try to merge development to mine

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Mario Picciani
 email: [email protected]
 project_name: spectrum_io
 project_short_description: IO related functionalities for oktoberfest.
-version: 0.2.0
+version: 0.4.2
 license: MIT

.flake8

@@ -5,8 +5,9 @@ max-line-length = 120
 max-complexity = 10
 docstring-convention = google
 per-file-ignores =
-	tests/*:S101
+	tests/*:S101,S301,S403
 	noxfile.py:DAR101
 	spectrum_io/raw/thermo_raw.py:S603,S404
 	spectrum_io/raw/msraw.py:S405,S314
-        docs/conf.py:S404,S607,S603
+	spectrum_io/d/masterSpectrum.py:C901
+    docs/conf.py:S404,S607,S603

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.2.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.2.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.4.2 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.4.2 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

.github/workflows/run_tests.yml

@@ -1,8 +1,14 @@
 name: Run spectrum_io Tests
 
 on:
-    - push
-    - pull_request
+    push:
+        branches:
+            - development
+            - main
+            - "release/*"
+    pull_request:
+        branches:
+            - "*"
 
 jobs:
     tests:

.readthedocs.yml

@@ -3,19 +3,20 @@
 
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
+# Set the OS, Python version and other tools you might need
+build:
+    os: ubuntu-22.04
+    tools:
+        python: "3.10"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
     configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-    version: 3.8
     install:
         - requirements: docs/requirements.txt

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022, Mario Picciani
+Copyright (c) 2023, Wilhelmlab at Technical University of Munich
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -21,7 +21,7 @@ spectrum_io
 .. |Tests| image:: https://github.com/wilhelm-lab/spectrum_io/workflows/Run%20spectrum_io%20Tests/badge.svg
    :target: https://github.com/wilhelm-lab/spectrum_io/actions?workflow=Tests
    :alt: Run Tests Status
-.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_io/branch/master/graph/badge.svg
+.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_io/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/wilhelm-lab/spectrum_io
    :alt: Codecov
 .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white

ReadMe.md

@@ -1,15 +1,33 @@
 # Spectrum IO
 
-Spectrum IO is a package we use in our rescoring pipeline. It was created to be able to handle several search engines.
+Spectrum IO is a package primarily developed for usage within oktoberfest (https://github.com/wilhelm-lab/oktoberfest). It handles file conversions and input / output operations for oktoberfest.
 
-## Features
+## Installation
 
--   Handle search results from different software (Mascot, MaxQuant, MSFragger).
+### Prerequisites
 
-## Installation
+If you want to convert raw files to mzml, make sure you have ThermoRawFileParser (https://github.com/compomics/ThermoRawFileParser) installed.
 
-Install with:
+If you are on linux or MacOS, make sure mono (https://www.mono-project.com/) is installed (for ThermoRawFileParser).
 
+### Using pip
+
+```bash
+pip install oktoberfest
 ```
-pip install git+https://github.com/wilhelm-lab/spectrum_io
-```
+
+## Features
+
+-   Read search results from different search engines (Mascot, MaxQuant, MSFragger, MS Amanda) and transform them to the internal format used by oktoberfest
+-   Read thermo raw files and convert them to mzml, required by oktoberfest
+-   Read a fasta file and digest with various configurations (protease, missed cleavages, length of peptides, fragmentation, ...) for spectral library generation
+-   Create spectral libraries from peptide lists and output as dlib, msp or spectronaut(csv) format
+-   read and write data created as part of oktoberfest in hdf5 libraries
+
+## Documentation
+
+Please refer to https://spectrum-io.readthedocs.io for further documentation.
+
+## License
+
+The project is licensed under the [MIT license](https://github.com/wilhelm-lab/spectrum_io/blob/main/LICENSE).

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.4.2
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_io/__init__.py

docs/conf.py

@@ -53,9 +53,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.2.0"
+version = "0.4.2"
 # The full version, including alpha/beta/rc tags.
-release = "0.2.0"
+release = "0.4.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

noxfile.py

@@ -1,4 +1,5 @@
 """Nox sessions."""
+
 import os
 import shlex
 import shutil