Merge branch 'JhonFlash3008-loop-from-file'

Closes https://codeberg.org/echemdata/galvani/pulls/124

See also:
8a9d475222
8a9d475222

.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

@@ -1,10 +1,8 @@
 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
+Source: https://codeberg.org/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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+
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README.md

@@ -7,21 +7,60 @@ 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:
+
+```shell
+pip install git+https://codeberg.org/echemdata/galvani
+```
+
+## Development installation and contributing 
+
+If you wish to contribute to galvani, please clone the repository and install the testing dependencies:
+
+```shell
+git clone git@codeberg.org:echemdata/galvani
+cd galvani
+pip install -e .\[tests\]
+```
+
+Code can be contributed back via [pull requests](https://codeberg.org/echemdata/galvani/pulls) and new features or bugs can be discussed in the [issue tracker](https://codeberg.org/echemdata/galvani/issues).

galvani/BioLogic.py

@@ -5,51 +5,120 @@
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
 
-__all__ = ['MPTfileCSV', 'MPTfile']
+__all__ = ["MPTfileCSV", "MPTfile"]
 
 import re
 import csv
 from os import SEEK_SET
+import os.path
 import time
 from datetime import date, datetime, timedelta
 from collections import defaultdict, OrderedDict
+import warnings
 
 import numpy as np
 
+UNKNOWN_COLUMN_TYPE_HIERARCHY = ("<f8", "<f4", "<u4", "<u2", "<u1")
+
 
 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 +126,15 @@ 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 +143,12 @@ 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 +161,15 @@ 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 +178,243 @@ 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"),
+    182: ("step time/s", "<f8"),
+    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:
@@ -261,23 +425,30 @@ 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)
 
 
-def VMPdata_dtype_from_colIDs(colIDs):
+def VMPdata_dtype_from_colIDs(colIDs, error_on_unknown_column: bool = True):
     """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
+    sequence into a list that can be used with numpy dtype 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.
 
+    If error_on_unknown_column is True, an error will be raised if an unknown
+    column ID is encountered. If it is False, a warning will be emited and attempts
+    will be made to read the column with a few different dtypes.
+
+
     """
     type_list = []
     field_name_counts = defaultdict(int)
@@ -289,9 +460,9 @@ 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?
@@ -302,16 +473,24 @@ 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]))
-    return np.dtype(type_list), flags_dict
+            if error_on_unknown_column:
+                raise NotImplementedError(
+                    "Column ID {cid} after column {prev} is unknown".format(
+                        cid=colID, prev=type_list[-1][0]
+                    )
+                )
+            warnings.warn(
+                "Unknown column ID %d -- will attempt to read as common dtypes"
+                % colID
+            )
+            type_list.append(("unknown_colID_%d" % colID, UNKNOWN_COLUMN_TYPE_HIERARCHY[0]))
+
+    return type_list, flags_dict
 
 
 def read_VMP_modules(fileobj, read_module_data=True):
@@ -321,36 +500,128 @@ 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'
+def loop_from_file(file: str, encoding: str = "latin1"):
+    """
+    When an experiment is still running and it includes loops,
+    a _LOOP.txt file is temporarily created to progressively store the indexes of new loops.
+    This function reads the file and creates the loop_index array for MPRfile initialization.
+
+    Parameters
+    ----------
+    file : str
+        Path of the loop file.
+    encoding : str, optional
+        Encoding of the text file. The default is "latin1".
+
+    Raises
+    ------
+    ValueError
+        If the file does not start with "VMP EXPERIMENT LOOP INDEXES".
+
+    Returns
+    -------
+    loop_index : np.array
+        Indexes of data points that start a new loop.
+
+    """
+    with open(file, "r", encoding=encoding) as f:
+        line = f.readline().strip()
+        if line != LOOP_MAGIC:
+            raise ValueError("Invalid magic for LOOP.txt file")
+        loop_index = np.array([int(line) for line in f], dtype="u4")
+
+    return loop_index
+
+
+def timestamp_from_file(file: str, encoding: str = "latin1"):
+    """
+    When an experiment is still running, a .mpl file is temporarily created to store
+    information that will be added in the log module and will be appended to the data
+    module in the .mpr file at the end of experiment.
+    This function reads the file and extracts the experimental starting date and time
+    as a timestamp for MPRfile initialization.
+
+    Parameters
+    ----------
+    file : str
+        Path of the log file.
+    encoding : str, optional
+        Encoding of the text file. The default is "latin1".
+
+    Raises
+    ------
+    ValueError
+        If the file does not start with "EC-Lab LOG FILE" or "BT-Lab LOG FILE".
+
+    Returns
+    -------
+    timestamp
+        Date and time of the start of data acquisition
+    """
+    with open(file, "r", encoding=encoding) as f:
+        line = f.readline().strip()
+        if line not in LOG_MAGIC:
+            raise ValueError("Invalid magic for .mpl file")
+        log = f.read()
+    start = tuple(
+        map(
+            int,
+            re.findall(
+                r"Acquisition started on : (\d+)\/(\d+)\/(\d+) (\d+):(\d+):(\d+)\.(\d+)",
+                "".join(log),
+            )[0],
+        )
+    )
+    return datetime(
+        int(start[2]), start[0], start[1], start[3], start[4], start[5], start[6] * 1000
+    )
+
+
+LOG_MAGIC = "EC-Lab LOG FILEBT-Lab LOG FILE"
+LOOP_MAGIC = "VMP EXPERIMENT LOOP INDEXES"
+MPR_MAGIC = b"BIO-LOGIC MODULAR FILE\x1a".ljust(48) + b"\x00\x00\x00\x00"
 
 
 class MPRfile:
@@ -369,83 +640,157 @@ class MPRfile:
     enddate - The date when the experiment finished
     """
 
-    def __init__(self, file_or_path):
+    def __init__(self, file_or_path, error_on_unknown_column: bool = True):
+        """Pass an EC-lab .mpr file to be parsed.
+
+        Parameters:
+            file_or_path: Either the open file data or a path to it.
+            error_on_unknown_column: Whether or not to raise an error if an
+                unknown column ID is encountered. A warning will be emited and
+                the column will be added 'unknown_<colID>', with an attempt to read
+                it with a few different dtypes.
+
+        """
         self.loop_index = None
         if isinstance(file_or_path, str):
-            mpr_file = open(file_or_path, 'rb')
+            mpr_file = open(file_or_path, "rb")
+            loop_file = file_or_path[:-4] + "_LOOP.txt"  # loop file for running experiment
+            log_file = file_or_path[:-1] + "l"  # log file for runnning experiment
         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)
+        dtypes, self.flags_dict = VMPdata_dtype_from_colIDs(
+            column_types, error_on_unknown_column=error_on_unknown_column
+        )
+
+        unknown_cols = []
+        # Iteratively work through the unknown columns and try to read them
+        if not error_on_unknown_column:
+            for col, _ in dtypes:
+                if col.startswith("unknown_colID"):
+                    unknown_cols.append(col)
+            if len(unknown_cols) > 3:
+                raise RuntimeError(
+                    "Too many unknown columns to attempt to read combinatorially: %s"
+                    % unknown_cols
+                )
+
+        if unknown_cols:
+            # create a list of all possible combinations of dtypes
+            # for the unknown columns
+            from itertools import product
+            perms = product(UNKNOWN_COLUMN_TYPE_HIERARCHY, repeat=len(unknown_cols))
+            for perm in perms:
+                for unknown_col_ind, c in enumerate(unknown_cols):
+                    for ind, (col, _) in enumerate(dtypes):
+                        if c == col:
+                            dtypes[ind] = (col, perm[unknown_col_ind])
+
+                try:
+                    self.dtype = np.dtype(dtypes)
+                    self.data = np.frombuffer(main_data, dtype=self.dtype)
+                    break
+                except ValueError:
+                    continue
+            else:
+                raise RuntimeError(
+                    "Unable to read data for unknown columns %s with any of the common dtypes %s",
+                    unknown_cols,
+                    UNKNOWN_COLUMN_TYPE_HIERARCHY
+                )
+
+        else:
+            self.dtype = np.dtype(dtypes)
+            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
-        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"]
+                )
+        else:
+            if os.path.isfile(loop_file):
+                self.loop_index = loop_from_file(loop_file)
+                if self.loop_index[-1] < n_data_points:
+                    self.loop_index = np.append(self.loop_index, n_data_points)
 
         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 +808,20 @@ 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
+                )
+        else:
+            if os.path.isfile(log_file):
+                self.timestamp = timestamp_from_file(log_file)
+                self.enddate = None
 
     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="0.5.0",
+    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://codeberg.org/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):
@@ -74,17 +99,20 @@ def test_colID_to_dtype(colIDs, expected):
         return
     expected_dtype = np.dtype(expected)
     dtype, flags_dict = BioLogic.VMPdata_dtype_from_colIDs(colIDs)
-    assert dtype == expected_dtype
+    assert np.dtype(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 +205,175 @@ 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)
+
+
+@pytest.mark.skip(reason="Test data file is missing")
+def test_loop_from_file(testdata_dir):
+    """Check if the loop_index is correctly extracted from the _LOOP.txt file
+    """
+    mpr = MPRfile(os.path.join(testdata_dir, "running", "running_OCV.mpr"))
+    assert mpr.loop_index is not None, "No loop_index found"
+    assert len(mpr.loop_index) == 4, "loop_index is not the right size"
+    assert_array_equal(mpr.loop_index, [0, 4, 8, 11], "loop_index values are wrong")
+
+
+@pytest.mark.skip(reason="Test data file is missing")
+def test_timestamp_from_file(testdata_dir):
+    """Check if the loop_index is correctly extracted from the _LOOP.txt file
+    """
+    mpr = MPRfile(os.path.join(testdata_dir, "running", "running_OCV.mpr"))
+    assert hasattr(mpr, "timestamp"), "No timestamp found"
+    assert mpr.timestamp.timestamp() == pytest.approx(1707299985.908), "timestamp value is wrong"

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