pyprophet

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I stumbled over an issue that the tests running by py.test, would not be able to import modules - I am actually not sure why. After removing the `__init__.py` from...

oliveralka

Assay RT calculation is not proper

7

https://github.com/PyProphet/pyprophet/blob/eb048de3014c676d704250cdd443e81af14e32f0/pyprophet/export.py#L59 To get assay_rt, we should be doing exp_rt - lib2expTrafo(delta_rt). Currently, we are subtracting library_space time from experimental_space time. lib2expTrafo function would convert delta_rt from library_space to experimental_space.

shubham1637

We had an issue when we tried to merge different `osw` files across runs that were analyzed using different libraries -- the results made no sense since the keys were...

hroest

singularity pull issue

6

Hi, I want to use it in the singularity containers but when I use the demand like: ``` singularity pull docker://pyprophet/pyprophet:2.1.3 ``` It is not working. Do you know the...

HFan11

Feature/speedup parquet export

1

Re-implementation of PR https://github.com/PyProphet/pyprophet/pull/111 This uses duckdb for parquet export instead of pandas. This allows for memory and SQL queries to be handled by duckdb which is faster and uses...

jcharkow

It seems that CI tests got disabled and recent changes might cause some of these tests to fail. Possibly we should enable these in github actions? @singjc

jcharkow

change to always select precursor table so scoring is performed correctly

jcharkow

Use duckdb loading throughout pyprophet

2

With export-parquet, we have an additional dependency of duckdb which allows for fast SQL queries, especially those involving lots of joins. Here roll out duckdb SQL queries in pyprophet for...

jcharkow

## Problem When training an XGBoost or HistGradientBoosting model with a specific `--ss_main_score` parameter and then applying the trained weights without specifying the same parameter, features become misaligned, causing incorrect...

Copilot

--apply_weights requires --ss_main_score to be specified as in the original command

1

I get unexpected results when using `--apply_weights` with XGBoost if a `--ss_main_score` was set manually. E.g. `pyprophet score --in in.oswpq --level=ms1ms2 --classifier=XGBoost --ss_main_score=var_dotprod_score` - Trains the model as expected However...

jcharkow