tests passing after cleanup

sensospot_data/__init__.py

@@ -10,10 +10,7 @@ from pathlib import Path
 
 import click
 
-from .parser import (  # noqa: F401
-    parse_file,
-    parse_folder,
-)
+from .parser import parse_file, parse_folder  # noqa: F401
 from .parameters import ExposureInfo, get_measurement_params  # noqa: F401
 
 

sensospot_data/columns.py

@@ -20,7 +20,7 @@ RAW_DATA_POS_NOM_Y = "Pos.Nom.Y"
 RAW_DATA_POS_ID = "Pos.Id"
 RAW_DATA_SPOT_FOUND = "Spot.Found"
 RAW_DATA_SPOT_DIAMETER = "Spot.Diameter"
-RAW_DATA_SPOT_SAT = "Spot.Sat[%]"
+RAW_DATA_SPOT_SAT = "Spot.Saturation"
 
 
 RAW_DATA_COLUMNS_RENAME_MAP = {

sensospot_data/parameters.py

@@ -10,9 +10,9 @@ import numpy
 from defusedxml import ElementTree
 
 from .columns import (
-    COL_NAME_EXPOSURE_ID,
-    COL_NAME_PARAMETERS_TIME,
-    COL_NAME_PARAMETERS_CHANNEL,
+    META_DATA_EXPOSURE_ID,
+    META_DATA_PARAMETERS_TIME,
+    META_DATA_PARAMETERS_CHANNEL,
 )
 
 ExposureInfo = namedtuple("ExposureInfo", ["channel", "time"])
@@ -59,22 +59,22 @@ def get_measurement_params(folder):
 def _add_measurement_params(data_frame, params):
     """ adds measurement parameters to a data frame """
     for exposure_id, info in params.items():
-        mask = data_frame[COL_NAME_EXPOSURE_ID] == exposure_id
-        data_frame.loc[mask, COL_NAME_PARAMETERS_CHANNEL] = info.channel
-        data_frame.loc[mask, COL_NAME_PARAMETERS_TIME] = info.time
-    data_frame[COL_NAME_PARAMETERS_CHANNEL] = data_frame[
-        COL_NAME_PARAMETERS_CHANNEL
+        mask = data_frame[META_DATA_EXPOSURE_ID] == exposure_id
+        data_frame.loc[mask, META_DATA_PARAMETERS_CHANNEL] = info.channel
+        data_frame.loc[mask, META_DATA_PARAMETERS_TIME] = info.time
+    data_frame[META_DATA_PARAMETERS_CHANNEL] = data_frame[
+        META_DATA_PARAMETERS_CHANNEL
     ].astype("category")
     return data_frame
 
 
 def add_optional_measurement_parameters(data_frame, folder):
     """ adds measurement params to the data frame, if they could be parsed """
-    data_frame[COL_NAME_PARAMETERS_CHANNEL] = numpy.nan
-    data_frame[COL_NAME_PARAMETERS_TIME] = numpy.nan
+    data_frame[META_DATA_PARAMETERS_CHANNEL] = numpy.nan
+    data_frame[META_DATA_PARAMETERS_TIME] = numpy.nan
     params = get_measurement_params(folder)
     if params:
-        available_exposures = set(data_frame[COL_NAME_EXPOSURE_ID].unique())
+        available_exposures = set(data_frame[META_DATA_EXPOSURE_ID].unique())
         if available_exposures == set(params.keys()):
             return _add_measurement_params(data_frame, params)
     return data_frame

sensospot_data/parser.py

@@ -10,14 +10,12 @@ from collections import namedtuple
 import pandas
 
 from .columns import (
-    COL_NAME_POS_ID,
-    COL_NAME_WELL_ROW,
-    COL_NAME_SPOT_FOUND,
+    RAW_DATA_POS_ID,
+    META_DATA_WELL_ROW,
     RAW_DATA_COLUMN_SET,
-    COL_NAME_EXPOSURE_ID,
-    COL_NAME_WELL_COLUMN,
-    COL_NAME_SPOT_DIAMETER,
-    COLUMNS_RENAME_MAP
+    META_DATA_EXPOSURE_ID,
+    META_DATA_WELL_COLUMN,
+    RAW_DATA_COLUMNS_RENAME_MAP,
 )
 from .parameters import add_optional_measurement_parameters
 
@@ -29,12 +27,6 @@ REGEX_WELL = re.compile(
     re.VERBOSE | re.IGNORECASE,
 )
 
-COLUMNS_RENAME_MAP = {
-    " ID ": COL_NAME_POS_ID,
-    "Found": COL_NAME_SPOT_FOUND,
-    "Dia.": COL_NAME_SPOT_DIAMETER,
-}
-
 FileInfo = namedtuple("FileInfo", ["row", "column", "exposure"])
 
 
@@ -71,7 +63,7 @@ def _extract_measurement_info(data_file):
 
 def _cleanup_data_columns(data_frame):
     """ renames some data columns for consistency and drops unused columns """
-    renamed = data_frame.rename(columns=COLUMNS_RENAME_MAP)
+    renamed = data_frame.rename(columns=RAW_DATA_COLUMNS_RENAME_MAP)
     surplus_columns = set(renamed.columns) - RAW_DATA_COLUMN_SET
     return renamed.drop(columns=surplus_columns)
 
@@ -86,9 +78,9 @@ def parse_file(data_file, silent=False):
         else:
             raise e
     data_frame = _parse_csv(data_file)
-    data_frame[COL_NAME_WELL_ROW] = measurement_info.row
-    data_frame[COL_NAME_WELL_COLUMN] = measurement_info.column
-    data_frame[COL_NAME_EXPOSURE_ID] = measurement_info.exposure
+    data_frame[META_DATA_WELL_ROW] = measurement_info.row
+    data_frame[META_DATA_WELL_COLUMN] = measurement_info.column
+    data_frame[META_DATA_EXPOSURE_ID] = measurement_info.exposure
     return _cleanup_data_columns(data_frame)
 
 
@@ -101,7 +93,7 @@ def parse_multiple_files(file_list):
     data_frame = next(filtered)
     for next_frame in filtered:
         data_frame = data_frame.append(next_frame, ignore_index=True)
-    data_frame[COL_NAME_WELL_ROW] = data_frame[COL_NAME_WELL_ROW].astype(
+    data_frame[META_DATA_WELL_ROW] = data_frame[META_DATA_WELL_ROW].astype(
         "category"
     )
     return data_frame
@@ -117,10 +109,10 @@ def list_csv_files(folder):
 
 def _sanity_check(data_frame):
     """ checks some basic constrains of a combined data frame """
-    field_rows = len(data_frame[COL_NAME_WELL_ROW].unique())
-    field_cols = len(data_frame[COL_NAME_WELL_COLUMN].unique())
-    exposures = len(data_frame[COL_NAME_EXPOSURE_ID].unique())
-    spot_positions = len(data_frame[COL_NAME_POS_ID].unique())
+    field_rows = len(data_frame[META_DATA_WELL_ROW].unique())
+    field_cols = len(data_frame[META_DATA_WELL_COLUMN].unique())
+    exposures = len(data_frame[META_DATA_EXPOSURE_ID].unique())
+    spot_positions = len(data_frame[RAW_DATA_POS_ID].unique())
     expected_rows = field_rows * field_cols * exposures * spot_positions
     if expected_rows != len(data_frame):
         raise ValueError("Measurements are missing")
@@ -129,7 +121,7 @@ def _sanity_check(data_frame):
 
 def parse_folder(folder):
     """ parses all csv files in a folder to one large dataframe """
-    file = list_csv_files(Path(folder))
+    file_list = list_csv_files(Path(folder))
     data_frame = parse_multiple_files(file_list)
     data_frame = add_optional_measurement_parameters(data_frame, folder)
     return _sanity_check(data_frame)

tests/test_parameters.py

@@ -50,9 +50,9 @@ def test_parse_channel_info(example_dir):
 
 
 def test_get_measurement_params_file_found(example_dir):
-    from sensospot_data.parameters import _get_measurement_params
+    from sensospot_data.parameters import get_measurement_params
 
-    result = _get_measurement_params(example_dir / EXAMPLE_DIR_WITH_PARAMS)
+    result = get_measurement_params(example_dir / EXAMPLE_DIR_WITH_PARAMS)
 
     assert set(result.keys()) == {1, 2, 3}
     assert result[1] == ("green", 100)
@@ -61,9 +61,9 @@ def test_get_measurement_params_file_found(example_dir):
 
 
 def test_get_measurement_params_file_not_found(example_dir):
-    from sensospot_data.parameters import _get_measurement_params
+    from sensospot_data.parameters import get_measurement_params
 
-    result = _get_measurement_params(example_dir / EXAMPLE_DIR_WO_PARAMS)
+    result = get_measurement_params(example_dir / EXAMPLE_DIR_WO_PARAMS)
 
     assert result is None
 

tests/test_parser.py

@@ -163,7 +163,7 @@ def test_parse_file(example_file):
         "Spot.Sum",
         "Bkg.Area",
         "Spot.Area",
-        "Spot.Sat. (%)",
+        "Spot.Saturation",
         "Spot.Found",
         "Pos.Nom.X",
         "Pos.Nom.Y",
@@ -221,9 +221,9 @@ def testparse_multiple_files_empty_array(example_dir):
 
 
 def test_list_csv_files(example_dir):
-    from sensospot_data.parser import _list_csv_files
+    from sensospot_data.parser import list_csv_files
 
-    result = list(_list_csv_files(example_dir / EXAMPLE_DIR_WITH_PARAMS))
+    result = list(list_csv_files(example_dir / EXAMPLE_DIR_WITH_PARAMS))
 
     assert len(result) == 36 * 3
     assert all(str(item).endswith(".csv") for item in result)
@@ -274,82 +274,3 @@ def test_sanity_check_raises_value_error(example_dir):
 
     with pytest.raises(ValueError):
         _sanity_check(data_frame)
-
-
-def test_get_cache_table_name():
-    from sensospot_data import VERSION_TABLE_NAME
-    from sensospot_data.parser import _get_cache_table_name
-
-    result = _get_cache_table_name()
-
-    assert result == VERSION_TABLE_NAME
-
-
-def test_process_folder_creates_cache(dir_for_caching):
-    from sensospot_data.parser import CACHE_FILE_NAME, process_folder
-
-    cache_path = dir_for_caching / CACHE_FILE_NAME
-    assert not cache_path.is_file()
-
-    result = process_folder(dir_for_caching)
-
-    assert len(result) == 100
-    assert cache_path.is_file()
-
-
-def test_process_folder_reads_from_cache(dir_for_caching, example_file):
-    from sensospot_data.parser import process_folder
-
-    process_folder(dir_for_caching)
-
-    csv_file = dir_for_caching / example_file.name
-    csv_file.unlink()
-
-    result = process_folder(dir_for_caching)
-    assert len(result) == 100
-
-
-def test_process_folder_read_cache_fails_silently(
-    dir_for_caching, exposure_df
-):
-    from sensospot_data.parser import CACHE_FILE_NAME, process_folder
-
-    cache_path = dir_for_caching / CACHE_FILE_NAME
-    exposure_df.to_hdf(cache_path, "unknown table")
-
-    result = process_folder(dir_for_caching)
-
-    assert result["Well.Row"][0] == "A"
-
-
-def test_process_folder_read_cache_no_cache_arg(dir_for_caching, exposure_df):
-    from sensospot_data.parser import (
-        CACHE_FILE_NAME,
-        process_folder,
-        _get_cache_table_name,
-    )
-
-    cache_path = dir_for_caching / CACHE_FILE_NAME
-    exposure_df.to_hdf(cache_path, _get_cache_table_name())
-
-    result = process_folder(dir_for_caching, use_cache=False)
-
-    assert result["Well.Row"][0] == "A"
-
-
-def test_process_folder_writes_cache(dir_for_caching):
-    from sensospot_data.parser import CACHE_FILE_NAME, process_folder
-
-    process_folder(dir_for_caching, use_cache=True)
-
-    cache_path = dir_for_caching / CACHE_FILE_NAME
-    assert cache_path.is_file()
-
-
-def test_process_folder_writes_cache_no_cache_arg(dir_for_caching):
-    from sensospot_data.parser import CACHE_FILE_NAME, process_folder
-
-    process_folder(dir_for_caching, use_cache=False)
-
-    cache_path = dir_for_caching / CACHE_FILE_NAME
-    assert not cache_path.is_file()

tests/test_sensovation_data_parser.py

@@ -2,11 +2,8 @@
 
 
 def test_import_api():
-    from sensospot_data import CACHE_FILE_NAME  # noqa: F401
     from sensospot_data import ExposureInfo  # noqa: F401
+    from sensospot_data import run  # noqa: F401
     from sensospot_data import parse_file  # noqa: F401
     from sensospot_data import parse_folder  # noqa: F401
-    from sensospot_data import process_folder  # noqa: F401
-    from sensospot_data import split_channels  # noqa: F401
-    from sensospot_data import normalize_channel  # noqa: F401
-    from sensospot_data import parse_multiple_files  # noqa: F401
+    from sensospot_data import get_measurement_params  # noqa: F401