Align docstrings with function signatures and add inspec GeoPackage marimo nb #59

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Merged

JoostGevaert merged 14 commits into main from dev

Jul 14, 2025

examples/geopackage/inspect_gpkg.py

-Original file line number
+Diff line change
@@ -0,0 +1,82 @@
+    # /// script
+    # requires-python = ">=3.12"
+    # dependencies = [
+    #     "folium==0.19.5",
+    #     "mapclassify==2.8.1",
+    #     "matplotlib==3.9.4",
+    #     "pandas==2.2.3",
+    #     "shapely==2.0.7",
+    # ]
+    # ///
+    import marimo
+    __generated_with = "0.13.2"
+    app = marimo.App(width="medium")
+    @app.cell(hide_code=True)
+    def _():
+        from pathlib import Path
+        import geopandas as gpd
+        import marimo as mo
+        import pandas as pd
+        import pyogrio
+        from shapely import Point
+        return Path, Point, gpd, mo, pd, pyogrio
+    @app.cell
+    def _(Path):
+        gpkg_path = Path(
+            r"S:\Shared drives\Bedrock\Case Studies\A2TunnelMaastricht\data\A2_Maastricht.gpkg"
+        )
+        return (gpkg_path,)
+    @app.cell(hide_code=True)
+    def _(gpd, gpkg_path, pyogrio):
+        gpkg_layers = gpd.list_layers(gpkg_path)
+        brgi_geodb = {}
+        for layer in gpkg_layers["name"]:
+            brgi_geodb[layer] = pyogrio.read_dataframe(gpkg_path, layer=layer)
+        gpkg_layers
+        return (brgi_geodb,)
+    @app.cell(hide_code=True)
+    def _(brgi_geodb, mo):
+        sel_brgi_table = mo.ui.dropdown(brgi_geodb, value="Project")
+        mo.md(f"Select the Bedrock GI table you want to explore: {sel_brgi_table}")
+        return (sel_brgi_table,)
+    @app.cell(hide_code=True)
+    def _(pd, sel_brgi_table):
+        df = pd.DataFrame(sel_brgi_table.value.copy())
+        if "geometry" in df.columns:
+            df = df.assign(geometry=df.geometry.astype(str))
+        df
+        return
+    @app.cell(hide_code=True)
+    def _(Point, sel_brgi_table):
+        if "geometry" in sel_brgi_table.value.columns:
+            gdf = sel_brgi_table.value.copy()
+            gdf = gdf["geometry"].apply(lambda geom: Point(geom.coords[0]))
+            map = gdf.explore()
+        else:
+            map = f"The {sel_brgi_table.selected_key} table doesn't contain GIS geometry."
+        map
+        return
+    if __name__ == "__main__":
+        app.run()

examples/hk_kaitak_ags3/hk_kaitak_ags3_to_brgi_geodb.py

-Original file line number
+Diff line change
@@ -1,7 +1,7 @@
     # /// script
     # requires-python = ">=3.12"
     # dependencies = [
-    #     "bedrock-ge==0.3.1",
+    #     "bedrock-ge==0.3.2",
     #     "folium==0.20.0",
     #     "geopandas==1.1.0",
     #     "mapclassify==2.9.0",
@@ Expand Down @@

pyproject.toml

-Original file line number
+Diff line change
@@ -1,6 +1,6 @@
     [project]
     name = "bedrock-ge"
-    version = "0.3.1"
+    version = "0.3.2"
     description = "Bedrock's Python library for geotechnical engineering."
     authors = [
         {name = "Bedrock", email = "[email protected]"}
@@ Expand Down @@

src/bedrock_ge/__init__.py

-Original file line number
+Diff line change
@@ -1,3 +1,3 @@
     """Bedrock, the open source foundation for ground engineering."""
-    __version__ = "0.3.1"
+    __version__ = "0.3.2"

src/bedrock_ge/gi/ags.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -17,23 +17,22 @@ def ags_to_brgi_db_mapping(
  
        """Map AGS 3 or AGS 4 data to the Bedrock GI data model.

        Args:

            source (str | Path | IO[str] | IO[bytes] | bytes): The AGS file (str or Path)

                or a file-like object that represents the AGS file.

            projected_crs (CRS): Projected Coordinate Reference System (CRS). For example:

            source: The AGS file (str or Path) or a file-like object that represents the AGS file.

            projected_crs: Projected Coordinate Reference System (CRS). For example:

                - OSGB36 / British National Grid: `pyproj.CRS("EPSG:27700")`

                - Hong Kong 1980 Grid System: `pyproj.CRS("EPSG:2326")`

            vertical_crs (CRS, optional): Vertical CRS. Defaults to EGM2008 height, EPSG:3855

            vertical_crs: Vertical CRS. Defaults to EGM2008 height, EPSG:3855,

                which measures the orthometric height w.r.t. the Earth Gravitational Model 2008.

                - Ordnance Datum Newlyn (ODN) Height: `pyproj.CRS("EPSG:5701")`

                - Hong Kong Principle Datum (HKPD) Height: `pyproj.CRS("EPSG:5738")`

            encoding (str | None, optional): Encoding of the text file or bytes stream.

                Defaults to None. An attempt at detecting the encoding will be made if None.

            encoding: Encoding of the text file or bytes stream. Defaults to None.

                An attempt at detecting the encoding will be made if None.

        Raises:

            ValueError: If the data does not match AGS 3 or AGS 4 format.

        Returns:

            BedrockGIDatabaseMapping: Object that maps AGS 3 or AGS 4 data to Bedrock GI data model.

            Object that maps AGS 3 or AGS 4 data to Bedrock GI data model.

        """

        if not encoding:

            encoding = detect_encoding(source)

src/bedrock_ge/gi/ags3.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -26,14 +26,13 @@ def ags3_to_dfs(
  
        make the rest of the code more generic.

        Args:

            source (str | Path | IO[str] | IO[bytes] | bytes): The AGS 3 file (str or Path)

                or a file-like object that represents the AGS 3 file.

            encoding (str):  Encoding of file or object.

            source: The AGS 3 file (str or Path) or a file-like object that represents the AGS 3 file.

            encoding: Encoding of the text file or bytes stream.

        Returns:

            dict[str, pd.DataFrame]: A dictionary of pandas DataFrames, i.e. a database,

                where each key is an AGS 3 group, and the corresponding value is

                a pandas DataFrame containing the data for that group.

            A dictionary of pandas DataFrames, i.e. a database, where each key is

                an AGS 3 group, and the corresponding value is a pandas DataFrame

                containing the data for that group.

        """

        # Initialize dictionary and variables used in the AGS 3 read loop

        ags3_dfs = {}

    @@ -134,16 +133,18 @@ def ags3_to_brgi_db_mapping(
  
        """Map AGS 3 data to the Bedrock GI data model.

        Args:

            ags3_db (dict[str, pd.DataFrame]): A dictionary of pandas DataFrames, i.e. database,

                where each key is an AGS 3 group, and the corresponding value is

                a pandas DataFrame containing the data for that group.

            projected_crs (CRS): Projected coordinate reference system (CRS).

            vertical_crs (CRS, optional): Vertical CRS. Defaults to EGM2008 height, EPSG:3855

            source: The AGS 3 file (str or Path) or a file-like object that represents the AGS 3 file.

            projected_crs: Projected Coordinate Reference System (CRS). For example:

                - OSGB36 / British National Grid: `pyproj.CRS("EPSG:27700")`

                - Hong Kong 1980 Grid System: `pyproj.CRS("EPSG:2326")`

            vertical_crs: Vertical CRS. Defaults to EGM2008 height, EPSG:3855,

                which measures the orthometric height w.r.t. the Earth Gravitational Model 2008.

            encoding (str): Encoding of the text file or bytes stream.

                - Ordnance Datum Newlyn (ODN) Height: `pyproj.CRS("EPSG:5701")`

                - Hong Kong Principle Datum (HKPD) Height: `pyproj.CRS("EPSG:5738")`

            encoding: Encoding of the text file or bytes stream.

        Returns:

            BedrockGIDatabaseMapping: Object that maps AGS 3 data to Bedrock GI data model.

            Object that maps AGS 3 data to Bedrock GI data model.

        """

        ags3_dfs = ags3_to_dfs(source, encoding)

    @@ -269,7 +270,7 @@ def _get_depth_columns(group: str, headers: list[str]) -> tuple[str | None, str
  
            base_depth = None

        if not top_depth and not base_depth:

            raise ValueError(

                'The in-situ test group "{group}" group in this AGS 3 file does not contain a top or base depth heading!'

                f'The in-situ test group "{group}" group in this AGS 3 file does not contain a top or base depth heading!'

            )

        return top_depth, base_depth

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