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

Pin and update release downloader action

.flake8

@@ -1,2 +0,0 @@
-# This file will be ignored - see http://flake8.pycqa.org/en/2.6.0/config.html#per-project
-# Edit the [flake8] section in tox.ini instead

.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

.github/workflows/codeql-analysis.yml

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

.gitignore

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: 2013-2017 Christopher Kerr <chris.kerr@mykolab.ch>
+# SPDX-License-Identifier: CC0-1.0
+
 *.py[cod]
 
 # C extensions
@@ -36,5 +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

@@ -0,0 +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
+
+Files: tests/testdata/*
+Copyright: 2010-2014 Christopher Kerr <chris.kerr@mykolab.ch>
+License: CC-BY-4.0

.travis.yml

@@ -1,10 +1,11 @@
+# SPDX-FileCopyrightText: 2017-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+# SPDX-License-Identifier: GPL-3.0-or-later
 sudo: false
 language: python
 cache:
   directories:
     - .tox
     - .pytest_cache
-    - tests/testdata
 python:
   - "3.6"
   - "3.7"
@@ -12,5 +13,4 @@ python:
   - "3.9"
 install:
   - pip install tox-travis
-  - sh get_testdata.sh
 script: tox

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+TERMS AND CONDITIONS
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+6. Conveying Non-Source Forms.
+You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:
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+
+7. Additional Terms.
+“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
+
+When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
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+Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
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+All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
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+Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
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+8. Termination.
+You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
+
+However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
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+Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
+
+Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
+
+9. Acceptance Not Required for Having Copies.
+You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
+
+10. Automatic Licensing of Downstream Recipients.
+Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
+
+An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
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+
+11. Patents.
+A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's “contributor version”.
+
+A contributor's “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
+
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+If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
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+
+A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
+
+12. No Surrender of Others' Freedom.
+If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
+
+13. Use with the GNU Affero General Public License.
+Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.
+
+14. Revised Versions of this License.
+The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
+
+15. Disclaimer of Warranty.
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+16. Limitation of Liability.
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+17. Interpretation of Sections 15 and 16.
+If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
+
+     <one line to give the program's name and a brief idea of what it does.>
+     Copyright (C) <year>  <name of author>
+
+     This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+     This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+
+     You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
+
+     <program>  Copyright (C) <year>  <name of author>
+     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+     This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
+
+The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.

LICENSES/MIT.txt

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

MANIFEST.in

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

README.md

@@ -1,21 +1,82 @@
 galvani
 =======
 
-Read proprietary file formats from electrochemical test stations
+<!---
+SPDX-FileCopyrightText: 2013-2020 Christopher Kerr, Peter Attia
 
-## Bio-Logic .mpr files ##
+SPDX-License-Identifier: GPL-3.0-or-later
+-->
+
+Read proprietary file formats from electrochemical test stations.
+
+# 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

@@ -1,7 +1,11 @@
 # -*- coding: utf-8 -*-
 """Code to read in data files from Bio-Logic instruments"""
 
-__all__ = ['MPTfileCSV', 'MPTfile']
+# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr, "bcolsen"
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+__all__ = ["MPTfileCSV", "MPTfile"]
 
 import re
 import csv
@@ -17,35 +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
@@ -53,16 +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)
@@ -71,14 +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
 
@@ -91,15 +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)
@@ -108,138 +174,259 @@ 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'),
-    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'),
-    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"]
+    if isinstance(date_text, bytes):
+        date_string = date_text.decode("ascii")
+    else:
+        date_string = date_text
+    for date_format in date_formats:
+        try:
+            tm = time.strptime(date_string, date_format)
+        except ValueError:
+            continue
+        else:
+            break
+    else:
+        raise ValueError(
+            f"Could not parse timestamp {date_string!r}"
+            f" with any of the formats {date_formats}"
+        )
+    return date(tm.tm_year, tm.tm_mon, tm.tm_mday)
+
+
 def VMPdata_dtype_from_colIDs(colIDs):
     """Get a numpy record type from a list of column ID numbers.
 
@@ -263,9 +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?
@@ -276,15 +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
 
 
@@ -295,36 +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:
@@ -346,89 +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
-
-        try:
-            tm = time.strptime(settings_mod['date'].decode('ascii'), '%m/%d/%y')
-        except ValueError:
-            tm = time.strptime(settings_mod['date'].decode('ascii'), '%m-%d-%y')
-        self.startdate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
+        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
-            try:
-                tm = time.strptime(log_module['date'].decode('ascii'), '%m/%d/%y')
-            except ValueError:
-                tm = time.strptime(log_module['date'].decode('ascii'), '%m-%d-%y')
-            self.enddate = date(tm.tm_year, tm.tm_mon, tm.tm_mday)
+            (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
@@ -446,14 +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

@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2014-2019 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from .BioLogic import MPRfile, MPTfile
 
-__all__ = ['MPRfile', 'MPTfile']
+__all__ = ["MPRfile", "MPTfile"]

galvani/res2sqlite.py

@@ -1,5 +1,9 @@
 #!/usr/bin/python
 
+# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import subprocess as sp
 import sqlite3
 import re
@@ -12,43 +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 = {
@@ -187,7 +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),
@@ -267,7 +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,
@@ -281,7 +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,
@@ -291,7 +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,
@@ -340,7 +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,
@@ -348,7 +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,
@@ -367,7 +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(
@@ -434,17 +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)
@@ -455,8 +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:
@@ -471,14 +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,
@@ -488,8 +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
 
@@ -500,7 +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):
@@ -510,9 +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)
@@ -521,33 +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)
@@ -572,17 +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

@@ -1,28 +0,0 @@
-#!/bin/sh
-
-## 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

requirements.txt

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

setup.cfg

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

setup.py

@@ -1,38 +1,41 @@
 # -*- coding: utf-8 -*-
+# SPDX-FileCopyrightText: 2014-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
 
 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='0.2.0',
-    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

@@ -1,11 +1,15 @@
 """Helpers for pytest tests."""
 
+# SPDX-FileCopyrightText: 2019 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import os
 
 import pytest
 
 
-@pytest.fixture(scope='session')
+@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

@@ -1,5 +1,9 @@
 """Tests for loading Arbin .res files."""
 
+# SPDX-FileCopyrightText: 2019-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import os
 import sqlite3
 import subprocess
@@ -9,8 +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():
@@ -18,39 +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

@@ -1,11 +1,15 @@
 # -*- coding: utf-8 -*-
 
+# SPDX-FileCopyrightText: 2013-2020 Christopher Kerr <chris.kerr@mykolab.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import os.path
 import re
-from datetime import datetime
+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
@@ -13,33 +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():
@@ -55,13 +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):
@@ -73,49 +102,76 @@ def test_colID_to_dtype(colIDs, expected):
     assert dtype == expected_dtype
 
 
-@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'),
-])
+@pytest.mark.parametrize(
+    "data, expected",
+    [
+        ("02/23/17", date(2017, 2, 23)),
+        ("10-03-05", date(2005, 10, 3)),
+        ("11.12.20", date(2020, 11, 12)),
+        (b"01/02/03", date(2003, 1, 2)),
+        ("13.08.07", ValueError),
+        ("03-04/05", ValueError),
+    ],
+)
+def test_parse_BioLogic_date(data, expected):
+    """Test the parse_BioLogic_date function."""
+    if isinstance(expected, type) and issubclass(expected, Exception):
+        with pytest.raises(expected):
+            BioLogic.parse_BioLogic_date(data)
+        return
+    result = BioLogic.parse_BioLogic_date(data)
+    assert result == expected
+
+
+@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:
@@ -130,18 +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
 
@@ -149,43 +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

@@ -1,13 +1,24 @@
+# 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
+  reuse
   pytest
 commands =
   flake8
+  reuse lint
   pytest
 
 [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