Merge pull request #59 from bedrock-engineer/dev

Align docstrings with function signatures and add inspec GeoPackage marimo nb

Author: JoostGevaert

examples/geopackage/inspect_gpkg.py

@@ -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

@@ -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",

pyproject.toml

@@ -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]"}

src/bedrock_ge/__init__.py

@@ -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

@@ -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

@@ -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