Update version in setup.py to 0.2.1

Add '%m.%d.%y' date format for .mpr file timestamps

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# SPDX-FileCopyrightText: 2006-2020 GitHub, Inc.
+# SPDX-License-Identifier: MIT
+
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+# ******** NOTE ********
+
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '22 23 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more...
+        # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.gitignore

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: 2013-2017 Christopher Kerr <chris.kerr@mykolab.ch>
+# SPDX-License-Identifier: CC0-1.0
+
 *.py[cod]
 
 # C extensions

.reuse/dep5

@@ -0,0 +1,10 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Galvani
+Upstream-Contact: Christopher Kerr <chris.kerr@mykolab.ch>
+Source: https://github.com/echemdata/galvani
+
+# Sample paragraph, commented out:
+#
+# Files: src/*
+# Copyright: $YEAR $NAME <$CONTACT>
+# License: ...

.travis.yml

@@ -1,13 +1,17 @@
+# SPDX-FileCopyrightText: 2017-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+# SPDX-License-Identifier: GPL-3.0-or-later
 sudo: false
 language: python
 cache:
   directories:
     - .tox
+    - .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

LICENSES/CC0-1.0.txt

@@ -0,0 +1,121 @@
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LICENSES/GPL-3.0-or-later.txt

@@ -0,0 +1,232 @@
+GNU GENERAL PUBLIC LICENSE
+Version 3, 29 June 2007
+
+Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
+
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+
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+
+The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.
+
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+
+You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
+
+11. Patents.
+A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's “contributor version”.
+
+A contributor's “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
+
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+
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+
+If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
+
+A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
+
+12. No Surrender of Others' Freedom.
+If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
+
+13. Use with the GNU Affero General Public License.
+Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
+
+14. Revised Versions of this License.
+The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
+
+15. Disclaimer of Warranty.
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+16. Limitation of Liability.
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+17. Interpretation of Sections 15 and 16.
+If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
+
+     <one line to give the program's name and a brief idea of what it does.>
+     Copyright (C) <year>  <name of author>
+
+     This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+     This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+
+     You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
+
+     <program>  Copyright (C) <year>  <name of author>
+     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+     This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
+
+The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.

LICENSES/MIT.txt

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) <year> <copyright holders>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

MANIFEST.in

@@ -0,0 +1,9 @@
+# SPDX-FileCopyrightText: 2021 Christopher Kerr
+# SPDX-License-Identifier: CC0-1.0
+
+recursive-include LICENSES *.txt
+include README.md
+
+# The GitHub CodeQL file is not included in the tarball,
+# so its licence does not need to be included either
+exclude LICENSES/MIT.txt

README.md

@@ -1,12 +1,26 @@
 galvani
 =======
 
+<!---
+SPDX-FileCopyrightText: 2013-2020 Christopher Kerr, Peter Attia
+
+SPDX-License-Identifier: GPL-3.0-or-later
+-->
+
 Read proprietary file formats from electrochemical test stations
 
 ## Bio-Logic .mpr files ##
 
 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

@@ -1,27 +1,22 @@
 # -*- coding: utf-8 -*-
 """Code to read in data files from Bio-Logic instruments"""
 
+# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr, "bcolsen"
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 __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 OrderedDict
+from collections import defaultdict, OrderedDict
 
 import numpy as np
 
 
-if sys.version_info.major <= 2:
-    str3 = str
-    from string import maketrans
-else:
-    str3 = lambda b: str(b, 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"""
@@ -48,13 +43,13 @@ 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
@@ -70,19 +65,20 @@ 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*$', next(mpt_file))
+    nb_headers_match = re.match(rb'Nb header lines : (\d+)\s*$',
+                                next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
         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')
+    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
+    # 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,
@@ -107,13 +103,13 @@ 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)
 
-    ## 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')
@@ -143,109 +139,179 @@ VMPmodule_hdr = np.dtype([('shortname', 'S10'),
                           ('version', '<u4'),
                           ('date', 'S8')])
 
+# Maps from colID to a tuple defining a numpy dtype
+VMPdata_colID_dtype_map = {
+    4: ('time/s', '<f8'),
+    5: ('control/V/mA', '<f4'),
+    6: ('Ewe/V', '<f4'),
+    7: ('dQ/mA.h', '<f8'),
+    8: ('I/mA', '<f4'),  # 8 is either I or <I> ??
+    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?
+    24: ('cycle number', '<f8'),
+    26: ('Rapp/Ohm', '<f4'),
+    32: ('freq/Hz', '<f4'),
+    33: ('|Ewe|/V', '<f4'),
+    34: ('|I|/A', '<f4'),
+    35: ('Phase(Z)/deg', '<f4'),
+    36: ('|Z|/Ohm', '<f4'),
+    37: ('Re(Z)/Ohm', '<f4'),
+    38: ('-Im(Z)/Ohm', '<f4'),
+    39: ('I Range', '<u2'),
+    69: ('R/Ohm', '<f4'),
+    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
+# The values in the map are (name, bitmask, dtype)
+VMPdata_colID_flag_map = {
+    1: ('mode', 0x03, np.uint8),
+    2: ('ox/red', 0x04, np.bool_),
+    3: ('error', 0x08, np.bool_),
+    21: ('control changes', 0x10, np.bool_),
+    31: ('Ns changes', 0x20, np.bool_),
+    65: ('counter inc.', 0x80, np.bool_),
+}
+
+
+def parse_BioLogic_date(date_text):
+    """Parse a date from one of the various formats used by Bio-Logic files."""
+    date_formats = ['%m/%d/%y', '%m-%d-%y', '%m.%d.%y']
+    if isinstance(date_text, bytes):
+        date_string = date_text.decode('ascii')
+    else:
+        date_string = date_text
+    for date_format in date_formats:
+        try:
+            tm = time.strptime(date_string, date_format)
+        except ValueError:
+            continue
+        else:
+            break
+    else:
+        raise ValueError(f'Could not parse timestamp {date_string!r}'
+                         f' with any of the formats {date_formats}')
+    return date(tm.tm_year, tm.tm_mon, tm.tm_mday)
+
 
 def VMPdata_dtype_from_colIDs(colIDs):
-    dtype_dict = OrderedDict()
+    """Get a numpy record type from a list of column ID numbers.
+
+    The binary layout of the data in the MPR file is described by the sequence
+    of column ID numbers in the file header. This function converts that
+    sequence into a numpy dtype which can then be used to load data from the
+    file with np.frombuffer().
+
+    Some column IDs refer to small values which are packed into a single byte.
+    The second return value is a dict describing the bit masks with which to
+    extract these columns from the flags byte.
+
+    """
+    type_list = []
+    field_name_counts = defaultdict(int)
     flags_dict = OrderedDict()
-    flags2_dict = OrderedDict()
     for colID in colIDs:
-        if colID in (1, 2, 3, 21, 31, 65):
-            dtype_dict['flags'] = 'u1'
-            if colID == 1:
-                flags_dict['mode'] = (np.uint8(0x03), np.uint8)
-            elif colID == 2:
-                flags_dict['ox/red'] = (np.uint8(0x04), np.bool_)
-            elif colID == 3:
-                flags_dict['error'] = (np.uint8(0x08), np.bool_)
-            elif colID == 21:
-                flags_dict['control changes'] = (np.uint8(0x10), np.bool_)
-            elif colID == 31:
-                flags_dict['Ns changes'] = (np.uint8(0x20), np.bool_)
-            elif colID == 65:
-                flags_dict['counter inc.'] = (np.uint8(0x80), np.bool_)
+        if colID in VMPdata_colID_flag_map:
+            # Some column IDs represent boolean flags or small integers
+            # These are all packed into a single 'flags' byte whose position
+            # in the overall record is determined by the position of the first
+            # column ID of flag type. If there are several flags present,
+            # there is still only one 'flags' int
+            if 'flags' not in field_name_counts:
+                type_list.append(('flags', 'u1'))
+                field_name_counts['flags'] = 1
+            flag_name, flag_mask, flag_type = VMPdata_colID_flag_map[colID]
+            # TODO what happens if a flag colID has already been seen
+            # i.e. if flag_name is already present in flags_dict?
+            # Does it create a second 'flags' byte in the record?
+            flags_dict[flag_name] = (np.uint8(flag_mask), flag_type)
+        elif colID in VMPdata_colID_dtype_map:
+            field_name, field_type = VMPdata_colID_dtype_map[colID]
+            field_name_counts[field_name] += 1
+            count = field_name_counts[field_name]
+            if count > 1:
+                unique_field_name = '%s %d' % (field_name, count)
             else:
-                raise NotImplementedError("flag %d not implemented" % colID)
-        elif colID == 4:
-            dtype_dict['time/s'] = '<f8'
-        elif colID == 5:
-            dtype_dict['control/V/mA'] = '<f4'
-        # 6 is Ewe, 77 is <Ewe>, I don't see the difference
-        elif colID in (6, 77):
-            dtype_dict['Ewe/V'] = '<f4'
-        # Can't see any difference between 7 and 23
-        elif colID in (7, 23):
-            dtype_dict['dQ/mA.h'] = '<f8'
-        # 76 is <I>, 8 is either I or <I> ??
-        elif colID in (8, 76):
-            dtype_dict['I/mA'] = '<f4'
-        elif colID == 9:
-            dtype_dict['Ece/V'] = '<f4'
-        elif colID == 11:
-            dtype_dict['I/mA'] = '<f8'
-        elif colID == 13:
-            dtype_dict['(Q-Qo)/mA.h'] = '<f8'
-        elif colID == 19:
-            dtype_dict['control/V'] = '<f4'
-        elif colID == 20:
-            dtype_dict['control/mA'] = '<f4'
-        elif colID == 24:
-            dtype_dict['cycle number'] = '<f8'
-        elif colID == 32:
-            dtype_dict['freq/Hz'] = '<f4'
-        elif colID == 33:
-            dtype_dict['|Ewe|/V'] = '<f4'
-        elif colID == 34:
-            dtype_dict['|I|/A'] = '<f4'
-        elif colID == 35:
-            dtype_dict['Phase(Z)/deg'] = '<f4'
-        elif colID == 36:
-            dtype_dict['|Z|/Ohm'] = '<f4'
-        elif colID == 37:
-            dtype_dict['Re(Z)/Ohm'] = '<f4'
-        elif colID == 38:
-            dtype_dict['-Im(Z)/Ohm'] = '<f4'
-        elif colID == 39:
-            dtype_dict['I Range'] = '<u2'
-        elif colID == 70:
-            dtype_dict['P/W'] = '<f4'
-        elif colID == 123:
-            dtype_dict['Energy charge/W.h'] = '<f8'
-        elif colID == 124:
-            dtype_dict['Energy discharge/W.h'] = '<f8'
-        elif colID == 125:
-            dtype_dict['Capacitance charge/µF'] = '<f8'
-        elif colID == 126:
-            dtype_dict['Capacitance discharge/µF'] = '<f8'
-        elif colID == 131:
-            dtype_dict['Ns'] = '<u2'
-        elif colID == 169:
-            dtype_dict['Cs/µF'] = '<f4'
-        elif colID == 172:
-            dtype_dict['Cp/µF'] = '<f4'
-        elif colID == 434:
-            dtype_dict['(Q-Qo)/C'] = '<f4'
-        elif colID == 435:
-            dtype_dict['dQ/C'] = '<f4'
-        elif colID == 467:
-            dtype_dict['Q charge/discharge/mA.h'] = '<f8'
-        elif colID == 468:
-            dtype_dict['half cycle'] = '<u4'
-        elif colID == 473:
-            dtype_dict['THD Ewe/%'] = '<f4'
-        elif colID == 476:
-            dtype_dict['NSD Ewe/%'] = '<f4'
-        elif colID == 479:
-            dtype_dict['NSR Ewe/%'] = '<f4'
-        elif colID == 474:
-            dtype_dict['THD I/%'] = '<f4'
-        elif colID == 477:
-            dtype_dict['NSD I/%'] = '<f4'
-        elif colID == 480:
-            dtype_dict['NSR I/%'] = '<f4'
+                unique_field_name = field_name
+            type_list.append((unique_field_name, field_type))
         else:
-            print(dtype_dict)
-            raise NotImplementedError("column type %d not implemented" % colID)
-    return np.dtype(list(dtype_dict.items())), flags_dict, flags2_dict
+            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
 
 
 def read_VMP_modules(fileobj, read_module_data=True):
@@ -259,13 +325,14 @@ 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:
             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:
@@ -283,6 +350,9 @@ 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
 
@@ -300,74 +370,81 @@ class MPRfile:
     """
 
     def __init__(self, file_or_path):
+        self.loop_index = None
         if isinstance(file_or_path, str):
             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))
         self.modules = modules
         settings_mod, = (m for m in modules if m['shortname'] == b'VMP Set   ')
         data_module, = (m for m in modules if m['shortname'] == b'VMP data  ')
+        maybe_loop_module = [m for m in modules if m['shortname'] == b'VMP loop  ']
         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_columns = np.fromstring(data_module['data'][4:5], dtype='u1')
-        n_columns = np.asscalar(n_columns)  # Compatibility with recent numpy
+        n_data_points = np.frombuffer(data_module['data'][:4], dtype='<u4')
+        n_columns = np.frombuffer(data_module['data'][4:5], dtype='u1').item()
 
         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',
+        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, self.flags2_dict = VMPdata_dtype_from_colIDs(column_types)
-        self.data = np.fromstring(main_data, dtype=self.dtype)
+        self.dtype, self.flags_dict = VMPdata_dtype_from_colIDs(column_types)
+        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
+        self.startdate = parse_BioLogic_date(settings_mod['date'])
 
-        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:
+            loop_module, = maybe_loop_module
+            if loop_module['version'] == 0:
+                self.loop_index = np.fromstring(loop_module['data'][4:],
+                                                dtype='<u4')
+                self.loop_index = np.trim_zeros(self.loop_index, 'b')
+            else:
+                raise ValueError("Unrecognised version for data module: %d" %
+                                 data_module['version'])
 
         if maybe_log_module:
             log_module, = maybe_log_module
-            tm = time.strptime(str3(log_module['date']), '%m/%d/%y')
-            self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
+            self.enddate = parse_BioLogic_date(log_module['date'])
 
-            ## 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:],
+            # 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.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:
@@ -386,17 +463,14 @@ 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:
             mask, dtype = self.flags_dict[flagname]
             return np.array(self.data['flags'] & mask, dtype=dtype)
-        elif flagname in self.flags2_dict:
-            mask, dtype = self.flags2_dict[flagname]
-            return np.array(self.data['flags2'] & mask, dtype=dtype)
         else:
             raise AttributeError("Flag '%s' not present" % flagname)

galvani/__init__.py

@@ -1 +1,7 @@
-from .BioLogic import MPTfile, MPRfile
+# SPDX-FileCopyrightText: 2014-2019 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from .BioLogic import MPRfile, MPTfile
+
+__all__ = ['MPRfile', 'MPTfile']

galvani/res2sqlite.py

@@ -1,30 +1,59 @@
 #!/usr/bin/python
 
+# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import subprocess as sp
 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
+# 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 +85,17 @@ 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 +103,7 @@ 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 +153,8 @@ 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
@@ -126,7 +165,9 @@ 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)
+    PRIMARY KEY (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 +178,9 @@ 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)
+    PRIMARY KEY (Test_ID, Data_Point, Auxiliary_Index),
+    FOREIGN KEY (Test_ID, Data_Point)
+        REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 ); """,
     "Event_Table": """
 CREATE TABLE Event_Table
@@ -151,7 +194,7 @@ 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,
@@ -220,9 +263,14 @@ 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)
+  -- 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
  (
@@ -233,7 +281,9 @@ 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)
+    PRIMARY KEY (Test_ID, Data_Point, Cell_Index),
+    FOREIGN KEY (Test_ID, Data_Point)
+        REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 );""",
     'Aux_Global_Data_Table': """
 CREATE TABLE Aux_Global_Data_Table
@@ -242,7 +292,8 @@ 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
@@ -288,8 +339,32 @@ 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)
-);"""}
+    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": """
@@ -306,11 +381,14 @@ 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 +406,14 @@ 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;
@@ -342,54 +423,79 @@ 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)
+        # 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 = 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():]
+                mdb_output += mdb_sql.stdout.read()
             s3db.commit()
-    except:
+
+    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
+    except BaseException:
         print("Error while importing %s" % table)
+        if mdb_output:
             print("Remaining mdb-export output:", mdb_output)
         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)
     try:
-        mdb_sql = sp.Popen(['mdb-export', filename, table],
-                           bufsize=-1, stdin=None, stdout=sp.PIPE,
-                           universal_newlines=True)
+        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]
             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:
-        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):
@@ -401,31 +507,69 @@ 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)
 
+    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(mdb_tables + mdb_5_23_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])
 
-    if (s3db.execute("SELECT Version_Schema_Field FROM Version_Table;").fetchone()[0] == "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)
 
@@ -434,7 +578,9 @@ 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
 

get_testdata.sh

@@ -1,5 +1,9 @@
 #!/bin/sh
 
+# SPDX-FileCopyrightText: 2014-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 ## Test data are posted on FigShare, listed in this article
 # http://figshare.com/articles/galvani_test_data/1228760
 
@@ -7,20 +11,22 @@ mkdir -p tests/testdata
 cd tests/testdata
 
 /usr/bin/wget --continue -i - <<END_FILELIST
-http://files.figshare.com/1778905/arbin1.res
-http://files.figshare.com/1778937/bio_logic2.mpt
-http://files.figshare.com/1778938/bio_logic5.mpt
-http://files.figshare.com/1778939/bio_logic1.mpr
-http://files.figshare.com/1778940/bio_logic6.mpr
-http://files.figshare.com/1778941/bio_logic4.mpt
-http://files.figshare.com/1778942/bio_logic5.mpr
-http://files.figshare.com/1778943/bio_logic2.mpr
-http://files.figshare.com/1778944/bio_logic6.mpt
-http://files.figshare.com/1778945/bio_logic1.mpt
-http://files.figshare.com/1778946/bio_logic3.mpr
-http://files.figshare.com/1780444/bio_logic4.mpr
-http://files.figshare.com/1780529/121_CA_455nm_6V_30min_C01.mpr
-http://files.figshare.com/1780530/121_CA_455nm_6V_30min_C01.mpt
-http://files.figshare.com/1780526/CV_C01.mpr
-http://files.figshare.com/1780527/CV_C01.mpt
+https://files.figshare.com/1778905/arbin1.res
+https://files.figshare.com/1778937/bio_logic2.mpt
+https://files.figshare.com/1778938/bio_logic5.mpt
+https://files.figshare.com/1778939/bio_logic1.mpr
+https://files.figshare.com/1778940/bio_logic6.mpr
+https://files.figshare.com/1778941/bio_logic4.mpt
+https://files.figshare.com/1778942/bio_logic5.mpr
+https://files.figshare.com/1778943/bio_logic2.mpr
+https://files.figshare.com/1778944/bio_logic6.mpt
+https://files.figshare.com/1778945/bio_logic1.mpt
+https://files.figshare.com/1778946/bio_logic3.mpr
+https://files.figshare.com/1780444/bio_logic4.mpr
+https://files.figshare.com/1780529/121_CA_455nm_6V_30min_C01.mpr
+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

requirements.txt

@@ -1 +1,3 @@
+# SPDX-FileCopyrightText: 2017 Christopher Kerr <chris.kerr@mykolab.ch>
+# SPDX-License-Identifier: CC0-1.0
 numpy

setup.cfg

@@ -0,0 +1,8 @@
+# SPDX-FileCopyrightText: 2021 Christopher Kerr
+# SPDX-License-Identifier: CC0-1.0
+[metadata]
+# N.B. The MIT-licensed CodeQL file and the CC0-licensed
+# config files are not included in the .whl package so
+# their licenses do not need to be packaged either.
+license_files =
+   LICENSES/GPL-3.0-or-later.txt

setup.py

@@ -1,4 +1,7 @@
 # -*- coding: utf-8 -*-
+# SPDX-FileCopyrightText: 2014-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
 
 import os.path
 
@@ -9,11 +12,11 @@ with open(os.path.join(os.path.dirname(__file__), 'README.md')) as f:
 
 setup(
     name='galvani',
-    version='0.0.1',
+    version='0.2.1',
     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+',
@@ -23,10 +26,16 @@ 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/conftest.py

@@ -0,0 +1,15 @@
+"""Helpers for pytest tests."""
+
+# SPDX-FileCopyrightText: 2019 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+import os
+
+import pytest
+
+
+@pytest.fixture(scope='session')
+def testdata_dir():
+    """Path to the testdata directory."""
+    return os.path.join(os.path.dirname(__file__), 'testdata')

tests/test_Arbin.py

@@ -0,0 +1,60 @@
+"""Tests for loading Arbin .res files."""
+
+# SPDX-FileCopyrightText: 2019-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+import os
+import sqlite3
+import subprocess
+
+import pytest
+
+from galvani import res2sqlite
+
+
+have_mdbtools = (subprocess.call(['which', 'mdb-export'],
+                                 stdout=subprocess.DEVNULL) == 0)
+
+
+def test_res2sqlite_help():
+    """Test running `res2sqlite --help`.
+
+    This should work even when mdbtools is not installed.
+    """
+    help_output = subprocess.check_output(['res2sqlite', '--help'])
+    assert b'Convert Arbin .res files to sqlite3 databases' in help_output
+
+
+@pytest.mark.skipif(have_mdbtools, reason='This tests the failure when mdbtools is not installed')
+def test_convert_Arbin_no_mdbtools(testdata_dir, tmpdir):
+    """Checks that the conversion fails with an appropriate error message."""
+    res_file = os.path.join(testdata_dir, 'arbin1.res')
+    sqlite_file = os.path.join(str(tmpdir), 'arbin1.s3db')
+    with pytest.raises(RuntimeError, match="Could not locate the `mdb-export` executable."):
+        res2sqlite.convert_arbin_to_sqlite(res_file, sqlite_file)
+
+
+@pytest.mark.skipif(not have_mdbtools, reason='Reading the Arbin file requires MDBTools')
+@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')
+    sqlite_file = os.path.join(str(tmpdir), basename + '.s3db')
+    res2sqlite.convert_arbin_to_sqlite(res_file, sqlite_file)
+    assert os.path.isfile(sqlite_file)
+    with sqlite3.connect(sqlite_file) as conn:
+        csr = conn.execute('SELECT * FROM Channel_Normal_Table;')
+        csr.fetchone()
+
+
+@pytest.mark.skipif(not have_mdbtools, reason='Reading the Arbin file requires MDBTools')
+def test_convert_cmdline(testdata_dir, tmpdir):
+    """Checks that the conversion fails with an appropriate error message."""
+    res_file = os.path.join(testdata_dir, 'arbin1.res')
+    sqlite_file = os.path.join(str(tmpdir), 'arbin1.s3db')
+    subprocess.check_call(['res2sqlite', res_file, sqlite_file])
+    assert os.path.isfile(sqlite_file)
+    with sqlite3.connect(sqlite_file) as conn:
+        csr = conn.execute('SELECT * FROM Channel_Normal_Table;')
+        csr.fetchone()

tests/test_BioLogic.py

@@ -1,99 +1,132 @@
 # -*- coding: utf-8 -*-
 
+# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import os.path
 import re
 from datetime import date, 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
-
-testdata_dir = os.path.join(os.path.dirname(__file__), 'testdata')
+from galvani import BioLogic, MPTfile, MPRfile
+from galvani.BioLogic import MPTfileCSV  # not exported
 
 
-def test_open_MPT():
+def test_open_MPT(testdata_dir):
     mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt'))
-    eq_(comments, [])
-    eq_(mpt1.dtype.names, ("mode", "ox/red", "error", "control changes",
-                           "Ns changes", "counter inc.", "time/s",
-                           "control/V/mA", "Ewe/V", "dQ/mA.h", "P/W",
-                           "I/mA", "(Q-Qo)/mA.h", "x"))
+    assert comments == []
+    assert mpt1.dtype.names == (
+        "mode", "ox/red", "error", "control changes", "Ns changes",
+        "counter inc.", "time/s", "control/V/mA", "Ewe/V", "dQ/mA.h", "P/W",
+        "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'))
+def test_open_MPT_fails_for_bad_file(testdata_dir):
+    with pytest.raises(ValueError, match='Bad first line'):
+        MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
 
 
-def test_open_MPT_csv():
+def test_open_MPT_csv(testdata_dir):
     mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpt'))
-    eq_(comments, [])
-    eq_(mpt1.fieldnames, ["mode", "ox/red", "error", "control changes",
-                          "Ns changes", "counter inc.", "time/s",
-                          "control/V/mA", "Ewe/V", "dq/mA.h", "P/W",
-                          "<I>/mA", "(Q-Qo)/mA.h", "x"])
+    assert comments == []
+    assert mpt1.fieldnames == [
+        "mode", "ox/red", "error", "control changes", "Ns changes",
+        "counter inc.", "time/s", "control/V/mA", "Ewe/V", "dq/mA.h", "P/W",
+        "<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'))
+def test_open_MPT_csv_fails_for_bad_file(testdata_dir):
+    with pytest.raises((ValueError, UnicodeDecodeError)):
+        MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpr'))
 
 
-def test_open_MPR1():
-    mpr1 = MPRfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
-    ## Check the dates as a basic test that it has been read properly
-    eq_(mpr1.startdate, date(2011, 10, 29))
-    eq_(mpr1.enddate, date(2011, 10, 31))
+def test_colID_map_uniqueness():
+    """Check some uniqueness properties of the VMPdata_colID_xyz maps."""
+    field_colIDs = set(BioLogic.VMPdata_colID_dtype_map.keys())
+    flag_colIDs = set(BioLogic.VMPdata_colID_flag_map.keys())
+    field_names = [v[0] for v in BioLogic.VMPdata_colID_dtype_map.values()]
+    flag_names = [v[0] for v in BioLogic.VMPdata_colID_flag_map.values()]
+    assert not field_colIDs.intersection(flag_colIDs)
+    # 'I/mA' and 'dQ/mA.h' are duplicated
+    # assert len(set(field_names)) == len(field_names)
+    assert len(set(flag_names)) == len(flag_names)
+    assert not set(field_names).intersection(flag_names)
 
 
-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))
+@pytest.mark.parametrize('colIDs, expected', [
+    ([1, 2, 3], [('flags', 'u1')]),
+    ([4, 6], [('time/s', '<f8'), ('Ewe/V', '<f4')]),
+    ([1, 4, 21], [('flags', 'u1'), ('time/s', '<f8')]),
+    ([4, 6, 4], [('time/s', '<f8'), ('Ewe/V', '<f4'), ('time/s 2', '<f8')]),
+    ([4, 9999], NotImplementedError),
+])
+def test_colID_to_dtype(colIDs, expected):
+    """Test converting column ID to numpy dtype."""
+    if isinstance(expected, type) and issubclass(expected, Exception):
+        with pytest.raises(expected):
+            BioLogic.VMPdata_dtype_from_colIDs(colIDs)
+        return
+    expected_dtype = np.dtype(expected)
+    dtype, flags_dict = BioLogic.VMPdata_dtype_from_colIDs(colIDs)
+    assert dtype == expected_dtype
 
 
-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))
+@pytest.mark.parametrize('data, expected', [
+    ('02/23/17', date(2017, 2, 23)),
+    ('10-03-05', date(2005, 10, 3)),
+    ('11.12.20', date(2020, 11, 12)),
+    (b'01/02/03', date(2003, 1, 2)),
+    ('13.08.07', ValueError),
+    ('03-04/05', ValueError),
+])
+def test_parse_BioLogic_date(data, expected):
+    """Test the parse_BioLogic_date function."""
+    if isinstance(expected, type) and issubclass(expected, Exception):
+        with pytest.raises(expected):
+            BioLogic.parse_BioLogic_date(data)
+        return
+    result = BioLogic.parse_BioLogic_date(data)
+    assert result == expected
 
 
-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))
+@pytest.mark.parametrize('filename, startdate, enddate', [
+    ('bio_logic1.mpr', '2011-10-29', '2011-10-31'),
+    ('bio_logic2.mpr', '2012-09-27', '2012-09-27'),
+    ('bio_logic3.mpr', '2013-03-27', '2013-03-27'),
+    ('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'),
+    ('Rapp_Error.mpr', '2010-12-02', '2010-12-02'),
+])
+def test_MPR_dates(testdata_dir, 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_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'))
+def test_open_MPR_fails_for_bad_file(testdata_dir):
+    with pytest.raises(ValueError, match='Invalid magic for .mpr file'):
+        MPRfile(os.path.join(testdata_dir, 'arbin1.res'))
 
 
 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")
@@ -117,7 +150,7 @@ 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"],
@@ -139,33 +172,34 @@ 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():
-    mpr1 = MPRfile(os.path.join(testdata_dir, 'bio_logic1.mpr'))
-    mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt'))
-    assert_MPR_matches_MPT(mpr1, mpt1, comments)
+@pytest.mark.parametrize('basename', [
+    'bio_logic1',
+    'bio_logic2',
+    # 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(testdata_dir, basename):
+    """Check the MPR parser against the MPT parser.
+
+    Load a binary .mpr file and a text .mpt file which should contain
+    exactly the same data. Check that the loaded data actually match.
+    """
+    binpath = os.path.join(testdata_dir, basename + '.mpr')
+    txtpath = os.path.join(testdata_dir, basename + '.mpt')
+    mpr = MPRfile(binpath)
+    mpt, comments = MPTfile(txtpath)
+    assert_MPR_matches_MPT(mpr, mpt, comments)
 
 
-def test_MPR2_matches_MPT2():
-    mpr2 = MPRfile(os.path.join(testdata_dir, 'bio_logic2.mpr'))
-    mpt2, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic2.mpt'))
-    assert_MPR_matches_MPT(mpr2, mpt2, comments)
-
-
-## No bio_logic3.mpt file
-
-
-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():
+def test_MPR5_matches_MPT5(testdata_dir):
     mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic5.mpr'))
     mpt, comments = MPTfile((re.sub(b'\tXXX\t', b'\t0\t', line) for line in
                              open(os.path.join(testdata_dir, 'bio_logic5.mpt'),
@@ -173,23 +207,8 @@ def test_MPR5_matches_MPT5():
     assert_MPR_matches_MPT(mpr, mpt, comments)
 
 
-def test_MPR6_matches_MPT6():
+def test_MPR6_matches_MPT6(testdata_dir):
     mpr = MPRfile(os.path.join(testdata_dir, 'bio_logic6.mpr'))
     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 +1,17 @@
+# SPDX-FileCopyrightText: 2017-2021 Christopher Kerr <chris.kerr@mykolab.ch>
+# SPDX-License-Identifier: GPL-3.0-or-later
 [tox]
-envlist = py27,py35,py37
+envlist = py36,py37,py38,py39
 [testenv]
-deps=nose
-commands=nosetests
+deps =
+  flake8
+  reuse
+  pytest
+commands =
+  flake8
+  reuse lint
+  pytest
+
+[flake8]
+exclude = build,dist,*.egg-info,.cache,.git,.tox,__pycache__
+max-line-length = 100