Release version 0.0.2

This tests for issue #20

Thanks @JBWarrington for providing this file

galvani/BioLogic.py

@@ -70,7 +70,8 @@ def MPTfile(file_or_path):
     if magic != b'EC-Lab ASCII FILE\r\n':
         raise ValueError("Bad first line for EC-Lab file: '%s'" % magic)
 
-    nb_headers_match = re.match(b'Nb header lines : (\d+)\s*$', next(mpt_file))
+    # TODO use rb'string' here once Python 2 is no longer supported
+    nb_headers_match = re.match(b'Nb header lines : (\\d+)\\s*$', next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
         raise ValueError("Too few header lines: %d" % nb_headers)
@@ -107,7 +108,7 @@ def MPTfileCSV(file_or_path):
     if magic.rstrip() != 'EC-Lab ASCII FILE':
         raise ValueError("Bad first line for EC-Lab file: '%s'" % magic)
 
-    nb_headers_match = re.match('Nb header lines : (\d+)\s*$', next(mpt_file))
+    nb_headers_match = re.match(r'Nb header lines : (\d+)\s*$', next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
         raise ValueError("Too few header lines: %d" % nb_headers)
@@ -184,6 +185,8 @@ def VMPdata_dtype_from_colIDs(colIDs):
             dtype_dict['I/mA'] = '<f8'
         elif colID == 13:
             dtype_dict['(Q-Qo)/mA.h'] = '<f8'
+        elif colID == 16:
+            dtype_dict['Analog IN 1/V'] = '<f4'
         elif colID == 19:
             dtype_dict['control/V'] = '<f4'
         elif colID == 20:
@@ -208,6 +211,10 @@ def VMPdata_dtype_from_colIDs(colIDs):
             dtype_dict['I Range'] = '<u2'
         elif colID == 70:
             dtype_dict['P/W'] = '<f4'
+        elif colID == 74:
+            dtype_dict['Energy/W.h'] = '<f8'
+        elif colID == 78:
+            dtype_dict['Cs-2/µf-2'] = '<f4'
         elif colID == 123:
             dtype_dict['Energy charge/W.h'] = '<f8'
         elif colID == 124:
@@ -222,6 +229,8 @@ def VMPdata_dtype_from_colIDs(colIDs):
             dtype_dict['Cs/µF'] = '<f4'
         elif colID == 172:
             dtype_dict['Cp/µF'] = '<f4'
+        elif colID == 173:
+            dtype_dict['Cp-2/µF-2'] = '<f4'
         elif colID == 434:
             dtype_dict['(Q-Qo)/C'] = '<f4'
         elif colID == 435:
@@ -230,6 +239,8 @@ def VMPdata_dtype_from_colIDs(colIDs):
             dtype_dict['Q charge/discharge/mA.h'] = '<f8'
         elif colID == 468:
             dtype_dict['half cycle'] = '<u4'
+        elif colID == 469:
+            dtype_dict['z cycle'] = '<u4'
         elif colID == 473:
             dtype_dict['THD Ewe/%'] = '<f4'
         elif colID == 476:
@@ -265,7 +276,7 @@ def read_VMP_modules(fileobj, read_module_data=True):
         if len(hdr_bytes) < VMPmodule_hdr.itemsize:
             raise IOError("Unexpected end of file while reading module header")
 
-        hdr = np.fromstring(hdr_bytes, dtype=VMPmodule_hdr, count=1)
+        hdr = np.frombuffer(hdr_bytes, dtype=VMPmodule_hdr, count=1)
         hdr_dict = dict(((n, hdr[n][0]) for n in VMPmodule_hdr.names))
         hdr_dict['offset'] = fileobj.tell()
         if read_module_data:
@@ -316,17 +327,16 @@ class MPRfile:
         data_module, = (m for m in modules if m['shortname'] == b'VMP data  ')
         maybe_log_module = [m for m in modules if m['shortname'] == b'VMP LOG   ']
 
-        n_data_points = np.fromstring(data_module['data'][:4], dtype='<u4')
+        n_data_points = np.frombuffer(data_module['data'][:4], dtype='<u4')
-        n_columns = np.fromstring(data_module['data'][4:5], dtype='u1')
+        n_columns = np.frombuffer(data_module['data'][4:5], dtype='u1').item()
-        n_columns = np.asscalar(n_columns)  # Compatibility with recent numpy
 
         if data_module['version'] == 0:
-            column_types = np.fromstring(data_module['data'][5:], dtype='u1',
+            column_types = np.frombuffer(data_module['data'][5:], dtype='u1',
                                          count=n_columns)
             remaining_headers = data_module['data'][5 + n_columns:100]
             main_data = data_module['data'][100:]
         elif data_module['version'] == 2:
-            column_types = np.fromstring(data_module['data'][5:], dtype='<u2',
+            column_types = np.frombuffer(data_module['data'][5:], dtype='<u2',
                                          count=n_columns)
             ## There is 405 bytes of data before the main array starts
             remaining_headers = data_module['data'][5 + 2 * n_columns:405]
@@ -341,7 +351,7 @@ class MPRfile:
             assert(not any(remaining_headers))
 
         self.dtype, self.flags_dict, self.flags2_dict = VMPdata_dtype_from_colIDs(column_types)
-        self.data = np.fromstring(main_data, dtype=self.dtype)
+        self.data = np.frombuffer(main_data, dtype=self.dtype)
         assert(self.data.shape[0] == n_data_points)
 
         ## No idea what these 'column types' mean or even if they are actually
@@ -350,24 +360,30 @@ class MPRfile:
         self.cols = column_types
         self.npts = n_data_points
 
-        tm = time.strptime(str3(settings_mod['date']), '%m/%d/%y')
+        try:
+            tm = time.strptime(str3(settings_mod['date']), '%m/%d/%y')
+        except ValueError:
+            tm = time.strptime(str3(settings_mod['date']), '%m-%d-%y')
         self.startdate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
 
         if maybe_log_module:
             log_module, = maybe_log_module
-            tm = time.strptime(str3(log_module['date']), '%m/%d/%y')
+            try:
+                tm = time.strptime(str3(log_module['date']), '%m/%d/%y')
+            except ValueError:
+                tm = time.strptime(str3(log_module['date']), '%m-%d-%y')
             self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
 
             ## There is a timestamp at either 465 or 469 bytes
             ## I can't find any reason why it is one or the other in any
             ## given file
-            ole_timestamp1 = np.fromstring(log_module['data'][465:],
+            ole_timestamp1 = np.frombuffer(log_module['data'][465:],
                                            dtype='<f8', count=1)
-            ole_timestamp2 = np.fromstring(log_module['data'][469:],
+            ole_timestamp2 = np.frombuffer(log_module['data'][469:],
                                            dtype='<f8', count=1)
-            ole_timestamp3 = np.fromstring(log_module['data'][473:],
+            ole_timestamp3 = np.frombuffer(log_module['data'][473:],
                                            dtype='<f8', count=1)
-            ole_timestamp4 = np.fromstring(log_module['data'][585:],
+            ole_timestamp4 = np.frombuffer(log_module['data'][585:],
                                            dtype='<f8', count=1)
 
             if ole_timestamp1 > 40000 and ole_timestamp1 < 50000:

get_testdata.sh

@@ -7,20 +7,21 @@ mkdir -p tests/testdata
 cd tests/testdata
 
 /usr/bin/wget --continue -i - <<END_FILELIST
-http://files.figshare.com/1778905/arbin1.res
+https://files.figshare.com/1778905/arbin1.res
-http://files.figshare.com/1778937/bio_logic2.mpt
+https://files.figshare.com/1778937/bio_logic2.mpt
-http://files.figshare.com/1778938/bio_logic5.mpt
+https://files.figshare.com/1778938/bio_logic5.mpt
-http://files.figshare.com/1778939/bio_logic1.mpr
+https://files.figshare.com/1778939/bio_logic1.mpr
-http://files.figshare.com/1778940/bio_logic6.mpr
+https://files.figshare.com/1778940/bio_logic6.mpr
-http://files.figshare.com/1778941/bio_logic4.mpt
+https://files.figshare.com/1778941/bio_logic4.mpt
-http://files.figshare.com/1778942/bio_logic5.mpr
+https://files.figshare.com/1778942/bio_logic5.mpr
-http://files.figshare.com/1778943/bio_logic2.mpr
+https://files.figshare.com/1778943/bio_logic2.mpr
-http://files.figshare.com/1778944/bio_logic6.mpt
+https://files.figshare.com/1778944/bio_logic6.mpt
-http://files.figshare.com/1778945/bio_logic1.mpt
+https://files.figshare.com/1778945/bio_logic1.mpt
-http://files.figshare.com/1778946/bio_logic3.mpr
+https://files.figshare.com/1778946/bio_logic3.mpr
-http://files.figshare.com/1780444/bio_logic4.mpr
+https://files.figshare.com/1780444/bio_logic4.mpr
-http://files.figshare.com/1780529/121_CA_455nm_6V_30min_C01.mpr
+https://files.figshare.com/1780529/121_CA_455nm_6V_30min_C01.mpr
-http://files.figshare.com/1780530/121_CA_455nm_6V_30min_C01.mpt
+https://files.figshare.com/1780530/121_CA_455nm_6V_30min_C01.mpt
-http://files.figshare.com/1780526/CV_C01.mpr
+https://files.figshare.com/1780526/CV_C01.mpr
-http://files.figshare.com/1780527/CV_C01.mpt
+https://files.figshare.com/1780527/CV_C01.mpt
+https://files.figshare.com/14752538/C019P-0ppb-A_C01.mpr
 END_FILELIST

setup.py

@@ -9,7 +9,7 @@ with open(os.path.join(os.path.dirname(__file__), 'README.md')) as f:
 
 setup(
     name='galvani',
-    version='0.0.1',
+    version='0.0.2',
     description='Open and process battery charger log data files',
     long_description=readme,
     long_description_content_type="text/markdown",
@@ -29,4 +29,5 @@ setup(
             'res2sqlite = galvani.res2sqlite:main',
     ]},
     install_requires=['numpy'],
+    tests_require=['pytest'],
 )

tests/test_BioLogic.py

@@ -2,11 +2,11 @@
 
 import os.path
 import re
-from datetime import date, datetime
+from datetime import datetime
 
 import numpy as np
 from numpy.testing import assert_array_almost_equal, assert_array_equal
-from nose.tools import ok_, eq_, raises
+import pytest
 
 from galvani import MPTfile, MPRfile
 from galvani.BioLogic import MPTfileCSV, str3  # not exported
@@ -16,77 +16,58 @@ testdata_dir = os.path.join(os.path.dirname(__file__), 'testdata')
 
 def test_open_MPT():
     mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt'))
-    eq_(comments, [])
+    assert comments == []
-    eq_(mpt1.dtype.names, ("mode", "ox/red", "error", "control changes",
+    assert mpt1.dtype.names == (
-                           "Ns changes", "counter inc.", "time/s",
+        "mode", "ox/red", "error", "control changes", "Ns changes",
-                           "control/V/mA", "Ewe/V", "dQ/mA.h", "P/W",
+        "counter inc.", "time/s", "control/V/mA", "Ewe/V", "dQ/mA.h", "P/W",
-                           "I/mA", "(Q-Qo)/mA.h", "x"))
+        "I/mA", "(Q-Qo)/mA.h", "x",
+    )
 
 
-@raises(ValueError)
 def test_open_MPT_fails_for_bad_file():
-    mpt1 = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
+    with pytest.raises(ValueError, match='Bad first line'):
+        MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
 
 
 def test_open_MPT_csv():
     mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpt'))
-    eq_(comments, [])
+    assert comments == []
-    eq_(mpt1.fieldnames, ["mode", "ox/red", "error", "control changes",
+    assert mpt1.fieldnames == [
-                          "Ns changes", "counter inc.", "time/s",
+        "mode", "ox/red", "error", "control changes", "Ns changes",
-                          "control/V/mA", "Ewe/V", "dq/mA.h", "P/W",
+        "counter inc.", "time/s", "control/V/mA", "Ewe/V", "dq/mA.h", "P/W",
-                          "<I>/mA", "(Q-Qo)/mA.h", "x"])
+        "<I>/mA", "(Q-Qo)/mA.h", "x",
+    ]
 
 
-@raises(ValueError)
 def test_open_MPT_csv_fails_for_bad_file():
-    mpt1 = MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpr'))
+    with pytest.raises((ValueError, UnicodeDecodeError)):
+        MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpr'))
 
 
-def test_open_MPR1():
+@pytest.mark.parametrize('filename, startdate, enddate', [
-    mpr1 = MPRfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
+    ('bio_logic1.mpr', '2011-10-29', '2011-10-31'),
-    ## Check the dates as a basic test that it has been read properly
+    ('bio_logic2.mpr', '2012-09-27', '2012-09-27'),
-    eq_(mpr1.startdate, date(2011, 10, 29))
+    ('bio_logic3.mpr', '2013-03-27', '2013-03-27'),
-    eq_(mpr1.enddate, date(2011, 10, 31))
+    ('bio_logic4.mpr', '2011-11-01', '2011-11-02'),
+    ('bio_logic5.mpr', '2013-01-28', '2013-01-28'),
+    # bio_logic6.mpr has no end date because it does not have a VMP LOG module
+    ('bio_logic6.mpr', '2012-09-11', None),
+    # C019P-0ppb-A_C01.mpr stores the date in a different format
+    ('C019P-0ppb-A_C01.mpr', '2019-03-14', '2019-03-14'),
+])
+def test_MPR_dates(filename, startdate, enddate):
+    """Check that the start and end dates in .mpr files are read correctly."""
+    mpr = MPRfile(os.path.join(testdata_dir, filename))
+    assert mpr.startdate.strftime('%Y-%m-%d') == startdate
+    if enddate:
+        assert mpr.enddate.strftime('%Y-%m-%d') == enddate
+    else:
+        assert not hasattr(mpr, 'enddate')
 
 
-def test_open_MPR2():
-    mpr2 = MPRfile(os.path.join(testdata_dir, 'bio_logic2.mpr'))
-    ## Check the dates as a basic test that it has been read properly
-    eq_(mpr2.startdate, date(2012, 9, 27))
-    eq_(mpr2.enddate, date(2012, 9, 27))
-
-
-def test_open_MPR3():
-    mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic3.mpr'))
-    ## Check the dates as a basic test that it has been read properly
-    eq_(mpr.startdate, date(2013, 3, 27))
-    eq_(mpr.enddate, date(2013, 3, 27))
-
-
-def test_open_MPR4():
-    mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic4.mpr'))
-    ## Check the dates as a basic test that it has been read properly
-    eq_(mpr.startdate, date(2011, 11, 1))
-    eq_(mpr.enddate, date(2011, 11, 2))
-
-
-def test_open_MPR5():
-    mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic5.mpr'))
-    ## Check the dates as a basic test that it has been read properly
-    eq_(mpr.startdate, date(2013, 1, 28))
-    eq_(mpr.enddate, date(2013, 1, 28))
-
-
-def test_open_MPR6():
-    mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic6.mpr'))
-    ## Check the dates as a basic test that it has been read properly
-    eq_(mpr.startdate, date(2012, 9, 11))
-    ## no end date because no VMP LOG module
-
-
-@raises(ValueError)
 def test_open_MPR_fails_for_bad_file():
-    mpr1 = MPRfile(os.path.join(testdata_dir, 'arbin1.res'))
+    with pytest.raises(ValueError, match='Invalid magic for .mpr file'):
+        MPRfile(os.path.join(testdata_dir, 'arbin1.res'))
 
 
 def timestamp_from_comments(comments):
@@ -139,30 +120,31 @@ def assert_MPR_matches_MPT(mpr, mpt, comments):
     assert_field_matches("(Q-Qo)/C", decimal=6)  # 32 bit float precision
     
     try:
-        eq_(timestamp_from_comments(comments), mpr.timestamp)
+        assert timestamp_from_comments(comments) == mpr.timestamp
     except AttributeError:
         pass
 
 
-def test_MPR1_matches_MPT1():
+@pytest.mark.parametrize('basename', [
-    mpr1 = MPRfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
+    'bio_logic1',
-    mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt'))
+    'bio_logic2',
-    assert_MPR_matches_MPT(mpr1, mpt1, comments)
+    # No bio_logic3.mpt file
+    'bio_logic4',
+    # bio_logic5 and bio_logic6 are special cases
+    'CV_C01',
+    '121_CA_455nm_6V_30min_C01',
+])
+def test_MPR_matches_MPT(basename):
+    """Check the MPR parser against the MPT parser.
 
-
+    Load a binary .mpr file and a text .mpt file which should contain
-def test_MPR2_matches_MPT2():
+    exactly the same data. Check that the loaded data actually match.
-    mpr2 = MPRfile(os.path.join(testdata_dir, 'bio_logic2.mpr'))
+    """
-    mpt2, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic2.mpt'))
+    binpath = os.path.join(testdata_dir, basename + '.mpr')
-    assert_MPR_matches_MPT(mpr2, mpt2, comments)
+    txtpath = os.path.join(testdata_dir, basename + '.mpt')
-
+    mpr = MPRfile(binpath)
-
+    mpt, comments = MPTfile(txtpath)
-## No bio_logic3.mpt file
+    assert_MPR_matches_MPT(mpr, mpt, comments)
-
-
-def test_MPR4_matches_MPT4():
-    mpr4 = MPRfile(os.path.join(testdata_dir, 'bio_logic4.mpr'))
-    mpt4, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic4.mpt'))
-    assert_MPR_matches_MPT(mpr4, mpt4, comments)
 
 
 def test_MPR5_matches_MPT5():
@@ -178,18 +160,3 @@ def test_MPR6_matches_MPT6():
     mpt, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic6.mpt'))
     mpr.data = mpr.data[:958]  # .mpt file is incomplete
     assert_MPR_matches_MPT(mpr, mpt, comments)
-
-
-## Tests for issue #1 -- new dtypes ##
-
-
-def test_CV_C01():
-    mpr = MPRfile(os.path.join(testdata_dir, 'CV_C01.mpr'))
-    mpt, comments = MPTfile(os.path.join(testdata_dir, 'CV_C01.mpt'))
-    assert_MPR_matches_MPT(mpr, mpt, comments)
-
-
-def test_CA_455nm():
-    mpr = MPRfile(os.path.join(testdata_dir, '121_CA_455nm_6V_30min_C01.mpr'))
-    mpt, comments = MPTfile(os.path.join(testdata_dir, '121_CA_455nm_6V_30min_C01.mpt'))
-    assert_MPR_matches_MPT(mpr, mpt, comments)

tox.ini

@@ -1,5 +1,5 @@
 [tox]
 envlist = py27,py35,py37
 [testenv]
-deps=nose
+deps=pytest
-commands=nosetests
+commands=pytest