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Release/0.5.0 #134

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merged 52 commits into from
Oct 4, 2023
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0240521
Added preprocessing, plotting submodules
victorgiurcoiu Jul 28, 2023
0c57a60
Fixed pre-commit
victorgiurcoiu Jul 28, 2023
e7cefa7
Added predict, preprocessing submodules
victorgiurcoiu Jul 29, 2023
e87a64b
Added rescore submodule
victorgiurcoiu Jul 31, 2023
52dd237
Modified runner to work with the new api
victorgiurcoiu Aug 16, 2023
cf561c4
Merge branch 'development' into feature/api
picciama Aug 25, 2023
309a428
correct line numbers and lists
picciama Aug 26, 2023
24cd7cd
2 levels of toc and hidden on page
picciama Aug 26, 2023
89c308e
removed files that are no longer required
picciama Aug 26, 2023
1dfeebb
rename submodules to use aliases
picciama Aug 26, 2023
01a8f35
added news and citations for publication
picciama Sep 12, 2023
1ff03bd
fix style of autosummary tables
picciama Sep 12, 2023
8298425
added all major important functions in sections
picciama Sep 13, 2023
674fe88
cleanup and added RST304 ignore to silence :doc:
picciama Sep 13, 2023
2eecae2
added exports for Spectra and FragmentType
picciama Sep 13, 2023
3ecd5f6
fixed variables
picciama Sep 13, 2023
4cba8be
move plotting to pl submodule and updated API docs
picciama Sep 13, 2023
703ebbd
moved logic to new api and updated runners
picciama Sep 13, 2023
f0af9cd
fixed nox tests
picciama Sep 13, 2023
a3de371
removed old API
picciama Sep 13, 2023
8dee1ea
added tmt tag model check and fixed default tag
picciama Sep 15, 2023
fcc9a8b
added missing space
picciama Sep 15, 2023
2313f3c
updated docs for new percolator version
picciama Sep 19, 2023
efdc5dc
changed fragment type to str type
picciama Sep 19, 2023
0bddf71
follow proforma standard
picciama Sep 19, 2023
0c7eabd
return correct default paths for thermo_exe
picciama Sep 19, 2023
8793802
exploit expmass for tdc within files
picciama Sep 19, 2023
c7d41a9
filter out phospho as it is not supported
picciama Sep 22, 2023
759806c
properly use classmethod to read from file
picciama Sep 22, 2023
bd3b061
bugfixes after runing tutorial notebook
picciama Sep 22, 2023
00ee30a
cleanup library generation and support dlib
picciama Sep 22, 2023
64c7ec8
updated spectrum io and fundamentals deps
picciama Sep 22, 2023
74761de
updated dependencies
picciama Sep 23, 2023
0467c63
restrict tritonclient to avoid cuda-python dep
picciama Sep 23, 2023
1b4e47c
support reading from csv
picciama Oct 2, 2023
a2241a7
added unit test for tmt prosit predictions
picciama Oct 2, 2023
baa5c5a
cleanup
picciama Oct 2, 2023
b53013b
cleanup and added unit test for processing step
picciama Oct 2, 2023
a78fb34
corrected koina URL
picciama Oct 2, 2023
fd66b66
migrate to new format required for readthedocs.io
picciama Oct 3, 2023
464ec54
better instructions for prerequisites
picciama Oct 3, 2023
edba9b9
make autosummary link to actual source
picciama Oct 3, 2023
9bba077
fix missing ssl for public koina server
picciama Oct 3, 2023
d445834
corrected port of publikc koina server
picciama Oct 3, 2023
e677999
Bump version from 0.4.0 to 0.5.0
picciama Oct 3, 2023
167c943
fix typeguard using correct typhint
picciama Oct 3, 2023
11ebc3b
Merge pull request #108 from wilhelm-lab/feature/api
picciama Oct 3, 2023
bf9461a
fixed news date style and added info about v0.5.0
picciama Oct 3, 2023
014e823
added numthreads option to minimal CE calib config
picciama Oct 3, 2023
0ce43ca
fix runner not parallelised for rescoring
picciama Oct 3, 2023
1ec6029
updated dependencies
picciama Oct 3, 2023
53da87e
added numThreads option to CE calib
picciama Oct 3, 2023
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fixed news date style and added info about v0.5.0
  • Loading branch information
picciama committed Oct 3, 2023
commit bf9461a77cc1d5d8dda5cf15aa2206b373dfaffc
4 changes: 4 additions & 0 deletions docs/_static/custom_cookietemple.css
Original file line number Diff line number Diff line change
@@ -57,3 +57,7 @@ table.align-default {
.digest-config-table tbody tr:not(:first-child) td:nth-child(1) {
padding-left: 50px;
}

.date {
font-size: 50%;
}
15 changes: 12 additions & 3 deletions docs/news.rst
Original file line number Diff line number Diff line change
@@ -1,16 +1,25 @@
News
====

.. role:: date
:class: date

Oktoberfest is published! :small:`2023-09-07`
-----------------------------------------------------------
Oktoberfest now provides a low level API :date:`2023-10-03`
------------------------------------------------------------

| With our new release 0.5.0, we refactored our code base to provide a low level API to the users. Check the new `API <./API.html>`_ section for more details.
| Please note: We dropped support for percolator version 3.05. Please update to version 3.06.1. See `installation <./installation.html>`_ for details.


Oktoberfest is published! :date:`2023-09-07`
---------------------------------------------

| Alongside the new 0.4.0 release, Oktoberfest was published in Proteomics.
| Check out the publication here: `https://doi.org/10.1002/pmic.202300112 <https://doi.org/10.1002/pmic.202300112>`_.
| Accordingly, please check `How to cite <./reference.html>`_.


The first Oktoberfest release is ready! :small:`2023-06-25`
The first Oktoberfest release is ready! :date:`2023-06-25`
-----------------------------------------------------------

Version 0.3.0 is available on `PyPI <https://pypi.org/project/oktoberfest/>`_.