Merge pull request #122 from echemdata/ml-evs/fix-ci

Pin and update release downloader action

.gitattributes

@@ -0,0 +1,8 @@
+# SPDX-FileCopyrightText: 2021 Christopher Kerr <chris.kerr@mykolab.ch>
+# SPDX-License-Identifier: CC0-1.0
+
+# Arbin data files
+*.res filter=lfs diff=lfs merge=lfs -text
+# Bio-Logic data files
+*.mpr filter=lfs diff=lfs merge=lfs -text
+*.mpt filter=lfs diff=lfs merge=lfs -text

.github/workflows/ci.yml

@@ -0,0 +1,71 @@
+# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr, "bcolsen"
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+name: CI tests
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+
+concurrency:
+  # cancels running checks on new pushes
+  group: check-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  pytest:
+    name: Run Python unit tests
+    runs-on: ubuntu-22.04
+
+    strategy:
+      fail-fast: false
+      max-parallel: 6
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          lfs: false
+
+      # Due to limited LFS bandwidth, it is preferable to download
+      # test files from the last release.
+      #
+      # This does mean that testing new LFS files in the CI is tricky;
+      # care should be taken to also test new files locally first
+      # Tests missing these files in the CI should still fail.
+      - name: Download static files from last release for testing
+        uses: robinraju/release-downloader@v1.12
+        with:
+          latest: true
+          tarBall: true
+          out-file-path: /home/runner/work/last-release
+          extract: true
+
+      - name: Copy test files from static downloaded release
+        run: |
+          cp -r /home/runner/work/last-release/*/tests/testdata tests
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install MDBTools OS dependency
+        run: |
+          sudo apt install -y mdbtools
+
+      # tox-gh workflow following instructions at https://github.com/tox-dev/tox-gh
+      - name: Install tox
+        run: python -m pip install tox-gh
+
+      - name: Setup tests
+        run: |
+          tox -vv --notest
+
+      - name: Run all tests
+        run: |-
+          tox --skip-pkg-install

.gitignore

@@ -39,5 +39,11 @@ nosetests.xml
 .project
 .pydevproject
 
-# Data for testing
-testdata
+# Compressed files used to transfer test data
+*.gz
+*.bz2
+*.xz
+*.zip
+*.tar
+*.tgz
+*.tbz2

.reuse/dep5

@@ -3,8 +3,6 @@ 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: ...
+Files: tests/testdata/*
+Copyright: 2010-2014 Christopher Kerr <chris.kerr@mykolab.ch>
+License: CC-BY-4.0

.travis.yml

@@ -6,7 +6,6 @@ cache:
   directories:
     - .tox
     - .pytest_cache
-    - tests/testdata
 python:
   - "3.6"
   - "3.7"
@@ -14,5 +13,4 @@ python:
   - "3.9"
 install:
   - pip install tox-travis
-  - sh get_testdata.sh
 script: tox

LICENSES/CC-BY-4.0.txt

@@ -0,0 +1,156 @@
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README.md

@@ -7,21 +7,76 @@ SPDX-FileCopyrightText: 2013-2020 Christopher Kerr, Peter Attia
 SPDX-License-Identifier: GPL-3.0-or-later
 -->
 
-Read proprietary file formats from electrochemical test stations
+Read proprietary file formats from electrochemical test stations.
 
-## Bio-Logic .mpr files ##
+# Usage
+
+## Bio-Logic .mpr files
 
 Use the `MPRfile` class from BioLogic.py (exported in the main package)
 
-````
+```python
 from galvani import BioLogic
 import pandas as pd
 
 mpr_file = BioLogic.MPRfile('test.mpr')
 df = pd.DataFrame(mpr_file.data)
-````
+```
 
-## Arbin .res files ##
+## Arbin .res files
 
-Use the res2sqlite.py script to convert the .res file to a sqlite3 database
-with the same schema.
+Use the `./galvani/res2sqlite.py` script to convert the .res file to a sqlite3 database with the same schema, which can then be interrogated with external tools or directly in Python.
+For example, to extract the data into a pandas DataFrame (will need to be installed separately):
+
+```python
+import sqlite3
+import pandas as pd
+from galvani.res2sqlite import convert_arbin_to_sqlite
+convert_arbin_to_sqlite("input.res", "output.sqlite")
+with sqlite3.connect("output.sqlite") as db:
+    df = pd.read_sql(sql="select * from Channel_Normal_Table", con=db)
+```
+
+This functionality requires [MDBTools](https://github.com/mdbtools/mdbtools) to be installed on the local system.
+
+# Installation
+
+The latest galvani releases can be installed from [PyPI](https://pypi.org/project/galvani/) via
+
+```shell
+pip install galvani
+```
+
+The latest development version can be installed with `pip` directly from GitHub (see note about git-lfs below):
+
+```shell
+GIT_LFS_SKIP_SMUDGE=1 pip install git+https://github.com/echemdata/galvani
+```
+
+## Development installation and contributing 
+
+> [!WARNING]
+> 
+> This project uses Git Large File Storage (LFS) to store its test files,
+> however the LFS quota provided by GitHub is frequently exceeded. 
+> This means that anyone cloning the repository with LFS installed will get
+> failures unless they set the `GIT_LFS_SKIP_SMUDGE=1` environment variable when
+> cloning. 
+> The full test data from the last release can always be obtained by
+> downloading the GitHub release archives (tar or zip), at
+> https://github.com/echemdata/galvani/releases/latest
+>
+> If you wish to add test files, please ensure they are as small as possible,
+> and take care that your tests work locally without the need for the LFS files.
+> Ideally, you could commit them to your fork when making a PR, and then they
+> can be converted to LFS files as part of the review.
+
+If you wish to contribute to galvani, please clone the repository and install the testing dependencies:
+
+```shell
+git clone git@github.com:echemdata/galvani
+cd galvani
+pip install -e .\[tests\]
+```
+
+Code can be contributed back via [GitHub pull requests](https://github.com/echemdata/galvani/pulls) and new features or bugs can be discussed in the [issue tracker](https://github.com/echemdata/galvani/issues).

galvani/BioLogic.py

@@ -5,7 +5,7 @@
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
 
-__all__ = ['MPTfileCSV', 'MPTfile']
+__all__ = ["MPTfileCSV", "MPTfile"]
 
 import re
 import csv
@@ -21,35 +21,100 @@ def fieldname_to_dtype(fieldname):
     """Converts a column header from the MPT file into a tuple of
     canonical name and appropriate numpy dtype"""
 
-    if fieldname == 'mode':
-        return ('mode', np.uint8)
-    elif fieldname in ("ox/red", "error", "control changes", "Ns changes",
-                       "counter inc."):
+    if fieldname == "mode":
+        return ("mode", np.uint8)
+    elif fieldname in (
+        "ox/red",
+        "error",
+        "control changes",
+        "Ns changes",
+        "counter inc.",
+    ):
         return (fieldname, np.bool_)
-    elif fieldname in ("time/s", "P/W", "(Q-Qo)/mA.h", "x", "control/V",
-                       "control/V/mA", "(Q-Qo)/C", "dQ/C", "freq/Hz",
-                       "|Ewe|/V", "|I|/A", "Phase(Z)/deg", "|Z|/Ohm",
-                       "Re(Z)/Ohm", "-Im(Z)/Ohm"):
-        return (fieldname, np.float_)
-    elif fieldname in ("cycle number", "I Range", "Ns", "half cycle"):
+    elif fieldname in (
+        "time/s",
+        "P/W",
+        "(Q-Qo)/mA.h",
+        "x",
+        "control/V",
+        "control/mA",
+        "control/V/mA",
+        "(Q-Qo)/C",
+        "dQ/C",
+        "freq/Hz",
+        "|Ewe|/V",
+        "|I|/A",
+        "Phase(Z)/deg",
+        "|Z|/Ohm",
+        "Re(Z)/Ohm",
+        "-Im(Z)/Ohm",
+        "Re(M)",
+        "Im(M)",
+        "|M|",
+        "Re(Permittivity)",
+        "Im(Permittivity)",
+        "|Permittivity|",
+        "Tan(Delta)",
+    ):
+        return (fieldname, np.float64)
+    elif fieldname in (
+        "Q charge/discharge/mA.h",
+        "step time/s",
+        "Q charge/mA.h",
+        "Q discharge/mA.h",
+        "Temperature/°C",
+        "Efficiency/%",
+        "Capacity/mA.h",
+    ):
+        return (fieldname, np.float64)
+    elif fieldname in ("cycle number", "I Range", "Ns", "half cycle", "z cycle"):
         return (fieldname, np.int_)
     elif fieldname in ("dq/mA.h", "dQ/mA.h"):
-        return ("dQ/mA.h", np.float_)
+        return ("dQ/mA.h", np.float64)
     elif fieldname in ("I/mA", "<I>/mA"):
-        return ("I/mA", np.float_)
-    elif fieldname in ("Ewe/V", "<Ewe>/V"):
-        return ("Ewe/V", np.float_)
+        return ("I/mA", np.float64)
+    elif fieldname in ("Ewe/V", "<Ewe>/V", "Ecell/V", "<Ewe/V>"):
+        return ("Ewe/V", np.float64)
+    elif fieldname.endswith(
+        (
+            "/s",
+            "/Hz",
+            "/deg",
+            "/W",
+            "/mW",
+            "/W.h",
+            "/mW.h",
+            "/A",
+            "/mA",
+            "/A.h",
+            "/mA.h",
+            "/V",
+            "/mV",
+            "/F",
+            "/mF",
+            "/uF",
+            "/µF",
+            "/nF",
+            "/C",
+            "/Ohm",
+            "/Ohm-1",
+            "/Ohm.cm",
+            "/mS/cm",
+            "/%",
+        )
+    ):
+        return (fieldname, np.float64)
     else:
         raise ValueError("Invalid column header: %s" % fieldname)
 
 
 def comma_converter(float_text):
     """Convert text to float whether the decimal point is '.' or ','"""
-    trans_table = bytes.maketrans(b',', b'.')
+    trans_table = bytes.maketrans(b",", b".")
     return float(float_text.translate(trans_table))
 
 
-def MPTfile(file_or_path, encoding='ascii'):
+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
@@ -57,16 +122,15 @@ def MPTfile(file_or_path, encoding='ascii'):
     """
 
     if isinstance(file_or_path, str):
-        mpt_file = open(file_or_path, 'rb')
+        mpt_file = open(file_or_path, "rb")
     else:
         mpt_file = file_or_path
 
     magic = next(mpt_file)
-    if magic != b'EC-Lab ASCII FILE\r\n':
+    if magic not in (b"EC-Lab ASCII FILE\r\n", b"BT-Lab ASCII FILE\r\n"):
         raise ValueError("Bad first line for EC-Lab file: '%s'" % magic)
 
-    nb_headers_match = re.match(rb'Nb header lines : (\d+)\s*$',
-                                next(mpt_file))
+    nb_headers_match = re.match(rb"Nb header lines : (\d+)\s*$", next(mpt_file))
     nb_headers = int(nb_headers_match.group(1))
     if nb_headers < 3:
         raise ValueError("Too few header lines: %d" % nb_headers)
@@ -75,14 +139,12 @@ def MPTfile(file_or_path, encoding='ascii'):
     # make three lines. Every additional line is a comment line.
     comments = [next(mpt_file) for i in range(nb_headers - 3)]
 
-    fieldnames = next(mpt_file).decode(encoding).strip().split('\t')
+    fieldnames = 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
-    converter_dict = dict(((i, comma_converter)
-                           for i in range(len(fieldnames))))
-    mpt_array = np.loadtxt(mpt_file, dtype=record_type,
-                           converters=converter_dict)
+    converter_dict = dict(((i, comma_converter) for i in range(len(fieldnames))))
+    mpt_array = np.loadtxt(mpt_file, dtype=record_type, converters=converter_dict)
 
     return mpt_array, comments
 
@@ -95,15 +157,15 @@ def MPTfileCSV(file_or_path):
     """
 
     if isinstance(file_or_path, str):
-        mpt_file = open(file_or_path, 'r')
+        mpt_file = open(file_or_path, "r")
     else:
         mpt_file = file_or_path
 
     magic = next(mpt_file)
-    if magic.rstrip() != 'EC-Lab ASCII FILE':
+    if magic.rstrip() != "EC-Lab ASCII FILE":
         raise ValueError("Bad first line for EC-Lab file: '%s'" % magic)
 
-    nb_headers_match = re.match(r'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)
@@ -112,145 +174,242 @@ def MPTfileCSV(file_or_path):
     # 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')
+    mpt_csv = csv.DictReader(mpt_file, dialect="excel-tab")
 
     expected_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"],
-        ['mode', 'ox/red', 'error', 'control changes', 'Ns changes',
-         'counter inc.', 'time/s', 'control/V', 'Ewe/V', 'dq/mA.h',
-         '<I>/mA', '(Q-Qo)/mA.h', 'x'],
-        ["mode", "ox/red", "error", "control changes", "Ns changes",
-         "counter inc.", "time/s", "control/V", "Ewe/V", "I/mA",
-         "dQ/mA.h", "P/W"],
-        ["mode", "ox/red", "error", "control changes", "Ns changes",
-         "counter inc.", "time/s", "control/V", "Ewe/V", "<I>/mA",
-         "dQ/mA.h", "P/W"])
+        [
+            "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",
+        ],
+        [
+            "mode",
+            "ox/red",
+            "error",
+            "control changes",
+            "Ns changes",
+            "counter inc.",
+            "time/s",
+            "control/V",
+            "Ewe/V",
+            "dq/mA.h",
+            "<I>/mA",
+            "(Q-Qo)/mA.h",
+            "x",
+        ],
+        [
+            "mode",
+            "ox/red",
+            "error",
+            "control changes",
+            "Ns changes",
+            "counter inc.",
+            "time/s",
+            "control/V",
+            "Ewe/V",
+            "I/mA",
+            "dQ/mA.h",
+            "P/W",
+        ],
+        [
+            "mode",
+            "ox/red",
+            "error",
+            "control changes",
+            "Ns changes",
+            "counter inc.",
+            "time/s",
+            "control/V",
+            "Ewe/V",
+            "<I>/mA",
+            "dQ/mA.h",
+            "P/W",
+        ],
+    )
     if mpt_csv.fieldnames not in expected_fieldnames:
         raise ValueError("Unrecognised headers for MPT file format")
 
     return mpt_csv, comments
 
 
-VMPmodule_hdr = np.dtype([('shortname', 'S10'),
-                          ('longname', 'S25'),
-                          ('length', '<u4'),
-                          ('version', '<u4'),
-                          ('date', 'S8')])
+VMPmodule_hdr_v1 = np.dtype(
+    [
+        ("shortname", "S10"),
+        ("longname", "S25"),
+        ("length", "<u4"),
+        ("version", "<u4"),
+        ("date", "S8"),
+    ]
+)
+
+VMPmodule_hdr_v2 = np.dtype(
+    [
+        ("shortname", "S10"),
+        ("longname", "S25"),
+        ("max length", "<u4"),
+        ("length", "<u4"),
+        ("version", "<u4"),
+        ("unknown2", "<u4"),  # 10 for set, log and loop, 11 for data
+        ("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'),
+    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"),
+    17: ("Analog IN 2/V", "<f4"),  # Probably column 18 is Analog IN 3/V, if anyone hits this error in the future  # noqa: E501
+    19: ("control/V", "<f4"),
+    20: ("control/mA", "<f4"),
+    23: ("dQ/mA.h", "<f8"),  # Same as 7?
+    24: ("cycle number", "<f8"),
+    26: ("Rapp/Ohm", "<f4"),
+    27: ("Ewe-Ece/V", "<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"),
+    174: ("<Ewe>/V", "<f4"),
+    178: ("(Q-Qo)/C", "<f4"),
+    179: ("dQ/C", "<f4"),
+    211: ("Q charge/discharge/mA.h", "<f8"),
+    212: ("half cycle", "<u4"),
+    213: ("z cycle", "<u4"),
+    217: ("THD Ewe/%", "<f4"),
+    218: ("THD I/%", "<f4"),
+    220: ("NSD Ewe/%", "<f4"),
+    221: ("NSD I/%", "<f4"),
+    223: ("NSR Ewe/%", "<f4"),
+    224: ("NSR I/%", "<f4"),
+    230: ("|Ewe h2|/V", "<f4"),
+    231: ("|Ewe h3|/V", "<f4"),
+    232: ("|Ewe h4|/V", "<f4"),
+    233: ("|Ewe h5|/V", "<f4"),
+    234: ("|Ewe h6|/V", "<f4"),
+    235: ("|Ewe h7|/V", "<f4"),
+    236: ("|I h2|/A", "<f4"),
+    237: ("|I h3|/A", "<f4"),
+    238: ("|I h4|/A", "<f4"),
+    239: ("|I h5|/A", "<f4"),
+    240: ("|I h6|/A", "<f4"),
+    241: ("|I h7|/A", "<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"),
+    438: ("step time/s", "<f8"),
+    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"),
+    498: ("Q charge/mA.h", "<f8"),
+    499: ("Q discharge/mA.h", "<f8"),
+    500: ("step time/s", "<f8"),
+    501: ("Efficiency/%", "<f8"),
+    502: ("Capacity/mA.h", "<f8"),
+    505: ("Rdc/Ohm", "<f4"),
+    509: ("Acir/Dcir Control", "<u1"),
 }
 
 # 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_),
+    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']
+    date_formats = ["%m/%d/%y", "%m-%d-%y", "%m.%d.%y"]
     if isinstance(date_text, bytes):
-        date_string = date_text.decode('ascii')
+        date_string = date_text.decode("ascii")
     else:
         date_string = date_text
     for date_format in date_formats:
@@ -261,8 +420,10 @@ def parse_BioLogic_date(date_text):
         else:
             break
     else:
-        raise ValueError(f'Could not parse timestamp {date_string!r}'
-                         f' with any of the formats {date_formats}')
+        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)
 
 
@@ -289,9 +450,9 @@ def VMPdata_dtype_from_colIDs(colIDs):
             # 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
+            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?
@@ -302,15 +463,15 @@ def VMPdata_dtype_from_colIDs(colIDs):
             field_name_counts[field_name] += 1
             count = field_name_counts[field_name]
             if count > 1:
-                unique_field_name = '%s %d' % (field_name, count)
+                unique_field_name = "%s %d" % (field_name, count)
             else:
                 unique_field_name = field_name
             type_list.append((unique_field_name, field_type))
         else:
-            raise NotImplementedError("Column ID {cid} after column {prev} "
-                                      "is unknown"
-                                      .format(cid=colID,
-                                              prev=type_list[-1][0]))
+            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
 
 
@@ -321,36 +482,49 @@ def read_VMP_modules(fileobj, read_module_data=True):
     N.B. the offset yielded is the offset to the start of the data i.e. after
     the end of the header. The data runs from (offset) to (offset+length)"""
     while True:
-        module_magic = fileobj.read(len(b'MODULE'))
+        module_magic = fileobj.read(len(b"MODULE"))
         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)
+        elif module_magic != b"MODULE":
+            raise ValueError(
+                "Found %r, expecting start of new VMP MODULE" % module_magic
+            )
+        VMPmodule_hdr = VMPmodule_hdr_v1
 
+        # Reading headers binary information
         hdr_bytes = fileobj.read(VMPmodule_hdr.itemsize)
         if len(hdr_bytes) < VMPmodule_hdr.itemsize:
             raise IOError("Unexpected end of file while reading module header")
 
+        # Checking if EC-Lab version is >= 11.50
+        if hdr_bytes[35:39] == b"\xff\xff\xff\xff":
+            VMPmodule_hdr = VMPmodule_hdr_v2
+            hdr_bytes += fileobj.read(VMPmodule_hdr_v2.itemsize - VMPmodule_hdr_v1.itemsize)
+
         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()
+        hdr_dict["offset"] = fileobj.tell()
         if read_module_data:
-            hdr_dict['data'] = fileobj.read(hdr_dict['length'])
-            if len(hdr_dict['data']) != hdr_dict['length']:
-                raise IOError("""Unexpected end of file while reading data
+            hdr_dict["data"] = fileobj.read(hdr_dict["length"])
+            if len(hdr_dict["data"]) != hdr_dict["length"]:
+                raise IOError(
+                    """Unexpected end of file while reading data
                     current module: %s
                     length read: %d
-                    length expected: %d""" % (hdr_dict['longname'],
-                                              len(hdr_dict['data']),
-                                              hdr_dict['length']))
+                    length expected: %d"""
+                    % (
+                        hdr_dict["longname"],
+                        len(hdr_dict["data"]),
+                        hdr_dict["length"],
+                    )
+                )
             yield hdr_dict
         else:
             yield hdr_dict
-            fileobj.seek(hdr_dict['offset'] + hdr_dict['length'], SEEK_SET)
+            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'
+MPR_MAGIC = b"BIO-LOGIC MODULAR FILE\x1a".ljust(48) + b"\x00\x00\x00\x00"
 
 
 class MPRfile:
@@ -372,80 +546,95 @@ 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')
+            mpr_file = open(file_or_path, "rb")
         else:
             mpr_file = file_or_path
         magic = mpr_file.read(len(MPR_MAGIC))
         if magic != MPR_MAGIC:
-            raise ValueError('Invalid magic for .mpr file: %s' % 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   ']
+        (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.frombuffer(data_module['data'][:4], dtype='<u4')
-        n_columns = np.frombuffer(data_module['data'][4:5], dtype='u1').item()
+        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.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'] in [2, 3]:
-            column_types = np.frombuffer(data_module['data'][5:], dtype='<u2',
-                                         count=n_columns)
+        if data_module["version"] == 0:
+            # If EC-Lab version >= 11.50, column_types is [0 1 0 3 0 174...] instead of [1 3 174...]
+            if np.frombuffer(data_module["data"][5:6], dtype="u1").item():
+                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:]
+            else:
+                column_types = np.frombuffer(
+                    data_module["data"][5:], dtype="u1", count=n_columns * 2
+                )
+                column_types = column_types[1::2]  # suppressing zeros in column types array
+                # remaining headers should be empty except for bytes 5 + n_columns * 2
+                # and 1006 which are sometimes == 1
+                remaining_headers = data_module["data"][6 + n_columns * 2:1006]
+                main_data = data_module["data"][1007:]
+        elif data_module["version"] in [2, 3]:
+            column_types = np.frombuffer(data_module["data"][5:], dtype="<u2", count=n_columns)
             # There are bytes of data before the main array starts
-            if data_module['version'] == 3:
+            if data_module["version"] == 3:
                 num_bytes_before = 406  # version 3 added `\x01` to the start
             else:
                 num_bytes_before = 405
-            remaining_headers = data_module['data'][5 + 2 * n_columns:405]
-            main_data = data_module['data'][num_bytes_before:]
+            remaining_headers = data_module["data"][5 + 2 * n_columns:405]
+            main_data = data_module["data"][num_bytes_before:]
         else:
-            raise ValueError("Unrecognised version for data module: %d" %
-                             data_module['version'])
+            raise ValueError(
+                "Unrecognised version for data module: %d" % data_module["version"]
+            )
 
-        assert(not any(remaining_headers))
+        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)
-        assert(self.data.shape[0] == n_data_points)
+        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
-        self.version = int(data_module['version'])
+        self.version = int(data_module["version"])
         self.cols = column_types
         self.npts = n_data_points
-        self.startdate = parse_BioLogic_date(settings_mod['date'])
+        self.startdate = parse_BioLogic_date(settings_mod["date"])
 
         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')
+            (loop_module,) = maybe_loop_module
+            if loop_module["version"] == 0:
+                self.loop_index = np.frombuffer(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'])
+                raise ValueError(
+                    "Unrecognised version for data module: %d" % data_module["version"]
+                )
 
         if maybe_log_module:
-            log_module, = maybe_log_module
-            self.enddate = parse_BioLogic_date(log_module['date'])
+            (log_module,) = maybe_log_module
+            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.frombuffer(log_module['data'][465:],
-                                           dtype='<f8', count=1)
-            ole_timestamp2 = np.frombuffer(log_module['data'][469:],
-                                           dtype='<f8', count=1)
-            ole_timestamp3 = np.frombuffer(log_module['data'][473:],
-                                           dtype='<f8', count=1)
-            ole_timestamp4 = np.frombuffer(log_module['data'][585:],
-                                           dtype='<f8', count=1)
+            ole_timestamp1 = np.frombuffer(
+                log_module["data"][465:], dtype="<f8", count=1
+            )
+            ole_timestamp2 = np.frombuffer(
+                log_module["data"][469:], dtype="<f8", count=1
+            )
+            ole_timestamp3 = np.frombuffer(
+                log_module["data"][473:], dtype="<f8", count=1
+            )
+            ole_timestamp4 = np.frombuffer(
+                log_module["data"][585:], dtype="<f8", count=1
+            )
 
             if ole_timestamp1 > 40000 and ole_timestamp1 < 50000:
                 ole_timestamp = ole_timestamp1
@@ -463,14 +652,16 @@ 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:\n"
-                                 + "    Start date: %s\n" % self.startdate
-                                 + "    End date: %s\n" % self.enddate
-                                 + "    Timestamp: %s\n" % 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)
+            return np.array(self.data["flags"] & mask, dtype=dtype)
         else:
             raise AttributeError("Flag '%s' not present" % flagname)

galvani/__init__.py

@@ -4,4 +4,4 @@
 
 from .BioLogic import MPRfile, MPTfile
 
-__all__ = ['MPRfile', 'MPTfile']
+__all__ = ["MPRfile", "MPTfile"]

galvani/res2sqlite.py

@@ -16,43 +16,43 @@ from copy import copy
 # $ 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',
+    "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',
+    "MCell_Aci_Data_Table",
+    "Aux_Global_Data_Table",
+    "Smart_Battery_Clock_Stretch_Table",
 ]
 mdb_5_26_tables = [
-    'Can_BMS_Info_Table',
-    'Can_BMS_Data_Table',
+    "Can_BMS_Info_Table",
+    "Can_BMS_Data_Table",
 ]
 
 mdb_tables_text = {
-    'Version_Table',
-    'Global_Table',
-    'Event_Table',
-    'Smart_Battery_Info_Table',
-    'Can_BMS_Info_Table',
+    "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',
+    "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 = {
@@ -191,7 +191,7 @@ CREATE TABLE Event_Table
     Event_Type              INTEGER,
     Event_Describe          TEXT
 ); """,
-    "Smart_Battery_Info_Table":  """
+    "Smart_Battery_Info_Table": """
 CREATE TABLE Smart_Battery_Info_Table
  (
     Test_ID                 INTEGER PRIMARY KEY REFERENCES Global_Table(Test_ID),
@@ -271,7 +271,7 @@ CREATE TABLE Smart_Battery_Data_Table
         REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 ); """,
     # The following tables are not present in version 1.14, but are in 5.23
-    'MCell_Aci_Data_Table': """
+    "MCell_Aci_Data_Table": """
 CREATE TABLE MCell_Aci_Data_Table
  (
     Test_ID			INTEGER,
@@ -285,7 +285,7 @@ CREATE TABLE MCell_Aci_Data_Table
     FOREIGN KEY (Test_ID, Data_Point)
         REFERENCES Channel_Normal_Table (Test_ID, Data_Point)
 );""",
-    'Aux_Global_Data_Table': """
+    "Aux_Global_Data_Table": """
 CREATE TABLE Aux_Global_Data_Table
  (
     Channel_Index		INTEGER,
@@ -295,7 +295,7 @@ CREATE TABLE Aux_Global_Data_Table
     Unit			TEXT,
     PRIMARY KEY (Channel_Index, Auxiliary_Index, Data_Type)
 );""",
-    'Smart_Battery_Clock_Stretch_Table': """
+    "Smart_Battery_Clock_Stretch_Table": """
 CREATE TABLE Smart_Battery_Clock_Stretch_Table
  (
     Test_ID			    INTEGER,
@@ -344,7 +344,7 @@ CREATE TABLE Smart_Battery_Clock_Stretch_Table
         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': """
+    "Can_BMS_Info_Table": """
 CREATE TABLE "Can_BMS_Info_Table"
  (
     Channel_Index        INTEGER PRIMARY KEY,
@@ -352,7 +352,7 @@ CREATE TABLE "Can_BMS_Info_Table"
     CAN_Configuration    TEXT
 );
 """,
-    'Can_BMS_Data_Table': """
+    "Can_BMS_Data_Table": """
 CREATE TABLE "Can_BMS_Data_Table"
  (
     Test_ID              INTEGER,
@@ -371,7 +371,8 @@ mdb_create_indices = {
 CREATE UNIQUE INDEX data_point_index ON Channel_Normal_Table (Test_ID, Data_Point);
 CREATE INDEX voltage_index ON Channel_Normal_Table (Test_ID, Voltage);
 CREATE INDEX test_time_index ON Channel_Normal_Table (Test_ID, Test_Time);
-"""}
+"""
+}
 
 helper_table_script = """
 CREATE TEMPORARY TABLE capacity_helper(
@@ -438,17 +439,20 @@ CREATE VIEW IF NOT EXISTS Capacity_View
 def mdb_get_data_text(s3db, filename, table):
     print("Reading %s..." % table)
     insert_pattern = re.compile(
-        r'INSERT INTO "\w+" \([^)]+?\) VALUES \(("[^"]*"|[^")])+?\);\n',
-        re.IGNORECASE
+        r"""INSERT INTO "\w+" \([^)]+?\) VALUES (\((('[^']*')|"[^"]*"|[^')])+?\),?\s*)+;\n""",
+        re.IGNORECASE,
     )
     try:
         # Initialize values to avoid NameError in except clause
-        mdb_output = ''
+        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:
-
+        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)
@@ -459,8 +463,10 @@ def mdb_get_data_text(s3db, filename, table):
 
     except OSError as e:
         if e.errno == 2:
-            raise RuntimeError('Could not locate the `mdb-export` executable. '
-                               'Check that mdbtools is properly installed.')
+            raise RuntimeError(
+                "Could not locate the `mdb-export` executable. "
+                "Check that mdbtools is properly installed."
+            )
         else:
             raise
     except BaseException:
@@ -475,14 +481,18 @@ def mdb_get_data_text(s3db, filename, table):
 def mdb_get_data_numeric(s3db, filename, table):
     print("Reading %s..." % table)
     try:
-        with sp.Popen(['mdb-export', filename, table],
-                      bufsize=-1, stdin=sp.DEVNULL, stdout=sp.PIPE,
-                      universal_newlines=True) as mdb_sql:
+        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])
+            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,
@@ -492,8 +502,10 @@ def mdb_get_data_numeric(s3db, filename, table):
             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.')
+            raise RuntimeError(
+                "Could not locate the `mdb-export` executable. "
+                "Check that mdbtools is properly installed."
+            )
         else:
             raise
 
@@ -504,7 +516,9 @@ def mdb_get_data(s3db, filename, table):
     elif table in mdb_tables_numeric:
         mdb_get_data_numeric(s3db, filename, table)
     else:
-        raise ValueError("'%s' is in neither mdb_tables_text nor mdb_tables_numeric" % table)
+        raise ValueError(
+            "'%s' is in neither mdb_tables_text nor mdb_tables_numeric" % table
+        )
 
 
 def mdb_get_version(filename):
@@ -514,9 +528,13 @@ def mdb_get_version(filename):
     """
     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:
+        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)
@@ -525,33 +543,53 @@ def mdb_get_version(filename):
             except StopIteration:
                 pass
             else:
-                raise ValueError('Version_Table of %s lists multiple versions' % filename)
+                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.')
+            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)
+    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)
+    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)
+        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('.')))
+    version_tuple = tuple(map(int, version_string.split(".")))
     return version_tuple
 
 
-def convert_arbin_to_sqlite(input_file, output_file):
+def convert_arbin_to_sqlite(input_file, output_file=None):
     """Read data from an Arbin .res data file and write to a sqlite file.
 
-    Any data currently in the sqlite file will be erased!
+    Any data currently in an sqlite file at `output_file` will be erased!
+
+    Parameters:
+        input_file (str): The path to the Arbin .res file to read from.
+        output_file (str or None): The path to the sqlite file to write to; if None,
+            return a `sqlite3.Connection` into an in-memory database.
+
+    Returns:
+        None or sqlite3.Connection
+
     """
     arbin_version = mdb_get_version(input_file)
 
+    if output_file is None:
+        output_file = ":memory:"
+
     s3db = sqlite3.connect(output_file)
 
     tables_to_convert = copy(mdb_tables)
@@ -576,17 +614,24 @@ def convert_arbin_to_sqlite(input_file, output_file):
     print("Vacuuming database...")
     s3db.executescript("VACUUM; ANALYZE;")
 
+    if output_file == ":memory:":
+        return s3db
+
+    s3db.close()
+
 
 def main(argv=None):
     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
+    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
 
     args = parser.parse_args(argv)
     convert_arbin_to_sqlite(args.input_file, args.output_file)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

get_testdata.sh

@@ -1,32 +0,0 @@
-#!/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
-
-mkdir -p tests/testdata
-cd tests/testdata
-
-/usr/bin/wget --continue -i - <<END_FILELIST
-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

setup.py

@@ -7,35 +7,35 @@ import os.path
 
 from setuptools import setup
 
-with open(os.path.join(os.path.dirname(__file__), 'README.md')) as f:
+with open(os.path.join(os.path.dirname(__file__), "README.md")) as f:
     readme = f.read()
 
 setup(
-    name='galvani',
-    version='0.2.1',
-    description='Open and process battery charger log data files',
+    name="galvani",
+    version="0.4.1",
+    description="Open and process battery charger log data files",
     long_description=readme,
     long_description_content_type="text/markdown",
-    url='https://github.com/echemdata/galvani',
-    author='Chris Kerr',
-    author_email='chris.kerr@mykolab.ch',
-    license='GPLv3+',
+    url="https://github.com/echemdata/galvani",
+    author="Chris Kerr",
+    author_email="chris.kerr@mykolab.ch",
+    license="GPLv3+",
     classifiers=[
-        'Development Status :: 4 - Beta',
-        'Intended Audience :: Developers',
-        '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',
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Developers",
+        "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'],
+    packages=["galvani"],
     entry_points={
-        'console_scripts': [
-            'res2sqlite = galvani.res2sqlite:main',
+        "console_scripts": [
+            "res2sqlite = galvani.res2sqlite:main",
         ],
     },
-    python_requires='>=3.6',
-    install_requires=['numpy'],
-    tests_require=['pytest'],
+    python_requires=">=3.6",
+    install_requires=["numpy"],
+    tests_require=["pytest"],
 )

tests/conftest.py

@@ -9,7 +9,7 @@ import os
 import pytest
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope="session")
 def testdata_dir():
     """Path to the testdata directory."""
-    return os.path.join(os.path.dirname(__file__), 'testdata')
+    return os.path.join(os.path.dirname(__file__), "testdata")

tests/test_Arbin.py

@@ -13,8 +13,7 @@ import pytest
 from galvani import res2sqlite
 
 
-have_mdbtools = (subprocess.call(['which', 'mdb-export'],
-                                 stdout=subprocess.DEVNULL) == 0)
+have_mdbtools = subprocess.call(["which", "mdb-export"], stdout=subprocess.DEVNULL) == 0
 
 
 def test_res2sqlite_help():
@@ -22,39 +21,57 @@ def test_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
+    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')
+@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."):
+    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'])
+@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')
+    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 = conn.execute("SELECT * FROM Channel_Normal_Table;")
         csr.fetchone()
 
 
-@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_in_memory(testdata_dir, tmpdir, basename):
+    """Convert an Arbin file to an in-memory SQLite database."""
+    res_file = os.path.join(testdata_dir, basename + ".res")
+    conn = None
+    with res2sqlite.convert_arbin_to_sqlite(res_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])
+    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 = conn.execute("SELECT * FROM Channel_Normal_Table;")
         csr.fetchone()

tests/test_BioLogic.py

@@ -9,7 +9,7 @@ import re
 from datetime import date, datetime
 
 import numpy as np
-from numpy.testing import assert_array_almost_equal, assert_array_equal
+from numpy.testing import assert_array_almost_equal, assert_array_equal, assert_allclose
 import pytest
 
 from galvani import BioLogic, MPTfile, MPRfile
@@ -17,33 +17,55 @@ from galvani.BioLogic import MPTfileCSV  # not exported
 
 
 def test_open_MPT(testdata_dir):
-    mpt1, comments = MPTfile(os.path.join(testdata_dir, 'bio_logic1.mpt'))
+    mpt1, comments = MPTfile(os.path.join(testdata_dir, "bio_logic1.mpt"))
     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",
+        "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",
     )
 
 
 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'))
+    with pytest.raises(ValueError, match="Bad first line"):
+        MPTfile(os.path.join(testdata_dir, "bio_logic1.mpr"))
 
 
 def test_open_MPT_csv(testdata_dir):
-    mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, 'bio_logic1.mpt'))
+    mpt1, comments = MPTfileCSV(os.path.join(testdata_dir, "bio_logic1.mpt"))
     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",
+        "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",
     ]
 
 
 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'))
+        MPTfileCSV(os.path.join(testdata_dir, "bio_logic1.mpr"))
 
 
 def test_colID_map_uniqueness():
@@ -59,13 +81,16 @@ def test_colID_map_uniqueness():
     assert not set(field_names).intersection(flag_names)
 
 
-@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),
-])
+@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):
@@ -77,14 +102,17 @@ def test_colID_to_dtype(colIDs, expected):
     assert dtype == expected_dtype
 
 
-@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),
-])
+@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):
@@ -95,50 +123,55 @@ def test_parse_BioLogic_date(data, expected):
     assert result == expected
 
 
-@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'),
-])
+@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"),
+        ("Ewe_Error.mpr", "2021-11-18", "2021-11-19"),
+        ("col_27_issue_74.mpr", "2022-07-28", "2022-07-28"),
+    ],
+)
 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
+    assert mpr.startdate.strftime("%Y-%m-%d") == startdate
     if enddate:
-        assert mpr.enddate.strftime('%Y-%m-%d') == enddate
+        assert mpr.enddate.strftime("%Y-%m-%d") == enddate
     else:
-        assert not hasattr(mpr, 'enddate')
+        assert not hasattr(mpr, "enddate")
 
 
 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'))
+    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)
+        time_match = re.match(b"Acquisition started on : ([0-9/]+ [0-9:]+)", line)
         if time_match:
-            timestamp = datetime.strptime(time_match.group(1).decode('ascii'),
-                                          '%m/%d/%Y %H:%M:%S')
+            timestamp = datetime.strptime(
+                time_match.group(1).decode("ascii"), "%m/%d/%Y %H:%M:%S"
+            )
             return timestamp
     raise AttributeError("No timestamp in comments")
 
 
 def assert_MPR_matches_MPT(mpr, mpt, comments):
-
     def assert_field_matches(fieldname, decimal):
         if fieldname in mpr.dtype.fields:
-            assert_array_almost_equal(mpr.data[fieldname],
-                                      mpt[fieldname],
-                                      decimal=decimal)
+            assert_array_almost_equal(
+                mpr.data[fieldname], mpt[fieldname], decimal=decimal
+            )
 
     def assert_field_exact(fieldname):
         if fieldname in mpr.dtype.fields:
@@ -153,18 +186,18 @@ def assert_MPR_matches_MPT(mpr, mpt, comments):
     # 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"],
-                              mpt["time/s"],
-                              decimal=2)  # 2 digits in CSV
+    assert_array_almost_equal(
+        mpr.data["time/s"], mpt["time/s"], decimal=2
+    )  # 2 digits in CSV
 
     assert_field_matches("control/V/mA", decimal=6)
     assert_field_matches("control/V", decimal=6)
 
-    assert_array_almost_equal(mpr.data["Ewe/V"],
-                              mpt["Ewe/V"],
-                              decimal=6)  # 32 bit float precision
+    assert_array_almost_equal(
+        mpr.data["Ewe/V"], mpt["Ewe/V"], decimal=6
+    )  # 32 bit float precision
 
-    assert_field_matches("dQ/mA.h", decimal=17)  # 64 bit float precision
+    assert_field_matches("dQ/mA.h", decimal=16)  # 64 bit float precision
     assert_field_matches("P/W", decimal=10)  # 32 bit float precision for 1.xxE-5
     assert_field_matches("I/mA", decimal=6)  # 32 bit float precision
 
@@ -172,43 +205,156 @@ def assert_MPR_matches_MPT(mpr, mpt, comments):
     assert_field_matches("(Q-Qo)/C", decimal=6)  # 32 bit float precision
 
     try:
-        assert timestamp_from_comments(comments) == mpr.timestamp
+        assert timestamp_from_comments(comments) == mpr.timestamp.replace(microsecond=0)
     except AttributeError:
         pass
 
 
-@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 assert_MPR_matches_MPT_v2(mpr, mpt, comments):
+    """
+    Asserts that the fields in the MPR.data ar the same as in the MPT.
+
+    Modified from assert_MPR_matches_MPT. Automatically converts dtype from MPT data
+    to dtype from MPR data before comparing the columns.
+
+    Special case for EIS_indicators: these fields are valid only at f<100kHz so their
+    values are replaced by -1 or 0 at high frequency in the MPT file, this is not the
+    case in the MPR data.
+
+    Parameters
+    ----------
+    mpr : MPRfile
+        Data extracted with the MPRfile class.
+    mpt : np.array
+        Data extracted with MPTfile method.
+
+    Returns
+    -------
+    None.
+
+    """
+
+    def assert_field_matches(fieldname):
+        EIS_quality_indicators = [
+            "THD Ewe/%",
+            "NSD Ewe/%",
+            "NSR Ewe/%",
+            "|Ewe h2|/V",
+            "|Ewe h3|/V",
+            "|Ewe h4|/V",
+            "|Ewe h5|/V",
+            "|Ewe h6|/V",
+            "|Ewe h7|/V",
+            "THD I/%",
+            "NSD I/%",
+            "NSR I/%",
+            "|I h2|/A",
+            "|I h3|/A",
+            "|I h4|/A",
+            "|I h5|/A",
+            "|I h6|/A",
+            "|I h7|/A",
+        ]
+
+        if fieldname in EIS_quality_indicators:  # EIS quality indicators only valid for f < 100kHz
+            index_inf_100k = np.where(mpr.data["freq/Hz"] < 100000)[0]
+            assert_allclose(
+                mpr.data[index_inf_100k][fieldname],
+                mpt[index_inf_100k][fieldname].astype(mpr.data[fieldname].dtype),
+            )
+        elif fieldname == "<Ewe>/V":
+            assert_allclose(
+                mpr.data[fieldname],
+                mpt["Ewe/V"].astype(mpr.data[fieldname].dtype),
+            )
+        elif fieldname == "<I>/mA":
+            assert_allclose(
+                mpr.data[fieldname],
+                mpt["I/mA"].astype(mpr.data[fieldname].dtype),
+            )
+        elif fieldname == "dq/mA.h":
+            assert_allclose(
+                mpr.data[fieldname],
+                mpt["dQ/mA.h"].astype(mpr.data[fieldname].dtype),
+            )
+        else:
+            assert_allclose(
+                mpr.data[fieldname],
+                mpt[fieldname].astype(mpr.data[fieldname].dtype),
+            )
+
+    def assert_field_exact(fieldname):
+        if fieldname in mpr.dtype.fields:
+            assert_array_equal(mpr.data[fieldname], mpt[fieldname])
+
+    for key in mpr.flags_dict.keys():
+        assert_array_equal(mpr.get_flag(key), mpt[key])
+
+    for d in mpr.dtype.descr[1:]:
+        assert_field_matches(d[0])
+
+    try:
+        assert timestamp_from_comments(comments) == mpr.timestamp.replace(microsecond=0)
+    except AttributeError:
+        pass
+
+
+@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",
+        "020-formation_CB5",
+    ],
+)
 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')
+    binpath = os.path.join(testdata_dir, basename + ".mpr")
+    txtpath = os.path.join(testdata_dir, basename + ".mpt")
     mpr = MPRfile(binpath)
-    mpt, comments = MPTfile(txtpath)
+    mpt, comments = MPTfile(txtpath, encoding="latin1")
     assert_MPR_matches_MPT(mpr, mpt, comments)
 
 
 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'),
-                                  mode='rb')))
+    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"), mode="rb")
+        )
+    )
     assert_MPR_matches_MPT(mpr, mpt, comments)
 
 
 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 = 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)
+
+
+@pytest.mark.parametrize(
+    "basename_v1150",
+    ["v1150_CA", "v1150_CP", "v1150_GCPL", "v1150_GEIS", "v1150_MB", "v1150_OCV", "v1150_PEIS"],
+)
+def test_MPR_matches_MPT_v1150(testdata_dir, basename_v1150):
+    """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, "v1150", basename_v1150 + ".mpr")
+    txtpath = os.path.join(testdata_dir, "v1150", basename_v1150 + ".mpt")
+    mpr = MPRfile(binpath)
+    mpt, comments = MPTfile(txtpath, encoding="latin1")
+    assert_MPR_matches_MPT_v2(mpr, mpt, comments)

tests/testdata/020-formation_CB5.mpr.license

@@ -0,0 +1,2 @@
+SPDX-FileCopyrightText Chihyu Chen <chihyu.chen@molicel.com>
+SPDX-License-Identifier CC-BY-4.0

tests/testdata/020-formation_CB5.mpt.license

@@ -0,0 +1,2 @@
+SPDX-FileCopyrightText Chihyu Chen <chihyu.chen@molicel.com>
+SPDX-License-Identifier CC-BY-4.0

tests/testdata/Ewe_Error.mpr.license

@@ -0,0 +1,2 @@
+SPDX-FileCopyrightText Danzi Federico
+SPDX-License-Identifier CC-BY-4.0

tests/testdata/Rapp_Error.mpr.license

@@ -0,0 +1,2 @@
+SPDX-FileCopyrightText Danzi Federico
+SPDX-License-Identifier CC-BY-4.0

tests/testdata/UM34_Test005E.res.license

@@ -0,0 +1,2 @@
+SPDX-FileCopyrightText Nikhil Shetty
+SPDX-License-Identifier CC-BY-4.0

tox.ini

@@ -1,7 +1,7 @@
 # SPDX-FileCopyrightText: 2017-2021 Christopher Kerr <chris.kerr@mykolab.ch>
 # SPDX-License-Identifier: GPL-3.0-or-later
 [tox]
-envlist = py36,py37,py38,py39
+envlist = py38,py39,py310,py311
 [testenv]
 deps =
   flake8
@@ -15,3 +15,10 @@ commands =
 [flake8]
 exclude = build,dist,*.egg-info,.cache,.git,.tox,__pycache__
 max-line-length = 100
+
+[gh]
+python =
+    3.11 = py311
+    3.10 = py310
+    3.9 = py39
+    3.8 = py38