Open winni2k opened 4 years ago
I will likely get started on this after #6 has been merged. It would be great if everyone could take look through this list and keep it in mind while coding up new things 👀
Thanks to @jonn-smith many of the warnings have been fixed! We still have some variable naming issues...
Here is the current list:
************* Module tesserae.tesserae
src/tesserae/tesserae.py:88:9: E1101: Module 'pysam' has no 'FastxFile' member (no-member)
src/tesserae/tesserae.py:88:45: C0103: Variable name "fh" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:125:8: C0103: Attribute name "piM" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:126:8: C0103: Attribute name "piI" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:127:8: C0103: Attribute name "mm" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:128:8: C0103: Attribute name "gm" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:129:8: C0103: Attribute name "dm" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:131:8: C0103: Attribute name "lpiM" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:132:8: C0103: Attribute name "lpiI" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:173:8: C0103: Attribute name "sm" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:175:8: C0103: Attribute name "si" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:179:8: C0103: Attribute name "editTrack" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:97:0: R0902: Too many instance attributes (53/7) (too-many-instance-attributes)
src/tesserae/tesserae.py:106:4: R0913: Too many arguments (7/5) (too-many-arguments)
src/tesserae/tesserae.py:106:4: R0915: Too many statements (58/50) (too-many-statements)
src/tesserae/tesserae.py:314:4: R0914: Too many local variables (20/15) (too-many-locals)
src/tesserae/tesserae.py:334:8: C0103: Variable name "l1" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:359:8: C0103: Variable name "cp" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:367:8: C0103: Variable name "l2" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:399:12: C0103: Variable name "cp" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:410:4: C0103: Argument name "cp" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:421:8: C0103: Variable name "sb" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:441:8: C0103: Variable name "sb" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:463:8: C0103: Variable name "sb" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:488:16: C0103: Variable name "sb" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:503:16: C0103: Variable name "sb" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:508:16: C0103: Variable name "c" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:509:16: C0103: Variable name "c" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:410:4: R0912: Too many branches (19/12) (too-many-branches)
src/tesserae/tesserae.py:410:4: R0915: Too many statements (63/50) (too-many-statements)
src/tesserae/tesserae.py:528:4: C0103: Argument name "l1" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:528:4: C0103: Argument name "cp" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:528:4: R0913: Too many arguments (6/5) (too-many-arguments)
src/tesserae/tesserae.py:566:4: C0103: Argument name "l1" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:566:4: R0913: Too many arguments (25/5) (too-many-arguments)
src/tesserae/tesserae.py:566:4: R0914: Too many local variables (52/15) (too-many-locals)
src/tesserae/tesserae.py:597:8: C0103: Variable name "C" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:610:8: C0103: Variable name "A" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:633:8: C0103: Variable name "B" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:579:8: W0613: Unused argument 'pos_target_trace' (unused-argument)
src/tesserae/tesserae.py:581:8: W0613: Unused argument 'l1' (unused-argument)
src/tesserae/tesserae.py:583:8: W0613: Unused argument 'mem_limit' (unused-argument)
src/tesserae/tesserae.py:591:8: W0613: Unused argument 'store_states' (unused-argument)
src/tesserae/tesserae.py:680:4: C0103: Argument name "l1" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:680:4: C0103: Argument name "l0" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:680:4: R0913: Too many arguments (12/5) (too-many-arguments)
src/tesserae/tesserae.py:680:4: R0914: Too many local variables (33/15) (too-many-locals)
src/tesserae/tesserae.py:742:16: C0415: Import outside toplevel (multiprocessing.pool) (import-outside-toplevel)
src/tesserae/tesserae.py:744:49: C0103: Variable name "p" doesn't conform to snake_case naming style (invalid-name)
src/tesserae/tesserae.py:839:8: C0103: Variable name "sb" doesn't conform to snake_case naming style (invalid-name)
I have similar issues with the pysam
module in the CLI code as well. I'm not sure how to fix them - the module most certainly does exist.
I think you are referring to E1101, which is the first message? This is almost certainly a false positive. E1101 is also triggered for attributes that are created dynamically, and I think that is a common coding style for an API that interfaces with C code.
I'll set up a .pylintrc
file and add pysam
as an exclusion for E1101.
Done. If you are still having issues with pysam
, try rebuilding your test environment with tox -r
or tox -re lint
.
Running
pylint -d C0330,C0114,C0116 src
returns the messages below. I have removed a few categories of messages that I don't think are relevant right now using the-d
option. I think the majority of messages below need addressing. The W* codes are the most pressing.