Release/0.5.0 #134

picciama · 2023-10-03T16:20:31Z

PR Checklist

This comment contains a description of changes (with reason)
Referenced issue is linked
If you've fixed a bug or added code that should be tested, add tests!
Documentation in docs is updated

Description of changes

Major release including new API structure and documentation
supports new spectrum-io and spectrum-fundamentals versions that fix TMT model issue with koina
see release notes

Technical details

see PRs in release notes

Additional context

Feature/api

victorgiurcoiu and others added 30 commits July 28, 2023 13:12

Added preprocessing, plotting submodules

0240521

Fixed pre-commit

0c57a60

Added predict, preprocessing submodules

e7cefa7

Added rescore submodule

e87a64b

Modified runner to work with the new api

52dd237

Merge branch 'development' into feature/api

cf561c4

correct line numbers and lists

309a428

2 levels of toc and hidden on page

24cd7cd

removed files that are no longer required

89c308e

rename submodules to use aliases

1dfeebb

added news and citations for publication

01a8f35

fix style of autosummary tables

1ff03bd

added all major important functions in sections

8298425

cleanup and added RST304 ignore to silence :doc:

674fe88

added exports for Spectra and FragmentType

2eecae2

fixed variables

3ecd5f6

move plotting to pl submodule and updated API docs

4cba8be

moved logic to new api and updated runners

703ebbd

fixed nox tests

f0af9cd

removed old API

a3de371

added tmt tag model check and fixed default tag

8dee1ea

added missing space

fcc9a8b

updated docs for new percolator version

2313f3c

changed fragment type to str type

efdc5dc

follow proforma standard

0bddf71

return correct default paths for thermo_exe

0c7eabd

exploit expmass for tdc within files

8793802

filter out phospho as it is not supported

c7d41a9

properly use classmethod to read from file

759806c

bugfixes after runing tutorial notebook

bd3b061

picciama and others added 22 commits September 22, 2023 23:56

cleanup library generation and support dlib

00ee30a

updated spectrum io and fundamentals deps

64c7ec8

updated dependencies

74761de

restrict tritonclient to avoid cuda-python dep

0467c63

support reading from csv

1b4e47c

added unit test for tmt prosit predictions

a2241a7

cleanup

baa5c5a

cleanup and added unit test for processing step

b53013b

corrected koina URL

a78fb34

migrate to new format required for readthedocs.io

fd66b66

better instructions for prerequisites

464ec54

make autosummary link to actual source

edba9b9

fix missing ssl for public koina server

9bba077

corrected port of publikc koina server

d445834

Bump version from 0.4.0 to 0.5.0

e677999

fix typeguard using correct typhint

167c943

Merge pull request #108 from wilhelm-lab/feature/api

11ebc3b

Feature/api

fixed news date style and added info about v0.5.0

bf9461a

added numthreads option to minimal CE calib config

014e823

fix runner not parallelised for rescoring

0ce43ca

updated dependencies

1ec6029

added numThreads option to CE calib

53da87e

picciama requested review from LLautenbacher and WassimG and removed request for LLautenbacher October 3, 2023 16:24

picciama merged commit 2b7b63a into main Oct 4, 2023
75 checks passed

picciama deleted the release/0.5.0 branch November 1, 2023 08:19

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Release/0.5.0 #134

Release/0.5.0 #134

picciama commented Oct 3, 2023 •

edited

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Release/0.5.0 #134

Release/0.5.0 #134

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picciama commented Oct 3, 2023 • edited Loading

picciama commented Oct 3, 2023 •

edited

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