fixing stratigraphic sorters (#144)

* fix: stratigraphic alpha sorter was inverted, reverse sorter * ignore units without contact for max contact length sorter * updated orientation sorter to use correct trigonometry for strike/dip lines. also change to using all intersections along line not only the first intersection. perhaps this should be a different sorter? * revert back to original orientation sorter * style: black * updating WA json to work * remove unused argument documentation * only run doc build on master
Loop3D · Nov 8, 2024 · 184663e · 184663e
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commit 184663e
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diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml
@@ -1,4 +1,4 @@
-# for this workflow to work, need to release LPF=1.0.5, map2model=1.0.1, use json instead of hjson 
+# for this workflow to work, need to release LPF=1.0.5, map2model=1.0.1, use json instead of hjson
 
 name: release-please
 
@@ -51,15 +51,14 @@ jobs:
         with:
           name: map2loop-dist
           path: dist/*.tar.gz
-          compression-level: 0        
+          compression-level: 0
 
   pypi-test-sdist:
     name: Test sdist
     needs: pypi-build-sdist
     runs-on: ubuntu-latest
     steps:
-
-      - name : Install GDAL 
+      - name: Install GDAL
         run: |
           sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
           sudo apt-get update
@@ -79,15 +78,15 @@ jobs:
           pip install geopandas shapely networkx owslib map2model loopprojectfile beartype gdal==3.8.4 hjson pytest scikit-learn
           pip install --no-cache dist/*.tar.gz
           pip list
-    
+
   pypi-build-wheels:
     needs: pypi-test-sdist
     name: Build Wheels
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: 
+        os:
           - ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -96,7 +95,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.x
-      
+
       - name: Build Wheels
         run: |
           pip install build 
@@ -128,14 +127,14 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
 
-      - name : Install GDAL - Linux
+      - name: Install GDAL - Linux
         if: runner.os == 'Linux'
         run: |
           sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
           sudo apt-get update
           sudo apt-get install -y libgdal-dev gdal-bin
 
-      - name: Upgrade pip 
+      - name: Upgrade pip
         run: |
           python -m pip install --upgrade pip
 
@@ -152,7 +151,7 @@ jobs:
           pip install numpy==1.26.4
           pip install -r dependencies.txt
           pip install --no-cache --pre --no-index --find-links dist map2loop
-          pip list    
+          pip list
 
       - name: Testing
         shell: bash -l {0}
@@ -165,10 +164,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os:   
-        - ubuntu-latest
-        # - macos-latest # currently not supported because needs libgcc>= 14 and not available for macos-latest (version available is 4.x.x)
-        - windows-latest
+        os:
+          - ubuntu-latest
+          # - macos-latest # currently not supported because needs libgcc>= 14 and not available for macos-latest (version available is 4.x.x)
+          - windows-latest
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
@@ -200,8 +199,8 @@ jobs:
           path: ~/conda_pkgs_dir
         shell: bash -l {0}
         run: |
-          conda build -c anaconda -c conda-forge -c loop3d --output-folder conda conda --python ${{ matrix.python-version }} 
-      
+          conda build -c anaconda -c conda-forge -c loop3d --output-folder conda conda --python ${{ matrix.python-version }}
+
       - name: upload artifacts
         uses: actions/upload-artifact@v4
         with:
@@ -217,14 +216,15 @@ jobs:
       - uses: googleapis/release-please-action@v4
         id: release
         with:
-          config-file: 'release-please-config.json'
-          manifest-file: '.release-please-manifest.json'
+          config-file: "release-please-config.json"
+          manifest-file: ".release-please-manifest.json"
     outputs:
       release_created: ${{ steps.release.outputs.release_created }}
       #if a release is created then run the deploy scripts for github.io, conda, pypi and docker
 
   documentation-test:
     runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/master'
     steps:
       - uses: actions/checkout@v4
       - run: |
@@ -255,17 +255,17 @@ jobs:
         with:
           branch: gh-pages # The branch the action should deploy to.
           folder: docs # The folder the action should deploy.
-  
+
   conda-upload:
     needs: [release-please, conda-build]
     runs-on: ${{matrix.os}}
     strategy:
       fail-fast: false
       matrix:
         os:
-        - ubuntu-latest
-        # - macos-latest
-        - windows-latest
+          - ubuntu-latest
+          # - macos-latest
+          - windows-latest
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     if: ${{ needs.release-please.outputs.release_created }}
     steps:
@@ -278,15 +278,15 @@ jobs:
         shell: bash -l {0}
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN  }}
-          with: 
+          with:
           skip-existing: true
           verbose: true
         run: |
           conda install -c anaconda anaconda-client -y
           anaconda upload --label main conda/*/*.tar.bz2
-        
+
   pypi-upload:
-    needs: [release-please, pypi-test-wheels] 
+    needs: [release-please, pypi-test-wheels]
     runs-on:
       - ubuntu-latest
     if: ${{ needs.release-please.outputs.release_created }}

diff --git a/map2loop/_datasets/config_files/WA.json b/map2loop/_datasets/config_files/WA.json
@@ -1,50 +1,49 @@
 {
-    "structure": {
-        "orientation_type": "strike",
-        "dipdir_column": "strike",
-        "dip_column": "dip",
-        "description_column": "DESCRIPTION",
-        "bedding_text": "Bed",
-        "overturned_column": "structypei",
-        "overturned_text": "BEOI",
-        "objectid_column": "objectid",
-        "desciption_column": "feature"
-    },
-    "geology": {
-        "unitname_column": "unitname",
-        "alt_unitname_column": "code",
-        "group_column": "group_",
-        "supergroup_column": "supersuite",
-        "description_column": "descriptn",
-        "minage_column": "min_age_ma",
-        "maxage_column": "max_age_ma",
-        "rocktype_column": "rocktype1",
-        "alt_rocktype_column": "rocktype2",
-        "sill_text": "sill",
-        "intrusive_text": "intrusive",
-        "volcanic_text": "volcanic",
-        "objectid_column": "ID",
-        "ignore_codes": ["cover"]
-    },
-    "fault": {
-        "structtype_column": "feature",
-        "fault_text": "Fault",
-        "dip_null_value": "0",
-        "dipdir_flag": "num",
-        "dipdir_column": "dip_dir",
-        "dip_column": "dip",
-        "orientation_type": "dip direction",
-        "dipestimate_column": "dip_est",
-        "dipestimate_text": "gentle,moderate,steep",
-        "name_column": "name",
-        "objectid_column": "objectid"
-    },
-    "fold": {
-        "structtype_column": "feature",
-        "fold_text": "Fold axial trace",
-        "description_column": "type",
-        "synform_text": "syncline",
-        "foldname_column": "NAME",
-        "objectid_column": "objectid"
-    }
-}
+  "structure": {
+    "orientation_type": "strike",
+    "dipdir_column": "strike",
+    "dip_column": "dip",
+    "description_column": "feature",
+    "bedding_text": "Bed",
+    "overturned_column": "structypei",
+    "overturned_text": "BEOI",
+    "objectid_column": "objectid"
+  },
+  "geology": {
+    "unitname_column": "unitname",
+    "alt_unitname_column": "code",
+    "group_column": "group_",
+    "supergroup_column": "supersuite",
+    "description_column": "descriptn",
+    "minage_column": "min_age_ma",
+    "maxage_column": "max_age_ma",
+    "rocktype_column": "rocktype1",
+    "alt_rocktype_column": "rocktype2",
+    "sill_text": "is a sill",
+    "intrusive_text": "intrusive",
+    "volcanic_text": "volcanic",
+    "objectid_column": "ID",
+    "ignore_codes": ["cover"]
+  },
+  "fault": {
+    "structtype_column": "feature",
+    "fault_text": "Fault",
+    "dip_null_value": "0",
+    "dipdir_flag": "num",
+    "dipdir_column": "dip_dir",
+    "dip_column": "dip",
+    "orientation_type": "dip direction",
+    "dipestimate_column": "dip_est",
+    "dipestimate_text": "gentle,moderate,steep",
+    "name_column": "name",
+    "objectid_column": "objectid"
+  },
+  "fold": {
+    "structtype_column": "feature",
+    "fold_text": "Fold axial trace",
+    "description_column": "type",
+    "synform_text": "syncline",
+    "foldname_column": "NAME",
+    "objectid_column": "objectid"
+  }
+}
diff --git a/map2loop/mapdata.py b/map2loop/mapdata.py
@@ -20,6 +20,7 @@
 from io import BytesIO
 from typing import Union
 
+
 class MapData:
     """
     A data structure containing all the map data loaded from map files
@@ -315,7 +316,7 @@ def set_filenames_from_australian_state(self, state: str):
             self.set_filename(Datatype.STRUCTURE, AustraliaStateUrls.aus_structure_urls[state])
             self.set_filename(Datatype.FAULT, AustraliaStateUrls.aus_fault_urls[state])
             self.set_filename(Datatype.FOLD, AustraliaStateUrls.aus_fold_urls[state])
-            self.set_filename(Datatype.DTM, "au")
+            self.set_filename(Datatype.DTM, "hawaii")
             lower = state == "SA"
 
             # Check if this is running a documentation test and use local datasets if so
@@ -483,8 +484,6 @@ def __check_and_create_tmp_path(self):
         if not os.path.isdir(self.tmp_path):
             os.mkdir(self.tmp_path)
 
-
-
     @beartype.beartype
     def __retrieve_tif(self, filename: str):
         """
@@ -498,10 +497,13 @@ def __retrieve_tif(self, filename: str):
             _type_: The open geotiff in a gdal handler
         """
         self.__check_and_create_tmp_path()
-        
+
         # For gdal debugging use exceptions
         gdal.UseExceptions()
-        bb_ll = tuple(float(coord) for coord in self.bounding_box_polygon.to_crs("EPSG:4326").geometry.total_bounds)
+        bb_ll = tuple(
+            float(coord)
+            for coord in self.bounding_box_polygon.to_crs("EPSG:4326").geometry.total_bounds
+        )
 
         if filename.lower() == "aus" or filename.lower() == "au":
 
@@ -511,7 +513,7 @@ def __retrieve_tif(self, filename: str):
             coverage = wcs.getCoverage(
                 identifier="1", bbox=bb_ll, format="GeoTIFF", crs=4326, width=2048, height=2048
             )
-            
+
             # This is stupid that gdal cannot read a byte stream and has to have a
             # file on the local system to open or otherwise create a gdal file
             # from scratch with Create
@@ -521,14 +523,14 @@ def __retrieve_tif(self, filename: str):
             with open(tmp_file, "wb") as fh:
                 fh.write(coverage.read())
             tif = gdal.Open(tmp_file)
-        
+
         elif filename == "hawaii":
             import netCDF4
 
             bbox_str = (
                 f"[({str(bb_ll[1])}):1:({str(bb_ll[3])})][({str(bb_ll[0])}):1:({str(bb_ll[2])})]"
             )
-            
+
             filename = f"https://pae-paha.pacioos.hawaii.edu/erddap/griddap/srtm30plus_v11_land.nc?elev{bbox_str}"
             f = urllib.request.urlopen(filename)
             ds = netCDF4.Dataset("in-mem-file", mode="r", memory=f.read())
@@ -734,10 +736,10 @@ def parse_structure_map(self) -> tuple:
                 structure["DIPDIR"] = self.raw_data[Datatype.STRUCTURE][config["dipdir_column"]]
         else:
             print(f"Structure map does not contain dipdir_column '{config['dipdir_column']}'")
-                    
+
         # Ensure all DIPDIR values are within [0, 360]
         structure["DIPDIR"] = structure["DIPDIR"] % 360.0
-        
+
         if config["dip_column"] in self.raw_data[Datatype.STRUCTURE]:
             structure["DIP"] = self.raw_data[Datatype.STRUCTURE][config["dip_column"]]
         else:
@@ -1491,9 +1493,9 @@ def colour_units(
             )
 
         colour_lookup["colour"] = colour_lookup["colour"].str.upper()
-        # if there are duplicates in the clut file, drop. 
+        # if there are duplicates in the clut file, drop.
         colour_lookup = colour_lookup.drop_duplicates(subset=["UNITNAME"])
-        
+
         if "UNITNAME" in colour_lookup.columns and "colour" in colour_lookup.columns:
             stratigraphic_units = stratigraphic_units.merge(
                 colour_lookup,
@@ -1511,3 +1513,15 @@ def colour_units(
                 f"Colour Lookup file {self.colour_filename} does not contain 'UNITNAME' or 'colour' field"
             )
         return stratigraphic_units
+
+    @property
+    def GEOLOGY(self):
+        return self.get_map_data(Datatype.GEOLOGY)
+
+    @property
+    def STRUCTURE(self):
+        return self.get_map_data(Datatype.STRUCTURE)
+
+    @property
+    def FAULT(self):
+        return self.get_map_data(Datatype.FAULT)