renamed project

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
     hooks:
     -   id: isort-project
         name: isort_project
-        entry: isort -rc sensovation_data_parser
+        entry: isort -rc sensospot_data
         language: system
         pass_filenames: false
     -   id: isort-test
@@ -22,12 +22,12 @@ repos:
         pass_filenames: false
     -   id: black
         name: black
-        entry: black sensovation_data_parser tests
+        entry: black sensospot_data tests
         language: system
         pass_filenames: false
     -   id: flake8
         name: flake8
-        entry: flake8 --ignore E231 sensovation_data_parser tests
+        entry: flake8 --ignore E231 sensospot_data tests
         language: system
         pass_filenames: false
     -   id: pytest

Makefile

@@ -51,16 +51,16 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr htmlcov/
 
 lint: ## reformat with black and check style with flake8
-	isort -rc sensovation_data_parser
+	isort -rc sensospot_data
 	isort -rc tests
-	black sensovation_data_parser tests
+	black sensospot_data tests
-	flake8 --ignore E231 sensovation_data_parser tests
+	flake8 --ignore E231 sensospot_data tests
 
 test: ## run tests quickly with the default Python
 	pytest tests -x --disable-warnings -k "not app"
 
 coverage: ## full test suite, check code coverage and open coverage report
-	pytest tests --cov=sensovation_data_parser
+	pytest tests --cov=sensospot_data
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
@@ -71,7 +71,7 @@ install:  ## install updated project.toml with flint
 	flit install --pth-file
 
 devenv: ## setup development environment
-	python3 -m venv --prompt sensovation .venv
+	python3 -m venv --prompt sensospot .venv
 	.venv/bin/pip3 install --upgrade pip
 	.venv/bin/pip3 install flit
 	.venv/bin/flit install --pth-file
@@ -80,7 +80,7 @@ repo: devenv ## complete project setup with development environment and git repo
 	git init .
 	git add .
 	git commit -m "import of project template"
-	git remote add origin https://git.cpi.imtek.uni-freiburg.de/holgi/sensovation-data-parser.git
+	git remote add origin https://git.cpi.imtek.uni-freiburg.de/holgi/sensospot_data.git
 	git push -u origin master --no-verify
 
 	.venv/bin/pre-commit install --install-hooks

pyproject.toml

@@ -3,11 +3,11 @@ requires = ["flit"]
 build-backend = "flit.buildapi"
 
 [tool.flit.metadata]
-module = "sensovation_data_parser"
+module = "sensospot_data"
-dist-name = "sensovation_data_parser"
+dist-name = "sensospot_data"
 author = "Holger Frey"
 author-email = "frey@imtek.de"
-home-page = "https://github.com/holgi/sensovation_data_parser"
+home-page = "https://git.cpi.imtek.uni-freiburg.de/holgi/sensospot_data.git"
 description-file = "README.md"
 license = "Beerware"
 

tests/test_parser.py

@@ -52,7 +52,7 @@ def dir_for_caching(tmpdir, example_file):
     ],
 )
 def test_parse_csv(example_dir, sub_dir, file_name):
-    from sensovation_data_parser.parser import _parse_csv
+    from sensospot_data.parser import _parse_csv
 
     result = _parse_csv(example_dir / sub_dir / file_name)
 
@@ -87,7 +87,7 @@ def test_parse_csv(example_dir, sub_dir, file_name):
 
 
 def test_parse_csv_no_array(example_dir):
-    from sensovation_data_parser.parser import _parse_csv
+    from sensospot_data.parser import _parse_csv
 
     result = _parse_csv(example_dir / "no_array_A1_1.csv")
 
@@ -99,7 +99,7 @@ def test_parse_csv_no_array(example_dir):
     "input, expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", "."),]
 )
 def test_guess_decimal_separator_returns_correct_separator(input, expected):
-    from sensovation_data_parser.parser import _guess_decimal_separator
+    from sensospot_data.parser import _guess_decimal_separator
     from io import StringIO
 
     handle = StringIO(f"header\n{input}\n")
@@ -109,7 +109,7 @@ def test_guess_decimal_separator_returns_correct_separator(input, expected):
 
 
 def test_guess_decimal_separator_rewinds_handle():
-    from sensovation_data_parser.parser import _guess_decimal_separator
+    from sensospot_data.parser import _guess_decimal_separator
     from io import StringIO
 
     handle = StringIO(f"header\n{input}\n")
@@ -119,7 +119,7 @@ def test_guess_decimal_separator_rewinds_handle():
 
 
 def test_well_regex_ok():
-    from sensovation_data_parser.parser import REGEX_WELL
+    from sensospot_data.parser import REGEX_WELL
 
     result = REGEX_WELL.match("AbC123")
 
@@ -129,7 +129,7 @@ def test_well_regex_ok():
 
 @pytest.mark.parametrize("input", ["", "A", "1", "1A", "-1", "A-"])
 def test_well_regex_no_match(input):
-    from sensovation_data_parser.parser import REGEX_WELL
+    from sensospot_data.parser import REGEX_WELL
 
     result = REGEX_WELL.match(input)
 
@@ -141,7 +141,7 @@ def test_well_regex_no_match(input):
     [("A1_1.csv", ("A", 1, 1)), ("test/measurement_1_H12_2", ("H", 12, 2)),],
 )
 def test_extract_measurement_info_ok(filename, expected):
-    from sensovation_data_parser.parser import _extract_measurement_info
+    from sensospot_data.parser import _extract_measurement_info
 
     result = _extract_measurement_info(filename)
 
@@ -150,14 +150,14 @@ def test_extract_measurement_info_ok(filename, expected):
 
 @pytest.mark.parametrize("filename", ["wrong_exposure_A1_B", "no_well_XX_1"])
 def test_extract_measurement_info_raises_error(filename):
-    from sensovation_data_parser.parser import _extract_measurement_info
+    from sensospot_data.parser import _extract_measurement_info
 
     with pytest.raises(ValueError):
         _extract_measurement_info(filename)
 
 
 def test_cleanup_data_columns():
-    from sensovation_data_parser.parser import _cleanup_data_columns
+    from sensospot_data.parser import _cleanup_data_columns
     from pandas import DataFrame
 
     columns = ["Rect.", "Contour", " ID ", "Found", "Dia."]
@@ -173,7 +173,7 @@ def test_cleanup_data_columns():
 
 
 def test_parse_file(example_file):
-    from sensovation_data_parser.parser import parse_file
+    from sensospot_data.parser import parse_file
 
     result = parse_file(example_file)
 
@@ -218,7 +218,7 @@ def test_parse_file(example_file):
     ],
 )
 def testparse_multiple_files_ok(example_dir, file_list):
-    from sensovation_data_parser.parser import parse_multiple_files
+    from sensospot_data.parser import parse_multiple_files
 
     sub_dir = example_dir / EXAMPLE_DIR_WO_PARAMS
     files = [sub_dir / file for file in file_list]
@@ -231,14 +231,14 @@ def testparse_multiple_files_ok(example_dir, file_list):
 
 
 def testparse_multiple_files_empty_file_list():
-    from sensovation_data_parser.parser import parse_multiple_files
+    from sensospot_data.parser import parse_multiple_files
 
     with pytest.raises(ValueError):
         parse_multiple_files([])
 
 
 def testparse_multiple_files_empty_array(example_dir):
-    from sensovation_data_parser.parser import parse_multiple_files
+    from sensospot_data.parser import parse_multiple_files
 
     files = [example_dir / "no_array_A1_1.csv"]
 
@@ -249,7 +249,7 @@ def testparse_multiple_files_empty_array(example_dir):
 
 
 def test_list_csv_files(example_dir):
-    from sensovation_data_parser.parser import _list_csv_files
+    from sensospot_data.parser import _list_csv_files
 
     result = list(_list_csv_files(example_dir / EXAMPLE_DIR_WITH_PARAMS))
 
@@ -259,7 +259,7 @@ def test_list_csv_files(example_dir):
 
 
 def test_parse_folder(example_dir):
-    from sensovation_data_parser.parser import parse_folder
+    from sensospot_data.parser import parse_folder
 
     data_frame = parse_folder(example_dir / EXAMPLE_DIR_WITH_PARAMS)
 
@@ -271,7 +271,7 @@ def test_parse_folder(example_dir):
 
 
 def test_sanity_check_ok(example_dir):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         _sanity_check,
         parse_multiple_files,
     )
@@ -290,7 +290,7 @@ def test_sanity_check_ok(example_dir):
 
 
 def test_sanity_check_raises_value_error(example_dir):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         _sanity_check,
         parse_multiple_files,
     )
@@ -309,7 +309,7 @@ def test_sanity_check_raises_value_error(example_dir):
 
 
 def test_search_channel_info_file_ok(example_dir):
-    from sensovation_data_parser.parser import _search_channel_info_file
+    from sensospot_data.parser import _search_channel_info_file
 
     result = _search_channel_info_file(example_dir / EXAMPLE_DIR_WITH_PARAMS)
 
@@ -317,7 +317,7 @@ def test_search_channel_info_file_ok(example_dir):
 
 
 def test_search_channel_info_file_no_parameters_folder(example_dir):
-    from sensovation_data_parser.parser import _search_channel_info_file
+    from sensospot_data.parser import _search_channel_info_file
 
     result = _search_channel_info_file(example_dir / EXAMPLE_DIR_WO_PARAMS)
 
@@ -325,7 +325,7 @@ def test_search_channel_info_file_no_parameters_folder(example_dir):
 
 
 def test_search_channel_info_file_no_parameters_file(tmpdir):
-    from sensovation_data_parser.parser import _search_channel_info_file
+    from sensospot_data.parser import _search_channel_info_file
 
     params_dir = tmpdir / "Parameters"
     params_dir.mkdir()
@@ -336,7 +336,7 @@ def test_search_channel_info_file_no_parameters_file(tmpdir):
 
 
 def test_parse_channel_info(example_dir):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         _search_channel_info_file,
         _parse_channel_info,
     )
@@ -351,7 +351,7 @@ def test_parse_channel_info(example_dir):
 
 
 def test_get_valid_exposure_map_provided_ok(exposure_df):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         _get_valid_exposure_map,
         ExposureInfo,
     )
@@ -367,7 +367,7 @@ def test_get_valid_exposure_map_provided_ok(exposure_df):
 
 
 def test_get_valid_exposure_map_provided_not_ok(exposure_df):
-    from sensovation_data_parser.parser import _get_valid_exposure_map
+    from sensospot_data.parser import _get_valid_exposure_map
 
     exposure_map = {1: None, 2: None}
 
@@ -380,7 +380,7 @@ def test_get_valid_exposure_map_provided_not_ok(exposure_df):
 
 
 def test_get_valid_exposure_map_info_from_file_ok(example_dir, exposure_df):
-    from sensovation_data_parser.parser import _get_valid_exposure_map
+    from sensospot_data.parser import _get_valid_exposure_map
 
     result = _get_valid_exposure_map(
         example_dir / EXAMPLE_DIR_WITH_PARAMS, exposure_df, exposure_map=None
@@ -395,7 +395,7 @@ def test_get_valid_exposure_map_info_from_file_ok(example_dir, exposure_df):
 def test_get_valid_exposure_map_info_from_file_not_ok(
     example_dir, exposure_df
 ):
-    from sensovation_data_parser.parser import _get_valid_exposure_map
+    from sensospot_data.parser import _get_valid_exposure_map
 
     data_frame = exposure_df.drop(exposure_df.index[1])
 
@@ -408,7 +408,7 @@ def test_get_valid_exposure_map_info_from_file_not_ok(
 
 
 def test_augment_exposure_map(exposure_df):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         _augment_exposure_map,
         ExposureInfo,
     )
@@ -433,7 +433,7 @@ def test_augment_exposure_map(exposure_df):
 
 
 def test_process_folder_with_exposure_map(example_dir):
-    from sensovation_data_parser.parser import _process_folder
+    from sensospot_data.parser import _process_folder
 
     result = _process_folder(example_dir / EXAMPLE_DIR_WITH_PARAMS)
 
@@ -448,7 +448,7 @@ def test_process_folder_with_exposure_map(example_dir):
 
 
 def test_process_folder_without_exposure_map(example_dir):
-    from sensovation_data_parser.parser import _process_folder
+    from sensospot_data.parser import _process_folder
     from pandas import isnull
 
     result = _process_folder(example_dir / EXAMPLE_DIR_WO_PARAMS)
@@ -464,7 +464,7 @@ def test_process_folder_without_exposure_map(example_dir):
 
 
 def test_process_folder_creates_cache(dir_for_caching):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         process_folder,
         CACHE_FILE_NAME,
     )
@@ -479,7 +479,7 @@ def test_process_folder_creates_cache(dir_for_caching):
 
 
 def test_process_folder_reads_from_cache(dir_for_caching, example_file):
-    from sensovation_data_parser.parser import process_folder
+    from sensospot_data.parser import process_folder
 
     process_folder(dir_for_caching)
 
@@ -493,7 +493,7 @@ 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 sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         process_folder,
         CACHE_FILE_NAME,
     )
@@ -507,8 +507,8 @@ def test_process_folder_read_cache_fails_silently(
 
 
 def test_get_cache_table_name():
-    from sensovation_data_parser.parser import _get_cache_table_name
+    from sensospot_data.parser import _get_cache_table_name
-    from sensovation_data_parser import __version__
+    from sensospot_data import __version__
 
     result = _get_cache_table_name()
 
@@ -517,7 +517,7 @@ def test_get_cache_table_name():
 
 
 def test_process_folder_read_cache_no_cache_arg(dir_for_caching, exposure_df):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         process_folder,
         _get_cache_table_name,
         CACHE_FILE_NAME,
@@ -532,7 +532,7 @@ def test_process_folder_read_cache_no_cache_arg(dir_for_caching, exposure_df):
 
 
 def test_process_folder_writes_cache(dir_for_caching):
-    from sensovation_data_parser.parser import (
+    from sensospot_data.parser import (
         process_folder,
         CACHE_FILE_NAME,
     )
@@ -544,7 +544,7 @@ def test_process_folder_writes_cache(dir_for_caching):
 
 
 def test_process_folder_writes_cache_no_cache_arg(dir_for_caching):
-    from sensovation_data_parser.parser import process_folder, CACHE_FILE_NAME
+    from sensospot_data.parser import process_folder, CACHE_FILE_NAME
 
     process_folder(dir_for_caching, use_cache=False)
 

tests/test_sensovation_data_parser.py

@@ -2,8 +2,8 @@
 
 
 def test_import_api():
-    from sensovation_data_parser import ExposureInfo  # noqa: F401
+    from sensospot_data import ExposureInfo  # noqa: F401
-    from sensovation_data_parser import parse_file  # noqa: F401
+    from sensospot_data import parse_file  # noqa: F401
-    from sensovation_data_parser import parse_multiple_files  # noqa: F401
+    from sensospot_data import parse_multiple_files  # noqa: F401
-    from sensovation_data_parser import parse_folder  # noqa: F401
+    from sensospot_data import parse_folder  # noqa: F401
-    from sensovation_data_parser import process_folder  # noqa: F401
+    from sensospot_data import process_folder  # noqa: F401