Comments (7)
ttung
commented on May 29, 2024
1
Turns out travis only supports osx and linux. :(
No longer true!
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bkmartinjr
commented on May 29, 2024
@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)?
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ttung
commented on May 29, 2024
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.
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bkmartinjr
commented on May 29, 2024
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>
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ttung
commented on May 29, 2024
Turns out travis only supports osx and linux. :(
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ambrosejcarr
commented on May 29, 2024
@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
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ttung
commented on May 29, 2024
This is basically done. We know that Windows works, but it's just slow. #1544 solves that.
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Related Issues (20)
- Quickstart and napari HOT 2
- Update open napari window? HOT 1
- Displaying example from data formatting tutorial HOT 3
- Include output in example notebooks HOT 2
- JOSS paper does not mention alternative tools
- JOSS MS comments HOT 1
- "ValueError: in1 and in2 should have the same dimensionality" when "is_volume=True" for Filter.DeconvolvePSF
- make install-dev got error
- 'Visualizing Data' tutorial crashes at viewer.add_image step HOT 3
- Tutorials making use of Napari should include screenshots of expected output. HOT 1
- Are the masks in the left in the tutorial really two cells? HOT 2
- JOSS paper should mention how starfish compares to the other available tools
- error importing scikit's 'match_histograms' HOT 2
- Link to raw data is not working HOT 2
- starfish is incompatible with Python 3.9 HOT 1
- AttributeError: 'DataArray' object has no attribute 'flags' in quick start run HOT 9
- Couldn't install without specifying an older version of scikit-image (0.17.2) HOT 5
- Update installation section in the README.rst and readthedocs.io
- ValueError when running BlobDetector HOT 2
- Unable to run dev install on Mac M2 HOT 1
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