Merge pull request #282 from wilhelm-lab/feature/cit_pipeline_tutorial

Feature/cit pipeline tutorial
wilhelm-lab · Oct 11, 2024 · a1dfb9f · a1dfb9f
2 parents 7135b18 + 558d27f
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diff --git a/.cookietemple.yml b/.cookietemple.yml
@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: victor.giurcoiu@tum.de
 project_name: oktoberfest
 project_short_description: Public repo oktoberfest
-version: 0.8.0
+version: 0.8.1
 license: MIT
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
-name-template: "0.8.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.8.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.8.1 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.8.1 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

diff --git a/.gitignore b/.gitignore
@@ -144,9 +144,7 @@ hash.file
 
 
 # output files in tutorials folder
-tutorials/
-!tutorials/Oktoberfest Tutorial.ipynb
-!tutorials/Oktoberfest_workshop.ipynb
+!tutorials/*.ipynb
 
 # example data
 data/

diff --git a/cookietemple.cfg b/cookietemple.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.0
+current_version = 0.8.1
 
 [bumpversion_files_whitelisted]
 init_file = oktoberfest/__init__.py

diff --git a/docs/_key_contributors.rst b/docs/_key_contributors.rst
@@ -1,14 +1,22 @@
 .. sidebar:: Key Contributors
 
-   * `Mario Picciani <https://github.com/picciama>`_: developer, maintainer
-   * `Wassim Gabriel <https://github.com/WassimG>`_: developer, maintainer
-   * `Matthew The <https://github.com/MatthewThe>`_: developer, maintainer
-   * `Ludwig Lautenbacher <https://github.com/LLautenbacher>`_: developer, maintainer
-   * `Victor-George Giurcoiu <https://github.com/victorgiurcoiu>`_: developer
-   * `Omar Shouman <https://github.com/omsh>`_: developer
-   * Firas Hamood: developer
-   * Cecilia Jensen: developer
-   * Julian Mueller: developer
-   * `Mostafa Kalhor <https://github.com/mostafakalhor>`_: developer
-   * `Armin Soleymaniniya <https://github.com/arminsl>`_: developer
-   * `Mathias Wilhelm <https://github.com/mwilhelm42>`_: advisor and PI of wilhelmlab
+   Current developers
+
+   * `Arne van den Berg <https://github.com/arne-vdb>`_
+   * `Wassim Gabriel <https://github.com/WassimG>`_
+   * `Victor-George Giurcoiu <https://github.com/victorgiurcoiu>`_
+   * `Firas Hamood <https://github.com/fhamood>`_
+   * `Cecilia Jensen`
+   * `Mostafa Kalhor <https://github.com/mostafakalhor>`_
+   * `Ludwig Lautenbacher <https://github.com/LLautenbacher>`_
+   * `Julian Mueller <https://github.com/jmueller95>`_
+   * `Mario Picciani <https://github.com/picciama>`_
+   * `Ayla Schröder <https://github.com/ayla-s>`_
+   * `Omar Shouman <https://github.com/omsh>`_
+   * `Armin Soleymaniniya <https://github.com/arminsl>`_
+   * `Matthew The <https://github.com/MatthewThe>`_
+   * `Zixuan Xiao <https://github.com/zix-xiao>`_
+
+   Other roles
+
+   * `Mathias Wilhelm <https://github.com/mwilhelm42>`_ advisor and PI of wilhelmlab
diff --git a/docs/_static/custom_cookietemple.css b/docs/_static/custom_cookietemple.css
@@ -75,6 +75,10 @@ table.align-default {
     padding-left: 50px;
 }
 
+.ptm-config-table tbody tr:nth-last-child(-n + 3) td:nth-child(1) {
+    padding-left: 50px;
+}
+
 .lib-refinement-learning-config-table
     tbody
     tr:nth-child(n + 2):nth-child(-n + 5)

diff --git a/docs/conf.py b/docs/conf.py
@@ -55,9 +55,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.8.0"
+version = "0.8.1"
 # The full version, including alpha/beta/rc tags.
-release = "0.8.0"
+release = "0.8.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/config.rst b/docs/config.rst
@@ -147,17 +147,37 @@ Applicable to in-silico digestion
    |     db                     | Defines whether the digestion should contain only targets, only decoys or both (concatenated); can be "target", "decoy" or "concat"; default = "concat"            |
    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
+Applicable to PTM pipeline
+---------------------------------
+
+.. table::
+   :class: fixed-table ptm-config-table
+
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   | Parameter                  |                             Description                                                                                                                            |
+   +============================+====================================================================================================================================================================+
+   | ptm_localization           | Flag to indicate whether the user want to run the PTM localization pipeline or not.                                                                                |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   | ptmLocalizationOptions     | Contains specific settings for the ptm pipele (see following 2 nested parameters)                                                                                  |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   |     unimod_id              | unimod_id from unimod.org to indicate the target ptm. e.g (7 for citrullination/deamidation)                                                                       |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   |     possible_sites         | List of Possible sites where the PTM can happen. e.g (['R','N','Q'] for citrullination/deamidation)                                                                |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   |     neutral_loss           | Flag to annotate neutral loss peaks or not.                                                                                                                        |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
 Applicable to local intensity prediction
 ----------------------------------------
 
 .. table::
    :class: fixed-table
 
-    +--------------------------+---------------------------------------------------+
-    | Parameter                | Description                                       |
-    +==========================+===================================================+
-    | dlomixInferenceBatchSize | Batch size to use for local inference with DLomix |
-    +--------------------------+---------------------------------------------------+
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   | Parameter                  | Description                                                                                                                                                        |
+   +============================+====================================================================================================================================================================+
+   | dlomixInferenceBatchSize   | Batch size to use for local inference with DLomix                                                                                                                  |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
 Applicable to transfer/refinement learning
 ------------------------------------------

diff --git a/oktoberfest/__init__.py b/oktoberfest/__init__.py
@@ -5,7 +5,7 @@
 __author__ = """The Oktoberfest development team (Wilhelmlab at Technical University of Munich)"""
 __copyright__ = f"Copyright {datetime.now():%Y}, Wilhelmlab at Technical University of Munich"
 __license__ = "MIT"
-__version__ = "0.8.0"
+__version__ = "0.8.1"
 
 import logging.handlers
 import sys