active, write_geometry,
                                 use_lattice, use_parametric_lines)
 
-    def x_section_points(self, axis, ref_slice0 = 0, plus_face = False, masked = False):
-        """Deprecated: please use `unsplit_x_section_points` instead."""
-        warnings.warn('Deprecated: please use `unsplit_x_section_points` instead.', DeprecationWarning)
-
-        return unsplit_x_section_points(self, axis, ref_slice0 = ref_slice0, plus_face = plus_face, masked = masked)
-
-    # The implementations of the below functions have been moved to separate modules.
+    # the implementations of the functions below have been moved to separate modules
 
     def cell_geometry_is_defined(self, cell_kji0 = None, cell_geometry_is_defined_root = None, cache_array = True):
         """Returns True if the geometry of the specified cell is defined.

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/grid_surface/_find_faces.py

@@ -558,6 +558,8 @@ def find_faces_to_represent_surface_regular_dense_optimised(grid,
         to a grid connection set; use the non-dense version of the function for a reduced memory footprint;
         this function is DEPRECATED pending proving of newer find_faces_to_represent_surface_regular_optimised()
     """
+    warnings.warn('DEPRECATED: grid_surface.find_faces_to_represent_surface_regular_dense_optimised() function; ' +
+                  'use find_faces_to_represent_surface_regular_optimised() instead')
 
     assert isinstance(grid, grr.RegularGrid)
     assert grid.is_aligned
@@ -1363,6 +1365,7 @@ def bisector_from_faces(  # type: ignore
           assigned to either the True or False part
         - this function is DEPRECATED, pending proving of newer indices based approach
     """
+    warnings.warn('DEPRECATED: grid_surface.bisector_from_faces() function; use bisector_from_face_indices() instead')
     assert len(grid_extent_kji) == 3
 
     # find the surface boundary (includes a buffer slice where surface does not reach edge of grid)

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/lines/_polyline.py

@@ -25,25 +25,22 @@ class Polyline(rql_c._BasePolyline):
 
     resqml_type = 'PolylineRepresentation'
 
-    def __init__(
-            self,
-            parent_model,
-            uuid = None,
-            set_bool = None,  #: DEPRECATED
-            set_coord = None,
-            set_crs = None,
-            is_closed = None,
-            title = None,
-            rep_int_root = None,
-            originator = None,
-            extra_metadata = None):
+    def __init__(self,
+                 parent_model,
+                 uuid = None,
+                 set_coord = None,
+                 set_crs = None,
+                 is_closed = None,
+                 title = None,
+                 rep_int_root = None,
+                 originator = None,
+                 extra_metadata = None):
         """Initialises a new polyline object.
 
         arguments:
             parent_model (model.Model object): the model which the new PolylineRepresentation belongs to
             uuid (uuid.UUID, optional): the uuid of an existing RESQML PolylineRepresentation from which
                 to initialise the resqpy Polyline
-            set_bool (boolean, optional): DEPRECATED: synonym for is_closed argument
             set_coord (numpy float array, optional): an ordered set of xyz values used to define a new polyline;
                 last dimension of array must have extent 3; ignored if uuid is not None
             set_crs (uuid.UUID, optional): the uuid of a crs to be used when initialising from coordinates;
@@ -65,10 +62,6 @@ class Polyline(rql_c._BasePolyline):
         """
 
         self.model = parent_model
-        if set_bool is not None:
-            warnings.warn('DEPRECATED: use is_closed argument instead of set_bool, in Polyline initialisation')
-            if is_closed is None:
-                is_closed = set_bool
         self.isclosed = is_closed
         self.nodepatch = None
         self.crs_uuid = set_crs
@@ -466,22 +459,20 @@ class Polyline(rql_c._BasePolyline):
         if cache and self.centre is not None:
             return self.centre
         assert mode in ['weighted', 'sampled']
-        if mode == 'sampled':  # this mode is deprecated as it simply approximates the weighted mode
-            sample_points = self.equidistant_points(n, in_xy = in_xy)
-            centre = np.mean(sample_points, axis = 0)
-        else:  # 'weighted'
-            sum = np.zeros(3)
-            seg_count = len(self.coordinates) - 1
-            if self.isclosed:
-                seg_count += 1
-            d = 2 if in_xy else 3
-            p1 = np.zeros(3)
-            p2 = np.zeros(3)
-            for seg_index in range(seg_count):
-                successor = (seg_index + 1) % len(self.coordinates)
-                p1[:d], p2[:d] = self.coordinates[seg_index, :d], self.coordinates[successor, :d]
-                sum += (p1 + p2) * vu.naive_length(p2 - p1)
-            centre = sum / (2.0 * self.full_length(in_xy = in_xy))
+        if mode != 'weighted':  # ignore any other mode, ie. sampled
+            warnings.warn('DEPRECATED: weighted mode is only mode now supported for Polyline.balanced_centre()')
+        sum = np.zeros(3)
+        seg_count = len(self.coordinates) - 1
+        if self.isclosed:
+            seg_count += 1
+        d = 2 if in_xy else 3
+        p1 = np.zeros(3)
+        p2 = np.zeros(3)
+        for seg_index in range(seg_count):
+            successor = (seg_index + 1) % len(self.coordinates)
+            p1[:d], p2[:d] = self.coordinates[seg_index, :d], self.coordinates[successor, :d]
+            sum += (p1 + p2) * vu.naive_length(p2 - p1)
+        centre = sum / (2.0 * self.full_length(in_xy = in_xy))
         if cache:
             self.centre = centre
         return centre

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/model/_model.py

@@ -1340,7 +1340,8 @@ class Model():
            an hdf5 file name is cached once determined for a given ext uuid; to clear the cache,
            call the h5_clear_filename_cache() method
         """
-
+        if isinstance(override, bool):
+            warnings.warn('DEPRECATED: boolean override argument to Model.h5_file_name(); use string instead')
         return m_h._h5_file_name(self, uuid = uuid, override = override, file_must_exist = file_must_exist)
 
     def h5_access(self, uuid = None, mode = 'r', override = 'default', file_path = None):
@@ -1366,7 +1367,8 @@ class Model():
            an exception will be raised if the hdf5 file cannot be opened; note that sometimes another
            piece of code accessing the file might cause a 'resource unavailable' exception
         """
-
+        if isinstance(override, bool):
+            warnings.warn('DEPRECATED: boolean override argument to Model.h5_access(); use string instead')
         return m_h._h5_access(self, uuid = uuid, mode = mode, override = override, file_path = file_path)
 
     def h5_release(self):

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/multi_processing/wrappers/grid_surface_mp.py

@@ -213,7 +213,7 @@ def find_faces_to_represent_surface_regular_wrapper(index: int,
         surface = rqs.Surface(model, crs_uuid = grid.crs.uuid, title = surf_title)
         flange_bool = surface.set_from_point_set(pset,
                                                  convexity_parameter = 2.0,
-                                                 reorient = True,
+                                                 reorient = reorient,
                                                  extend_with_flange = extend_fault_representation,
                                                  flange_inner_ring = flange_inner_ring,
                                                  saucer_parameter = saucer_parameter,

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/olio/triangulation.py

@@ -25,7 +25,7 @@ import resqpy.olio.vector_utilities as vec
 
 def _dt_scipy(points: np.ndarray) -> Tuple[np.ndarray, np.ndarray]:
     """Calculates the Delaunay triangulation for an array of points and the convex hull indices.
-    
+
     arguments:
         points (np.ndarray): coordinates of the points to triangulate; array has shape
             (npoints, ndim)
@@ -871,6 +871,7 @@ def surrounding_xy_ring(p,
        numpy float array of shape (N, 3) being xyz points in surrounding ring(s); z is set constant to
        mean value of z in p (optionally adjussted based on saucer_angle);
        N is count if inner_ring is False, 3 * count if True
+       radius used for ring of additional points
     """
 
     def make_ring(count, centre, radius, saucer_angle):
@@ -898,8 +899,8 @@ def surrounding_xy_ring(p,
         inner_radius = p_radius * 1.1
         assert radius > inner_radius
         in_ring = make_ring(2 * count, centre, inner_radius, saucer_angle)
-        return np.concatenate((in_ring, ring), axis = 0)
-    return ring
+        return np.concatenate((in_ring, ring), axis = 0), radius
+    return ring, radius
 
 
 def edges(t):

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/olio/volume.py

@@ -77,26 +77,6 @@ def tetra_cell_volume(cp, centre = None, off_hand = False):
     return v / 6.0
 
 
-def tetra_volumes_slow(cp, centres = None, off_hand = False):
-    """Returns volume array for all hexahedral cells assuming bilinear faces, using loop over cells."""
-
-    # NB: deprecated, superceded by much faster function below
-    # todo: handle NaNs
-    # Pagoda style corner point data
-    assert cp.ndim == 7
-
-    flat = cp.reshape(-1, 2, 2, 2, 3)
-    cells = flat.shape[0]
-    if centres is None:
-        centres = np.mean(flat, axis = (1, 2, 3))
-    else:
-        centres = centres.reshape((-1, 3))
-    volumes = np.zeros(cells)
-    for cell in range(cells):
-        volumes[cell] = tetra_cell_volume(flat[cell], centre = centres[cell], off_hand = off_hand)
-    return volumes.reshape(cp.shape[0:3])
-
-
 def tetra_volumes(cp, centres = None, off_hand = False):
     """Returns volume array for all hexahedral cells assuming bilinear faces, using numpy operations.
 

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/property/__init__.py

@@ -8,7 +8,8 @@ __all__ = [
     'reformat_column_edges_from_resqml_format', 'same_property_kind', 'selective_version_of_collection',
     'supported_local_property_kind_list', 'supported_property_kind_list', 'supported_facet_type_list',
     'expected_facet_type_dict', 'create_transmisibility_multiplier_property_kind',
-    'property_kind_and_facet_from_keyword', 'guess_uom', 'property_parts', 'property_part', 'make_aps_key'
+    'property_kind_and_facet_from_keyword', 'guess_uom', 'property_parts', 'property_part', 'make_aps_key',
+    'establish_zone_property_kind'
 ]
 
 from .property_common import property_collection_for_keyword,  \
@@ -27,7 +28,7 @@ from .property_common import property_collection_for_keyword,  \
     guess_uom,  \
     property_parts,  \
     property_part
-from .property_kind import PropertyKind, create_transmisibility_multiplier_property_kind
+from .property_kind import PropertyKind, create_transmisibility_multiplier_property_kind, establish_zone_property_kind
 from .string_lookup import StringLookup
 from .property_collection import PropertyCollection
 from .attribute_property_set import AttributePropertySet, ApsProperty, make_aps_key

{resqpy-4.18.11 → resqpy-5.0.0}/resqpy/rq_import/_grid_from_cp.py

@@ -511,8 +511,8 @@ class _GridFromCp:
                 assert len(where_defined) == 3 and len(where_defined[0]) > 0, 'no extant cell geometries'
                 sample_kji0 = (where_defined[0][0], where_defined[1][0], where_defined[2][0])
             sample_cp = self.__cp_array[sample_kji0]
-            self.__cell_ijk_lefthanded = (vec.clockwise(sample_cp[0, 0, 0], sample_cp[0, 1, 0], sample_cp[0, 0, 1]) >=
-                                          0.0)
+            self.__cell_ijk_lefthanded =  \
+                (vec.clockwise(sample_cp[0, 0, 0], sample_cp[0, 1, 0], sample_cp[0, 0, 1]) >= 0.0)
             if not self.grid.k_direction_is_down:
                 self.__cell_ijk_lefthanded = not self.__cell_ijk_lefthanded
             if self.__crs.is_right_handed_xyz():