Release version 0.1.0

Update package URL to the new echemdata repo

.travis.yml

@@ -6,10 +6,9 @@ cache:
     - .pytest_cache
     - tests/testdata
 python:
-  - "3.6"
+  - "2.7"
-  - "3.7"
+  - "3.5"
-  - "3.8"
+#  - "3.7"  # Python 3.7 is not available on travis CI yet
-  - "3.9"
 install:
   - pip install tox-travis
   - sh get_testdata.sh

README.md

@@ -7,14 +7,6 @@ Read proprietary file formats from electrochemical test stations
 
 Use the `MPRfile` class from BioLogic.py (exported in the main package)
 
-````
-from galvani import BioLogic
-import pandas as pd
-
-mpr_file = BioLogic.MPRfile('test.mpr')
-df = pd.DataFrame(mpr_file.data)
-````
-
 ## Arbin .res files ##
 
 Use the res2sqlite.py script to convert the .res file to a sqlite3 database

galvani/BioLogic.py

@@ -3,16 +3,26 @@
 
 __all__ = ['MPTfileCSV', 'MPTfile']
 
+import sys
 import re
 import csv
 from os import SEEK_SET
 import time
 from datetime import date, datetime, timedelta
 from collections import defaultdict, OrderedDict
+import functools
 
 import numpy as np
 
 
+if sys.version_info.major <= 2:
+    str3 = str
+    from string import maketrans
+else:
+    str3 = functools.partial(str, encoding='ascii')
+    maketrans = bytes.maketrans
+
+
 def fieldname_to_dtype(fieldname):
     """Converts a column header from the MPT file into a tuple of
     canonical name and appropriate numpy dtype"""
@@ -39,13 +49,13 @@ def fieldname_to_dtype(fieldname):
         raise ValueError("Invalid column header: %s" % fieldname)
 
 
-def comma_converter(float_text):
+def comma_converter(float_string):
-    """Convert text to float whether the decimal point is '.' or ','"""
+    """Convert numbers to floats whether the decimal point is '.' or ','"""
-    trans_table = bytes.maketrans(b',', b'.')
+    trans_table = maketrans(b',', b'.')
-    return float(float_text.translate(trans_table))
+    return float(float_string.translate(trans_table))
 
 
-def MPTfile(file_or_path, encoding='ascii'):
+def MPTfile(file_or_path):
     """Opens .mpt files as numpy record arrays
 
     Checks for the correct headings, skips any comments and returns a
@@ -61,7 +71,8 @@ def MPTfile(file_or_path, encoding='ascii'):
     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(rb'Nb header lines : (\d+)\s*$',
+    # TODO use rb'string' here once Python 2 is no longer supported
+    nb_headers_match = re.match(b'Nb header lines : (\\d+)\\s*$',
                                 next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
@@ -71,7 +82,7 @@ def MPTfile(file_or_path, encoding='ascii'):
     # make three lines. Every additional line is a comment line.
     comments = [next(mpt_file) for i in range(nb_headers - 3)]
 
-    fieldnames = next(mpt_file).decode(encoding).strip().split('\t')
+    fieldnames = str3(next(mpt_file)).strip().split('\t')
     record_type = np.dtype(list(map(fieldname_to_dtype, fieldnames)))
 
     # Must be able to parse files where commas are used for decimal points
@@ -145,7 +156,6 @@ VMPdata_colID_dtype_map = {
     9: ('Ece/V', '<f4'),
     11: ('I/mA', '<f8'),
     13: ('(Q-Qo)/mA.h', '<f8'),
-    16: ('Analog IN 1/V', '<f4'),
     19: ('control/V', '<f4'),
     20: ('control/mA', '<f4'),
     23: ('dQ/mA.h', '<f8'),  # Same as 7?
@@ -159,73 +169,25 @@ VMPdata_colID_dtype_map = {
     38: ('-Im(Z)/Ohm', '<f4'),
     39: ('I Range', '<u2'),
     70: ('P/W', '<f4'),
-    74: ('Energy/W.h', '<f8'),
-    75: ('Analog OUT/V', '<f4'),
     76: ('<I>/mA', '<f4'),
     77: ('<Ewe>/V', '<f4'),
-    78: ('Cs-2/µF-2', '<f4'),
-    96: ('|Ece|/V', '<f4'),
-    98: ('Phase(Zce)/deg', '<f4'),
-    99: ('|Zce|/Ohm', '<f4'),
-    100: ('Re(Zce)/Ohm', '<f4'),
-    101: ('-Im(Zce)/Ohm', '<f4'),
     123: ('Energy charge/W.h', '<f8'),
     124: ('Energy discharge/W.h', '<f8'),
     125: ('Capacitance charge/µF', '<f8'),
     126: ('Capacitance discharge/µF', '<f8'),
     131: ('Ns', '<u2'),
-    163: ('|Estack|/V', '<f4'),
-    168: ('Rcmp/Ohm', '<f4'),
     169: ('Cs/µF', '<f4'),
     172: ('Cp/µF', '<f4'),
-    173: ('Cp-2/µF-2', '<f4'),
-    241: ('|E1|/V', '<f4'),
-    242: ('|E2|/V', '<f4'),
-    271: ('Phase(Z1) / deg', '<f4'),
-    272: ('Phase(Z2) / deg', '<f4'),
-    301: ('|Z1|/Ohm', '<f4'),
-    302: ('|Z2|/Ohm', '<f4'),
-    331: ('Re(Z1)/Ohm', '<f4'),
-    332: ('Re(Z2)/Ohm', '<f4'),
-    361: ('-Im(Z1)/Ohm', '<f4'),
-    362: ('-Im(Z2)/Ohm', '<f4'),
-    391: ('<E1>/V', '<f4'),
-    392: ('<E2>/V', '<f4'),
-    422: ('Phase(Zstack)/deg', '<f4'),
-    423: ('|Zstack|/Ohm', '<f4'),
-    424: ('Re(Zstack)/Ohm', '<f4'),
-    425: ('-Im(Zstack)/Ohm', '<f4'),
-    426: ('<Estack>/V', '<f4'),
-    430: ('Phase(Zwe-ce)/deg', '<f4'),
-    431: ('|Zwe-ce|/Ohm', '<f4'),
-    432: ('Re(Zwe-ce)/Ohm', '<f4'),
-    433: ('-Im(Zwe-ce)/Ohm', '<f4'),
     434: ('(Q-Qo)/C', '<f4'),
     435: ('dQ/C', '<f4'),
-    441: ('<Ecv>/V', '<f4'),
-    462: ('Temperature/°C', '<f4'),
     467: ('Q charge/discharge/mA.h', '<f8'),
     468: ('half cycle', '<u4'),
-    469: ('z cycle', '<u4'),
-    471: ('<Ece>/V', '<f4'),
     473: ('THD Ewe/%', '<f4'),
     474: ('THD I/%', '<f4'),
     476: ('NSD Ewe/%', '<f4'),
     477: ('NSD I/%', '<f4'),
     479: ('NSR Ewe/%', '<f4'),
     480: ('NSR I/%', '<f4'),
-    486: ('|Ewe h2|/V', '<f4'),
-    487: ('|Ewe h3|/V', '<f4'),
-    488: ('|Ewe h4|/V', '<f4'),
-    489: ('|Ewe h5|/V', '<f4'),
-    490: ('|Ewe h6|/V', '<f4'),
-    491: ('|Ewe h7|/V', '<f4'),
-    492: ('|I h2|/A', '<f4'),
-    493: ('|I h3|/A', '<f4'),
-    494: ('|I h4|/A', '<f4'),
-    495: ('|I h5|/A', '<f4'),
-    496: ('|I h6|/A', '<f4'),
-    497: ('|I h7|/A', '<f4'),
 }
 
 # These column IDs define flags which are all stored packed in a single byte
@@ -281,10 +243,7 @@ def VMPdata_dtype_from_colIDs(colIDs):
                 unique_field_name = field_name
             type_list.append((unique_field_name, field_type))
         else:
-            raise NotImplementedError("Column ID {cid} after column {prev} "
+            raise NotImplementedError("column type %d not implemented" % colID)
-                                      "is unknown"
-                                      .format(cid=colID,
-                                              prev=type_list[-1][0]))
     return np.dtype(type_list), flags_dict
 
 
@@ -368,21 +327,20 @@ class MPRfile:
                                          count=n_columns)
             remaining_headers = data_module['data'][5 + n_columns:100]
             main_data = data_module['data'][100:]
-        elif data_module['version'] in [2, 3]:
+        elif data_module['version'] == 2:
             column_types = np.frombuffer(data_module['data'][5:], dtype='<u2',
                                          count=n_columns)
-            # There are bytes of data before the main array starts
+            # There is 405 bytes of data before the main array starts
-            if data_module['version'] == 3:
-                num_bytes_before = 406  # version 3 added `\x01` to the start
-            else:
-                num_bytes_before = 405
             remaining_headers = data_module['data'][5 + 2 * n_columns:405]
-            main_data = data_module['data'][num_bytes_before:]
+            main_data = data_module['data'][405:]
         else:
             raise ValueError("Unrecognised version for data module: %d" %
                              data_module['version'])
 
-        assert(not any(remaining_headers))
+        if sys.version_info.major <= 2:
+            assert(all((b == '\x00' for b in remaining_headers)))
+        else:
+            assert(not any(remaining_headers))
 
         self.dtype, self.flags_dict = VMPdata_dtype_from_colIDs(column_types)
         self.data = np.frombuffer(main_data, dtype=self.dtype)
@@ -395,9 +353,9 @@ class MPRfile:
         self.npts = n_data_points
 
         try:
-            tm = time.strptime(settings_mod['date'].decode('ascii'), '%m/%d/%y')
+            tm = time.strptime(str3(settings_mod['date']), '%m/%d/%y')
         except ValueError:
-            tm = time.strptime(settings_mod['date'].decode('ascii'), '%m-%d-%y')
+            tm = time.strptime(str3(settings_mod['date']), '%m-%d-%y')
         self.startdate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
 
         if maybe_loop_module:
@@ -413,9 +371,9 @@ class MPRfile:
         if maybe_log_module:
             log_module, = maybe_log_module
             try:
-                tm = time.strptime(log_module['date'].decode('ascii'), '%m/%d/%y')
+                tm = time.strptime(str3(log_module['date']), '%m/%d/%y')
             except ValueError:
-                tm = time.strptime(log_module['date'].decode('ascii'), '%m-%d-%y')
+                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

galvani/res2sqlite.py

@@ -5,51 +5,26 @@ import sqlite3
 import re
 import csv
 import argparse
-from copy import copy
 
 
 # The following scripts are adapted from the result of running
 # $ mdb-schema <result.res> oracle
 
-mdb_tables = [
+mdb_tables = ["Version_Table", "Global_Table", "Resume_Table",
-    'Version_Table',
+              "Channel_Normal_Table", "Channel_Statistic_Table",
-    'Global_Table',
+              "Auxiliary_Table", "Event_Table",
-    'Resume_Table',
+              "Smart_Battery_Info_Table", "Smart_Battery_Data_Table"]
-    'Channel_Normal_Table',
-    'Channel_Statistic_Table',
-    'Auxiliary_Table',
-    'Event_Table',
-    'Smart_Battery_Info_Table',
-    'Smart_Battery_Data_Table',
-]
-mdb_5_23_tables = [
-    'MCell_Aci_Data_Table',
-    'Aux_Global_Data_Table',
-    'Smart_Battery_Clock_Stretch_Table',
-]
-mdb_5_26_tables = [
-    'Can_BMS_Info_Table',
-    'Can_BMS_Data_Table',
-]
 
-mdb_tables_text = {
+mdb_tables_text = ["Version_Table", "Global_Table", "Event_Table",
-    'Version_Table',
+                   "Smart_Battery_Info_Table"]
-    'Global_Table',
+mdb_tables_numeric = ["Resume_Table", "Channel_Normal_Table",
-    'Event_Table',
+                      "Channel_Statistic_Table", "Auxiliary_Table",
-    'Smart_Battery_Info_Table',
+                      "Smart_Battery_Data_Table", 'MCell_Aci_Data_Table',
-    'Can_BMS_Info_Table',
+                      'Aux_Global_Data_Table',
-}
+                      'Smart_Battery_Clock_Stretch_Table']
-mdb_tables_numeric = {
+
-    'Resume_Table',
+mdb_5_23_tables = ['MCell_Aci_Data_Table', 'Aux_Global_Data_Table',
-    'Channel_Normal_Table',
+                   'Smart_Battery_Clock_Stretch_Table']
-    'Channel_Statistic_Table',
-    'Auxiliary_Table',
-    'Smart_Battery_Data_Table',
-    'MCell_Aci_Data_Table',
-    'Aux_Global_Data_Table',
-    'Smart_Battery_Clock_Stretch_Table',
-    'Can_BMS_Data_Table',
-}
 
 mdb_create_scripts = {
     "Version_Table": """
@@ -81,17 +56,8 @@ CREATE TABLE Global_Table
     Log_Aux_Data_Flag               INTEGER,
     Log_Event_Data_Flag             INTEGER,
     Log_Smart_Battery_Data_Flag     INTEGER,
-  -- The following items are in 5.26 but not in 5.23
-    Log_Can_BMS_Data_Flag           INTEGER DEFAULT NULL,
-    Software_Version                TEXT DEFAULT NULL,
-    Serial_Number                   TEXT DEFAULT NULL,
-    Schedule_Version                TEXT DEFAULT NULL,
-    MASS                            REAL DEFAULT NULL,
-    Specific_Capacity               REAL DEFAULT NULL,
-    Capacity                        REAL DEFAULT NULL,
-  -- Item_ID exists in all versions
     Item_ID                         TEXT,
-  -- These items are in 5.26 and 5.23 but not in 1.14
+  -- Version 1.14 ends here, version 5.23 continues
     Mapped_Aux_Conc_CNumber         INTEGER DEFAULT NULL,
     Mapped_Aux_DI_CNumber           INTEGER DEFAULT NULL,
     Mapped_Aux_DO_CNumber           INTEGER DEFAULT NULL
@@ -99,7 +65,7 @@ CREATE TABLE Global_Table
     "Resume_Table": """
 CREATE TABLE Resume_Table
  (
-    Test_ID         INTEGER PRIMARY KEY REFERENCES Global_Table(Test_ID),
+    Test_ID         INTEGER REFERENCES Global_Table(Test_ID),
     Step_Index      INTEGER,
     Cycle_Index     INTEGER,
     Channel_Status  INTEGER,
@@ -149,8 +115,7 @@ CREATE TABLE Channel_Normal_Table
     "dV/dt"                 REAL,
     Internal_Resistance     REAL,
     AC_Impedance            REAL,
-    ACI_Phase_Angle         REAL,
+    ACI_Phase_Angle         REAL
-    PRIMARY KEY (Test_ID, Data_Point)
 ); """,
     "Channel_Statistic_Table": """
 CREATE TABLE Channel_Statistic_Table
@@ -161,7 +126,6 @@ CREATE TABLE Channel_Statistic_Table
   -- Version 1.14 ends here, version 5.23 continues
     Charge_Time             REAL DEFAULT NULL,
     Discharge_Time          REAL DEFAULT NULL,
-    PRIMARY KEY (Test_ID, Data_Point),
     FOREIGN KEY (Test_ID, Data_Point)
         REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 ); """,
@@ -174,7 +138,6 @@ CREATE TABLE Auxiliary_Table
     Data_Type               INTEGER,
     X                       REAL,
     "dX/dt"                 REAL,
-    PRIMARY KEY (Test_ID, Data_Point, Auxiliary_Index),
     FOREIGN KEY (Test_ID, Data_Point)
         REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 ); """,
@@ -190,7 +153,7 @@ CREATE TABLE Event_Table
     "Smart_Battery_Info_Table":  """
 CREATE TABLE Smart_Battery_Info_Table
  (
-    Test_ID                 INTEGER PRIMARY KEY REFERENCES Global_Table(Test_ID),
+    Test_ID                 INTEGER REFERENCES Global_Table(Test_ID),
     ManufacturerDate        REAL,
     ManufacturerAccess      TEXT,
     SpecificationInfo       TEXT,
@@ -259,14 +222,10 @@ CREATE TABLE Smart_Battery_Data_Table
     ChargingCurrent         REAL DEFAULT NULL,
     ChargingVoltage         REAL DEFAULT NULL,
     ManufacturerData        REAL DEFAULT NULL,
-  -- Version 5.23 ends here, version 5.26 continues
-    BATMAN_Status           INTEGER DEFAULT NULL,
-    DTM_PDM_Status          INTEGER DEFAULT NULL,
-    PRIMARY KEY (Test_ID, Data_Point),
     FOREIGN KEY (Test_ID, Data_Point)
         REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 ); """,
-    # The following tables are not present in version 1.14, but are in 5.23
+    # The following tables are not present in version 1.14
     'MCell_Aci_Data_Table': """
 CREATE TABLE MCell_Aci_Data_Table
  (
@@ -277,7 +236,6 @@ CREATE TABLE MCell_Aci_Data_Table
     Phase_Shift		REAL,
     Voltage			REAL,
     Current			REAL,
-    PRIMARY KEY (Test_ID, Data_Point, Cell_Index),
     FOREIGN KEY (Test_ID, Data_Point)
         REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 );""",
@@ -288,8 +246,7 @@ CREATE TABLE Aux_Global_Data_Table
     Auxiliary_Index	INTEGER,
     Data_Type		INTEGER,
     Nickname		TEXT,
-    Unit			TEXT,
+    Unit			TEXT
-    PRIMARY KEY (Channel_Index, Auxiliary_Index, Data_Type)
 );""",
     'Smart_Battery_Clock_Stretch_Table': """
 CREATE TABLE Smart_Battery_Clock_Stretch_Table
@@ -335,32 +292,9 @@ CREATE TABLE Smart_Battery_Clock_Stretch_Table
     VCELL3			    INTEGER,
     VCELL2			    INTEGER,
     VCELL1			    INTEGER,
-    PRIMARY KEY (Test_ID, Data_Point),
     FOREIGN KEY (Test_ID, Data_Point)
         REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
-);""",
+);"""}
-    # The following tables are not present in version 5.23, but are in 5.26
-    'Can_BMS_Info_Table': """
-CREATE TABLE "Can_BMS_Info_Table"
- (
-    Channel_Index        INTEGER PRIMARY KEY,
-    CAN_Cfg_File_Name    TEXT,
-    CAN_Configuration    TEXT
-);
-""",
-    'Can_BMS_Data_Table': """
-CREATE TABLE "Can_BMS_Data_Table"
- (
-    Test_ID              INTEGER,
-    Data_Point           INTEGER,
-    CAN_MV_Index         INTEGER,
-    Signal_Value_X       REAL,
-    PRIMARY KEY (Test_ID, Data_Point, CAN_MV_Index),
-    FOREIGN KEY (Test_ID, Data_Point)
-        REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
-);
-""",
-}
 
 mdb_create_indices = {
     "Channel_Normal_Table": """
@@ -437,28 +371,27 @@ def mdb_get_data_text(s3db, filename, table):
         r'INSERT INTO "\w+" \([^)]+?\) VALUES \(("[^"]*"|[^")])+?\);\n',
         re.IGNORECASE
     )
+    # TODO after dropping Python 2 support - use Popen as contextmanager
     try:
-        # Initialize values to avoid NameError in except clause
+        mdb_sql = sp.Popen(['mdb-export', '-I', 'postgres', filename, table],
-        mdb_output = ''
+                           bufsize=-1, stdin=None, stdout=sp.PIPE,
-        insert_match = None
+                           universal_newlines=True)
-        with sp.Popen(['mdb-export', '-I', 'postgres', filename, table],
-                      bufsize=-1, stdin=sp.DEVNULL, stdout=sp.PIPE,
-                      universal_newlines=True) as mdb_sql:
-
-            mdb_output = mdb_sql.stdout.read()
-            while len(mdb_output) > 0:
-                insert_match = insert_pattern.match(mdb_output)
-                s3db.execute(insert_match.group())
-                mdb_output = mdb_output[insert_match.end():]
-                mdb_output += mdb_sql.stdout.read()
-            s3db.commit()
-
     except OSError as e:
         if e.errno == 2:
             raise RuntimeError('Could not locate the `mdb-export` executable. '
                                'Check that mdbtools is properly installed.')
         else:
             raise
+    try:
+        # Initialize values to avoid NameError in except clause
+        mdb_output = ''
+        insert_match = None
+        mdb_output = mdb_sql.stdout.read()
+        while len(mdb_output) > 0:
+            insert_match = insert_pattern.match(mdb_output)
+            s3db.execute(insert_match.group())
+            mdb_output = mdb_output[insert_match.end():]
+        s3db.commit()
     except BaseException:
         print("Error while importing %s" % table)
         if mdb_output:
@@ -466,32 +399,38 @@ def mdb_get_data_text(s3db, filename, table):
         if insert_match:
             print("insert_re match:", insert_match)
         raise
+    finally:
+        mdb_sql.terminate()
 
 
 def mdb_get_data_numeric(s3db, filename, table):
     print("Reading %s..." % table)
+    # TODO after dropping Python 2 support - use Popen as contextmanager
     try:
-        with sp.Popen(['mdb-export', filename, table],
+        mdb_sql = sp.Popen(['mdb-export', filename, table],
-                      bufsize=-1, stdin=sp.DEVNULL, stdout=sp.PIPE,
+                           bufsize=-1, stdin=None, stdout=sp.PIPE,
-                      universal_newlines=True) as mdb_sql:
+                           universal_newlines=True)
-            mdb_csv = csv.reader(mdb_sql.stdout)
-            mdb_headers = next(mdb_csv)
-            quoted_headers = ['"%s"' % h for h in mdb_headers]
-            joined_headers = ', '.join(quoted_headers)
-            joined_placemarks = ', '.join(['?' for h in mdb_headers])
-            insert_stmt = 'INSERT INTO "{0}" ({1}) VALUES ({2});'.format(
-                table,
-                joined_headers,
-                joined_placemarks,
-            )
-            s3db.executemany(insert_stmt, mdb_csv)
-            s3db.commit()
     except OSError as e:
         if e.errno == 2:
             raise RuntimeError('Could not locate the `mdb-export` executable. '
                                'Check that mdbtools is properly installed.')
         else:
             raise
+    try:
+        mdb_csv = csv.reader(mdb_sql.stdout)
+        mdb_headers = next(mdb_csv)
+        quoted_headers = ['"%s"' % h for h in mdb_headers]
+        joined_headers = ', '.join(quoted_headers)
+        joined_placemarks = ', '.join(['?' for h in mdb_headers])
+        insert_stmt = 'INSERT INTO "{0}" ({1}) VALUES ({2});'.format(
+            table,
+            joined_headers,
+            joined_placemarks,
+        )
+        s3db.executemany(insert_stmt, mdb_csv)
+        s3db.commit()
+    finally:
+        mdb_sql.terminate()
 
 
 def mdb_get_data(s3db, filename, table):
@@ -503,69 +442,32 @@ def mdb_get_data(s3db, filename, table):
         raise ValueError("'%s' is in neither mdb_tables_text nor mdb_tables_numeric" % table)
 
 
-def mdb_get_version(filename):
-    """Get the version number from an Arbin .res file.
-
-    Reads the Version_Table and parses the version from Version_Schema_Field.
-    """
-    print("Reading version number...")
-    try:
-        with sp.Popen(['mdb-export', filename, 'Version_Table'],
-                      bufsize=-1, stdin=sp.DEVNULL, stdout=sp.PIPE,
-                      universal_newlines=True) as mdb_sql:
-            mdb_csv = csv.reader(mdb_sql.stdout)
-            mdb_headers = next(mdb_csv)
-            mdb_values = next(mdb_csv)
-            try:
-                next(mdb_csv)
-            except StopIteration:
-                pass
-            else:
-                raise ValueError('Version_Table of %s lists multiple versions' % filename)
-    except OSError as e:
-        if e.errno == 2:
-            raise RuntimeError('Could not locate the `mdb-export` executable. '
-                               'Check that mdbtools is properly installed.')
-        else:
-            raise
-    if 'Version_Schema_Field' not in mdb_headers:
-        raise ValueError('Version_Table of %s does not contain a Version_Schema_Field column'
-                         % filename)
-    version_fields = dict(zip(mdb_headers, mdb_values))
-    version_text = version_fields['Version_Schema_Field']
-    version_match = re.fullmatch('Results File ([.0-9]+)', version_text)
-    if not version_match:
-        raise ValueError('File version "%s" did not match expected format' % version_text)
-    version_string = version_match.group(1)
-    version_tuple = tuple(map(int, version_string.split('.')))
-    return version_tuple
-
-
 def convert_arbin_to_sqlite(input_file, output_file):
     """Read data from an Arbin .res data file and write to a sqlite file.
 
     Any data currently in the sqlite file will be erased!
     """
-    arbin_version = mdb_get_version(input_file)
-
     s3db = sqlite3.connect(output_file)
 
-    tables_to_convert = copy(mdb_tables)
+    for table in reversed(mdb_tables + mdb_5_23_tables):
-    if arbin_version >= (5, 23):
-        tables_to_convert.extend(mdb_5_23_tables)
-    if arbin_version >= (5, 26):
-        tables_to_convert.extend(mdb_5_26_tables)
-
-    for table in reversed(tables_to_convert):
         s3db.execute('DROP TABLE IF EXISTS "%s";' % table)
 
-    for table in tables_to_convert:
+    for table in mdb_tables:
         s3db.executescript(mdb_create_scripts[table])
         mdb_get_data(s3db, input_file, table)
         if table in mdb_create_indices:
             print("Creating indices for %s..." % table)
             s3db.executescript(mdb_create_indices[table])
 
+    csr = s3db.execute("SELECT Version_Schema_Field FROM Version_Table;")
+    version_text, = csr.fetchone()
+    if (version_text == "Results File 5.23"):
+        for table in mdb_5_23_tables:
+            s3db.executescript(mdb_create_scripts[table])
+            mdb_get_data(input_file, table)
+            if table in mdb_create_indices:
+                s3db.executescript(mdb_create_indices[table])
+
     print("Creating helper table for capacity and energy totals...")
     s3db.executescript(helper_table_script)
 

get_testdata.sh

@@ -24,5 +24,4 @@ https://files.figshare.com/1780530/121_CA_455nm_6V_30min_C01.mpt
 https://files.figshare.com/1780526/CV_C01.mpr
 https://files.figshare.com/1780527/CV_C01.mpt
 https://files.figshare.com/14752538/C019P-0ppb-A_C01.mpr
-https://files.figshare.com/25331510/UM34_Test005E.res
 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='0.2.0',
+    version='0.1.0',
     description='Open and process battery charger log data files',
     long_description=readme,
     long_description_content_type="text/markdown",
@@ -23,8 +23,6 @@ setup(
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3 :: Only',
-        'Topic :: Scientific/Engineering :: Chemistry',
     ],
     packages=['galvani'],
     entry_points={
@@ -32,7 +30,6 @@ setup(
             'res2sqlite = galvani.res2sqlite:main',
         ],
     },
-    python_requires='>=3.6',
     install_requires=['numpy'],
     tests_require=['pytest'],
 )

tests/test_Arbin.py

@@ -9,8 +9,8 @@ import pytest
 from galvani import res2sqlite
 
 
-have_mdbtools = (subprocess.call(['which', 'mdb-export'],
+# TODO - change to subprocess.DEVNULL when python 2 support is removed
-                                 stdout=subprocess.DEVNULL) == 0)
+have_mdbtools = (subprocess.call(['which', 'mdb-export'], stdout=None) == 0)
 
 
 def test_res2sqlite_help():
@@ -32,7 +32,7 @@ def test_convert_Arbin_no_mdbtools(testdata_dir, tmpdir):
 
 
 @pytest.mark.skipif(not have_mdbtools, reason='Reading the Arbin file requires MDBTools')
-@pytest.mark.parametrize('basename', ['arbin1', 'UM34_Test005E'])
+@pytest.mark.parametrize('basename', ['arbin1'])
 def test_convert_Arbin_to_sqlite_function(testdata_dir, tmpdir, basename):
     """Convert an Arbin file to SQLite using the functional interface."""
     res_file = os.path.join(testdata_dir, basename + '.res')

tests/test_BioLogic.py

@@ -9,7 +9,7 @@ from numpy.testing import assert_array_almost_equal, assert_array_equal
 import pytest
 
 from galvani import BioLogic, MPTfile, MPRfile
-from galvani.BioLogic import MPTfileCSV  # not exported
+from galvani.BioLogic import MPTfileCSV, str3  # not exported
 
 
 def test_open_MPT(testdata_dir):
@@ -103,7 +103,7 @@ def timestamp_from_comments(comments):
     for line in comments:
         time_match = re.match(b'Acquisition started on : ([0-9/]+ [0-9:]+)', line)
         if time_match:
-            timestamp = datetime.strptime(time_match.group(1).decode('ascii'),
+            timestamp = datetime.strptime(str3(time_match.group(1)),
                                           '%m/%d/%Y %H:%M:%S')
             return timestamp
     raise AttributeError("No timestamp in comments")

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py36,py37,py38,py39
+envlist = py27,py35,py37
 [testenv]
 deps =
   flake8