linted

Makefile

@@ -51,10 +51,10 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr htmlcov/
 
 lint: ## reformat with black and check style with flake8
-	isort -rc sensospot_data
-	isort -rc tests
+	isort sensospot_data
+	isort tests
 	black sensospot_data tests
-	flake8 --ignore E231,W503 sensospot_data tests
+	flake8 --ignore E231,W503,E402 sensospot_data tests
 
 test: ## run tests quickly with the default Python
 	pytest tests -x --disable-warnings

sensospot_data/normalisation.py

@@ -24,7 +24,7 @@ def _split_data_frame(data_frame, column):
 
 
 def _infer_exposure_from_parameters(data_frame):
-    """ infer the exposures from measurement parameters
+    """infer the exposures from measurement parameters
 
     will raise a ValueError if the parameters contain NaNs
     """
@@ -42,7 +42,7 @@ def _infer_exposure_from_parameters(data_frame):
 
 
 def apply_exposure_map(data_frame, exposure_map=None):
-    """ applies the parameters of a exposure map to the data frame
+    """applies the parameters of a exposure map to the data frame
 
     exposure map:
         keys: must be the same as the exposure ids,
@@ -124,7 +124,7 @@ def _infer_normalization_map(split_data_frames):
 
 
 def normalize_exposure_time(split_data_frames):
-    """ add time normalized values to the split data frames
+    """add time normalized values to the split data frames
 
     The max exposure time per channel is used for normalization.
     """
@@ -153,7 +153,7 @@ def normalize_measurement(
     overflow_column=COL_NAME_SPOT_MEAN,
     overflow_limit=0.5,
 ):
-    """ augment normalize the measurement exposures
+    """augment normalize the measurement exposures
 
     exposure map:
         keys: must be the same as the exposure ids,

tests/test_normailsation.py

@@ -127,8 +127,8 @@ def test_check_overflow_limit_custom_limit():
 
 def test_reduce_overflow_in_channel(normalization_data_frame):
     from sensospot_data.normalisation import (
-        _reduce_overflow_in_channel,
         _check_overflow_limit,
+        _reduce_overflow_in_channel,
     )
 
     data_frame = _check_overflow_limit(
@@ -158,8 +158,8 @@ def test_reduce_overflow_in_channel(normalization_data_frame):
 
 def test_reduce_overflow_in_channel_shortcut(normalization_data_frame):
     from sensospot_data.normalisation import (
-        _reduce_overflow_in_channel,
         _check_overflow_limit,
+        _reduce_overflow_in_channel,
     )
 
     normalization_data_frame["Exposure.Time"] = 1
@@ -201,8 +201,8 @@ def test_reduce_overflow(normalization_data_frame):
 
 def test_infer_normalization_map(normalization_data_frame):
     from sensospot_data.normalisation import (
-        _infer_normalization_map,
         _split_data_frame,
+        _infer_normalization_map,
     )
 
     normalization_data_frame.loc[5, "Exposure.Channel"] = "Cy3"
@@ -216,11 +216,11 @@ def test_infer_normalization_map(normalization_data_frame):
 
 
 def test_normalize_exposure(normalization_data_frame):
+    from sensospot_data.columns import COLUMN_NORMALIZATION
     from sensospot_data.normalisation import (
-        _normalize_exposure,
         reduce_overflow,
+        _normalize_exposure,
     )
-    from sensospot_data.columns import COLUMN_NORMALIZATION
 
     reduced = reduce_overflow(normalization_data_frame, "Saturation", 1)
     result = _normalize_exposure(reduced["Cy5"], 100)
@@ -236,8 +236,8 @@ def test_normalize_exposure(normalization_data_frame):
 
 def test_normalize_exposure_time(normalization_data_frame):
     from sensospot_data.normalisation import (
-        normalize_exposure_time,
         reduce_overflow,
+        normalize_exposure_time,
     )
 
     reduced = reduce_overflow(normalization_data_frame, "Saturation", 1)
@@ -255,8 +255,8 @@ def test_normalize_exposure_time(normalization_data_frame):
 
 def test_normalize_exposure_time_infered_map(normalization_data_frame):
     from sensospot_data.normalisation import (
-        normalize_exposure_time,
         reduce_overflow,
+        normalize_exposure_time,
     )
 
     reduced = reduce_overflow(normalization_data_frame, "Saturation", 1)
@@ -273,8 +273,8 @@ def test_normalize_exposure_time_infered_map(normalization_data_frame):
 
 
 def test_normalize_measurement(example_dir):
-    from sensospot_data.normalisation import normalize_measurement
     from sensospot_data.parser import process_folder
+    from sensospot_data.normalisation import normalize_measurement
 
     sub_dir = example_dir / EXAMPLE_DIR_WITH_PARAMS
     data_frame = process_folder(sub_dir)

tests/test_parameters.py

@@ -34,8 +34,8 @@ def test_ssearch_measurement_params_file_parameters_file(tmpdir):
 
 def test_parse_channel_info(example_dir):
     from sensospot_data.parameters import (
-        _search_measurement_params_file,
         _parse_measurement_params,
+        _search_measurement_params_file,
     )
 
     params = _search_measurement_params_file(
@@ -70,8 +70,8 @@ def test_get_measurement_params_file_not_found(example_dir):
 
 def test_add_measurement_params(exposure_df):
     from sensospot_data.parameters import (
-        _add_measurement_params,
         MeasurementParams,
+        _add_measurement_params,
     )
 
     params = {

tests/test_parser.py

@@ -68,9 +68,10 @@ def test_parse_csv_no_array(example_dir):
     "input, expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")]
 )
 def test_guess_decimal_separator_returns_correct_separator(input, expected):
-    from sensospot_data.parser import _guess_decimal_separator
     from io import StringIO
 
+    from sensospot_data.parser import _guess_decimal_separator
+
     handle = StringIO(f"header\n{input}\n")
     result = _guess_decimal_separator(handle)
 
@@ -78,9 +79,10 @@ def test_guess_decimal_separator_returns_correct_separator(input, expected):
 
 
 def test_guess_decimal_separator_rewinds_handle():
-    from sensospot_data.parser import _guess_decimal_separator
     from io import StringIO
 
+    from sensospot_data.parser import _guess_decimal_separator
+
     handle = StringIO("\n".join(["header", "data_line"]))
     _guess_decimal_separator(handle)
 
@@ -126,9 +128,10 @@ def test_extract_measurement_info_raises_error(filename):
 
 
 def test_cleanup_data_columns():
-    from sensospot_data.parser import _cleanup_data_columns
     from pandas import DataFrame
 
+    from sensospot_data.parser import _cleanup_data_columns
+
     columns = ["Rect.", "Contour", " ID ", "Found", "Dia."]
     data = {col: [i] for i, col in enumerate(columns)}
     data_frame = DataFrame(data=data)
@@ -274,8 +277,8 @@ def test_sanity_check_raises_value_error(example_dir):
 
 
 def test_get_cache_table_name():
-    from sensospot_data.parser import _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()
 
@@ -283,7 +286,7 @@ def test_get_cache_table_name():
 
 
 def test_process_folder_creates_cache(dir_for_caching):
-    from sensospot_data.parser import process_folder, CACHE_FILE_NAME
+    from sensospot_data.parser import CACHE_FILE_NAME, process_folder
 
     cache_path = dir_for_caching / CACHE_FILE_NAME
     assert not cache_path.is_file()
@@ -309,7 +312,7 @@ def test_process_folder_reads_from_cache(dir_for_caching, example_file):
 def test_process_folder_read_cache_fails_silently(
     dir_for_caching, exposure_df
 ):
-    from sensospot_data.parser import process_folder, CACHE_FILE_NAME
+    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")
@@ -321,9 +324,9 @@ def test_process_folder_read_cache_fails_silently(
 
 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_FILE_NAME,
     )
 
     cache_path = dir_for_caching / CACHE_FILE_NAME
@@ -335,7 +338,7 @@ def test_process_folder_read_cache_no_cache_arg(dir_for_caching, exposure_df):
 
 
 def test_process_folder_writes_cache(dir_for_caching):
-    from sensospot_data.parser import process_folder, CACHE_FILE_NAME
+    from sensospot_data.parser import CACHE_FILE_NAME, process_folder
 
     process_folder(dir_for_caching, use_cache=True)
 
@@ -344,7 +347,7 @@ def test_process_folder_writes_cache(dir_for_caching):
 
 
 def test_process_folder_writes_cache_no_cache_arg(dir_for_caching):
-    from sensospot_data.parser import process_folder, CACHE_FILE_NAME
+    from sensospot_data.parser import CACHE_FILE_NAME, process_folder
 
     process_folder(dir_for_caching, use_cache=False)
 

tests/test_sensovation_data_parser.py

@@ -5,6 +5,6 @@ def test_import_api():
     from sensospot_data import CACHE_FILE_NAME  # noqa: F401
     from sensospot_data import parse_file  # noqa: F401
     from sensospot_data import parse_folder  # noqa: F401
-    from sensospot_data import parse_multiple_files  # noqa: F401
     from sensospot_data import process_folder  # noqa: F401
+    from sensospot_data import parse_multiple_files  # noqa: F401
     from sensospot_data import normalize_measurement  # noqa: F401