hguturu

Using bgz extension instead of gz for bgziped files

13

Would make it very clear what type of file is being dealth with. Additionally, can avoid issues with things like vim being able to read bgziped files saved with .gz...

PhilosopherFilter fails with `Cannot decode packed binary. expected element type <msms_pipeline_analysis> but have <msms_run_summary>`

18

**Describe the bug** I was running the `LFQ-phospho` workflow on a set of mzML files from Bruker data. After running the whole process during the `PhilosopherFilter` step one of the...

Accelerate single threaded jobs using multiple parallel processes

3

**Is your feature request related to a problem? Please describe.** Currently, FragPipe parallelizes jobs based on if the tool supports multiple threads. But, single threaded jobs like initializing philosopher, annotating...

Consider moving plotting to screen or figure logic in utility rather than library function

2

https://github.com/ShujiaHuang/qmplot/blob/ed1d5a82055ba8c787c2dbae69d533893438390e/qmplot/modules/_qq.py#L232-L235 It would be nice if the above logic can be moved to https://github.com/ShujiaHuang/qmplot/blob/ed1d5a82055ba8c787c2dbae69d533893438390e/qmplot/main.py#L113. That way the underlying qqplot function can be used as a plotting library function, where it...

Consider adding `figure.titlesize` and `figure.labelsize` rcmods

4

https://github.com/mwaskom/seaborn/blob/9087437ad28e872ff73e5ff10ce6c2e7d511d650/seaborn/rcmod.py#L386-L387 This would allow the figure `suptitle` to also scale up with `plotting_context`.

localconverter solution doesn't work with python classes for multi-threaded logic

1

**Describe the issue or bug** I believe this is a variant of https://github.com/rpy2/rpy2/issues/965 where I am unable to use an class that implements RPy2 in a multi-threading context. We discovered...

Comparision of performance of regenie WGR and glow WGR

2

Are there any comparisons of the two methods? In https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-021-00870-7/MediaObjects/41588_2021_870_MOESM1_ESM.pdf, I see a discussion of the implementation, but no comparison of two implementations similar to how regenie is compared against...

AnnData can be created with pd.MultiIndex dimension labels without erroring with pandas<2

10

The following line breaks in pandas>2 for MultiIndex X columns. https://github.com/scverse/anndata/blob/ff64448c44836b8134b67f828fb91f70dc59e347/anndata/_core/anndata.py#L120. Due to change in behavior of `is_string_dtype`. ```py import pandas as pd from pandas.api.types import is_string_dtype is_string_dtype(pd.MultiIndex.from_tuples([('a','b')])) # False...

Allow formatting the categorical encoded variables

4

Currently they get formatted as `C({parameter})[T.{value}]` or `{parameter}[T.{value}]` if its already a string. E.g., ```py BinGrp = [0, 0, 0, 1, 1, 1] becomes C(BinGrp)[T.0] C(BinGrp)[T.1] 0 1 0 1...

Unable to install from `sdist` using force-include with `hatchling>=1.19`

3

Following up on #1130 since I don't know if its being tracked due to being closed. I think this issue of being unable to install from `sdist` with `force-includes` for...