Merge pull request #56 from chatcannon/release-0.2.0

Bump release version to 0.2.0

.travis.yml

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

README.md

@@ -7,6 +7,14 @@ 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

@@ -3,26 +3,16 @@
 
 __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"""
@@ -49,13 +39,13 @@ def fieldname_to_dtype(fieldname):
         raise ValueError("Invalid column header: %s" % fieldname)
 
 
-def comma_converter(float_string):
-    """Convert numbers to floats whether the decimal point is '.' or ','"""
-    trans_table = maketrans(b',', b'.')
-    return float(float_string.translate(trans_table))
+def comma_converter(float_text):
+    """Convert text to float whether the decimal point is '.' or ','"""
+    trans_table = bytes.maketrans(b',', b'.')
+    return float(float_text.translate(trans_table))
 
 
-def MPTfile(file_or_path):
+def MPTfile(file_or_path, encoding='ascii'):
     """Opens .mpt files as numpy record arrays
 
     Checks for the correct headings, skips any comments and returns a
@@ -71,8 +61,7 @@ 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)
 
-    # TODO use rb'string' here once Python 2 is no longer supported
-    nb_headers_match = re.match(b'Nb header lines : (\\d+)\\s*$',
+    nb_headers_match = re.match(rb'Nb header lines : (\d+)\s*$',
                                 next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
@@ -82,7 +71,7 @@ def MPTfile(file_or_path):
     # make three lines. Every additional line is a comment line.
     comments = [next(mpt_file) for i in range(nb_headers - 3)]
 
-    fieldnames = str3(next(mpt_file)).strip().split('\t')
+    fieldnames = next(mpt_file).decode(encoding).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
@@ -156,6 +145,7 @@ 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?
@@ -169,25 +159,73 @@ 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
@@ -243,7 +281,10 @@ def VMPdata_dtype_from_colIDs(colIDs):
                 unique_field_name = field_name
             type_list.append((unique_field_name, field_type))
         else:
-            raise NotImplementedError("column type %d not implemented" % colID)
+            raise NotImplementedError("Column ID {cid} after column {prev} "
+                                      "is unknown"
+                                      .format(cid=colID,
+                                              prev=type_list[-1][0]))
     return np.dtype(type_list), flags_dict
 
 
@@ -327,19 +368,20 @@ class MPRfile:
                                          count=n_columns)
             remaining_headers = data_module['data'][5 + n_columns:100]
             main_data = data_module['data'][100:]
-        elif data_module['version'] == 2:
+        elif data_module['version'] in [2, 3]:
             column_types = np.frombuffer(data_module['data'][5:], dtype='<u2',
                                          count=n_columns)
-            # There is 405 bytes of data before the main array starts
+            # There are 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'][405:]
+            main_data = data_module['data'][num_bytes_before:]
         else:
             raise ValueError("Unrecognised version for data module: %d" %
                              data_module['version'])
 
-        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)
@@ -353,9 +395,9 @@ class MPRfile:
         self.npts = n_data_points
 
         try:
-            tm = time.strptime(str3(settings_mod['date']), '%m/%d/%y')
+            tm = time.strptime(settings_mod['date'].decode('ascii'), '%m/%d/%y')
         except ValueError:
-            tm = time.strptime(str3(settings_mod['date']), '%m-%d-%y')
+            tm = time.strptime(settings_mod['date'].decode('ascii'), '%m-%d-%y')
         self.startdate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
 
         if maybe_loop_module:
@@ -371,9 +413,9 @@ class MPRfile:
         if maybe_log_module:
             log_module, = maybe_log_module
             try:
-                tm = time.strptime(str3(log_module['date']), '%m/%d/%y')
+                tm = time.strptime(log_module['date'].decode('ascii'), '%m/%d/%y')
             except ValueError:
-                tm = time.strptime(str3(log_module['date']), '%m-%d-%y')
+                tm = time.strptime(log_module['date'].decode('ascii'), '%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

@@ -5,26 +5,51 @@ 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 = ["Version_Table", "Global_Table", "Resume_Table",
-              "Channel_Normal_Table", "Channel_Statistic_Table",
-              "Auxiliary_Table", "Event_Table",
-              "Smart_Battery_Info_Table", "Smart_Battery_Data_Table"]
-
-mdb_tables_text = ["Version_Table", "Global_Table", "Event_Table",
-                   "Smart_Battery_Info_Table"]
-mdb_tables_numeric = ["Resume_Table", "Channel_Normal_Table",
-                      "Channel_Statistic_Table", "Auxiliary_Table",
-                      "Smart_Battery_Data_Table", 'MCell_Aci_Data_Table',
+mdb_tables = [
+    'Version_Table',
+    'Global_Table',
+    'Resume_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']
+    'Smart_Battery_Clock_Stretch_Table',
+]
+mdb_5_26_tables = [
+    'Can_BMS_Info_Table',
+    'Can_BMS_Data_Table',
+]
 
-mdb_5_23_tables = ['MCell_Aci_Data_Table', 'Aux_Global_Data_Table',
-                   'Smart_Battery_Clock_Stretch_Table']
+mdb_tables_text = {
+    'Version_Table',
+    'Global_Table',
+    'Event_Table',
+    'Smart_Battery_Info_Table',
+    'Can_BMS_Info_Table',
+}
+mdb_tables_numeric = {
+    'Resume_Table',
+    'Channel_Normal_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": """
@@ -56,8 +81,17 @@ 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,
-  -- Version 1.14 ends here, version 5.23 continues
+  -- These items are in 5.26 and 5.23 but not in 1.14
     Mapped_Aux_Conc_CNumber         INTEGER DEFAULT NULL,
     Mapped_Aux_DI_CNumber           INTEGER DEFAULT NULL,
     Mapped_Aux_DO_CNumber           INTEGER DEFAULT NULL
@@ -65,7 +99,7 @@ CREATE TABLE Global_Table
     "Resume_Table": """
 CREATE TABLE Resume_Table
  (
-    Test_ID         INTEGER REFERENCES Global_Table(Test_ID),
+    Test_ID         INTEGER PRIMARY KEY REFERENCES Global_Table(Test_ID),
     Step_Index      INTEGER,
     Cycle_Index     INTEGER,
     Channel_Status  INTEGER,
@@ -115,7 +149,8 @@ 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
@@ -126,6 +161,7 @@ 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)
 ); """,
@@ -138,6 +174,7 @@ 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)
 ); """,
@@ -153,7 +190,7 @@ CREATE TABLE Event_Table
     "Smart_Battery_Info_Table":  """
 CREATE TABLE Smart_Battery_Info_Table
  (
-    Test_ID                 INTEGER REFERENCES Global_Table(Test_ID),
+    Test_ID                 INTEGER PRIMARY KEY REFERENCES Global_Table(Test_ID),
     ManufacturerDate        REAL,
     ManufacturerAccess      TEXT,
     SpecificationInfo       TEXT,
@@ -222,10 +259,14 @@ 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
+    # The following tables are not present in version 1.14, but are in 5.23
     'MCell_Aci_Data_Table': """
 CREATE TABLE MCell_Aci_Data_Table
  (
@@ -236,6 +277,7 @@ 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)
 );""",
@@ -246,7 +288,8 @@ 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
@@ -292,9 +335,32 @@ 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": """
@@ -371,27 +437,28 @@ 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:
-        mdb_sql = sp.Popen(['mdb-export', '-I', 'postgres', filename, table],
-                           bufsize=-1, stdin=None, stdout=sp.PIPE,
-                           universal_newlines=True)
+        # Initialize values to avoid NameError in except clause
+        mdb_output = ''
+        insert_match = None
+        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:
@@ -399,24 +466,14 @@ 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:
-        mdb_sql = sp.Popen(['mdb-export', filename, table],
-                           bufsize=-1, stdin=None, stdout=sp.PIPE,
-                           universal_newlines=True)
-    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:
+        with sp.Popen(['mdb-export', filename, 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)
             quoted_headers = ['"%s"' % h for h in mdb_headers]
@@ -429,8 +486,12 @@ def mdb_get_data_numeric(s3db, filename, table):
             )
             s3db.executemany(insert_stmt, mdb_csv)
             s3db.commit()
-    finally:
-        mdb_sql.terminate()
+    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
 
 
 def mdb_get_data(s3db, filename, table):
@@ -442,32 +503,69 @@ 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)
 
-    for table in reversed(mdb_tables + mdb_5_23_tables):
+    tables_to_convert = copy(mdb_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 mdb_tables:
+    for table in tables_to_convert:
         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

@@ -24,4 +24,5 @@ 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

@@ -9,11 +9,11 @@ with open(os.path.join(os.path.dirname(__file__), 'README.md')) as f:
 
 setup(
     name='galvani',
-    version='0.0.2',
+    version='0.2.0',
     description='Open and process battery charger log data files',
     long_description=readme,
     long_description_content_type="text/markdown",
-    url='https://github.com/chatcannon/galvani',
+    url='https://github.com/echemdata/galvani',
     author='Chris Kerr',
     author_email='chris.kerr@mykolab.ch',
     license='GPLv3+',
@@ -23,11 +23,16 @@ 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={'console_scripts': [
+    entry_points={
+        'console_scripts': [
             '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
 
 
-# TODO - change to subprocess.DEVNULL when python 2 support is removed
-have_mdbtools = (subprocess.call(['which', 'mdb-export'], stdout=None) == 0)
+have_mdbtools = (subprocess.call(['which', 'mdb-export'],
+                                 stdout=subprocess.DEVNULL) == 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'])
+@pytest.mark.parametrize('basename', ['arbin1', 'UM34_Test005E'])
 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, str3  # not exported
+from galvani.BioLogic import MPTfileCSV  # 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(str3(time_match.group(1)),
+            timestamp = datetime.strptime(time_match.group(1).decode('ascii'),
                                           '%m/%d/%Y %H:%M:%S')
             return timestamp
     raise AttributeError("No timestamp in comments")

tox.ini

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