Merge pull request #32 from chatcannon/flake8

Add code style checking with flake8
2025-12-14 01:15:34 +00:00 · 2019-05-16 17:25:36 +02:00
parent a41b40c7a4 aab135391a
commit a4cf8c1420
6 changed files with 106 additions and 66 deletions
--- a/.flake8
+++ b/.flake8
@@ -0,0 +1,2 @@
+# This file will be ignored - see http://flake8.pycqa.org/en/2.6.0/config.html#per-project
+# Edit the [flake8] section in tox.ini instead
--- a/galvani/BioLogic.py
+++ b/galvani/BioLogic.py
@@ -10,6 +10,7 @@ from os import SEEK_SET
 import time
 from datetime import date, datetime, timedelta
 from collections import defaultdict, OrderedDict
+import functools

 import numpy as np

@@ -18,7 +19,7 @@ if sys.version_info.major <= 2:
    str3 = str
    from string import maketrans
 else:
-    str3 = lambda b: str(b, encoding='ascii')
+    str3 = functools.partial(str, encoding='ascii')
    maketrans = bytes.maketrans


@@ -71,19 +72,20 @@ def MPTfile(file_or_path):
        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*$', next(mpt_file))
+    nb_headers_match = re.match(b'Nb header lines : (\\d+)\\s*$',
+                                next(mpt_file))
    nb_headers = int(nb_headers_match.group(1))
    if nb_headers < 3:
        raise ValueError("Too few header lines: %d" % nb_headers)

-    ## The 'magic number' line, the 'Nb headers' line and the column headers
-    ## make three lines. Every additional line is a comment line.
+    # The 'magic number' line, the 'Nb headers' line and the column headers
+    # 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')
    record_type = np.dtype(list(map(fieldname_to_dtype, fieldnames)))

-    ## Must be able to parse files where commas are used for decimal points
+    # Must be able to parse files where commas are used for decimal points
    converter_dict = dict(((i, comma_converter)
                           for i in range(len(fieldnames))))
    mpt_array = np.loadtxt(mpt_file, dtype=record_type,
@@ -113,8 +115,8 @@ def MPTfileCSV(file_or_path):
    if nb_headers < 3:
        raise ValueError("Too few header lines: %d" % nb_headers)

-    ## The 'magic number' line, the 'Nb headers' line and the column headers
-    ## make three lines. Every additional line is a comment line.
+    # The 'magic number' line, the 'Nb headers' line and the column headers
+    # make three lines. Every additional line is a comment line.
    comments = [next(mpt_file) for i in range(nb_headers - 3)]

    mpt_csv = csv.DictReader(mpt_file, dialect='excel-tab')
@@ -256,7 +258,8 @@ def read_VMP_modules(fileobj, read_module_data=True):
        if len(module_magic) == 0:  # end of file
            break
        elif module_magic != b'MODULE':
-            raise ValueError("Found %r, expecting start of new VMP MODULE" % module_magic)
+            raise ValueError("Found %r, expecting start of new VMP MODULE"
+                             % module_magic)

        hdr_bytes = fileobj.read(VMPmodule_hdr.itemsize)
        if len(hdr_bytes) < VMPmodule_hdr.itemsize:
@@ -280,6 +283,9 @@ def read_VMP_modules(fileobj, read_module_data=True):
            fileobj.seek(hdr_dict['offset'] + hdr_dict['length'], SEEK_SET)


+MPR_MAGIC = b'BIO-LOGIC MODULAR FILE\x1a'.ljust(48) + b'\x00\x00\x00\x00'
+
+
 class MPRfile:
    """Bio-Logic .mpr file

@@ -302,10 +308,8 @@ class MPRfile:
            mpr_file = open(file_or_path, 'rb')
        else:
            mpr_file = file_or_path
-
-        mpr_magic = b'BIO-LOGIC MODULAR FILE\x1a                         \x00\x00\x00\x00'
-        magic = mpr_file.read(len(mpr_magic))
-        if magic != mpr_magic:
+        magic = mpr_file.read(len(MPR_MAGIC))
+        if magic != MPR_MAGIC:
            raise ValueError('Invalid magic for .mpr file: %s' % magic)

        modules = list(read_VMP_modules(mpr_file))
@@ -326,7 +330,7 @@ class MPRfile:
        elif data_module['version'] == 2:
            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 is 405 bytes of data before the main array starts
            remaining_headers = data_module['data'][5 + 2 * n_columns:405]
            main_data = data_module['data'][405:]
        else:
@@ -342,8 +346,8 @@ class MPRfile:
        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
-        ## column types at all
+        # No idea what these 'column types' mean or even if they are actually
+        # column types at all
        self.version = int(data_module['version'])
        self.cols = column_types
        self.npts = n_data_points
@@ -372,9 +376,9 @@ class MPRfile:
                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
+            # 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.frombuffer(log_module['data'][465:],
                                           dtype='<f8', count=1)
            ole_timestamp2 = np.frombuffer(log_module['data'][469:],
@@ -400,10 +404,10 @@ class MPRfile:
            ole_timedelta = timedelta(days=ole_timestamp[0])
            self.timestamp = ole_base + ole_timedelta
            if self.startdate != self.timestamp.date():
-                raise ValueError("""Date mismatch:
-                Start date: %s
-                End date: %s
-                Timestamp: %s""" % (self.startdate, self.enddate, self.timestamp))
+                raise ValueError("Date mismatch:\n"
+                                 + "    Start date: %s\n" % self.startdate
+                                 + "    End date: %s\n" % self.enddate
+                                 + "    Timestamp: %s\n" % self.timestamp)

    def get_flag(self, flagname):
        if flagname in self.flags_dict:
--- a/galvani/init.py
+++ b/galvani/init.py
@@ -1 +1,3 @@
-from .BioLogic import MPTfile, MPRfile
+from .BioLogic import MPRfile, MPTfile
+
+__all__ = ['MPRfile', 'MPTfile']
--- a/galvani/res2sqlite.py
+++ b/galvani/res2sqlite.py
@@ -7,8 +7,8 @@ import csv
 import argparse


-## The following scripts are adapted from the result of running
-## $ mdb-schema <result.res> oracle
+# 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",
@@ -126,7 +126,8 @@ CREATE TABLE Channel_Statistic_Table
  -- Version 1.14 ends here, version 5.23 continues
    Charge_Time             REAL DEFAULT NULL,
    Discharge_Time          REAL DEFAULT NULL,
-    FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
+    FOREIGN KEY (Test_ID, Data_Point)
+        REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 ); """,
    "Auxiliary_Table": """
 CREATE TABLE Auxiliary_Table
@@ -137,7 +138,8 @@ CREATE TABLE Auxiliary_Table
    Data_Type               INTEGER,
    X                       REAL,
    "dX/dt"                 REAL,
-    FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
+    FOREIGN KEY (Test_ID, Data_Point)
+        REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 ); """,
    "Event_Table": """
 CREATE TABLE Event_Table
@@ -220,9 +222,10 @@ CREATE TABLE Smart_Battery_Data_Table
    ChargingCurrent         REAL DEFAULT NULL,
    ChargingVoltage         REAL DEFAULT NULL,
    ManufacturerData        REAL DEFAULT NULL,
-    FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (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
    'MCell_Aci_Data_Table': """
 CREATE TABLE MCell_Aci_Data_Table
 (
@@ -233,7 +236,8 @@ CREATE TABLE MCell_Aci_Data_Table
    Phase_Shift		REAL,
    Voltage			REAL,
    Current			REAL,
-    FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
+    FOREIGN KEY (Test_ID, Data_Point)
+        REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 );""",
    'Aux_Global_Data_Table': """
 CREATE TABLE Aux_Global_Data_Table
@@ -288,7 +292,8 @@ CREATE TABLE Smart_Battery_Clock_Stretch_Table
    VCELL3			    INTEGER,
    VCELL2			    INTEGER,
    VCELL1			    INTEGER,
-    FOREIGN KEY (Test_ID, Data_Point) REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
+    FOREIGN KEY (Test_ID, Data_Point)
+        REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 );"""}

 mdb_create_indices = {
@@ -306,11 +311,14 @@ CREATE TEMPORARY TABLE capacity_helper(
    Discharge_Capacity     REAL NOT NULL,
    Charge_Energy          REAL NOT NULL,
    Discharge_Energy       REAL NOT NULL,
-    FOREIGN KEY (Test_ID, Cycle_Index) REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
+    FOREIGN KEY (Test_ID, Cycle_Index)
+        REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
 );

 INSERT INTO capacity_helper
-    SELECT Test_ID, Cycle_Index, max(Charge_Capacity), max(Discharge_Capacity), max(Charge_Energy), max(Discharge_Energy) 
+    SELECT Test_ID, Cycle_Index,
+           max(Charge_Capacity), max(Discharge_Capacity),
+           max(Charge_Energy), max(Discharge_Energy)
        FROM Channel_Normal_Table
        GROUP BY Test_ID, Cycle_Index;

@@ -328,11 +336,14 @@ CREATE TABLE Capacity_Sum_Table(
    Discharge_Capacity_Sum REAL NOT NULL,
    Charge_Energy_Sum      REAL NOT NULL,
    Discharge_Energy_Sum   REAL NOT NULL,
-    FOREIGN KEY (Test_ID, Cycle_Index) REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
+    FOREIGN KEY (Test_ID, Cycle_Index)
+        REFERENCES Channel_Normal_Table (Test_ID, Cycle_Index)
 );

 INSERT INTO Capacity_Sum_Table
-    SELECT a.Test_ID, a.Cycle_Index, total(b.Charge_Capacity), total(b.Discharge_Capacity), total(b.Charge_Energy), total(b.Discharge_Energy) 
+    SELECT a.Test_ID, a.Cycle_Index,
+           total(b.Charge_Capacity), total(b.Discharge_Capacity),
+           total(b.Charge_Energy), total(b.Discharge_Energy)
        FROM capacity_helper AS a LEFT JOIN capacity_helper AS b
            ON (a.Test_ID = b.Test_ID AND a.Cycle_Index > b.Cycle_Index)
        GROUP BY a.Test_ID, a.Cycle_Index;
@@ -342,28 +353,35 @@ DROP TABLE capacity_helper;
 CREATE VIEW IF NOT EXISTS Capacity_View
    AS SELECT Test_ID, Data_Point, Test_Time, Step_Time, DateTime,
              Step_Index, Cycle_Index, Current, Voltage, "dV/dt",
-              Discharge_Capacity + Discharge_Capacity_Sum - Charge_Capacity - Charge_Capacity_Sum AS Net_Capacity,
-              Discharge_Capacity + Discharge_Capacity_Sum + Charge_Capacity + Charge_Capacity_Sum AS Gross_Capacity,
-              Discharge_Energy + Discharge_Energy_Sum - Charge_Energy - Charge_Energy_Sum AS Net_Energy,
-              Discharge_Energy + Discharge_Energy_Sum + Charge_Energy + Charge_Energy_Sum AS Gross_Energy
+              ( (Discharge_Capacity + Discharge_Capacity_Sum)
+              - (Charge_Capacity + Charge_Capacity_Sum) ) AS Net_Capacity,
+              ( (Discharge_Capacity + Discharge_Capacity_Sum)
+              + (Charge_Capacity + Charge_Capacity_Sum) ) AS Gross_Capacity,
+              ( (Discharge_Energy + Discharge_Energy_Sum)
+              - (Charge_Energy + Charge_Energy_Sum) ) AS Net_Energy,
+              ( (Discharge_Energy + Discharge_Energy_Sum)
+              + (Charge_Energy + Charge_Energy_Sum) ) AS Gross_Energy
        FROM Channel_Normal_Table NATURAL JOIN Capacity_Sum_Table;
 """


 def mdb_get_data_text(s3db, filename, table):
    print("Reading %s..." % table)
+    insert_pattern = re.compile(
+        r'INSERT INTO "\w+" \([^)]+?\) VALUES \(("[^"]*"|[^")])+?\);\n',
+        re.IGNORECASE
+    )
    try:
        mdb_sql = sp.Popen(['mdb-export', '-I', 'postgres', filename, table],
                           bufsize=-1, stdin=None, stdout=sp.PIPE,
                           universal_newlines=True)
        mdb_output = mdb_sql.stdout.read()
        while len(mdb_output) > 0:
-            insert_match = re.match(r'INSERT INTO "\w+" \([^)]+?\) VALUES \(("[^"]*"|[^")])+?\);\n',
-                                    mdb_output, re.IGNORECASE)
+            insert_match = insert_pattern.match(mdb_output)
            s3db.execute(insert_match.group())
            mdb_output = mdb_output[insert_match.end():]
        s3db.commit()
-    except:
+    except BaseException:
        print("Error while importing %s" % table)
        print("Remaining mdb-export output:", mdb_output)
        if insert_match:
@@ -384,8 +402,11 @@ def mdb_get_data_numeric(s3db, filename, table):
        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)
+        insert_stmt = 'INSERT INTO "{0}" ({1}) VALUES ({2});'.format(
+            table,
+            joined_headers,
+            joined_placemarks,
+        )
        s3db.executemany(insert_stmt, mdb_csv)
        s3db.commit()
    finally:
@@ -408,7 +429,6 @@ def convert_arbin_to_sqlite(input_file, output_file):
    """
    s3db = sqlite3.connect(output_file)

-    
    for table in reversed(mdb_tables + mdb_5_23_tables):
        s3db.execute('DROP TABLE IF EXISTS "%s";' % table)

@@ -419,7 +439,9 @@ def convert_arbin_to_sqlite(input_file, output_file):
            print("Creating indices for %s..." % table)
            s3db.executescript(mdb_create_indices[table])

-    if (s3db.execute("SELECT Version_Schema_Field FROM Version_Table;").fetchone()[0] == "Results File 5.23"):
+    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)
@@ -434,7 +456,9 @@ def convert_arbin_to_sqlite(input_file, output_file):


 def main(argv=None):
-    parser = argparse.ArgumentParser(description="Convert Arbin .res files to sqlite3 databases using mdb-export")
+    parser = argparse.ArgumentParser(
+        description="Convert Arbin .res files to sqlite3 databases using mdb-export",
+    )
    parser.add_argument('input_file', type=str)  # need file name to pass to sp.Popen
    parser.add_argument('output_file', type=str)  # need file name to pass to sqlite3.connect

--- a/tests/test_BioLogic.py
+++ b/tests/test_BioLogic.py
@@ -129,7 +129,7 @@ def assert_MPR_matches_MPT(mpr, mpt, comments):
    assert_array_equal(mpr.get_flag("control changes"), mpt["control changes"])
    if "Ns changes" in mpt.dtype.fields:
        assert_array_equal(mpr.get_flag("Ns changes"), mpt["Ns changes"])
-    ## 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_almost_equal(mpr.data["time/s"],
--- a/tox.ini
+++ b/tox.ini
@@ -1,5 +1,13 @@
 [tox]
 envlist = py27,py35,py37
 [testenv]
-deps=pytest
-commands=pytest
+deps =
+  flake8
+  pytest
+commands =
+  flake8
+  pytest
+
+[flake8]
+exclude = build,dist,*.egg-info,.cache,.git,.tox,__pycache__
+max-line-length = 100