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Add BLE, C4, ISC, and PERF lints - #3579

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Add BLE, C4, ISC, and PERF lints#3579
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pa/sim-lints

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@flying-sheep flying-sheep added Development Process 🚀 needs retroactive review This PR has been merged but could use some eyes on it labels Apr 11, 2025
@flying-sheep flying-sheep added this to the 1.11.2 milestone Apr 11, 2025
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@flying-sheep flying-sheep changed the title Add C4, ISC, and PERF lints Add BLE, C4, ISC, and PERF lints Apr 11, 2025
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❌ 1 Tests Failed:

Tests completed Failed Passed Skipped
1973 1 1972 90
View the top 1 failed test(s) by shortest run time 
tests/test_datasets.py::test_burczynski06
Stack Traces | 125s run time 
#x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.internet#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_burczynski06#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m pytest.warns(#x1B[96mUserWarning#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mVariable names are not unique#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
>           adata = sc.datasets.burczynski06()#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_datasets.py#x1B[0m:38: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13.../scanpy/datasets/_utils.py#x1B[0m:24: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m f(*args, **kwargs)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13.../scanpy/datasets/_datasets.py#x1B[0m:132: in burczynski06
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m read(filename, backup_url=url)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13.../site-packages/legacy_api_wrap/__init__.py#x1B[0m:82: in fn_compatible
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m fn(*args_all, **kw)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13........./site-packages/scanpy/readwrite.py#x1B[0m:150: in read
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m _read(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13........./site-packages/scanpy/readwrite.py#x1B[0m:880: in _read
    #x1B[0madata = _read_softgz(filename)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13........./site-packages/scanpy/readwrite.py#x1B[0m:954: in _read_softgz
    #x1B[0m#x1B[94mfor#x1B[39;49;00m line #x1B[95min#x1B[39;49;00m file:#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13/gzip.py#x1B[0m:339: in read1
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._buffer.read1(size)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13/_compression.py#x1B[0m:68: in readinto
    #x1B[0mdata = #x1B[96mself#x1B[39;49;00m.read(#x1B[96mlen#x1B[39;49;00m(byte_view))#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <gzip._GzipReader object at 0x7fbf48f2dc00>, size = 8192

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mread#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, size=-#x1B[94m1#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m size < #x1B[94m0#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.readall()#x1B[90m#x1B[39;49;00m
        #x1B[90m# size=0 is special because decompress(max_length=0) is not supported#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m size:#x1B[90m#x1B[39;49;00m
            #x1B[94mreturn#x1B[39;49;00m #x1B[33mb#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# For certain input data, a single#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# call to decompress() may not return#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# any data. In this case, retry until we get some data or reach EOF.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mwhile#x1B[39;49;00m #x1B[94mTrue#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._decompressor.eof:#x1B[90m#x1B[39;49;00m
                #x1B[90m# Ending case: we've come to the end of a member in the file,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# so finish up this member, and read a new gzip header.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# Check the CRC and file size, and set the flag so we read#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# a new member#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[96mself#x1B[39;49;00m._read_eof()#x1B[90m#x1B[39;49;00m
                #x1B[96mself#x1B[39;49;00m._new_member = #x1B[94mTrue#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[96mself#x1B[39;49;00m._decompressor = #x1B[96mself#x1B[39;49;00m._decomp_factory(#x1B[90m#x1B[39;49;00m
                    **#x1B[96mself#x1B[39;49;00m._decomp_args)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._new_member:#x1B[90m#x1B[39;49;00m
                #x1B[90m# If the _new_member flag is set, we have to#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# jump to the next member, if there is one.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[96mself#x1B[39;49;00m._init_read()#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._read_gzip_header():#x1B[90m#x1B[39;49;00m
                    #x1B[96mself#x1B[39;49;00m._size = #x1B[96mself#x1B[39;49;00m._pos#x1B[90m#x1B[39;49;00m
                    #x1B[94mreturn#x1B[39;49;00m #x1B[33mb#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[96mself#x1B[39;49;00m._new_member = #x1B[94mFalse#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[90m# Read a chunk of data from the file#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._decompressor.needs_input:#x1B[90m#x1B[39;49;00m
                buf = #x1B[96mself#x1B[39;49;00m._fp.read(READ_BUFFER_SIZE)#x1B[90m#x1B[39;49;00m
                uncompress = #x1B[96mself#x1B[39;49;00m._decompressor.decompress(buf, size)#x1B[90m#x1B[39;49;00m
            #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                uncompress = #x1B[96mself#x1B[39;49;00m._decompressor.decompress(#x1B[33mb#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, size)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._decompressor.unused_data != #x1B[33mb#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[90m# Prepend the already read bytes to the fileobj so they can#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# be seen by _read_eof() and _read_gzip_header()#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[96mself#x1B[39;49;00m._fp.prepend(#x1B[96mself#x1B[39;49;00m._decompressor.unused_data)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m uncompress != #x1B[33mb#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[94mbreak#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m buf == #x1B[33mb#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>               #x1B[94mraise#x1B[39;49;00m #x1B[96mEOFError#x1B[39;49;00m(#x1B[33m"#x1B[39;49;00m#x1B[33mCompressed file ended before the #x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                               #x1B[33m"#x1B[39;49;00m#x1B[33mend-of-stream marker was reached#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               EOFError: Compressed file ended before the end-of-stream marker was reached#x1B[0m

#x1B[1m#x1B[.../hostedtoolcache/Python/3.13.2.........................../x64/lib/python3.13/gzip.py#x1B[0m:549: EOFError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.internet#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_burczynski06#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
>       #x1B[94mwith#x1B[39;49;00m pytest.warns(#x1B[96mUserWarning#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mVariable names are not unique#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       Failed: DID NOT WARN. No warnings of type (<class 'UserWarning'>,) were emitted.#x1B[0m
#x1B[1m#x1B[31mE        Emitted warnings: [].#x1B[0m

#x1B[1m#x1B[31mtests/test_datasets.py#x1B[0m:37: Failed

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@flying-sheep
flying-sheep merged commit 1c5432b into main Apr 11, 2025
@flying-sheep
flying-sheep deleted the pa/sim-lints branch April 11, 2025 14:14
flying-sheep added a commit that referenced this pull request Apr 11, 2025
@flying-sheep
Backport PR #3579: Add BLE, C4, ISC, and PERF lints
707040d
@flying-sheep flying-sheep mentioned this pull request Apr 11, 2025
Merged
@scverse scverse deleted a comment from lumberbot-app Bot Apr 11, 2025
flying-sheep added a commit that referenced this pull request Apr 11, 2025
@flying-sheep
Backport PR #3579: Add BLE, C4, ISC, and PERF lints (#3581)
73b3917
selmanozleyen pushed a commit to selmanozleyen/scanpy that referenced this pull request Apr 14, 2025
@flying-sheep @selmanozleyen
Add BLE, C4, ISC, and PERF lints (scverse#3579)
b7aa8e3
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