Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Release/0.7.0 #127

Merged
merged 84 commits into from
Jul 31, 2024
Merged

Release/0.7.0 #127

merged 84 commits into from
Jul 31, 2024

Conversation

picciama
Copy link
Contributor

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

  • custom modifications support
  • additional columns to percolator support

Technical details

Additional context

victorgiurcoiu and others added 30 commits July 11, 2023 10:44
@victorgiurcoiu
Updated documentation (scanpydoc)
c32452a
@victorgiurcoiu
Updated contributors
eb00859
@victorgiurcoiu
Updated git links for contributors
362a701
@victorgiurcoiu
Added docs requirements, changed installation.rst
60036c9
@pfeifferpi
added ion_types parameter to function initialize peaks
b665290
@pfeifferpi
new and changed functions for calculating masses of new iontypes
35a1f2f
@pfeifferpi
changed parameter from ion_types to fragmentation_method
425912c
@laralechner
changed order of arguments in initialize peaks
4d6110c
@laralechner
added compute ion mass function again such that unit tests run now
ed8042b
@laralechner
corrected typo in docstring
522d1af
@laralechner
corrected formal issues raised by tests
44b6d5d
@pfeifferpi
modified funtcions to assemble dataframe after annotating spectra
af1943c
@pfeifferpi
Merge branch 'feature/add_new_iontypes' of github.com:wilhelm-lab/spe…
1072a29 
…ctrum_fundamentals into feature/add_new_iontypes
@laralechner
changed noxfile to python 3.10 and changed some formal stuff in fragm…
0c082aa 
…ents.py to pass more tests
@laralechner
tried to improve initizialze peaks by using more matrix operations
493f32d
@laralechner
can handle all fragmentation methods now
075f968
@laralechner
changed some data type things raised by tests
a1a1c13
@pfeifferpi
fixed error with parameters in call of initialize peaks
b414cf9
@pfeifferpi
Merge branch 'feature/add_new_iontypes' of github.com:wilhelm-lab/spe…
506ee0a 
…ctrum_fundamentals into feature/add_new_iontypes
@laralechner
changed order in which ion_types are returned from retrieve_ion_types…
d528714 
… function
@laralechner
changed order in which ion_types are returned from retrieve_ion_types…
210289b 
… function
handling all custom modifications depending on the search engine
681162f
switched stat & var
f633c5f
@dependabot
[DEPENDABOT]: Bump coverage from 7.5.4 to 7.6.0
f1294bb 
Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.5.4 to 7.6.0.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](nedbat/coveragepy@7.5.4...7.6.0)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump types-requests
79dcd73 
Bumps [types-requests](https://github.com/python/typeshed) from 2.32.0.20240622 to 2.32.0.20240712.
- [Commits](https://github.com/python/typeshed/commits)

---
updated-dependencies:
- dependency-name: types-requests
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump actions/setup-python from 5.1.0 to 5.1.1
2c8eb78 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.1.0 to 5.1.1.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v5.1.0...v5.1.1)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
@laralechner
added lines for addition of beta mass if xl, but does not work yet
6af3e36
@picciama
Merge branch 'development' into feature/add_new_iontypes
27aa31f
@picciama
updated workflows to use python 3.9
080b05c
@picciama
Merge branch 'feature/add_new_iontypes' of github.com:wilhelm-lab/spe…
cc81413 
…ctrum_fundamentals into feature/add_new_iontypes
Fabian Basso and others added 28 commits July 28, 2024 14:21
all tests succesfully passed except typeguard because of test_constants
b36f863
@dependabot
[DEPENDABOT]: Bump pyupgrade from 3.16.0 to 3.17.0
66590ae 
Bumps [pyupgrade](https://github.com/asottile/pyupgrade) from 3.16.0 to 3.17.0.
- [Commits](asottile/pyupgrade@v3.16.0...v3.17.0)

---
updated-dependencies:
- dependency-name: pyupgrade
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump pre-commit from 3.7.1 to 3.8.0
a27bb4a 
Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 3.7.1 to 3.8.0.
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v3.7.1...v3.8.0)

---
updated-dependencies:
- dependency-name: pre-commit
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump pytest from 8.3.1 to 8.3.2
9aa2867 
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.3.1 to 8.3.2.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.1...8.3.2)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
corrected docstrings for documentation
472230a
@arne-vdb
removed unnamed columns from features
b8c42ef
@arne-vdb
added unittests for all three possible parameter configurations
3a06600
@arne-vdb
moved function call so that it only applies to rescore searchtype
052a565
added optional parameter for custom_mods
69872bd
fixed pre-commit tests
5a35b61
@pfeifferpi
added new function to fragments.py with new order of iontypes and res…
9f1e5df 
…pective tests
@picciama
removed negative testing of update_mod_masses
623f586
@picciama
added additional column option to original mode
4377e20
@picciama
Merge pull request #120 from wilhelm-lab/feature/custom-modifications
82d5fed 
Feature/custom modifications
@picciama
Merge pull request #125 from wilhelm-lab/dependabot/pip/development/p…
726054f 
…ytest-8.3.2

[DEPENDABOT]: Bump pytest from 8.3.1 to 8.3.2
@picciama
Merge pull request #124 from wilhelm-lab/dependabot/pip/development/p…
92ee8d7 
…re-commit-3.8.0

[DEPENDABOT]: Bump pre-commit from 3.7.1 to 3.8.0
@picciama
Merge pull request #123 from wilhelm-lab/dependabot/pip/development/p…
4d1d495 
…yupgrade-3.17.0

[DEPENDABOT]: Bump pyupgrade from 3.16.0 to 3.17.0
@picciama
Merge pull request #122 from wilhelm-lab/feature/additional_columns
a2f97ea 
use custom columns as input features for percolator
@picciama
Merge branch 'development' into feature/change_iontype_order_for_dlmoix
aac0655
@picciama
Bump version from 0.6.0 to 0.7.0
5bad90d
@picciama
Merge branch 'development' of github.com:wilhelm-lab/spectrum_fundame…
cbf3bb9 
…ntals into development
@picciama
Merge pull request #126 from wilhelm-lab/feature/change_iontype_order…
2ca4c8d 
…_for_dlmoix

changed order of iontypes in preprocessing
@picciama
added new documentation template
638fed0
@picciama
Merge branch 'development' into feature/documentation
241bdda
@picciama
updated requirements.txt
0484fcd
@picciama
documentation prepared for filling
3fa1562
@picciama
Merge pull request #69 from wilhelm-lab/feature/documentation
73929d9 
Feature/documentation
@picciama
fix broken links
0a372f2
@picciama picciama merged commit 9fa9632 into main Jul 31, 2024
37 checks passed
@picciama picciama deleted the release/0.7.0 branch July 31, 2024 19:18
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
5 participants
@picciama @victorgiurcoiu @pfeifferpi @laralechner @arne-vdb