From 8b1e5df596b702f0c4bb3c56734aa03d15622c28 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 11:01:30 +1000
Subject: [PATCH 01/40] fix: remove calls to map2model

---
 map2loop/map2model_wrapper.py | 223 ++--------------------------------
 1 file changed, 13 insertions(+), 210 deletions(-)

diff --git a/map2loop/map2model_wrapper.py b/map2loop/map2model_wrapper.py
index 08738e60..3be25f2e 100644
--- a/map2loop/map2model_wrapper.py
+++ b/map2loop/map2model_wrapper.py
@@ -37,7 +37,7 @@ class Map2ModelWrapper:
     """
 
     def __init__(
-        self, map_data, mode: str = 'geopandas', verbose_level: VerboseLevel = VerboseLevel.NONE
+        self, map_data, *,  verbose_level: VerboseLevel = VerboseLevel.NONE
     ):
         """
         The initialiser for the map2model wrapper
@@ -48,7 +48,6 @@ def __init__(
             verbose_level (VerboseLevel, optional):
                 How much console output is sent. Defaults to VerboseLevel.ALL.
         """
-        self.mode = mode
         self.sorted_units = None
         self._fault_fault_relationships = None
         self._unit_fault_relationships = None
@@ -60,28 +59,22 @@ def __init__(
     @property
     def fault_fault_relationships(self):
         if self._fault_fault_relationships is None:
-            if self.mode == 'geopandas':
-                self._calculate_fault_fault_relationships()
-            else:
-                self.run()
+            self._calculate_fault_fault_relationships()
+            
         return self._fault_fault_relationships
 
     @property
     def unit_fault_relationships(self):
         if self._unit_fault_relationships is None:
-            if self.mode == 'geopandas':
-                self._calculate_fault_unit_relationships()
-            else:
-                self.run()
+            self._calculate_fault_unit_relationships()
+            
         return self._unit_fault_relationships
 
     @property
     def unit_unit_relationships(self):
         if self._unit_unit_relationships is None:
-            if self.mode == 'geopandas':
-                self._calculate_unit_unit_relationships()
-            else:
-                self.run()
+            self._calculate_unit_unit_relationships()
+            
         return self._unit_unit_relationships
 
     def reset(self):
@@ -101,12 +94,8 @@ def get_sorted_units(self):
         Returns:
             list: The map2model stratigraphic column estimate
         """
-        if self.mode == 'geopandas':
-            raise NotImplementedError("This method is not implemented")
-        else:
-            if self.sorted_units is None:
-                self.run()
-        return self.sorted_units
+        raise NotImplementedError("This method is not implemented")
+        
 
     def get_fault_fault_relationships(self):
         """
@@ -199,194 +188,8 @@ def run(self, verbose_level: VerboseLevel = None):
             verbose_level (VerboseLevel, optional):
                 How much console output is sent. Defaults to None (which uses the wrapper attribute).
         """
-        if self.mode == 'geopandas':
 
-            self.get_fault_fault_relationships()
-            self.get_unit_fault_relationships()
-            self.get_unit_unit_relationships()
-            return
-        else:
-
-            if verbose_level is None:
-                verbose_level = self.verbose_level
-            logger.info("Exporting map data for map2model")
-            self.map_data.export_wkt_format_files()
-            logger.info("Running map2model...")
-
-            map2model_code_map = {
-                "o": "ID",  # FIELD_COORDINATES
-                "f": "FEATURE",  # FIELD_FAULT_ID
-                "u": "CODE",  # FIELD_POLYGON_LEVEL1_NAME
-                "g": "GROUP",  # FIELD_POLYGON_LEVEL2_NAME
-                "min": "MIN_AGE",  # FIELD_POLYGON_MIN_AGE
-                "max": "MAX_AGE",  # FIELD_POLYGON_MAX_AGE
-                "c": "UNITNAME",  # FIELD_POLYGON_CODE
-                "ds": "DESCRIPTION",  # FIELD_POLYGON_DESCRIPTION
-                "r1": "ROCKTYPE1",  # FIELD_POLYGON_ROCKTYPE1
-                "r2": "ROCKTYPE2",  # FIELD_POLYGON_ROCKTYPE2
-                "msc": "",  # FIELD_SITE_CODE
-                "mst": "",  # FIELD_SITE_TYPE
-                "mscm": "",  # FIELD_SITE_COMMO
-                "fold": self.map_data.config.fold_config["fold_text"],  # FAULT_AXIAL_FEATURE_NAME
-                "sill": self.map_data.config.geology_config["sill_text"],  # SILL_STRING
-                "intrusive": self.map_data.config.geology_config[
-                    "intrusive_text"
-                ],  # IGNEOUS_STRING
-                "volcanic": self.map_data.config.geology_config["volcanic_text"],  # VOLCANIC_STRING
-                "deposit_dist": 100,  # deposit_dist
-            }
-            logger.info(f"map2model params: {map2model_code_map}")
-            # TODO: Simplify. Note: this is external so have to match fix to map2model module
-            logger.info(os.path.join(self.map_data.map2model_tmp_path, "map2model_data"))
-            logger.info(
-                os.path.join(self.map_data.map2model_tmp_path, "map2model_data", "geology_wkt.csv")
-            )
-            logger.info(
-                os.path.join(self.map_data.map2model_tmp_path, "map2model_data", "faults_wkt.csv")
-            )
-            logger.info(self.map_data.get_bounding_box())
-            logger.info(map2model_code_map)
-            logger.info(verbose_level == VerboseLevel.NONE)
-
-            run_log = map2model.run(
-                os.path.join(self.map_data.map2model_tmp_path),
-                os.path.join(self.map_data.map2model_tmp_path, "geology_wkt.csv"),
-                os.path.join(self.map_data.map2model_tmp_path, "faults_wkt.csv"),
-                "",
-                self.map_data.get_bounding_box(),
-                map2model_code_map,
-                verbose_level == VerboseLevel.NONE,
-                "None",
-            )
-        # Parse fault intersections
-        out = []
-        fault_fault_intersection_filename = os.path.join(
-            self.map_data.map2model_tmp_path, 'fault-fault-intersection.txt'
-        )
-        logger.info(f"Reading fault-fault intersections from {fault_fault_intersection_filename}")
-        if (
-            os.path.isfile(fault_fault_intersection_filename)
-            and os.path.getsize(fault_fault_intersection_filename) > 0
-        ):
-            df = pandas.read_csv(fault_fault_intersection_filename, delimiter="{", header=None)
-            df[1] = list(df[1].str.replace("}", "", regex=False))
-            df[1] = [re.findall("\(.*?\)", i) for i in df[1]]  # Valid escape for regex
-            df[0] = list(df[0].str.replace("^[0-9]*, ", "", regex=True))
-            df[0] = list(df[0].str.replace(", ", "", regex=False))
-
-            # df[0] = "Fault_" + df[0] #removed 7/10/24 as it seems to break the merge in
-            relations = df[1]
-            for j in range(len(relations)):
-                relations[j] = [i.strip("()").replace(" ", "").split(",") for i in relations[j]]
-            df[1] = relations
-
-            for _, row in df.iterrows():
-                for i in numpy.arange(len(row[1])):
-
-                    out += [[row[0], row[1][i][0], row[1][i][1], float(row[1][i][2])]]
-
-        else:
-            logger.warning(
-                f"Fault-fault intersections file {fault_fault_intersection_filename} not found"
-            )
-            logger.info("Parsing map2model output")
-            logger.info(run_log)
-
-            logger.info("map2model complete")
-
-            # Parse units sorted
-            units_sorted = pandas.read_csv(
-                os.path.join(self.map_data.map2model_tmp_path, "units_sorted.txt"),
-                header=None,
-                sep=' ',
-            )
-            if units_sorted.shape == 0:
-                self.sorted_units = []
-            else:
-                self.sorted_units = list(units_sorted[5])
-
-            # Parse fault intersections
-            out = []
-            fault_fault_intersection_filename = os.path.join(
-                self.map_data.map2model_tmp_path, "fault-fault-intersection.txt"
-            )
-            logger.info(
-                f"Reading fault-fault intersections from {fault_fault_intersection_filename}"
-            )
-            if (
-                os.path.isfile(fault_fault_intersection_filename)
-                and os.path.getsize(fault_fault_intersection_filename) > 0
-            ):
-                df = pandas.read_csv(fault_fault_intersection_filename, delimiter="{", header=None)
-                df[1] = list(df[1].str.replace("}", "", regex=False))
-                df[1] = [re.findall("\(.*?\)", i) for i in df[1]]  # Valid escape for regex
-                df[0] = list(df[0].str.replace("^[0-9]*, ", "", regex=True))
-                df[0] = list(df[0].str.replace(", ", "", regex=False))
-                # df[0] = "Fault_" + df[0] #removed 7/10/24 as it seems to break the merge in
-                relations = df[1]
-                for j in range(len(relations)):
-                    relations[j] = [i.strip("()").replace(" ", "").split(",") for i in relations[j]]
-                df[1] = relations
-
-                for _, row in df.iterrows():
-                    for i in numpy.arange(len(row[1])):
-                        out += [[row[0], row[1][i][0], row[1][i][1], float(row[1][i][2])]]
-
-            else:
-                logger.warning(
-                    f"Fault-fault intersections file {fault_fault_intersection_filename} not found"
-                )
-
-            df_out = pandas.DataFrame(columns=["Fault1", "Fault2", "Type", "Angle"], data=out)
-            logger.info('Fault intersections')
-            logger.info(df_out.to_string())
-            self.fault_fault_relationships = df_out
-
-            # Parse unit fault relationships
-            out = []
-            unit_fault_intersection_filename = os.path.join(
-                self.map_data.map2model_tmp_path, "unit-fault-intersection.txt"
-            )
-            if (
-                os.path.isfile(unit_fault_intersection_filename)
-                and os.path.getsize(unit_fault_intersection_filename) > 0
-            ):
-                df = pandas.read_csv(unit_fault_intersection_filename, header=None, sep='{')
-                df[1] = list(df[1].str.replace("}", "", regex=False))
-                df[1] = df[1].astype(str).str.split(", ")
-                df[0] = list(df[0].str.replace("^[0-9]*, ", "", regex=True))
-                df[0] = list(df[0].str.replace(", ", "", regex=False))
-
-                for _, row in df.iterrows():
-                    for i in numpy.arange(len(row[1])):
-                        out += [[row[0], "Fault_" + row[1][i]]]
-
-            df_out = pandas.DataFrame(columns=["Unit", "Fault"], data=out)
-            self.unit_fault_relationships = df_out
-
-            # Parse unit unit relationships
-            units = []
-            links = []
-            graph_filename = os.path.join(
-                self.map_data.map2model_tmp_path, "graph_all_None.gml.txt"
-            )
-            if os.path.isfile(graph_filename) and os.path.getsize(graph_filename) > 0:
-                with open(
-                    os.path.join(self.map_data.map2model_tmp_path, "graph_all_None.gml.txt")
-                ) as file:
-                    contents = file.read()
-                    segments = contents.split("\n\n")
-                    for line in segments[0].split("\n"):
-                        units += [line.split(" ")]
-                    for line in segments[1].split("\n")[:-1]:
-                        links += [line.split(" ")]
-
-            df = pandas.DataFrame(columns=["index", "unit"], data=units)
-            df.set_index("index", inplace=True)
-            out = []
-            for row in links:
-                out += [[int(row[0]), df["unit"][row[0]], int(row[1]), df["unit"][row[1]]]]
-            df_out = pandas.DataFrame(
-                columns=["Index1", "UnitName1", "Index2", "UnitName2"], data=out
-            )
-            self.unit_unit_relationships = df_out
+        self.get_fault_fault_relationships()
+        self.get_unit_fault_relationships()
+        self.get_unit_unit_relationships()
+        

From 078a366602abc37dece68b92fe63704661270283 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 11:02:12 +1000
Subject: [PATCH 02/40] fix: remove m2m from deps

---
 dependencies.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dependencies.txt b/dependencies.txt
index 7a1d95e7..889b05cc 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -4,7 +4,6 @@ geopandas
 shapely
 networkx
 owslib
-map2model
 loopprojectfile==0.2.2
 beartype
 pytest

From 975f6026f19585793931e332f722a1081e2ed7bc Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 11:08:34 +1000
Subject: [PATCH 03/40] fix: use os/python matrix

---
 .github/workflows/linting_and_testing.yml | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index dc2ed2fe..44543679 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -21,10 +21,18 @@ jobs:
  
           
   testing:
-    name: Testing
-    runs-on: ubuntu-24.04
+    name: Testing${{ matrix.os }} python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ${{ fromJSON(vars.BUILD_OS)}}
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}}
     steps:
       - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+            python-version: ${{ matrix.python }}
       - name: Install GDAL
         run: |
           sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable

From c8ef7ac0c8ed5b0ba1826d8be5507c432bcd5a1c Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 11:11:25 +1000
Subject: [PATCH 04/40] remove gdal install from test

---
 .github/workflows/linting_and_testing.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 44543679..68d96460 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -33,11 +33,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v3
         with:
             python-version: ${{ matrix.python }}
-      - name: Install GDAL
-        run: |
-          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
-          sudo apt-get update
-          sudo apt-get install -y libgdal-dev gdal-bin
+      
 
       - name: Install dependencies
         run: |

From a5273a70e3ce5f43a573dc2d8e99308ebe3b464e Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 11:16:32 +1000
Subject: [PATCH 05/40] only run for changes of python files or the workflow

---
 .github/workflows/linting_and_testing.yml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 68d96460..7d7e217a 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -1,7 +1,20 @@
 name: Linting and Testing
 
 on:
-    [push]
+  push:
+    branches:
+      - master
+    paths:
+      - '**.py'
+      - .github/workflows/linting_and_testing.yml
+
+  pull_request:
+    branches:
+      - master
+    paths:
+      - '**.py'
+      - .github/workflows/linting_and_testing.yml
+  workflow_dispatch:
 
 jobs:
   linting:

From febdada3c8e43b37103c30a9c68323a26dd6aecb Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 11:26:50 +1000
Subject: [PATCH 06/40] remove conda defaults channel

---
 .github/workflows/linting_and_testing.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 7d7e217a..482fcf86 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -46,7 +46,8 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v3
         with:
             python-version: ${{ matrix.python }}
-      
+            conda-remove-defaults: "true"
+
 
       - name: Install dependencies
         run: |

From b955c5d419097dfbc5b200a29d24bd1668f9496c Mon Sep 17 00:00:00 2001
From: lachlangrose <7371904+lachlangrose@users.noreply.github.com>
Date: Thu, 5 Jun 2025 01:33:08 +0000
Subject: [PATCH 07/40] style: style fixes by ruff and autoformatting by black

---
 map2loop/map2model_wrapper.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/map2loop/map2model_wrapper.py b/map2loop/map2model_wrapper.py
index 3be25f2e..115b8702 100644
--- a/map2loop/map2model_wrapper.py
+++ b/map2loop/map2model_wrapper.py
@@ -2,14 +2,9 @@
 from .m2l_enums import VerboseLevel
 
 # external imports
-import map2model
-import pandas
-import numpy
 import geopandas as gpd
 import pandas as pd
 import numpy as np
-import os
-import re
 
 from .logging import getLogger
 

From 628c3528b39df0a0cf356eecfa8a2316ff7b2764 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 11:34:47 +1000
Subject: [PATCH 08/40] remove map2model import

---
 map2loop/map2model_wrapper.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/map2loop/map2model_wrapper.py b/map2loop/map2model_wrapper.py
index 3be25f2e..2aae93ef 100644
--- a/map2loop/map2model_wrapper.py
+++ b/map2loop/map2model_wrapper.py
@@ -2,7 +2,6 @@
 from .m2l_enums import VerboseLevel
 
 # external imports
-import map2model
 import pandas
 import numpy
 import geopandas as gpd

From f4de309e89069a4352212b3f289a78e21a1cddba Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@monash.edu>
Date: Thu, 5 Jun 2025 14:23:47 +1000
Subject: [PATCH 09/40] Update linting_and_testing.yml

---
 .github/workflows/linting_and_testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 482fcf86..a73d0944 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -45,7 +45,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
-            python-version: ${{ matrix.python }}
+            python-version: ${{ matrix.python-version }}
             conda-remove-defaults: "true"
 
 

From 5be2b238e6ece081f72fb0afec571edf04c22e76 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@monash.edu>
Date: Thu, 5 Jun 2025 14:30:29 +1000
Subject: [PATCH 10/40] Update linting_and_testing.yml

---
 .github/workflows/linting_and_testing.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index a73d0944..683ea4eb 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -41,6 +41,7 @@ jobs:
       matrix:
         os: ${{ fromJSON(vars.BUILD_OS)}}
         python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}}
+        
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
@@ -51,6 +52,7 @@ jobs:
 
       - name: Install dependencies
         run: |
+            conda info
             conda update -n base -c defaults conda -y 
             conda install -n base conda-libmamba-solver -c conda-forge -y
             conda install -c conda-forge gdal -y

From 4820d5e1926e92c2d14b9c12ac3e82d6b0e7e552 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@monash.edu>
Date: Thu, 5 Jun 2025 14:36:49 +1000
Subject: [PATCH 11/40] Update linting_and_testing.yml

---
 .github/workflows/linting_and_testing.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 683ea4eb..edae6edf 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -53,8 +53,7 @@ jobs:
       - name: Install dependencies
         run: |
             conda info
-            conda update -n base -c defaults conda -y 
-            conda install -n base conda-libmamba-solver -c conda-forge -y
+            conda activate test
             conda install -c conda-forge gdal -y
             conda install -c conda-forge -c loop3d --file dependencies.txt -y
             conda install pytest -y

From 9ed4bd14e88b6276936f0bee204781b4d65af6d9 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@monash.edu>
Date: Thu, 5 Jun 2025 14:39:58 +1000
Subject: [PATCH 12/40] Update linting_and_testing.yml

---
 .github/workflows/linting_and_testing.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index edae6edf..20bb03d6 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -52,11 +52,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-            conda info
-            conda activate test
-            conda install -c conda-forge gdal -y
-            conda install -c conda-forge -c loop3d --file dependencies.txt -y
-            conda install pytest -y
+            conda run -n test conda info
+            conda run -n test conda install -c conda-forge gdal -y
+            conda run -n test conda install -c conda-forge -c loop3d --file dependencies.txt -y
+            conda run -n test conda install pytest -y
 
       - name: Install map2loop
         run: |

From c858a0c70e4ce03ee9f8feaef1c5aca844783453 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@monash.edu>
Date: Thu, 5 Jun 2025 14:47:47 +1000
Subject: [PATCH 13/40] trying to specify python version in conda install

---
 .github/workflows/linting_and_testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 20bb03d6..bd869878 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -53,7 +53,7 @@ jobs:
       - name: Install dependencies
         run: |
             conda run -n test conda info
-            conda run -n test conda install -c conda-forge gdal -y
+            conda run -n test conda install -c conda-forge gdal python=${{ matrix.python-version }} -y
             conda run -n test conda install -c conda-forge -c loop3d --file dependencies.txt -y
             conda run -n test conda install pytest -y
 

From d52968e4dba51c3e063c9747bd422c2e689d9db9 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@monash.edu>
Date: Thu, 5 Jun 2025 14:51:26 +1000
Subject: [PATCH 14/40] Update linting_and_testing.yml

---
 .github/workflows/linting_and_testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index bd869878..7a707a4d 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -59,9 +59,9 @@ jobs:
 
       - name: Install map2loop
         run: |
-            python -m pip install .
+            conda run -n test python -m pip install .
 
       - name: Run tests
         run: |
-            pytest
+            conda run -n test  pytest
 

From 87338ea8f4c61a7d72e08ae4e1b150363ab81343 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@monash.edu>
Date: Thu, 5 Jun 2025 15:03:47 +1000
Subject: [PATCH 15/40] Update linting_and_testing.yml

---
 .github/workflows/linting_and_testing.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 7a707a4d..c8c89126 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -53,9 +53,7 @@ jobs:
       - name: Install dependencies
         run: |
             conda run -n test conda info
-            conda run -n test conda install -c conda-forge gdal python=${{ matrix.python-version }} -y
-            conda run -n test conda install -c conda-forge -c loop3d --file dependencies.txt -y
-            conda run -n test conda install pytest -y
+            conda run -n test conda install -c conda-forge -c loop3d --file dependencies.txt gdal python=${{ matrix.python-version }} pytest -y
 
       - name: Install map2loop
         run: |

From 154c77538cf2082f64bef5ac3ab89b4e44a96b84 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 15:27:00 +1000
Subject: [PATCH 16/40] fix: make shapely imports backwards compatible

---
 .../geodata_files/load_map2loop_data.py       |  2 +-
 map2loop/mapdata.py                           |  6 ++--
 map2loop/thickness_calculator.py              |  6 ++--
 map2loop/utils.py                             | 28 +++++++++----------
 tests/mapdata/test_mapdata_dipdir.py          |  2 +-
 .../test_set_get_recreate_bounding_box.py     |  2 +-
 tests/sampler/test_SamplerSpacing.py          | 10 +++----
 .../sampler/test_SamplerSpacing_featureId.py  |  4 +--
 8 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/map2loop/_datasets/geodata_files/load_map2loop_data.py b/map2loop/_datasets/geodata_files/load_map2loop_data.py
index d625af9b..854e776b 100644
--- a/map2loop/_datasets/geodata_files/load_map2loop_data.py
+++ b/map2loop/_datasets/geodata_files/load_map2loop_data.py
@@ -42,4 +42,4 @@ def load_hamersley_dtm():
         gdal.Dataset: The DTM data
     """
     path = files("map2loop._datasets.geodata_files.hamersley").joinpath("dtm_rp.tif")
-    return gdal.Open(path)
+    return gdal.Open(str(path))
diff --git a/map2loop/mapdata.py b/map2loop/mapdata.py
index 6948d3c3..960d264b 100644
--- a/map2loop/mapdata.py
+++ b/map2loop/mapdata.py
@@ -52,7 +52,7 @@ class MapData:
         A string containing the projection e.g. "EPSG:28350"
     bounding_box: dict
         The bounding box in cartesian coordinates with 6 elements
-    bounding_box_polygon: shapely.Polygon
+    bounding_box_polygon: shapely.geometry.Polygon
         The bounding box in polygonal form
     bounding_box_str: str
         The bounding box in string form (used for url requests)
@@ -182,7 +182,7 @@ def set_bounding_box(self, bounding_box):
         self.bounding_box_polygon = geopandas.GeoDataFrame(
             index=[0],
             crs=self.working_projection,
-            geometry=[shapely.Polygon(zip(lon_point_list, lat_point_list))],
+            geometry=[shapely.geometry.Polygon(zip(lon_point_list, lat_point_list))],
         )
         self.recreate_bounding_box_str()
 
@@ -209,7 +209,7 @@ def get_bounding_box(self, polygon: bool = False):
             polygon (bool, optional): Flag to get the bounding box in polygon form. Defaults to False.
 
         Returns:
-            dict or shapely.Polygon: The bounding box in the requested form
+            dict or shapely.geometry.Polygon: The bounding box in the requested form
         """
         if polygon:
             return self.bounding_box_polygon
diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py
index eb8a2a67..5d7844d8 100644
--- a/map2loop/thickness_calculator.py
+++ b/map2loop/thickness_calculator.py
@@ -274,7 +274,7 @@ def compute(
         contacts = map_data.get_value_from_raster_df(Datatype.DTM, contacts)
         # update the geometry of the contact points to include the Z value
         contacts["geometry"] = contacts.apply(
-            lambda row: shapely.Point(row.geometry.x, row.geometry.y, row["Z"]), axis=1
+            lambda row: shapely.geometry.Point(row.geometry.x, row.geometry.y, row["Z"]), axis=1
         )
         # spatial join the contact points with the basal contacts to get the unit for each contact point
         contacts = contacts.sjoin(basal_contacts, how="inner", predicate="intersects")
@@ -302,7 +302,7 @@ def compute(
         interpolated = map_data.get_value_from_raster_df(Datatype.DTM, interpolated_orientations)
         # update the geometry of the interpolated points to include the Z value
         interpolated["geometry"] = interpolated.apply(
-            lambda row: shapely.Point(row.geometry.x, row.geometry.y, row["Z"]), axis=1
+            lambda row: shapely.geometry.Point(row.geometry.x, row.geometry.y, row["Z"]), axis=1
         )
         # for each interpolated point, assign name of unit using spatial join
         units = map_data.get_map_data(Datatype.GEOLOGY)
@@ -531,7 +531,7 @@ def compute(
 
             # make a shapely point from the measurement
             measurement = sampled_structures.iloc[s]
-            measurement_pt = shapely.Point(measurement.X, measurement.Y)
+            measurement_pt = shapely.geometry.Point(measurement.X, measurement.Y)
 
             # find unit and strike
             litho_in = measurement['unit_name']
diff --git a/map2loop/utils.py b/map2loop/utils.py
index 00e8fa57..25dc8b4c 100644
--- a/map2loop/utils.py
+++ b/map2loop/utils.py
@@ -130,15 +130,15 @@ def create_points(xy: Union[list, tuple, numpy.ndarray]) -> numpy.ndarray:
         where each coordinate contains two elements representing the x and y coordinates of a point.
 
     Returns:
-        shapely.points: A list of Point objects created from the input list of coordinates.
+        shapely.geometry.Points: A list of Point objects created from the input list of coordinates.
     """
-    points = shapely.points(xy)
+    points = shapely.geometry.Points(xy)
     return points
 
 
 @beartype.beartype
 def find_segment_strike_from_pt(
-    line: shapely.LineString, point: shapely.Point, measurement: pandas.Series
+    line: shapely.geometry.LineString, point: shapely.geometry.Point, measurement: pandas.Series
 ) -> float:
     """
     Finds the strike of a line segment (contact) closest to a given point (structural measurement).
@@ -154,7 +154,7 @@ def find_segment_strike_from_pt(
 
     lines = []
     for c1, c2 in zip(line.coords, line.coords[1:]):
-        lines.append(shapely.LineString([c1, c2]))
+        lines.append(shapely.geometry.LineString([c1, c2]))
     distances = [segment.distance(point) for segment in lines]
     nearest_line = lines[distances.index(min(distances))]
 
@@ -183,7 +183,7 @@ def find_segment_strike_from_pt(
 
 @beartype.beartype
 def calculate_endpoints(
-    start_point: shapely.Point, azimuth_deg: float, distance: int, bbox: pandas.DataFrame
+    start_point: shapely.geometry.Point, azimuth_deg: float, distance: int, bbox: pandas.DataFrame
 ) -> shapely.geometry.LineString:
     """
     Calculate the endpoints of a line segment given a start point, azimuth angle, distance, and bounding box.
@@ -195,7 +195,7 @@ def calculate_endpoints(
     bbox (dict): The bounding box coordinates (minx, miny, maxx, maxy).
 
     Returns:
-    shapely.LineString: A LineString object representing the line segment with endpoints clipped by the bounding box.
+    shapely.geometry.LineString: A LineString object representing the line segment with endpoints clipped by the bounding box.
     """
     bbox = numpy.array(bbox)[0]
     minx, miny, maxx, maxy = bbox[0], bbox[1], bbox[2], bbox[3]
@@ -216,7 +216,7 @@ def calculate_endpoints(
     dy_left = distance * math.sin(left_azimuth_rad)
     left_endpoint = (x + dx_left, y + dy_left)
 
-    line = shapely.LineString([left_endpoint, right_endpoint])
+    line = shapely.geometry.LineString([left_endpoint, right_endpoint])
 
     new_line = shapely.ops.clip_by_rect(line, minx, miny, maxx, maxy)
 
@@ -236,11 +236,11 @@ def multiline_to_line(
     Returns:
         LineString: The converted line geometry.
     """
-    if isinstance(geometry, shapely.LineString):
+    if isinstance(geometry, shapely.geometry.LineString):
         return geometry
     coords = [list(part.coords) for part in geometry.geoms]
-    flat_coords = [shapely.Point(*point) for segment in coords for point in segment]
-    return shapely.LineString(flat_coords)
+    flat_coords = [shapely.geometry.Point(*point) for segment in coords for point in segment]
+    return shapely.geometry.LineString(flat_coords)
 
 
 @beartype.beartype
@@ -280,7 +280,7 @@ def rebuild_sampled_basal_contacts(
 
         if len(unique_segments) == 1:
             # make a linestring with all the points in subset
-            line = shapely.LineString(subset.geometry)
+            line = shapely.geometry.LineString(subset.geometry)
             r.append(line)
 
         else:
@@ -289,7 +289,7 @@ def rebuild_sampled_basal_contacts(
             for featureId in unique_segments:
                 seg_subset = subset[subset['featureId'] == featureId]
                 if len(seg_subset) > 1:  # Ensure each segment has at least two points
-                    line_ = shapely.LineString(seg_subset.geometry.tolist())
+                    line_ = shapely.geometry.LineString(seg_subset.geometry.tolist())
                     lines.append(line_)
 
             # If multiple lines were created, combine them into a MultiLineString
@@ -439,7 +439,7 @@ def read_hjson_with_json(file_path: str) -> dict:
         raise FileNotFoundError(f"HJSON file not found: {file_path}") from e
     except json.JSONDecodeError as e:
         raise ValueError(f"Failed to decode preprocessed HJSON as JSON: {e}") from e
-    
+
 @beartype.beartype
 def update_from_legacy_file(
     filename: str,
@@ -527,4 +527,4 @@ def update_from_legacy_file(
         with open(json_save_path, "w") as f:
             json.dump(parsed_data, f, indent=4)
     
-    return file_map
\ No newline at end of file
+    return file_map
diff --git a/tests/mapdata/test_mapdata_dipdir.py b/tests/mapdata/test_mapdata_dipdir.py
index cc156253..e6107aea 100644
--- a/tests/mapdata/test_mapdata_dipdir.py
+++ b/tests/mapdata/test_mapdata_dipdir.py
@@ -28,7 +28,7 @@ def test_if_m2l_returns_all_sampled_structures_with_DIPDIR_lower_than_360():
 
     # create mock data
     data = {
-        'geometry': [shapely.Point(1, 1), shapely.Point(2, 2), shapely.Point(3, 3)],
+        'geometry': [shapely.geometry.Point(1, 1), shapely.geometry.Point(2, 2), shapely.geometry.Point(3, 3)],
         'DIPDIR': [45.0, 370.0, 420.0],
         'DIP': [30.0, 60.0, 50],
         'OVERTURNED': ["False", "True", "True"],
diff --git a/tests/mapdata/test_set_get_recreate_bounding_box.py b/tests/mapdata/test_set_get_recreate_bounding_box.py
index 5a6e9368..6e131c39 100644
--- a/tests/mapdata/test_set_get_recreate_bounding_box.py
+++ b/tests/mapdata/test_set_get_recreate_bounding_box.py
@@ -48,7 +48,7 @@ def test_bounding_box_polygon(md):
     expected_polygon = geopandas.GeoDataFrame(
         index=[0],
         crs=md.working_projection,
-        geometry=[shapely.Polygon(zip(lon_point_list, lat_point_list))],
+        geometry=[shapely.geometry.Polygon(zip(lon_point_list, lat_point_list))],
     )
 
     assert md.bounding_box_polygon.equals(
diff --git a/tests/sampler/test_SamplerSpacing.py b/tests/sampler/test_SamplerSpacing.py
index e69c7650..b4708567 100644
--- a/tests/sampler/test_SamplerSpacing.py
+++ b/tests/sampler/test_SamplerSpacing.py
@@ -18,10 +18,10 @@ def sampler_spacing():
 def correct_geodata():
     data = {
         'geometry': [
-            shapely.LineString([(0, 0), (1, 1), (2, 2)]),
-            shapely.Polygon([(0, 0), (1, 1), (1, 0), (0, 0)]),
+            shapely.geometry.LineString([(0, 0), (1, 1), (2, 2)]),
+            shapely.geometry.Polygon([(0, 0), (1, 1), (1, 0), (0, 0)]),
             shapely.MultiLineString(
-                [shapely.LineString([(0, 0), (1, 1)]), shapely.LineString([(2, 2), (3, 3)])]
+                [shapely.geometry.LineString([(0, 0), (1, 1)]), shapely.geometry.LineString([(2, 2), (3, 3)])]
             ),
         ],
         'ID': ['1', '2', '3'],
@@ -31,7 +31,7 @@ def correct_geodata():
 
 @pytest.fixture
 def incorrect_geodata():
-    data = {'geometry': [shapely.Point(0, 0), "Not a geometry"], 'ID': ['1', '2']}
+    data = {'geometry': [shapely.geometry.Point(0, 0), "Not a geometry"], 'ID': ['1', '2']}
     return pandas.DataFrame(data)
 
 
@@ -54,7 +54,7 @@ def test_sample_function_incorrect_data(sampler_spacing, incorrect_geodata):
 def test_sample_function_target_less_than_or_equal_to_2():
     sampler_spacing = SamplerSpacing(spacing=1.0)
     data = {
-        'geometry': [shapely.LineString([(0, 0), (0, 1)]), shapely.LineString([(0, 0), (1, 0)])],
+        'geometry': [shapely.geometry.LineString([(0, 0), (0, 1)]), shapely.geometry.LineString([(0, 0), (1, 0)])],
         'ID': ['1', '2'],
     }
     gdf = geopandas.GeoDataFrame(data, geometry='geometry')
diff --git a/tests/sampler/test_SamplerSpacing_featureId.py b/tests/sampler/test_SamplerSpacing_featureId.py
index a84df370..73faaa3e 100644
--- a/tests/sampler/test_SamplerSpacing_featureId.py
+++ b/tests/sampler/test_SamplerSpacing_featureId.py
@@ -30,7 +30,7 @@ def test_featureId():
 
             # check if in the right place
             for _, sample in corresponding_rows.iterrows():
-                point = shapely.Point(sample['X'], sample['Y']).buffer(1)
+                point = shapely.geometry.Point(sample['X'], sample['Y']).buffer(1)
                 assert point.intersects(
                     poly.geometry
                 ), f"Point from featureId 0 is not in the correct polygon segment of ID {poly['ID']}."
@@ -48,7 +48,7 @@ def test_featureId():
                 polygon_samples = corresponding_rows[corresponding_rows['featureId'] == str(i)]
                 print(polygon_samples)
                 for _, sample in polygon_samples.iterrows():
-                    point = shapely.Point(sample['X'], sample['Y']).buffer(
+                    point = shapely.geometry.Point(sample['X'], sample['Y']).buffer(
                         1
                     )  # buffer just to make sure
                     assert point.intersects(

From 8ff2964432f524d45f7ff5513e2b482a6346d1d3 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 15:28:13 +1000
Subject: [PATCH 17/40] points reverted

---
 map2loop/utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/map2loop/utils.py b/map2loop/utils.py
index 25dc8b4c..ba17aa26 100644
--- a/map2loop/utils.py
+++ b/map2loop/utils.py
@@ -130,9 +130,9 @@ def create_points(xy: Union[list, tuple, numpy.ndarray]) -> numpy.ndarray:
         where each coordinate contains two elements representing the x and y coordinates of a point.
 
     Returns:
-        shapely.geometry.Points: A list of Point objects created from the input list of coordinates.
+        shapely.geometry.Point: A list of Point objects created from the input list of coordinates.
     """
-    points = shapely.geometry.Points(xy)
+    points = shapely.points(xy)
     return points
 
 

From 408b523a7842a4917c739df11cb088c11042567f Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 15:39:43 +1000
Subject: [PATCH 18/40] remove incorrect type hinting

---
 map2loop/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/map2loop/utils.py b/map2loop/utils.py
index ba17aa26..4a4ee7e5 100644
--- a/map2loop/utils.py
+++ b/map2loop/utils.py
@@ -380,7 +380,7 @@ def hex_to_rgb(hex_color: str) -> tuple:
 
 @beartype.beartype
 def calculate_minimum_fault_length(
-    bbox: dict[str, int | float], area_percentage: float
+    bbox: dict[str, Union[int, float]], area_percentage: float
 ) -> float:
 
     """

From be97deeaa8aec1cd4b169b423cbd20f61862930c Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 15:58:59 +1000
Subject: [PATCH 19/40] fix: making test work on ALL python. use pathlib and
 not importlib to find files

---
 .../geodata_files/load_map2loop_data.py       | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/map2loop/_datasets/geodata_files/load_map2loop_data.py b/map2loop/_datasets/geodata_files/load_map2loop_data.py
index 854e776b..d1c8be1f 100644
--- a/map2loop/_datasets/geodata_files/load_map2loop_data.py
+++ b/map2loop/_datasets/geodata_files/load_map2loop_data.py
@@ -1,8 +1,12 @@
 import geopandas
-from importlib.resources import files
+import map2loop
+import pathlib
 from osgeo import gdal
 gdal.UseExceptions()
-
+def map2loop_dir(folder)-> pathlib.Path:
+    path = pathlib.Path(map2loop.__file__).parent
+    path = path / "_datasets"/"geodata_files"/f'{folder}'
+    return path
 def load_hamersley_geology():
     """
     Loads Hamersley geology data from a shapefile
@@ -14,8 +18,9 @@ def load_hamersley_geology():
     Returns:
         geopandas.GeoDataFrame: The geology data
     """
-    stream = files("map2loop._datasets.geodata_files.hamersley").joinpath("geology.geojson")
-    return geopandas.read_file(stream)
+    
+    path = map2loop_dir('hamersley') / "geology.geojson"
+    return geopandas.read_file(str(path))
 
 
 def load_hamersley_structure():
@@ -30,8 +35,8 @@ def load_hamersley_structure():
         geopandas.GeoDataFrame: The structure data
     """
 
-    path = files("map2loop._datasets.geodata_files.hamersley").joinpath("structure.geojson")
-    return geopandas.read_file(path)
+    path = map2loop_dir('hamersley') / "structure.geojson"
+    return geopandas.read_file(str(path))
 
 
 def load_hamersley_dtm():
@@ -41,5 +46,5 @@ def load_hamersley_dtm():
     Returns:
         gdal.Dataset: The DTM data
     """
-    path = files("map2loop._datasets.geodata_files.hamersley").joinpath("dtm_rp.tif")
+    path = map2loop_dir('hamersley') / "dtm_rp.tif"
     return gdal.Open(str(path))

From a29e9c4ca669c6149cff771585257ca068cca725 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 17:10:49 +1000
Subject: [PATCH 20/40] fix: multilinestring import

---
 map2loop/utils.py                    | 2 +-
 tests/sampler/test_SamplerSpacing.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/map2loop/utils.py b/map2loop/utils.py
index 4a4ee7e5..c3ed7795 100644
--- a/map2loop/utils.py
+++ b/map2loop/utils.py
@@ -294,7 +294,7 @@ def rebuild_sampled_basal_contacts(
 
             # If multiple lines were created, combine them into a MultiLineString
             if lines:
-                line = shapely.MultiLineString(lines)
+                line = shapely.geometry.MultiLineString(lines)
                 r.append(line)
 
     sampled_basal_contacts = geopandas.GeoDataFrame(
diff --git a/tests/sampler/test_SamplerSpacing.py b/tests/sampler/test_SamplerSpacing.py
index b4708567..017f2467 100644
--- a/tests/sampler/test_SamplerSpacing.py
+++ b/tests/sampler/test_SamplerSpacing.py
@@ -20,7 +20,7 @@ def correct_geodata():
         'geometry': [
             shapely.geometry.LineString([(0, 0), (1, 1), (2, 2)]),
             shapely.geometry.Polygon([(0, 0), (1, 1), (1, 0), (0, 0)]),
-            shapely.MultiLineString(
+            shapely.geometry.MultiLineString(
                 [shapely.geometry.LineString([(0, 0), (1, 1)]), shapely.geometry.LineString([(2, 2), (3, 3)])]
             ),
         ],

From bfd2eecfa7b35e8ba8d8cd22760c6ddf263da4a0 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Thu, 5 Jun 2025 20:03:19 +1000
Subject: [PATCH 21/40] fixing more shapley bugs

---
 map2loop/data_checks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/map2loop/data_checks.py b/map2loop/data_checks.py
index 6c7af1db..732464d8 100644
--- a/map2loop/data_checks.py
+++ b/map2loop/data_checks.py
@@ -41,7 +41,7 @@ def check_geology_fields_validity(mapdata) -> tuple[bool, str]:
     # 2. Validate geometry
     failed, message = validate_geometry(
         geodata=geology_data,
-        expected_geom_types=[shapely.Polygon, shapely.MultiPolygon],
+        expected_geom_types=[shapely.geometry.Polygon, shapely.geometry.MultiPolygon],
         datatype_name="GEOLOGY"
     )
     if failed:

From 3e50fc4ff2c059862778071047f7ea21d5ae691f Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Fri, 6 Jun 2025 09:06:10 +1000
Subject: [PATCH 22/40] add version constraint on shapely

---
 dependencies.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dependencies.txt b/dependencies.txt
index 889b05cc..945b9640 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -1,7 +1,7 @@
 numpy
 scipy
 geopandas
-shapely
+shapely>=2.
 networkx
 owslib
 loopprojectfile==0.2.2

From 190d5c88b8cb3a1b988f131d30ec74dff8f4df1e Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Fri, 6 Jun 2025 09:58:14 +1000
Subject: [PATCH 23/40] remove . add gdal back

---
 dependencies.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dependencies.txt b/dependencies.txt
index 945b9640..76f0f574 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -1,7 +1,7 @@
 numpy
 scipy
 geopandas
-shapely>=2.
+shapely>=2
 networkx
 owslib
 loopprojectfile==0.2.2

From 323ba9cacb7416bb12043416c661a4de70a8b614 Mon Sep 17 00:00:00 2001
From: Lachlan Grose <lachlan.grose@gmail.com>
Date: Fri, 6 Jun 2025 09:58:26 +1000
Subject: [PATCH 24/40] actually add gdal

---
 dependencies.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dependencies.txt b/dependencies.txt
index 76f0f574..80e02915 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -7,4 +7,5 @@ owslib
 loopprojectfile==0.2.2
 beartype
 pytest
-scikit-learn
\ No newline at end of file
+scikit-learn
+gdal
\ No newline at end of file

From e6b182ab445a7855723aa8e07b89e2d3fdfe646d Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Sun, 8 Jun 2025 10:20:06 +0800
Subject: [PATCH 25/40] make workflow runs on all pushes

---
 .github/workflows/linting_and_testing.yml | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index c8c89126..aeb1a206 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -2,19 +2,6 @@ name: Linting and Testing
 
 on:
   push:
-    branches:
-      - master
-    paths:
-      - '**.py'
-      - .github/workflows/linting_and_testing.yml
-
-  pull_request:
-    branches:
-      - master
-    paths:
-      - '**.py'
-      - .github/workflows/linting_and_testing.yml
-  workflow_dispatch:
 
 jobs:
   linting:

From 1b8f33641eac4ebfb377b6881c0046c9aae03472 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Sun, 8 Jun 2025 13:54:20 +0800
Subject: [PATCH 26/40] replace dwithin

---
 map2loop/thickness_calculator.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py
index 5d7844d8..8072d580 100644
--- a/map2loop/thickness_calculator.py
+++ b/map2loop/thickness_calculator.py
@@ -365,7 +365,8 @@ def compute(
                         # calculate the length of the shortest line
                         line_length = scipy.spatial.distance.euclidean(p1, p2)
                         # find the indices of the points that are within 5% of the length of the shortest line
-                        indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
+                        # indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
+                        indices= numpy.array([shapely.distance(short_line,point)<= (line_length * 0.25) for point in interp_points])
                         # get the dip of the points that are within
                         _dip = numpy.deg2rad(dip[indices])
                         _dips.append(_dip)

From ee1864054ea058731e919eae7b8d24fc775ecef5 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Sun, 8 Jun 2025 16:27:34 +0800
Subject: [PATCH 27/40] fix short_line

---
 map2loop/thickness_calculator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py
index 8072d580..b8cbfa3b 100644
--- a/map2loop/thickness_calculator.py
+++ b/map2loop/thickness_calculator.py
@@ -366,7 +366,7 @@ def compute(
                         line_length = scipy.spatial.distance.euclidean(p1, p2)
                         # find the indices of the points that are within 5% of the length of the shortest line
                         # indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
-                        indices= numpy.array([shapely.distance(short_line,point)<= (line_length * 0.25) for point in interp_points])
+                        indices= numpy.array([shapely.distance(short_line[0],point)<= (line_length * 0.25) for point in interp_points])
                         # get the dip of the points that are within
                         _dip = numpy.deg2rad(dip[indices])
                         _dips.append(_dip)

From 97016eca8f3b3c6a83c240d18acde352ed793684 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Sun, 8 Jun 2025 16:52:20 +0800
Subject: [PATCH 28/40] fix dependency file path and handle >= version
 condition in check_all_dependencies

---
 map2loop/__init__.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/map2loop/__init__.py b/map2loop/__init__.py
index d7ccac11..8723f4ef 100644
--- a/map2loop/__init__.py
+++ b/map2loop/__init__.py
@@ -30,7 +30,7 @@ class DependencyChecker:
 
     def __init__(self, package_name, dependency_file="dependencies.txt"):
         self.package_name = package_name
-        self.dependency_file = pathlib.Path(__file__).parent / dependency_file
+        self.dependency_file = pathlib.Path(__file__).parent.parent / dependency_file
         self.required_version = self.get_required_version()
         self.installed_version = self.get_installed_version()
 
@@ -93,7 +93,7 @@ def check_version(self):
 
 
 def check_all_dependencies(dependency_file="dependencies.txt"):
-    dependencies_path = pathlib.Path(__file__).parent / dependency_file
+    dependencies_path = pathlib.Path(__file__).parent.parent / dependency_file
     try:
         with dependencies_path.open("r") as file:
             for line in file:
@@ -103,6 +103,8 @@ def check_all_dependencies(dependency_file="dependencies.txt"):
                 if line:
                     if "==" in line:
                         package_name, _ = line.split("==")
+                    elif ">=" in line:
+                        package_name, _ = line.split(">=")
                     else:
                         package_name = line
 

From 1f429562c4c8013fe9ff7675a59a3ed3d8ae1a3f Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Mon, 9 Jun 2025 12:51:27 +0800
Subject: [PATCH 29/40] remove gdal from dependencies.txt

---
 dependencies.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/dependencies.txt b/dependencies.txt
index 80e02915..76f0f574 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -7,5 +7,4 @@ owslib
 loopprojectfile==0.2.2
 beartype
 pytest
-scikit-learn
-gdal
\ No newline at end of file
+scikit-learn
\ No newline at end of file

From 291cdd78c7be93f202a2762d64679e90e9736d70 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Mon, 9 Jun 2025 14:04:45 +0800
Subject: [PATCH 30/40] change order of dependencies

---
 .github/workflows/linting_and_testing.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index aeb1a206..c58048ed 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -40,7 +40,9 @@ jobs:
       - name: Install dependencies
         run: |
             conda run -n test conda info
-            conda run -n test conda install -c conda-forge -c loop3d --file dependencies.txt gdal python=${{ matrix.python-version }} pytest -y
+            conda run -n test conda install -c loop3d -c conda-forge gdal python=${{ 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 map2loop
         run: |

From e6f363c58d3ea87de469361d70b71f6d75b466d5 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Mon, 9 Jun 2025 16:46:29 +0800
Subject: [PATCH 31/40] display gdal owslib versions

---
 .github/workflows/linting_and_testing.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index c58048ed..b057b0e7 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -44,6 +44,12 @@ jobs:
             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: displace gdal owslib version
+        run: |
+            echo "${{ matrix.os }} ${{ matrix.python-version }}"
+            conda run -n test conda list gdal
+            conda run -n test conda list owslib
+            
       - name: Install map2loop
         run: |
             conda run -n test python -m pip install .

From e58156da80bc4ae34cb49677ea8f4f5b8c56cee7 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Wed, 11 Jun 2025 21:13:56 +0800
Subject: [PATCH 32/40] fix: specify gdal 3.4.3 for windows python 3.10

---
 .github/workflows/linting_and_testing.yml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index b057b0e7..d5906d65 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -37,18 +37,22 @@ jobs:
             conda-remove-defaults: "true"
 
 
-      - name: Install dependencies
+      - name: Install dependencies for windows python 3.10
+        if: ${{ matrix.os == 'windows-latest' && matrix.python-version == '3.10' }}
         run: |
             conda run -n test conda info
-            conda run -n test conda install -c loop3d -c conda-forge gdal python=${{ matrix.python-version }} -y
+            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: displace gdal owslib version
+      - name: Install dependencies for other environments
+        if: ${{ matrix.os != 'windows-latest' || matrix.python-version != '3.10' }}
         run: |
-            echo "${{ matrix.os }} ${{ matrix.python-version }}"
-            conda run -n test conda list gdal
-            conda run -n test conda list owslib
+            conda run -n test conda info
+            conda run -n test conda install -c loop3d -c conda-forge gdal python=${{ 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 map2loop
         run: |

From 10378065d00705a2f61bb0b6dfd8d6895e633596 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Fri, 13 Jun 2025 18:10:29 +0800
Subject: [PATCH 33/40] print gdal owslib shapely version

---
 .github/workflows/linting_and_testing.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index d5906d65..09bc3efb 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -53,6 +53,13 @@ jobs:
             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: displace gdal owslib version
+        run: |
+            echo "${{ matrix.os }} ${{ matrix.python-version }}"
+            conda run -n test conda list gdal
+            conda run -n test conda list owslib
+            conda run -n test python -c "from shapely import geos_version; print('geos_version: ', geos_version)"
+            conda run -n test python -c "import shapely; print('shapely version: ',shapely.__version__)"
             
       - name: Install map2loop
         run: |

From 2dd81b652d3b4aaa48d7740ac6b98553376f49f6 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Fri, 13 Jun 2025 20:05:11 +0800
Subject: [PATCH 34/40] set gdal>=3.6.2 and shapely>=2.0.2 in dependencies.txt

---
 .github/workflows/linting_and_testing.yml | 12 +-----------
 dependencies.txt                          |  3 ++-
 map2loop/thickness_calculator.py          |  3 +--
 3 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 09bc3efb..a0f0ff77 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -37,19 +37,9 @@ jobs:
             conda-remove-defaults: "true"
 
 
-      - 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 other environments
-        if: ${{ matrix.os != 'windows-latest' || matrix.python-version != '3.10' }}
+      - name: Install dependencies
         run: |
             conda run -n test conda info
-            conda run -n test conda install -c loop3d -c conda-forge gdal python=${{ 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
 
diff --git a/dependencies.txt b/dependencies.txt
index 76f0f574..d7bd1e53 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -1,7 +1,8 @@
+gdal>=3.6.2
 numpy
 scipy
 geopandas
-shapely>=2
+shapely>=2.0.2
 networkx
 owslib
 loopprojectfile==0.2.2
diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py
index b8cbfa3b..5d7844d8 100644
--- a/map2loop/thickness_calculator.py
+++ b/map2loop/thickness_calculator.py
@@ -365,8 +365,7 @@ def compute(
                         # calculate the length of the shortest line
                         line_length = scipy.spatial.distance.euclidean(p1, p2)
                         # find the indices of the points that are within 5% of the length of the shortest line
-                        # indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
-                        indices= numpy.array([shapely.distance(short_line[0],point)<= (line_length * 0.25) for point in interp_points])
+                        indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
                         # get the dip of the points that are within
                         _dip = numpy.deg2rad(dip[indices])
                         _dips.append(_dip)

From 1419270a5ab543e0879abc4258dcfc7d63b59a06 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Fri, 13 Jun 2025 21:06:01 +0800
Subject: [PATCH 35/40] change back to shapely>=2 in dependencies.txt

---
 dependencies.txt                 | 2 +-
 map2loop/thickness_calculator.py | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/dependencies.txt b/dependencies.txt
index d7bd1e53..c9014571 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -2,7 +2,7 @@ gdal>=3.6.2
 numpy
 scipy
 geopandas
-shapely>=2.0.2
+shapely>=2
 networkx
 owslib
 loopprojectfile==0.2.2
diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py
index 5d7844d8..d7a9aad1 100644
--- a/map2loop/thickness_calculator.py
+++ b/map2loop/thickness_calculator.py
@@ -23,7 +23,7 @@
 import geopandas
 import shapely
 import math
-
+from shapely.errors import UnsupportedGEOSVersionError
 
 class ThicknessCalculator(ABC):
     """
@@ -365,7 +365,11 @@ def compute(
                         # calculate the length of the shortest line
                         line_length = scipy.spatial.distance.euclidean(p1, p2)
                         # find the indices of the points that are within 5% of the length of the shortest line
-                        indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
+                        try:
+                            # GEOS 3.10.0+
+                            indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
+                        except UnsupportedGEOSVersionError:
+                            indices= numpy.array([shapely.distance(short_line[0],point)<= (line_length * 0.25) for point in interp_points])
                         # get the dip of the points that are within
                         _dip = numpy.deg2rad(dip[indices])
                         _dips.append(_dip)

From 75f08c9df680b44b18c8a62ef165323ceae983d1 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Fri, 13 Jun 2025 21:25:42 +0800
Subject: [PATCH 36/40] remove gdal>=3.6.2 from dependencies.txt

---
 .github/workflows/linting_and_testing.yml | 1 +
 dependencies.txt                          | 1 -
 map2loop/thickness_calculator.py          | 7 +------
 3 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index a0f0ff77..2dbe7e2b 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -40,6 +40,7 @@ jobs:
       - name: Install dependencies
         run: |
             conda run -n test conda info
+            conda run -n test conda install -c loop3d -c conda-forge "gdal>=3.6.2" 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
 
diff --git a/dependencies.txt b/dependencies.txt
index c9014571..76f0f574 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -1,4 +1,3 @@
-gdal>=3.6.2
 numpy
 scipy
 geopandas
diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py
index d7a9aad1..2e3bf1f5 100644
--- a/map2loop/thickness_calculator.py
+++ b/map2loop/thickness_calculator.py
@@ -23,7 +23,6 @@
 import geopandas
 import shapely
 import math
-from shapely.errors import UnsupportedGEOSVersionError
 
 class ThicknessCalculator(ABC):
     """
@@ -365,11 +364,7 @@ def compute(
                         # calculate the length of the shortest line
                         line_length = scipy.spatial.distance.euclidean(p1, p2)
                         # find the indices of the points that are within 5% of the length of the shortest line
-                        try:
-                            # GEOS 3.10.0+
-                            indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
-                        except UnsupportedGEOSVersionError:
-                            indices= numpy.array([shapely.distance(short_line[0],point)<= (line_length * 0.25) for point in interp_points])
+                        indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
                         # get the dip of the points that are within
                         _dip = numpy.deg2rad(dip[indices])
                         _dips.append(_dip)

From a4331fe8d9221fca39c6b465e67a29ea825e5b2e Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Fri, 13 Jun 2025 21:53:36 +0800
Subject: [PATCH 37/40] windows python 3.10 glda=3.4.3

---
 .github/workflows/linting_and_testing.yml | 13 +++++++++++--
 dependencies.txt                          |  2 +-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 2dbe7e2b..09bc3efb 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -37,10 +37,19 @@ jobs:
             conda-remove-defaults: "true"
 
 
-      - name: Install dependencies
+      - 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 other environments
+        if: ${{ matrix.os != 'windows-latest' || matrix.python-version != '3.10' }}
         run: |
             conda run -n test conda info
-            conda run -n test conda install -c loop3d -c conda-forge "gdal>=3.6.2" python=${{ 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
 
diff --git a/dependencies.txt b/dependencies.txt
index 76f0f574..7f7a2447 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -1,7 +1,7 @@
 numpy
 scipy
 geopandas
-shapely>=2
+shapely>=2.0.2
 networkx
 owslib
 loopprojectfile==0.2.2

From 0d583cb20f519ed42fd382023a706a894cbdb2ed Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Fri, 13 Jun 2025 22:47:21 +0800
Subject: [PATCH 38/40] add geos version compatibility for shapely.dwithin

---
 dependencies.txt                 | 2 +-
 map2loop/thickness_calculator.py | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/dependencies.txt b/dependencies.txt
index 7f7a2447..76f0f574 100644
--- a/dependencies.txt
+++ b/dependencies.txt
@@ -1,7 +1,7 @@
 numpy
 scipy
 geopandas
-shapely>=2.0.2
+shapely>=2
 networkx
 owslib
 loopprojectfile==0.2.2
diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py
index 2e3bf1f5..d7a9aad1 100644
--- a/map2loop/thickness_calculator.py
+++ b/map2loop/thickness_calculator.py
@@ -23,6 +23,7 @@
 import geopandas
 import shapely
 import math
+from shapely.errors import UnsupportedGEOSVersionError
 
 class ThicknessCalculator(ABC):
     """
@@ -364,7 +365,11 @@ def compute(
                         # calculate the length of the shortest line
                         line_length = scipy.spatial.distance.euclidean(p1, p2)
                         # find the indices of the points that are within 5% of the length of the shortest line
-                        indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
+                        try:
+                            # GEOS 3.10.0+
+                            indices = shapely.dwithin(short_line, interp_points, line_length * 0.25)
+                        except UnsupportedGEOSVersionError:
+                            indices= numpy.array([shapely.distance(short_line[0],point)<= (line_length * 0.25) for point in interp_points])
                         # get the dip of the points that are within
                         _dip = numpy.deg2rad(dip[indices])
                         _dips.append(_dip)

From e3aef22dae78bfcfebc93156d611753151c44fff Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Mon, 16 Jun 2025 13:08:54 +0800
Subject: [PATCH 39/40] add back branch and path restrictions

---
 .github/workflows/linting_and_testing.yml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 09bc3efb..03eab6dc 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -2,6 +2,19 @@ name: Linting and Testing
 
 on:
   push:
+    branches:
+    - master
+    paths:
+      - '**.py'
+      - .github/workflows/linting_and_testing.yml
+  
+  pull_request:
+    branches:
+      - master
+    paths:
+      - '**.py'
+      - .github/workflows/linting_and_testing.yml
+  workflow_dispatch:
 
 jobs:
   linting:
@@ -67,5 +80,4 @@ jobs:
 
       - name: Run tests
         run: |
-            conda run -n test  pytest
-
+            conda run -n test  pytest
\ No newline at end of file

From 18dd00da3d769b64b087658282e619e1f3a040b7 Mon Sep 17 00:00:00 2001
From: Noelle Cheng <noellechengheiman@gmail.com>
Date: Mon, 16 Jun 2025 13:10:52 +0800
Subject: [PATCH 40/40] remove print statements

---
 .github/workflows/linting_and_testing.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
index 03eab6dc..9570a3bb 100644
--- a/.github/workflows/linting_and_testing.yml
+++ b/.github/workflows/linting_and_testing.yml
@@ -65,14 +65,6 @@ jobs:
             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=${{ matrix.python-version }} -y
-
-      - name: displace gdal owslib version
-        run: |
-            echo "${{ matrix.os }} ${{ matrix.python-version }}"
-            conda run -n test conda list gdal
-            conda run -n test conda list owslib
-            conda run -n test python -c "from shapely import geos_version; print('geos_version: ', geos_version)"
-            conda run -n test python -c "import shapely; print('shapely version: ',shapely.__version__)"
             
       - name: Install map2loop
         run: |