wfondrie/mokapot issues and pull requests

#134 - [BUG] FDR to QValue Numba Typing Error

Issue - State: open - Opened by singjc 10 days ago

#133 - Storey's method for q-value computation (draft)

Pull Request - State: closed - Opened by ezander about 2 months ago - 2 comments

#132 - [WIP] v0.11.0 RC

Pull Request - State: open - Opened by jspaezp about 2 months ago - 5 comments

#131 - Small changes for FlashLFQ writer

Pull Request - State: closed - Opened by unholyparrot 2 months ago - 3 comments

#130 - Add (minimal) ProForma support in `mokapot.picked_protein.strip_peptides`

Issue - State: open - Opened by RalfG 3 months ago - 2 comments

#129 - [Issue] docker build stage does not get tested in CI

Issue - State: open - Opened by jspaezp 4 months ago

#128 - Feature/streaming fix windows

Pull Request - State: closed - Opened by gessulat 4 months ago - 1 comment

#127 - Feature/confidence streaming

Pull Request - State: closed - Opened by gessulat 4 months ago - 1 comment

#126 - (feat) added auto handling of traditional pin and testing

Pull Request - State: closed - Opened by jspaezp 5 months ago - 2 comments

#125 - Update Actions and Enable Dependabot for GH Actions

Pull Request - State: open - Opened by wfondrie 5 months ago - 2 comments

#124 - Also load scaler when loading model

Issue - State: open - Opened by gessulat 6 months ago

#123 - Chunksize should be derived from MEMORY env variable

Issue - State: open - Opened by gessulat 6 months ago

#122 - Consolidate naming of LinearPSMDataset OnDiskPSMDataset

Issue - State: open - Opened by gessulat 6 months ago - 1 comment

#121 - Revert file suffix change for output files

Issue - State: open - Opened by gessulat 6 months ago

#120 - Remove MSAID's SQLite output support

Issue - State: open - Opened by gessulat 6 months ago

#119 - Add parquet and sqlite support; add NNLS-based PEP and Q-value calculation

Pull Request - State: closed - Opened by gessulat 8 months ago - 10 comments

#118 - [Feature Request] mokapot output as a pepXML file

Issue - State: open - Opened by sciordia 10 months ago

#117 - Enzyme Free Digestion results in "0 digested proteins"

Issue - State: open - Opened by jonathan-krieger-bruker about 1 year ago - 4 comments

#115 - sorting proteins for protein group FDR

Issue - State: closed - Opened by bmx8177 about 1 year ago - 1 comment

#114 - Issue with decoy prefix when trying to get protein level confidence.

Issue - State: open - Opened by louisebuur about 1 year ago - 2 comments

#113 - Can't get protein level confidence. "IndexError: index -3 is out of bounds for axis 0 with size 1"

Issue - State: open - Opened by roushrsh over 1 year ago - 3 comments

#112 - updated gh actions

Pull Request - State: closed - Opened by jspaezp over 1 year ago - 1 comment

#111 - Add workflow for building Windows installer

Pull Request - State: open - Opened by RalfG over 1 year ago - 5 comments

#110 - Mokapot sub commands and `brew()` restructuring

Issue - State: open - Opened by gessulat over 1 year ago

#109 - File schema via pydantic

Issue - State: open - Opened by gessulat over 1 year ago - 3 comments

#108 - WIP: intermediary file format specification

Issue - State: open - Opened by gessulat over 1 year ago

#107 - Multi-threaded writing of output files

Issue - State: open - Opened by gessulat over 1 year ago - 2 comments

#106 - Add copy to multiprocessing

Pull Request - State: closed - Opened by wfondrie over 1 year ago - 1 comment

#105 - Replace logging.[...] with LOGGER.[...]

Pull Request - State: closed - Opened by RalfG over 1 year ago - 3 comments

#104 - max_workers issue

Issue - State: closed - Opened by wenbostar over 1 year ago - 1 comment
Labels: bug

#102 - Decoy Prefix results in many unmapped peptides

Issue - State: open - Opened by jonathan-krieger-bruker over 1 year ago - 1 comment

#101 - [Question] executable(e.g. pyinstaller)

Issue - State: open - Opened by timosachsenberg almost 2 years ago - 7 comments
Labels: enhancement

#100 - Feature/improve speed and limit memory (#11)

Pull Request - State: closed - Opened by sambenfredj almost 2 years ago - 3 comments

#99 - Main

Pull Request - State: closed - Opened by sambenfredj almost 2 years ago

#98 - Lint with Ruff and add other pre-commit hooks

Pull Request - State: closed - Opened by wfondrie almost 2 years ago - 1 comment
Labels: enhancement

#97 - Combine mokapot scores from multiple files

Issue - State: open - Opened by wfondrie almost 2 years ago
Labels: enhancement

#96 - [Breaking enhancement] Swap out Pandas for Polars

Pull Request - State: closed - Opened by wfondrie almost 2 years ago - 1 comment

#95 - Fixed typo in contributing.rst

Pull Request - State: closed - Opened by danielgeiszler almost 2 years ago

#94 - Update dataset.py

Pull Request - State: closed - Opened by danielgeiszler almost 2 years ago

#93 - Migrate to main

Pull Request - State: closed - Opened by wfondrie almost 2 years ago - 1 comment

#92 - [Pitch] Lazy data loading

Issue - State: closed - Opened by jspaezp almost 2 years ago - 1 comment

#91 - ✨ Add `seed` keyword to deterministically shuffle splits

Pull Request - State: closed - Opened by sjust-seerbio almost 2 years ago - 2 comments

#89 - [Upgrade] Migrate from Pandas to Polars

Issue - State: open - Opened by wfondrie about 2 years ago - 4 comments
Labels: enhancement

#86 - changed metadata import to allow the groups arg

Pull Request - State: closed - Opened by jspaezp about 2 years ago - 4 comments

#85 - [BUG] `importlib.metadata` doesn't allow `groups` kwarg in Python <3.10

Issue - State: closed - Opened by wfondrie about 2 years ago

#82 - Add scipy to the Docker image.

Pull Request - State: closed - Opened by wfondrie about 2 years ago

#81 - Add procps to the docker image

Pull Request - State: closed - Opened by wfondrie over 2 years ago

#80 - Fix Docker workflow

Pull Request - State: closed - Opened by wfondrie over 2 years ago

#79 - Add a custom Docker image

Pull Request - State: closed - Opened by wfondrie over 2 years ago

#78 - Make Confidence objects picklable.

Pull Request - State: closed - Opened by wfondrie over 2 years ago
Labels: bug

#77 - migration to pyproject toml

Pull Request - State: closed - Opened by jspaezp over 2 years ago - 2 comments

#76 - Migration to full pyproject toml

Pull Request - State: closed - Opened by jspaezp over 2 years ago - 1 comment

#75 - Feature/plugin arch

Pull Request - State: closed - Opened by jspaezp over 2 years ago - 10 comments

#74 - [Pitch] Plugin architecture

Issue - State: closed - Opened by jspaezp over 2 years ago - 5 comments

#66 - [Upgrade] Migrate to full pyproject.toml build

Issue - State: closed - Opened by wfondrie over 2 years ago - 3 comments

#65 - Fixed grouped scores and added test

Pull Request - State: closed - Opened by wfondrie over 2 years ago - 1 comment

#64 - [BUG] Different scores for LinearConfidence and GroupConfidence

Issue - State: closed - Opened by bittremieux over 2 years ago - 2 comments

#63 - [BUG] 'GridSearchCV' object has no attribute 'intercept_'

Issue - State: closed - Opened by lazear over 2 years ago - 3 comments

#62 - Fixed need for intercept

Pull Request - State: closed - Opened by wfondrie over 2 years ago - 1 comment

#61 - AttributeError when using alternative machine learning algorithms

Issue - State: closed - Opened by surya-money over 2 years ago - 1 comment

#60 - Fix missing values caused by logging

Pull Request - State: closed - Opened by wfondrie over 2 years ago - 1 comment

#59 - Docstring fix

Pull Request - State: closed - Opened by surya-money over 2 years ago - 1 comment

#58 - Change CLI argument and minor style changes

Pull Request - State: closed - Opened by wfondrie over 2 years ago

#57 - Supervised learning step

Pull Request - State: closed - Opened by surya-money over 2 years ago - 1 comment

#56 - Refactor trained models implementation

Pull Request - State: closed - Opened by sambenfredj over 2 years ago

#55 - [Upgrade] Migrate to using `numpy.random.Generator` for random number generation.

Issue - State: closed - Opened by wfondrie over 2 years ago

#54 - First commit

Pull Request - State: closed - Opened by surya-money over 2 years ago - 1 comment

#53 - Added .idea files to .gitignore and tweaked docstring in model.py

Pull Request - State: closed - Opened by surya-money over 2 years ago - 1 comment

#52 - fix non-deterministic multi-threading and reproduce results using trained models

Pull Request - State: closed - Opened by sambenfredj over 2 years ago - 4 comments

#51 - Update the documentation

Pull Request - State: closed - Opened by wfondrie almost 3 years ago - 1 comment

#49 - Enforce `min_length` with `clip_nterm_methionine=True`

Pull Request - State: closed - Opened by wfondrie almost 3 years ago

#48 - Corrected the mentioning of FlashLFQ

Pull Request - State: closed - Opened by tkschmidt almost 3 years ago

#47 - Update data links in docs

Issue - State: closed - Opened by wfondrie almost 3 years ago

#45 - Prepare release v0.8.0

Pull Request - State: closed - Opened by wfondrie almost 3 years ago - 1 comment

#44 - Improve runtime

Pull Request - State: closed - Opened by sambenfredj almost 3 years ago - 12 comments

#43 - pepxml parser Error: float() argument must be a string or a number, not 'NoneType'

Issue - State: closed - Opened by stsour almost 3 years ago - 2 comments
Labels: wontfix

#42 - [BUG] ValueError: X has 31 features, but StandardScaler is expecting 19 features as input.

Issue - State: closed - Opened by jamc1996 about 3 years ago - 4 comments

#41 - Fix typo in open_modification_bin_size help text

Pull Request - State: closed - Opened by mobiusklein about 3 years ago - 1 comment

#40 - added support for subset > data size

Pull Request - State: closed - Opened by wfondrie over 3 years ago - 1 comment

#39 - added support for subset > data size

Pull Request - State: closed - Opened by jspaezp over 3 years ago - 2 comments

#38 - [BUG] CLI fails when passing a --subset_max_train smaller than the data

Issue - State: closed - Opened by jspaezp over 3 years ago - 6 comments

#37 - [Feature Request] Explicit support for DIA results.

Issue - State: open - Opened by wfondrie over 3 years ago

#36 - fixed bug where aggregating ignored --keep_decoys flag

Pull Request - State: closed - Opened by jspaezp over 3 years ago - 4 comments

#35 - [0.7.2rc1] Updated tests, pandas code, and resolve oustanding issues

Pull Request - State: closed - Opened by wfondrie over 3 years ago - 1 comment

#34 - [Upgrade] Use pytest-datadir to manage data files for tests

Issue - State: open - Opened by wfondrie over 3 years ago - 2 comments

#33 - Small test improvements

Pull Request - State: closed - Opened by wfondrie over 3 years ago

#32 - added keep_args cli argument

Pull Request - State: closed - Opened by jspaezp over 3 years ago - 5 comments

#31 - [Feature request] Add a "keep-decoys" argument to the main command line entry point

Issue - State: closed - Opened by jspaezp over 3 years ago - 2 comments

#30 - Add information about setting a random seed to the docs

Issue - State: closed - Opened by wfondrie almost 4 years ago