Merge pull request #40 from chatcannon/remove-python-2

Remove Python 2 support

.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"
 install:
   - pip install tox-travis
   - sh get_testdata.sh

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):
+def comma_converter(float_text):
-    """Convert numbers to floats whether the decimal point is '.' or ','"""
+    """Convert text to float whether the decimal point is '.' or ','"""
-    trans_table = maketrans(b',', b'.')
+    trans_table = bytes.maketrans(b',', b'.')
-    return float(float_string.translate(trans_table))
+    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(rb'Nb header lines : (\d+)\s*$',
-    nb_headers_match = re.match(b'Nb header lines : (\\d+)\\s*$',
                                 next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
@@ -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
@@ -345,10 +334,7 @@ class MPRfile:
             raise ValueError("Unrecognised version for data module: %d" %
                              data_module['version'])
 
-        if sys.version_info.major <= 2:
+        assert(not any(remaining_headers))
-            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)
@@ -361,9 +347,9 @@ 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:
@@ -379,9 +365,9 @@ 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

@@ -371,27 +371,28 @@ 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],
+        # Initialize values to avoid NameError in except clause
-                           bufsize=-1, stdin=None, stdout=sp.PIPE,
+        mdb_output = ''
-                           universal_newlines=True)
+        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:
@@ -399,38 +400,32 @@ 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],
+        with sp.Popen(['mdb-export', filename, table],
-                           bufsize=-1, stdin=None, stdout=sp.PIPE,
+                      bufsize=-1, stdin=sp.DEVNULL, stdout=sp.PIPE,
-                           universal_newlines=True)
+                      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]
+            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):

setup.py

@@ -23,6 +23,8 @@ 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={
@@ -30,6 +32,7 @@ setup(
             'res2sqlite = galvani.res2sqlite:main',
         ],
     },
+    python_requires='>=3.5',
     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'],
-have_mdbtools = (subprocess.call(['which', 'mdb-export'], stdout=None) == 0)
+                                 stdout=subprocess.DEVNULL) == 0)
 
 
 def test_res2sqlite_help():

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 = py35,py36,py37,py38
 [testenv]
 deps =
   flake8