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Revert "3.3.0" #227

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2 changes: 1 addition & 1 deletion .github/workflows/conda.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ jobs:
conda install -c conda-forge conda-build scikit-build-core numpy anaconda-client conda-libmamba-solver -y
conda config --set solver libmamba
conda build --output-folder conda conda --python ${{matrix.python-version}}
anaconda upload --label main conda/*/*.conda
anaconda upload --label main conda/*/*.tar.bz2

- name: upload artifacts
uses: actions/upload-artifact@v4
Expand Down
21 changes: 8 additions & 13 deletions .github/workflows/linting_and_testing.yml
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Expand Up @@ -48,33 +48,28 @@ jobs:
with:
python-version: ${{ matrix.python-version }}
conda-remove-defaults: "true"

- name: Install dependencies for windows python 3.9 and 3.10
if: ${{ matrix.os == 'windows-latest' && (matrix.python-version == '3.9' || matrix.python-version == '3.10') }}


- name: Install dependencies for windows python 3.10
if: ${{ matrix.os == 'windows-latest' && matrix.python-version == '3.10' }}
run: |
conda run -n test conda info
conda run -n test conda install -c loop3d -c conda-forge "gdal=3.4.3" python=${{ matrix.python-version }} -y
conda run -n test conda install -c loop3d -c conda-forge --file dependencies.txt python=${{ matrix.python-version }} -y
conda run -n test conda install pytest python=${{ matrix.python-version }} -y

- name: Install dependencies for windows python 3.11
if: ${{ matrix.os == 'windows-latest' && matrix.python-version == '3.11' }}
- name: Install dependencies for other environments
if: ${{ matrix.os != 'windows-latest' || matrix.python-version != '3.10' }}
run: |
conda run -n test conda info
conda run -n test conda install -c loop3d -c conda-forge gdal "netcdf4=*=nompi_py311*" python=${{ matrix.python-version }} -y
conda run -n test conda install -c loop3d -c conda-forge gdal python=${{ matrix.python-version }} -y
conda run -n test conda install -c loop3d -c conda-forge --file dependencies.txt python=${{ matrix.python-version }} -y
conda run -n test conda install pytest python=${{ matrix.python-version }} -y

- name: Install dependencies for other environments
if: ${{ !(matrix.os == 'windows-latest' && (matrix.python-version == '3.9' || matrix.python-version == '3.10' || matrix.python-version == '3.11')) }}
run: |
conda run -n test conda info
conda run -n test conda install -c loop3d -c conda-forge python=${{ matrix.python-version }} gdal pytest --file dependencies.txt -y

- name: Install map2loop
run: |
conda run -n test python -m pip install .

- name: Run tests
run: |
conda run -n test pytest -v
conda run -n test pytest
96 changes: 0 additions & 96 deletions map2loop/contact_extractor.py
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11 changes: 4 additions & 7 deletions map2loop/data_checks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -471,13 +471,11 @@ def check_keys(d: dict, parent_key=""):
"fault": {
"structtype_column", "fault_text", "dip_null_value",
"dipdir_flag", "dipdir_column", "dip_column", "orientation_type",
"dipestimate_column", "dipestimate_text","displacement_column",
"displacement_text", "name_column","objectid_column", "featureid_column", "minimum_fault_length",
"fault_length_column", "fault_length_text", "ignore_fault_codes",
"dipestimate_column", "dipestimate_text", "name_column",
"objectid_column", "minimum_fault_length", "ignore_fault_codes",
},
"fold": {
"structtype_column", "fold_text", "axial_plane_dipdir_column",
"axial_plane_dip_column","tightness_column", "description_column",
"structtype_column", "fold_text", "description_column",
"synform_text", "foldname_column","objectid_column",
},
}
Expand Down Expand Up @@ -855,7 +853,6 @@ def validate_structtype_column(
if text_keys:
for text_key, config_key in text_keys.items():
text_value = config.get(config_key, None)
text_pattern = '|'.join(text_value) if text_value else None
if text_value:
if not isinstance(text_value, str):
error_msg = (
Expand All @@ -865,7 +862,7 @@ def validate_structtype_column(
logger.error(error_msg)
return (True, error_msg)

if not geodata[structtype_column].str.contains(text_pattern, case=False, regex=True, na=False).any():
if not geodata[structtype_column].str.contains(text_value, na=False).any():
if text_key == "synform_text":
warning_msg = (
f"Datatype {datatype_name.upper()}: The '{text_key}' value '{text_value}' is not found in column '{structtype_column}'. "
Expand Down
70 changes: 31 additions & 39 deletions map2loop/topology.py → map2loop/map2model_wrapper.py
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Original file line number Diff line number Diff line change
@@ -1,26 +1,24 @@
from typing import Optional
# internal imports
from .m2l_enums import VerboseLevel
from .contact_extractor import ContactExtractor

# external imports
import geopandas
import pandas
import numpy
import geopandas as gpd
import pandas as pd
import numpy as np

from .logging import getLogger

logger = getLogger(__name__)


class Topology:
class Map2ModelWrapper:
"""
Topology calculator for units and faults relationships
A wrapper around map2model functionality

Attributes
----------
sorted_units: None or list
the stratigraphic column
map2model's estimate of the stratigraphic column
fault_fault_relationships: None or pandas.DataFrame
data frame of fault to fault relationships with columns ["Fault1", "Fault2", "Type", "Angle"]
unit_fault_relationships: None or pandas.DataFrame
Expand All @@ -34,9 +32,7 @@ class Topology:
"""

def __init__(
self, geology_data: geopandas.GeoDataFrame,
fault_data: Optional[geopandas.GeoDataFrame] = None,
verbose_level: VerboseLevel = VerboseLevel.NONE
self, map_data, *, verbose_level: VerboseLevel = VerboseLevel.NONE
):
"""
The initialiser for the map2model wrapper
Expand All @@ -51,8 +47,7 @@ def __init__(
self._fault_fault_relationships = None
self._unit_fault_relationships = None
self._unit_unit_relationships = None
self.geology_data = geology_data
self.fault_data = fault_data
self.map_data = map_data
self.verbose_level = verbose_level
self.buffer_radius = 500

Expand All @@ -79,13 +74,13 @@ def unit_unit_relationships(self):

def reset(self):
"""
Reset before the next run
Reset the wrapper to before the map2model process
"""
logger.info("Resetting topology calculator")
logger.info("Resetting map2model wrapper")
self.sorted_units = None
self._fault_fault_relationships = None
self._unit_fault_relationships = None
self._unit_unit_relationships = None
self.fault_fault_relationships = None
self.unit_fault_relationships = None
self.unit_unit_relationships = None

def get_sorted_units(self):
"""
Expand Down Expand Up @@ -129,23 +124,23 @@ def get_unit_unit_relationships(self):

def _calculate_fault_fault_relationships(self):

faults = self.fault_data.copy()
faults = self.map_data.FAULT.copy()
# reset index so that we can index the adjacency matrix with the index
faults.reset_index(inplace=True)
buffers = faults.buffer(self.buffer_radius)
# create the adjacency matrix
intersection = geopandas.sjoin(
geopandas.GeoDataFrame(geometry=buffers), geopandas.GeoDataFrame(geometry=faults["geometry"])
intersection = gpd.sjoin(
gpd.GeoDataFrame(geometry=buffers), gpd.GeoDataFrame(geometry=faults["geometry"])
)
intersection["index_left"] = intersection.index
intersection.reset_index(inplace=True)

adjacency_matrix = numpy.zeros((faults.shape[0], faults.shape[0]), dtype=bool)
adjacency_matrix = np.zeros((faults.shape[0], faults.shape[0]), dtype=bool)
adjacency_matrix[
intersection.loc[:, "index_left"], intersection.loc[:, "index_right"]
] = True
f1, f2 = numpy.where(numpy.tril(adjacency_matrix, k=-1))
df = pandas.DataFrame(
f1, f2 = np.where(np.tril(adjacency_matrix, k=-1))
df = pd.DataFrame(
{'Fault1': faults.loc[f1, 'ID'].to_list(), 'Fault2': faults.loc[f2, 'ID'].to_list()}
)
df['Angle'] = 60 # make it big to prevent LS from making splays
Expand All @@ -156,29 +151,26 @@ def _calculate_fault_unit_relationships(self):
"""Calculate unit/fault relationships using geopandas sjoin.
This will return
"""
units = self.geology_data["UNITNAME"].unique()
faults = self.fault_data.copy().reset_index().drop(columns=['index'])
adjacency_matrix = numpy.zeros((len(units), faults.shape[0]), dtype=bool)
units = self.map_data.GEOLOGY["UNITNAME"].unique()
faults = self.map_data.FAULT.copy().reset_index().drop(columns=['index'])
adjacency_matrix = np.zeros((len(units), faults.shape[0]), dtype=bool)
for i, u in enumerate(units):
unit = self.geology_data[self.geology_data["UNITNAME"] == u]
intersection = geopandas.sjoin(
geopandas.GeoDataFrame(geometry=faults["geometry"]),
geopandas.GeoDataFrame(geometry=unit["geometry"]),
unit = self.map_data.GEOLOGY[self.map_data.GEOLOGY["UNITNAME"] == u]
intersection = gpd.sjoin(
gpd.GeoDataFrame(geometry=faults["geometry"]),
gpd.GeoDataFrame(geometry=unit["geometry"]),
)
intersection["index_left"] = intersection.index
intersection.reset_index(inplace=True)
adjacency_matrix[i, intersection.loc[:, "index_left"]] = True
u, f = numpy.where(adjacency_matrix)
df = pandas.DataFrame({"Unit": units[u].tolist(), "Fault": faults.loc[f, "ID"].to_list()})
u, f = np.where(adjacency_matrix)
df = pd.DataFrame({"Unit": units[u].tolist(), "Fault": faults.loc[f, "ID"].to_list()})
self._unit_fault_relationships = df

def _calculate_unit_unit_relationships(self):
extractor = ContactExtractor(
self.geology_data,
self.fault_data,
)
contacts = extractor.extract_all_contacts()
self._unit_unit_relationships = contacts.copy().drop(
if self.map_data.contacts is None:
self.map_data.extract_all_contacts()
self._unit_unit_relationships = self.map_data.contacts.copy().drop(
columns=['length', 'geometry']
)
return self._unit_unit_relationships
Expand Down
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