liningtonlab/madbyte

Metabolomics And Dereplication By Two-dimensional Experiments - MADByTE NMR Metabolomics Platform

madbyte's Issues

Application does not start on Big Sur

A fresh install on an Apple M1 chipset (Macbook pro 2021) running Big Sur 11.5.1 does not launch the program.

Behavior: Applications appears to begin to launch, printing the opening statements and gets frozen when trying to launch main window.

It appears to be tied to pyqt (and QT in general) - https://bugreports.qt.io/browse/QTBUG-87014

[Windows 11] Compatibility issues on Windows 11

Windows 11 and python 3.7 have some dependencies that keep MADByTE from running the processing step.

Error Seen in Dialog:

module '_winapi' has no attribute 'synchronize'

Proposed Solutions:

• remove multi threading (not optimal)
• update python to >3.7
• pin joblib <1.3.0 in requirements as work around (not long lived)

Running `pytest` on freshly cloned repo results in errors

In trying to address #8 , I installed pytest via conda install pytest and encountered the following:

=========================================================== test session starts ===========================================================
platform darwin -- Python 3.7.10, pytest-6.2.2, py-1.10.0, pluggy-0.13.1
rootdir: /Users/chananas2/Documents/madbytetesting/madbyte
collected 14 items

tests/test_madbyte_filter.py ...........                                                                                            [ 78%]
tests/test_madbyte_utils.py FF.                                                                                                     [100%]

================================================================ FAILURES =================================================================
______________________________________________________ test_establish_file_structure ______________________________________________________

project_dir = PosixPath('/private/var/folders/ws/4b3kt9f12jn3jvlp50f_x_ljl4jcfb/T/pytest-of-chananas2/pytest-3/data0')

    def test_establish_file_structure(project_dir: Path):
        out_dir = project_dir.joinpath("test")
>       utils.establish_file_structure("test", out_dir, project_dir)
E       TypeError: establish_file_structure() takes 1 positional argument but 3 were given

tests/test_madbyte_utils.py:11: TypeError
_____________________________________________________________ test_get_master _____________________________________________________________

project_dir = PosixPath('/private/var/folders/ws/4b3kt9f12jn3jvlp50f_x_ljl4jcfb/T/pytest-of-chananas2/pytest-3/data0')

    def test_get_master(project_dir: Path):
>       df = utils.get_master(project_dir)

tests/test_madbyte_utils.py:18:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
madbyte/utils.py:631: in get_master
    return pd.read_json(master_path)
/usr/local/Caskroom/miniconda/base/envs/madbyte/lib/python3.7/site-packages/pandas/util/_decorators.py:199: in wrapper
    return func(*args, **kwargs)
/usr/local/Caskroom/miniconda/base/envs/madbyte/lib/python3.7/site-packages/pandas/util/_decorators.py:299: in wrapper
    return func(*args, **kwargs)
/usr/local/Caskroom/miniconda/base/envs/madbyte/lib/python3.7/site-packages/pandas/io/json/_json.py:563: in read_json
    return json_reader.read()
/usr/local/Caskroom/miniconda/base/envs/madbyte/lib/python3.7/site-packages/pandas/io/json/_json.py:694: in read
    obj = self._get_object_parser(self.data)
/usr/local/Caskroom/miniconda/base/envs/madbyte/lib/python3.7/site-packages/pandas/io/json/_json.py:716: in _get_object_parser
    obj = FrameParser(json, **kwargs).parse()
/usr/local/Caskroom/miniconda/base/envs/madbyte/lib/python3.7/site-packages/pandas/io/json/_json.py:831: in parse
    self._parse_no_numpy()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <pandas.io.json._json.FrameParser object at 0x7fa785a90dd0>

    def _parse_no_numpy(self):

        json = self.json
        orient = self.orient

        if orient == "columns":
            self.obj = DataFrame(
>               loads(json, precise_float=self.precise_float), dtype=None
E               ValueError: Expected object or value

/usr/local/Caskroom/miniconda/base/envs/madbyte/lib/python3.7/site-packages/pandas/io/json/_json.py:1079: ValueError
========================================================= short test summary info =========================================================
FAILED tests/test_madbyte_utils.py::test_establish_file_structure - TypeError: establish_file_structure() takes 1 positional argument bu...
FAILED tests/test_madbyte_utils.py::test_get_master - ValueError: Expected object or value
====================================================== 2 failed, 12 passed in 1.31s =======================================================

~/Documents/madbytetesting/madbyte main

MADByte Installation - enviroment

Hello hello,
I'm trying to install MADByTE to try it, but even though I have Anaconda 3, I'm using another (NMRfilter) environment. This is probably a question about the Anaconda 3, but can I just remove the environment I'm using to add MADByTE's without having to install the first environment again?

• can I have several environments installed?
  Thanks!

[Popup] Error message contains typo

The "MADByTE Network Construction" popup contains a spelling error.

BUG

The MADByTE developed by your team has a good application, but there is a bug in use, how to solve it?

Warning needed when processing networks

Generating networks from only one sample causes the program to throw an error.

Need:
Design pop up explaining that the other two networks cannot be generated - rather than a default error in the terminal.

Drop Down menu for "NMR Data Type" only shows one option properly

OR

Similar things happen for other drop down menus as well:

Clicking Help > Examples in GUI results in nothing

Upon clicking Help > Examples I get this error in the command line:

python madbyte_gui.py
MADByTE is loading...
Multithreading with maximum 16 threads
/bin/sh: Documentation/MADByTE_Quick_Start_Tutorial.pdf: Permission denied

Clicking Help > Documentation results in a similar error:

/bin/sh: Documentation/MADByTE_User_Manual.pdf: Permission denied

I'm running madbyte v1.2.0 on macOS Catalina (10.15.7) on a MacBook Pro (16" 2019)

[Parsers] CSV Parser Switching Columns

When the CSV input is used, it might switch the H_PPM and C_PPM columns around (observed once), resulting in incorrect labeling between nuclei and no spin system formation for the sample.

A workaround for now: Try switching the columns around.

Fix incoming.

Import errors with some pulse sequences

Some pulse sequences are not what the system expects. This is due to other TOCSY pulse sequences being used and differences in pulse sequence programming (comments at the top).

TOCSY or HSQC-TOCSY

Hello again,
I wonder (1) if it accepts HSQC-TOCSY data instead of TOCSY (or if there is a plan for it); and (2) would it run on peak lists as entrees?

Thanks

1D plotting error - zg30

zg30 pulse sequences are not being recognized.