Verify native Windows compatibility #42

ttung · 2018-02-05T20:58:41Z

Many collaborators are on Windows machines. We should make sure pip installation works for them w/ no usability issues.

Dependencies: #834

bkmartinjr · 2018-02-08T21:13:08Z

@ttung - feel free to frame what tests you want run and I can do it. Also, do you require Win32 or can you have people use WSL (ie, Ubuntu)?

ttung · 2018-02-08T21:35:56Z

if you clone the repo and can pass pip install -r REQUIREMENTS.txt && pip install -e . && python -m unittest discover tests, we're in good shape. We should just add a windows run to travis and make sure we stay in good shape.

bkmartinjr · 2018-02-08T21:46:58Z

Almost, but no cigar. Win10 native shell:

C:\Users\bruce\projects\starfish>python -m unittest discover tests
Downloading data ...
Data downloaded to: C:\Users\bruce\AppData\Local\Temp\tmpsyaiu1_q\raw/ExampleInSituSequencing/
{
    "data": [
        {
            "hyb": 0,
            "ch": 0,
            "file": "fov_0_H_0_C_0.tiff"
        },
        {
            "hyb": 0,
            "ch": 1,
            "file": "fov_0_H_0_C_1.tiff"
        },
        {
            "hyb": 0,
            "ch": 2,
            "file": "fov_0_H_0_C_2.tiff"
        },
        {
            "hyb": 0,
            "ch": 3,
            "file": "fov_0_H_0_C_3.tiff"
        },
        {
            "hyb": 1,
            "ch": 0,
            "file": "fov_0_H_1_C_0.tiff"
        },
        {
            "hyb": 1,
            "ch": 1,
            "file": "fov_0_H_1_C_1.tiff"
        },
        {
            "hyb": 1,
            "ch": 2,
            "file": "fov_0_H_1_C_2.tiff"
        },
        {
            "hyb": 1,
            "ch": 3,
            "file": "fov_0_H_1_C_3.tiff"
        },
        {
            "hyb": 2,
            "ch": 0,
            "file": "fov_0_H_2_C_0.tiff"
        },
        {
            "hyb": 2,
            "ch": 1,
            "file": "fov_0_H_2_C_1.tiff"
        },
        {
            "hyb": 2,
            "ch": 2,
            "file": "fov_0_H_2_C_2.tiff"
        },
        {
            "hyb": 2,
            "ch": 3,
            "file": "fov_0_H_2_C_3.tiff"
        },
        {
            "hyb": 3,
            "ch": 0,
            "file": "fov_0_H_3_C_0.tiff"
        },
        {
            "hyb": 3,
            "ch": 1,
            "file": "fov_0_H_3_C_1.tiff"
        },
        {
            "hyb": 3,
            "ch": 2,
            "file": "fov_0_H_3_C_2.tiff"
        },
        {
            "hyb": 3,
            "ch": 3,
            "file": "fov_0_H_3_C_3.tiff"
        }
    ],
    "aux": [
        {
            "type": "dapi",
            "file": "fov_0_dapi.tiff",
            "format": "TIFF"
        },
        {
            "type": "dots",
            "file": "fov_0_dots.tiff",
            "format": "TIFF"
        }
    ],
    "metadata": {
        "num_hybs": 4,
        "num_chs": 4,
        "shape": [
            980,
            1330
        ],
        "is_volume": false,
        "format": "TIFF"
    }
}
Writing org.json to: C:\Users\bruce\AppData\Local\Temp\tmpsyaiu1_q\formatted/org.json
python examples/get_iss_data.py  ==> 6.489300966262817 seconds

         _              __ _     _
        | |            / _(_)   | |
     ___| |_ __ _ _ __| |_ _ ___| |__
    / __| __/ _` | '__|  _| / __| '_  `
    \__ \ || (_| | |  | | | \__ \ | | |
    |___/\__\__,_|_|  |_| |_|___/_| |_|


Registering ...
For hyb: 0, Shift: [  3.118 -11.021], Error: 0.37367679340203525
For hyb: 1, Shift: [-2.22   2.874], Error: 0.427452955088995
For hyb: 2, Shift: [ 4.994  0.348], Error: 0.4128292497462391
For hyb: 3, Shift: [ 5.912  0.548], Error: 0.4278942160521561
starfish register  ==> 14.382418394088745 seconds

         _              __ _     _
        | |            / _(_)   | |
     ___| |_ __ _ _ __| |_ _ ___| |__
    / __| __/ _` | '__|  _| / __| '_  `
    \__ \ || (_| | |  | | | \__ \ | | |
    |___/\__\__,_|_|  |_| |_|___/_| |_|


Filtering ...
Reading data
Filtering image: 0...
Filtering image: 1...
Filtering image: 2...
Filtering image: 3...
Filtering image: 4...
Filtering image: 5...
Filtering image: 6...
Filtering image: 7...
Filtering image: 8...
Filtering image: 9...
Filtering image: 10...
Filtering image: 11...
Filtering image: 12...
Filtering image: 13...
Filtering image: 14...
Filtering image: 15...
Filtering dots ...
Writing results ...
starfish filter  ==> 56.3315110206604 seconds

         _              __ _     _
        | |            / _(_)   | |
     ___| |_ __ _ _ __| |_ _ ___| |__
    / __| __/ _` | '__|  _| / __| '_  `
    \__ \ || (_| | |  | | | \__ \ | | |
    |___/\__\__,_|_|  |_| |_|___/_| |_|


Traceback (most recent call last):
  File "C:\Users\bruce\projects\starfish\starfish\__main__.py", line 3, in <module>
    starfish()
  File "C:\Users\bruce\projects\starfish\starfish\starfish.py", line 103, in starfish
    args.starfish_command(args)
  File "C:\Users\bruce\projects\starfish\starfish\starfish.py", line 150, in detect_spots
    from .spots.gaussian import GaussianSpotDetector
  File "C:\Users\bruce\projects\starfish\starfish\spots\gaussian.py", line 6, in <module>
    from showit import image
  File "c:\users\bruce\appdata\local\programs\python\python36\lib\site-packages\showit\__init__.py", line 24, in <module>
    __version__ = get_version()
  File "c:\users\bruce\appdata\local\programs\python\python36\lib\site-packages\showit\__init__.py", line 20, in get_version
    raise ValueError("Cannot find VERSION file")
ValueError: Cannot find VERSION file
E
         _              __ _     _
        | |            / _(_)   | |
     ___| |_ __ _ _ __| |_ _ ___| |__
    / __| __/ _` | '__|  _| / __| '_  `
    \__ \ || (_| | |  | | | \__ \ | | |
    |___/\__\__,_|_|  |_| |_|___/_| |_|


         9 function calls in 0.000 seconds

   Ordered by: internal time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000    0.000    0.000 c:\users\bruce\appdata\local\programs\python\python36\lib\pstats.py:75(init)
        1    0.000    0.000    0.000    0.000 c:\users\bruce\appdata\local\programs\python\python36\lib\pstats.py:65(__init__)
        1    0.000    0.000    0.000    0.000 c:\users\bruce\appdata\local\programs\python\python36\lib\pstats.py:94(load_stats)
        1    0.000    0.000    0.000    0.000 c:\users\bruce\appdata\local\programs\python\python36\lib\cProfile.py:50(create_stats)
        1    0.000    0.000    0.000    0.000 {built-in method builtins.isinstance}
        1    0.000    0.000    0.000    0.000 C:\Users\bruce\projects\starfish\starfish\starfish.py:257(noop)
        1    0.000    0.000    0.000    0.000 {built-in method builtins.len}
        1    0.000    0.000    0.000    0.000 {method 'disable' of '_lsprof.Profiler' objects}
        1    0.000    0.000    0.000    0.000 {built-in method builtins.hasattr}


.
======================================================================
ERROR: test_run_pipeline (test_iss_data.TestWithIssData)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Users\bruce\projects\starfish\tests\test_iss_data.py", line 98, in test_run_pipeline
    subprocess.check_call(cmdline)
  File "C:\Users\bruce\AppData\Local\Programs\Python\Python36\lib\subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['coverage', 'run', '-p', '--source', 'starfish', '-m', 'starfish', 'detect_spots', 'C:\\Users\\bruce\\AppData\\Local\\Temp\\tmpsyaiu1_q\\filtered\\org.json', 'C:\\Users\\bruce\\AppData\\Local\\Temp\\tmpsyaiu1_q\\results', 'dots', '--min_sigma', '4', '--max_sigma', '6', '--num_sigma', '20', '--t', '0.01']' returned non-zero exit status 1.

----------------------------------------------------------------------
Ran 2 tests in 78.472s

FAILED (errors=1)

C:\Users\bruce\projects\starfish>

ttung · 2018-02-08T23:11:40Z

Turns out travis only supports osx and linux. :(

ttung · 2018-12-07T10:12:02Z

Turns out travis only supports osx and linux. :(

No longer true!

ambrosejcarr · 2019-07-26T19:19:46Z

@dany-fu recorded the following path problem:

Hi, a Windows-specific error that we're encountering is regarding loading an `Experiment` from a json file. We can run the Starfish example notebooks just fine when it's pulling directly from aws for the test data, but when we try to load the json file after formatting our own images, the path gets warped:

`experiment = starfish.Experiment.from_json("C:/Users/path-to-file/experiment.json")`

`OSError: [Errno 22] Invalid argument: /C:/Users/path-to-file\\experiment.json` <-double backslash in front of the file

I feel like I've tried every combination of `os.join`, `\\`, `/`,  string literals

source link: https://spacetx.slack.com/archives/CCU5DN4DV/p1564162437019900

ttung · 2019-09-11T16:05:51Z

This is basically done. We know that Windows works, but it's just slow. #1544 solves that.

ttung self-assigned this Feb 5, 2018

dganguli added the usability label Feb 7, 2018

dganguli changed the title ~~windows pip~~ Verify Windows compatibility Feb 7, 2018

ttung added the low priority label Sep 13, 2018

ambrosejcarr unassigned ttung Sep 21, 2018

neuromusic added this to the 0.1.0 milestone Dec 19, 2018

neuromusic modified the milestones: 0.2.0, 0.1.0 Mar 13, 2019

ttung mentioned this issue Mar 18, 2019

Verify WSL Windows compatibility #1092

Closed

ttung changed the title ~~Verify Windows compatibility~~ Verify native Windows compatibility Mar 18, 2019

ttung removed this from the 0.1.0 milestone Mar 18, 2019

shanaxel42 added this to the 0.2.0 milestone May 7, 2019

neuromusic removed the low priority label May 7, 2019

shanaxel42 added research issues/questions opened for research purposes and removed ux labels May 7, 2019

ttung closed this as completed Sep 11, 2019

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Verify native Windows compatibility #42

Verify native Windows compatibility #42

ttung commented Feb 5, 2018 •

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bkmartinjr commented Feb 8, 2018

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bkmartinjr commented Feb 8, 2018 •

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ttung commented Feb 8, 2018

ttung commented Dec 7, 2018

ambrosejcarr commented Jul 26, 2019

ttung commented Sep 11, 2019

Verify native Windows compatibility #42

Verify native Windows compatibility #42

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