Merge pull request #115 from MiraGeoscience/GEOPY-1800

GEOPY-1800

Author: domfournier

las_geoh5/export_las.py

@@ -82,10 +82,12 @@ def add_curve_data(file: LASFile, drillhole: Drillhole, group):
         file.append_curve(datum.name, datum.values)
 
         if isinstance(datum, ReferencedData) and datum.value_map is not None:
-            for k, v in datum.value_map().items():  # pylint: disable=invalid-name
+            for name, value in datum.value_map().items():
                 file.params.append(
                     HeaderItem(
-                        mnemonic=f"{datum.name} ({k})", value=v, descr="REFERENCE"
+                        mnemonic=f"{datum.name} ({name})",
+                        value=value,
+                        descr="REFERENCE",
                     )
                 )
 
@@ -164,8 +166,8 @@ def write_curves(
             subpath = basepath
 
         filename = f"{drillhole.name}_{group.name}.las"
-        with open(subpath / filename, "a", encoding="utf8") as io:  # pylint: disable=invalid-name
-            file.write(io)
+        with open(subpath / filename, "a", encoding="utf8") as output:
+            file.write(output)
 
 
 def write_survey(
@@ -195,8 +197,8 @@ def write_survey(
             basepath.mkdir()
 
     filename = f"{drillhole.name}_survey.las"
-    with open(basepath / filename, "a", encoding="utf8") as io:  # pylint: disable=invalid-name
-        file.write(io)
+    with open(basepath / filename, "a", encoding="utf8") as output:
+        file.write(output)
 
 
 def drillhole_to_las(

las_geoh5/import_directories/uijson.py

@@ -13,6 +13,8 @@
 from geoh5py.ui_json.constants import default_ui_json
 
 
+# pylint: disable=duplicate-code
+
 ui_json = dict(
     deepcopy(default_ui_json),
     **{

las_geoh5/import_files/uijson.py

@@ -13,8 +13,6 @@
 from geoh5py.ui_json.constants import default_ui_json
 
 
-# pylint: disable=duplicate-code
-
 ui_json = dict(
     deepcopy(default_ui_json),
     **{

las_geoh5/import_las.py

@@ -324,7 +324,7 @@ def create_or_append_drillhole(
         )
 
     collar = get_collar(lasfile, translator, logger)
-    drillhole = drillhole_group.get_entity(name)[0]  # type: ignore
+    drillhole = drillhole_group.get_entity(name)[0]
 
     if not isinstance(drillhole, Drillhole):
         name = find_copy_name(drillhole_group.workspace, name)

las_geoh5/scripts/las_to_geoh5.py

@@ -16,6 +16,8 @@
 from las_geoh5.import_files import driver
 
 
+# pylint: disable=duplicate-code
+
 _logger = logging.getLogger(__package__ + "." + Path(__file__).stem)
 
 

las_geoh5/uijson/write_uijson.py

@@ -63,7 +63,7 @@ def main(args):
             "import_files",
             "import_directories",
             "export_files",
-        ]:  # pylint: disable=invalid-name
+        ]:
             write_uijson(args.path, mode)
     else:
         write_uijson(args.path, args.mode)

tests/geoh5_to_las_test.py

@@ -348,6 +348,7 @@ def test_collocation_tolerance(tmp_path: Path):
 
     dh1 = add_data(dh1, lasfile, group_name, collocation_tolerance=0.1)
 
+    assert dh1.property_groups is not None
     assert dh1.property_groups[0].name == group_name
 
     lasfile = lasio.LASFile()
@@ -356,6 +357,7 @@ def test_collocation_tolerance(tmp_path: Path):
 
     dh1 = add_data(dh1, lasfile, group_name, collocation_tolerance=0.01)
 
+    assert dh1.property_groups is not None
     assert len(dh1.property_groups) == 2
     assert all(
         k.name in ["my_property_group", "my_property_group (1)"]

tests/import_las_test.py

@@ -324,6 +324,7 @@ def test_add_data_increments_property_group(tmp_path: Path):
 
     drillhole = add_data(drillhole, file, "my group")
 
+    assert drillhole.property_groups is not None
     assert len(drillhole.property_groups) == 2
     assert [k.name in ["my group", "my group (1)"] for k in drillhole.property_groups]
 
@@ -334,11 +335,12 @@ def test_add_data_increments_property_group(tmp_path: Path):
 
     drillhole = add_data(drillhole, file, "my group")
 
+    assert drillhole.property_groups is not None
     assert len(drillhole.property_groups) == 3
-    assert [
+    assert all(
         k.name in ["my group", "my group (1)", "my group (2)"]
         for k in drillhole.property_groups
-    ]
+    )
 
 
 def test_add_data_increments_data_name(tmp_path: Path):
@@ -362,8 +364,11 @@ def test_add_data_increments_data_name(tmp_path: Path):
 
     drillhole = add_data(drillhole, file, "my group")
 
+    assert drillhole.property_groups is not None
     assert len(drillhole.property_groups) == 2
-    assert [k.name in ["my group", "my group (1)"] for k in drillhole.property_groups]
+    assert all(
+        k.name in ["my group", "my group (1)"] for k in drillhole.property_groups
+    )
     assert all(
         k in [c.name for c in drillhole.children] for k in ["my data", "my data (1)"]
     )
@@ -375,6 +380,7 @@ def test_add_data_increments_data_name(tmp_path: Path):
 
     drillhole = add_data(drillhole, file, "my group")
 
+    assert drillhole.property_groups is not None
     assert len(drillhole.property_groups) == 3
     assert [
         k.name in ["my group", "my group (1)", "my group (2)"]