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Reformatted test scripts with black 23.12.1

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This commit is contained in:
Chris Kerr
2024-01-20 21:57:31 +02:00
parent 239db97c69
commit 1cd5bd6239
3 changed files with 140 additions and 96 deletions
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4
tests/conftest.py
View File

@@ -9,7 +9,7 @@ import os
import pytest import pytest
@pytest.fixture(scope='session') @pytest.fixture(scope="session")
def testdata_dir(): def testdata_dir():
"""Path to the testdata directory.""" """Path to the testdata directory."""
return os.path.join(os.path.dirname(__file__), 'testdata') return os.path.join(os.path.dirname(__file__), "testdata")

43
tests/test_Arbin.py
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@@ -13,8 +13,7 @@ import pytest
from galvani import res2sqlite from galvani import res2sqlite
have_mdbtools = (subprocess.call(['which', 'mdb-export'], have_mdbtools = subprocess.call(["which", "mdb-export"], stdout=subprocess.DEVNULL) == 0
stdout=subprocess.DEVNULL) == 0)
def test_res2sqlite_help(): def test_res2sqlite_help():
@@ -22,39 +21,47 @@ def test_res2sqlite_help():
This should work even when mdbtools is not installed. This should work even when mdbtools is not installed.
""" """
help_output = subprocess.check_output(['res2sqlite', '--help']) help_output = subprocess.check_output(["res2sqlite", "--help"])
assert b'Convert Arbin .res files to sqlite3 databases' in help_output assert b"Convert Arbin .res files to sqlite3 databases" in help_output
@pytest.mark.skipif(have_mdbtools, reason='This tests the failure when mdbtools is not installed') @pytest.mark.skipif(
have_mdbtools, reason="This tests the failure when mdbtools is not installed"
)
def test_convert_Arbin_no_mdbtools(testdata_dir, tmpdir): def test_convert_Arbin_no_mdbtools(testdata_dir, tmpdir):
"""Checks that the conversion fails with an appropriate error message.""" """Checks that the conversion fails with an appropriate error message."""
res_file = os.path.join(testdata_dir, 'arbin1.res') res_file = os.path.join(testdata_dir, "arbin1.res")
sqlite_file = os.path.join(str(tmpdir), 'arbin1.s3db') sqlite_file = os.path.join(str(tmpdir), "arbin1.s3db")
with pytest.raises(RuntimeError, match="Could not locate the `mdb-export` executable."): with pytest.raises(
RuntimeError, match="Could not locate the `mdb-export` executable."
):
res2sqlite.convert_arbin_to_sqlite(res_file, sqlite_file) res2sqlite.convert_arbin_to_sqlite(res_file, sqlite_file)
@pytest.mark.skipif(not have_mdbtools, reason='Reading the Arbin file requires MDBTools') @pytest.mark.skipif(
@pytest.mark.parametrize('basename', ['arbin1', 'UM34_Test005E']) not have_mdbtools, reason="Reading the Arbin file requires MDBTools"
)
@pytest.mark.parametrize("basename", ["arbin1", "UM34_Test005E"])
def test_convert_Arbin_to_sqlite_function(testdata_dir, tmpdir, basename): def test_convert_Arbin_to_sqlite_function(testdata_dir, tmpdir, basename):
"""Convert an Arbin file to SQLite using the functional interface.""" """Convert an Arbin file to SQLite using the functional interface."""
res_file = os.path.join(testdata_dir, basename + '.res') res_file = os.path.join(testdata_dir, basename + ".res")
sqlite_file = os.path.join(str(tmpdir), basename + '.s3db') sqlite_file = os.path.join(str(tmpdir), basename + ".s3db")
res2sqlite.convert_arbin_to_sqlite(res_file, sqlite_file) res2sqlite.convert_arbin_to_sqlite(res_file, sqlite_file)
assert os.path.isfile(sqlite_file) assert os.path.isfile(sqlite_file)
with sqlite3.connect(sqlite_file) as conn: with sqlite3.connect(sqlite_file) as conn:
csr = conn.execute('SELECT * FROM Channel_Normal_Table;') csr = conn.execute("SELECT * FROM Channel_Normal_Table;")
csr.fetchone() csr.fetchone()
@pytest.mark.skipif(not have_mdbtools, reason='Reading the Arbin file requires MDBTools') @pytest.mark.skipif(
not have_mdbtools, reason="Reading the Arbin file requires MDBTools"
)
def test_convert_cmdline(testdata_dir, tmpdir): def test_convert_cmdline(testdata_dir, tmpdir):
"""Checks that the conversion fails with an appropriate error message.""" """Checks that the conversion fails with an appropriate error message."""
res_file = os.path.join(testdata_dir, 'arbin1.res') res_file = os.path.join(testdata_dir, "arbin1.res")
sqlite_file = os.path.join(str(tmpdir), 'arbin1.s3db') sqlite_file = os.path.join(str(tmpdir), "arbin1.s3db")
subprocess.check_call(['res2sqlite', res_file, sqlite_file]) subprocess.check_call(["res2sqlite", res_file, sqlite_file])
assert os.path.isfile(sqlite_file) assert os.path.isfile(sqlite_file)
with sqlite3.connect(sqlite_file) as conn: with sqlite3.connect(sqlite_file) as conn:
csr = conn.execute('SELECT * FROM Channel_Normal_Table;') csr = conn.execute("SELECT * FROM Channel_Normal_Table;")
csr.fetchone() csr.fetchone()

189
tests/test_BioLogic.py
View File

@@ -17,33 +17,55 @@ from galvani.BioLogic import MPTfileCSV # not exported
def test_open_MPT(testdata_dir): def test_open_MPT(testdata_dir):
mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt')) mpt1, comments = MPTfile(os.path.join(testdata_dir, "bio_logic1.mpt"))
assert comments == [] assert comments == []
assert mpt1.dtype.names == ( assert mpt1.dtype.names == (
"mode", "ox/red", "error", "control changes", "Ns changes", "mode",
"counter inc.", "time/s", "control/V/mA", "Ewe/V", "dQ/mA.h", "P/W", "ox/red",
"I/mA", "(Q-Qo)/mA.h", "x", "error",
"control changes",
"Ns changes",
"counter inc.",
"time/s",
"control/V/mA",
"Ewe/V",
"dQ/mA.h",
"P/W",
"I/mA",
"(Q-Qo)/mA.h",
"x",
) )
def test_open_MPT_fails_for_bad_file(testdata_dir): def test_open_MPT_fails_for_bad_file(testdata_dir):
with pytest.raises(ValueError, match='Bad first line'): with pytest.raises(ValueError, match="Bad first line"):
MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpr')) MPTfile(os.path.join(testdata_dir, "bio_logic1.mpr"))
def test_open_MPT_csv(testdata_dir): def test_open_MPT_csv(testdata_dir):
mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpt')) mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, "bio_logic1.mpt"))
assert comments == [] assert comments == []
assert mpt1.fieldnames == [ assert mpt1.fieldnames == [
"mode", "ox/red", "error", "control changes", "Ns changes", "mode",
"counter inc.", "time/s", "control/V/mA", "Ewe/V", "dq/mA.h", "P/W", "ox/red",
"<I>/mA", "(Q-Qo)/mA.h", "x", "error",
"control changes",
"Ns changes",
"counter inc.",
"time/s",
"control/V/mA",
"Ewe/V",
"dq/mA.h",
"P/W",
"<I>/mA",
"(Q-Qo)/mA.h",
"x",
] ]
def test_open_MPT_csv_fails_for_bad_file(testdata_dir): def test_open_MPT_csv_fails_for_bad_file(testdata_dir):
with pytest.raises((ValueError, UnicodeDecodeError)): with pytest.raises((ValueError, UnicodeDecodeError)):
MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpr')) MPTfileCSV(os.path.join(testdata_dir, "bio_logic1.mpr"))
def test_colID_map_uniqueness(): def test_colID_map_uniqueness():
@@ -59,13 +81,16 @@ def test_colID_map_uniqueness():
assert not set(field_names).intersection(flag_names) assert not set(field_names).intersection(flag_names)
@pytest.mark.parametrize('colIDs, expected', [ @pytest.mark.parametrize(
([1, 2, 3], [('flags', 'u1')]), "colIDs, expected",
([4, 6], [('time/s', '<f8'), ('Ewe/V', '<f4')]), [
([1, 4, 21], [('flags', 'u1'), ('time/s', '<f8')]), ([1, 2, 3], [("flags", "u1")]),
([4, 6, 4], [('time/s', '<f8'), ('Ewe/V', '<f4'), ('time/s 2', '<f8')]), ([4, 6], [("time/s", "<f8"), ("Ewe/V", "<f4")]),
([4, 9999], NotImplementedError), ([1, 4, 21], [("flags", "u1"), ("time/s", "<f8")]),
]) ([4, 6, 4], [("time/s", "<f8"), ("Ewe/V", "<f4"), ("time/s 2", "<f8")]),
([4, 9999], NotImplementedError),
],
)
def test_colID_to_dtype(colIDs, expected): def test_colID_to_dtype(colIDs, expected):
"""Test converting column ID to numpy dtype.""" """Test converting column ID to numpy dtype."""
if isinstance(expected, type) and issubclass(expected, Exception): if isinstance(expected, type) and issubclass(expected, Exception):
@@ -77,14 +102,17 @@ def test_colID_to_dtype(colIDs, expected):
assert dtype == expected_dtype assert dtype == expected_dtype
@pytest.mark.parametrize('data, expected', [ @pytest.mark.parametrize(
('02/23/17', date(2017, 2, 23)), "data, expected",
('10-03-05', date(2005, 10, 3)), [
('11.12.20', date(2020, 11, 12)), ("02/23/17", date(2017, 2, 23)),
(b'01/02/03', date(2003, 1, 2)), ("10-03-05", date(2005, 10, 3)),
('13.08.07', ValueError), ("11.12.20", date(2020, 11, 12)),
('03-04/05', ValueError), (b"01/02/03", date(2003, 1, 2)),
]) ("13.08.07", ValueError),
("03-04/05", ValueError),
],
)
def test_parse_BioLogic_date(data, expected): def test_parse_BioLogic_date(data, expected):
"""Test the parse_BioLogic_date function.""" """Test the parse_BioLogic_date function."""
if isinstance(expected, type) and issubclass(expected, Exception): if isinstance(expected, type) and issubclass(expected, Exception):
@@ -95,51 +123,54 @@ def test_parse_BioLogic_date(data, expected):
assert result == expected assert result == expected
@pytest.mark.parametrize('filename, startdate, enddate', [ @pytest.mark.parametrize(
('bio_logic1.mpr', '2011-10-29', '2011-10-31'), "filename, startdate, enddate",
('bio_logic2.mpr', '2012-09-27', '2012-09-27'), [
('bio_logic3.mpr', '2013-03-27', '2013-03-27'), ("bio_logic1.mpr", "2011-10-29", "2011-10-31"),
('bio_logic4.mpr', '2011-11-01', '2011-11-02'), ("bio_logic2.mpr", "2012-09-27", "2012-09-27"),
('bio_logic5.mpr', '2013-01-28', '2013-01-28'), ("bio_logic3.mpr", "2013-03-27", "2013-03-27"),
# bio_logic6.mpr has no end date because it does not have a VMP LOG module ("bio_logic4.mpr", "2011-11-01", "2011-11-02"),
('bio_logic6.mpr', '2012-09-11', None), ("bio_logic5.mpr", "2013-01-28", "2013-01-28"),
# C019P-0ppb-A_C01.mpr stores the date in a different format # bio_logic6.mpr has no end date because it does not have a VMP LOG module
('C019P-0ppb-A_C01.mpr', '2019-03-14', '2019-03-14'), ("bio_logic6.mpr", "2012-09-11", None),
('Rapp_Error.mpr', '2010-12-02', '2010-12-02'), # C019P-0ppb-A_C01.mpr stores the date in a different format
('Ewe_Error.mpr', '2021-11-18', '2021-11-19'), ("C019P-0ppb-A_C01.mpr", "2019-03-14", "2019-03-14"),
]) ("Rapp_Error.mpr", "2010-12-02", "2010-12-02"),
("Ewe_Error.mpr", "2021-11-18", "2021-11-19"),
],
)
def test_MPR_dates(testdata_dir, filename, startdate, enddate): def test_MPR_dates(testdata_dir, filename, startdate, enddate):
"""Check that the start and end dates in .mpr files are read correctly.""" """Check that the start and end dates in .mpr files are read correctly."""
mpr = MPRfile(os.path.join(testdata_dir, filename)) mpr = MPRfile(os.path.join(testdata_dir, filename))
assert mpr.startdate.strftime('%Y-%m-%d') == startdate assert mpr.startdate.strftime("%Y-%m-%d") == startdate
if enddate: if enddate:
assert mpr.enddate.strftime('%Y-%m-%d') == enddate assert mpr.enddate.strftime("%Y-%m-%d") == enddate
else: else:
assert not hasattr(mpr, 'enddate') assert not hasattr(mpr, "enddate")
def test_open_MPR_fails_for_bad_file(testdata_dir): def test_open_MPR_fails_for_bad_file(testdata_dir):
with pytest.raises(ValueError, match='Invalid magic for .mpr file'): with pytest.raises(ValueError, match="Invalid magic for .mpr file"):
MPRfile(os.path.join(testdata_dir, 'arbin1.res')) MPRfile(os.path.join(testdata_dir, "arbin1.res"))
def timestamp_from_comments(comments): def timestamp_from_comments(comments):
for line in comments: for line in comments:
time_match = re.match(b'Acquisition started on : ([0-9/]+ [0-9:]+)', line) time_match = re.match(b"Acquisition started on : ([0-9/]+ [0-9:]+)", line)
if time_match: if time_match:
timestamp = datetime.strptime(time_match.group(1).decode('ascii'), timestamp = datetime.strptime(
'%m/%d/%Y %H:%M:%S') time_match.group(1).decode("ascii"), "%m/%d/%Y %H:%M:%S"
)
return timestamp return timestamp
raise AttributeError("No timestamp in comments") raise AttributeError("No timestamp in comments")
def assert_MPR_matches_MPT(mpr, mpt, comments): def assert_MPR_matches_MPT(mpr, mpt, comments):
def assert_field_matches(fieldname, decimal): def assert_field_matches(fieldname, decimal):
if fieldname in mpr.dtype.fields: if fieldname in mpr.dtype.fields:
assert_array_almost_equal(mpr.data[fieldname], assert_array_almost_equal(
mpt[fieldname], mpr.data[fieldname], mpt[fieldname], decimal=decimal
decimal=decimal) )
def assert_field_exact(fieldname): def assert_field_exact(fieldname):
if fieldname in mpr.dtype.fields: if fieldname in mpr.dtype.fields:
@@ -154,16 +185,16 @@ def assert_MPR_matches_MPT(mpr, mpt, comments):
# Nothing uses the 0x40 bit of the flags # Nothing uses the 0x40 bit of the flags
assert_array_equal(mpr.get_flag("counter inc."), mpt["counter inc."]) assert_array_equal(mpr.get_flag("counter inc."), mpt["counter inc."])
assert_array_almost_equal(mpr.data["time/s"], assert_array_almost_equal(
mpt["time/s"], mpr.data["time/s"], mpt["time/s"], decimal=2
decimal=2) # 2 digits in CSV ) # 2 digits in CSV
assert_field_matches("control/V/mA", decimal=6) assert_field_matches("control/V/mA", decimal=6)
assert_field_matches("control/V", decimal=6) assert_field_matches("control/V", decimal=6)
assert_array_almost_equal(mpr.data["Ewe/V"], assert_array_almost_equal(
mpt["Ewe/V"], mpr.data["Ewe/V"], mpt["Ewe/V"], decimal=6
decimal=6) # 32 bit float precision ) # 32 bit float precision
assert_field_matches("dQ/mA.h", decimal=16) # 64 bit float precision assert_field_matches("dQ/mA.h", decimal=16) # 64 bit float precision
assert_field_matches("P/W", decimal=10) # 32 bit float precision for 1.xxE-5 assert_field_matches("P/W", decimal=10) # 32 bit float precision for 1.xxE-5
@@ -178,39 +209,45 @@ def assert_MPR_matches_MPT(mpr, mpt, comments):
pass pass
@pytest.mark.parametrize('basename', [ @pytest.mark.parametrize(
'bio_logic1', "basename",
'bio_logic2', [
# No bio_logic3.mpt file "bio_logic1",
'bio_logic4', "bio_logic2",
# bio_logic5 and bio_logic6 are special cases # No bio_logic3.mpt file
'CV_C01', "bio_logic4",
'121_CA_455nm_6V_30min_C01', # bio_logic5 and bio_logic6 are special cases
'020-formation_CB5', "CV_C01",
]) "121_CA_455nm_6V_30min_C01",
"020-formation_CB5",
],
)
def test_MPR_matches_MPT(testdata_dir, basename): def test_MPR_matches_MPT(testdata_dir, basename):
"""Check the MPR parser against the MPT parser. """Check the MPR parser against the MPT parser.
Load a binary .mpr file and a text .mpt file which should contain Load a binary .mpr file and a text .mpt file which should contain
exactly the same data. Check that the loaded data actually match. exactly the same data. Check that the loaded data actually match.
""" """
binpath = os.path.join(testdata_dir, basename + '.mpr') binpath = os.path.join(testdata_dir, basename + ".mpr")
txtpath = os.path.join(testdata_dir, basename + '.mpt') txtpath = os.path.join(testdata_dir, basename + ".mpt")
mpr = MPRfile(binpath) mpr = MPRfile(binpath)
mpt, comments = MPTfile(txtpath, encoding='latin1') mpt, comments = MPTfile(txtpath, encoding="latin1")
assert_MPR_matches_MPT(mpr, mpt, comments) assert_MPR_matches_MPT(mpr, mpt, comments)
def test_MPR5_matches_MPT5(testdata_dir): def test_MPR5_matches_MPT5(testdata_dir):
mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic5.mpr')) mpr = MPRfile(os.path.join(testdata_dir, "bio_logic5.mpr"))
mpt, comments = MPTfile((re.sub(b'\tXXX\t', b'\t0\t', line) for line in mpt, comments = MPTfile(
open(os.path.join(testdata_dir, 'bio_logic5.mpt'), (
mode='rb'))) re.sub(b"\tXXX\t", b"\t0\t", line)
for line in open(os.path.join(testdata_dir, "bio_logic5.mpt"), mode="rb")
)
)
assert_MPR_matches_MPT(mpr, mpt, comments) assert_MPR_matches_MPT(mpr, mpt, comments)
def test_MPR6_matches_MPT6(testdata_dir): def test_MPR6_matches_MPT6(testdata_dir):
mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic6.mpr')) mpr = MPRfile(os.path.join(testdata_dir, "bio_logic6.mpr"))
mpt, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic6.mpt')) mpt, comments = MPTfile(os.path.join(testdata_dir, "bio_logic6.mpt"))
mpr.data = mpr.data[:958] # .mpt file is incomplete mpr.data = mpr.data[:958] # .mpt file is incomplete
assert_MPR_matches_MPT(mpr, mpt, comments) assert_MPR_matches_MPT(mpr, mpt, comments)