Code

Release/0.7.0#127

Code

Merged

picciama merged 84 commits intomainwilhelm-lab/spectrum_fundamentals:mainfrom release/0.7.0wilhelm-lab/spectrum_fundamentals:release/0.7.0Copy head branch name to clipboardJul 31, 2024

+68,443-69,136

Commits

Commits on Jul 11, 2023

• Updated documentation (scanpydoc)

  victorgiurcoiu

  committed
  c32452a

• Updated contributors

  victorgiurcoiu

  committed
  eb00859

• Updated git links for contributors

  victorgiurcoiu

  committed
  362a701

Commits on Jul 12, 2023

• Added docs requirements, changed installation.rst

  victorgiurcoiu

  committed
  60036c9

Commits on Jun 14, 2024

• added ion_types parameter to function initialize peaks

  pfeifferpi

  committed
  b665290

• new and changed functions for calculating masses of new iontypes

  pfeifferpi

  committed
  35a1f2f

Commits on Jun 20, 2024

• changed parameter from ion_types to fragmentation_method

  pfeifferpi

  committed
  425912c

• changed order of arguments in initialize peaks

  laralechner

  committed
  4d6110c

Commits on Jun 21, 2024

• added compute ion mass function again such that unit tests run now

  laralechner

  committed
  ed8042b

Commits on Jun 23, 2024

• corrected typo in docstring

  laralechner

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  522d1af

Commits on Jun 30, 2024

• corrected formal issues raised by tests

  laralechner

  committed
  44b6d5d

Commits on Jul 1, 2024

• modified funtcions to assemble dataframe after annotating spectra

  pfeifferpi

  committed
  af1943c

• Merge branch 'feature/add_new_iontypes' of github.com:wilhelm-lab/spectrum_fundamentals into feature/add_new_iontypes

  pfeifferpi

  committed
  1072a29

• changed noxfile to python 3.10 and changed some formal stuff in fragments.py to pass more tests

  laralechner

  committed
  0c082aa

Commits on Jul 3, 2024

• tried to improve initizialze peaks by using more matrix operations

  laralechner

  committed
  493f32d

• can handle all fragmentation methods now

  laralechner

  committed
  075f968

Commits on Jul 7, 2024

• changed some data type things raised by tests

  laralechner

  committed
  a1a1c13

Commits on Jul 9, 2024

• fixed error with parameters in call of initialize peaks

  pfeifferpi

  committed
  b414cf9

• Merge branch 'feature/add_new_iontypes' of github.com:wilhelm-lab/spectrum_fundamentals into feature/add_new_iontypes

  pfeifferpi

  committed
  506ee0a

• changed order in which ion_types are returned from retrieve_ion_types function

  laralechner

  committed
  d528714

• changed order in which ion_types are returned from retrieve_ion_types function

  laralechner

  committed
  210289b

Commits on Jul 12, 2024

• handling all custom modifications depending on the search engine

  

  Fabian Basso

  committed
  681162f

• switched stat & var

  

  Fabian Basso

  committed
  f633c5f

Commits on Jul 15, 2024

• [DEPENDABOT]: Bump coverage from 7.5.4 to 7.6.0

  Show description for f1294bb
  dependabot[bot]

  authored
  f1294bb

• [DEPENDABOT]: Bump types-requests

  Show description for 79dcd73
  dependabot[bot]

  authored
  79dcd73

• [DEPENDABOT]: Bump actions/setup-python from 5.1.0 to 5.1.1

  Show description for 2c8eb78
  dependabot[bot]

  authored
  2c8eb78

Commits on Jul 16, 2024

• added lines for addition of beta mass if xl, but does not work yet

  laralechner

  committed
  6af3e36

• Merge branch 'development' into feature/add_new_iontypes

  picciama

  committed
  27aa31f

• updated workflows to use python 3.9

  picciama

  committed
  080b05c

• Merge branch 'feature/add_new_iontypes' of github.com:wilhelm-lab/spectrum_fundamentals into feature/add_new_iontypes

  picciama

  committed
  cc81413

• fixed non_cleavable_xl mode

  picciama

  committed
  d890fdb

• changed calculation ion_masses_all_charges as suggested

  laralechner

  committed
  fe395cc

• changed some formalities raised by flake8

  laralechner

  committed
  42602b8

Commits on Jul 18, 2024

• updated custom mods feature

  

  Fabian Basso

  committed
  7e3e474

Commits on Jul 19, 2024

• fixed code for mypy and flake8

  pfeifferpi

  committed
  6768538

Commits on Jul 24, 2024

• added test for retrieving ion types

  laralechner

  committed
  6d85ed1

Commits on Jul 25, 2024

• updated deps and moved to python>=3.9

  picciama

  committed
  6caa335

• fixed xl issue and used numpy where possible

  picciama

  committed
  b8ee59a

• Merge branch 'feature/add_new_iontypes' of github.com:wilhelm-lab/spectrum_fundamentals into feature/add_new_iontypes

  picciama

  committed
  714208c

• created function to add additional features from custom search results

  arne-vdb

  committed
  84c2b80

• added . to conform to documentation requirements

  arne-vdb

  committed
  dc2c942

• made additional_columns argument optional

  arne-vdb

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  59b0f5b

• fixed bug in logic

  arne-vdb

  committed
  2182207

Commits on Jul 26, 2024

• added unit tests

  laralechner

  committed
  b212a0f

• added data/fragments_meta_data_all_ions.json

  laralechner

  committed
  205e1c7

• fixed flake8

  picciama

  committed
  92ed0cd

Commits on Jul 27, 2024

• Updated Unit tests and fixed bugs

  

  Fabian Basso

  committed
  4f5d172

• fixed annotation and peak init and unit tests:

  Show description for 610ea36
  picciama

  committed
  610ea36

• fixed mypy

  picciama

  committed
  711ff64

• Merge pull request #119 from wilhelm-lab/dependabot/github_actions/development/actions/setup-python-5.1.1

  Show description for 083d6d0
  picciama

  authored
  083d6d0

• Merge pull request #118 from wilhelm-lab/dependabot/pip/development/types-requests-2.32.0.20240712

  Show description for 39ea5e7
  picciama

  authored
  39ea5e7

• Merge pull request #117 from wilhelm-lab/dependabot/pip/development/coverage-7.6.0

  Show description for 664285a
  picciama

  authored
  664285a

• Merge branch 'development' into feature/add_new_iontypes

  picciama

  authored
  7139560

• Merge pull request #112 from wilhelm-lab/feature/add_new_iontypes

  Show description for 5fb9de2
  picciama

  authored
  5fb9de2

• Merge branch 'development' into feature/custom-modifications

  picciama

  committed
  2018f25

Commits on Jul 28, 2024

• separated msfragger and custom to internal

  

  Fabian Basso

  committed
  e1f468a

• all tests succesfully passed except typeguard because of test_constants

  

  Fabian Basso

  committed
  b36f863

Commits on Jul 29, 2024

• [DEPENDABOT]: Bump pyupgrade from 3.16.0 to 3.17.0

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  dependabot[bot]

  authored
  66590ae

• [DEPENDABOT]: Bump pre-commit from 3.7.1 to 3.8.0

  Show description for a27bb4a
  dependabot[bot]

  authored
  a27bb4a

• [DEPENDABOT]: Bump pytest from 8.3.1 to 8.3.2

  Show description for 9aa2867
  dependabot[bot]

  authored
  9aa2867

Commits on Jul 30, 2024

• corrected docstrings for documentation

  

  Fabian Basso

  committed
  472230a

• removed unnamed columns from features

  arne-vdb

  committed
  b8c42ef

• added unittests for all three possible parameter configurations

  arne-vdb

  committed
  3a06600

• moved function call so that it only applies to rescore searchtype

  arne-vdb

  committed
  052a565

• added optional parameter for custom_mods

  

  Fabian Basso

  committed
  69872bd

• fixed pre-commit tests

  

  Fabian Basso

  committed
  5a35b61

Commits on Jul 31, 2024

• added new function to fragments.py with new order of iontypes and respective tests

  pfeifferpi

  committed
  9f1e5df

• removed negative testing of update_mod_masses

  picciama

  committed
  623f586

• added additional column option to original mode

  picciama

  committed
  4377e20

• Merge pull request #120 from wilhelm-lab/feature/custom-modifications

  Show description for 82d5fed
  picciama

  authored
  82d5fed

• Merge pull request #125 from wilhelm-lab/dependabot/pip/development/pytest-8.3.2

  Show description for 726054f
  picciama

  authored
  726054f

• Merge pull request #124 from wilhelm-lab/dependabot/pip/development/pre-commit-3.8.0

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  picciama

  authored
  92ee8d7

• Merge pull request #123 from wilhelm-lab/dependabot/pip/development/pyupgrade-3.17.0

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  picciama

  authored
  4d1d495

• Merge pull request #122 from wilhelm-lab/feature/additional_columns

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  picciama

  authored
  a2f97ea

• Merge branch 'development' into feature/change_iontype_order_for_dlmoix

  picciama

  authored
  aac0655

• Bump version from 0.6.0 to 0.7.0

  picciama

  committed
  5bad90d

• Merge branch 'development' of github.com:wilhelm-lab/spectrum_fundamentals into development

  picciama

  committed
  cbf3bb9

• Merge pull request #126 from wilhelm-lab/feature/change_iontype_order_for_dlmoix

  Show description for 2ca4c8d
  picciama

  authored
  2ca4c8d

• added new documentation template

  picciama

  committed
  638fed0

• Merge branch 'development' into feature/documentation

  picciama

  committed
  241bdda

• updated requirements.txt

  picciama

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  0484fcd

• documentation prepared for filling

  picciama

  committed
  3fa1562

• Merge pull request #69 from wilhelm-lab/feature/documentation

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  picciama

  authored
  73929d9

• fix broken links

  picciama

  committed
  0a372f2