Merge remote-tracking branch 'wilhelmlab/development' into OpenMS_sup…

…port

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: [email protected]
 project_name: spectrum_fundamentals
 project_short_description: Fundamentals public repo
-version: 0.5.2
+version: 0.7.8
 license: MIT

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.5.2 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.5.2 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.7.8 " # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.7.8 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

.github/workflows/build_package.yml

@@ -9,14 +9,14 @@ jobs:
         strategy:
             matrix:
                 os: [macos-latest, ubuntu-latest, windows-latest]
-                python: [3.8, 3.9]
+                python: ["3.9", "3.10"]
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: ${{ matrix.python }}
 

.github/workflows/labeler.yml

@@ -11,7 +11,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.3
+              uses: actions/checkout@v4
 
             - name: Run Labeler
               uses: crazy-max/[email protected]

.github/workflows/main_master_branch_protection.yml

@@ -40,9 +40,9 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Set up Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: "3.8"
+                  python-version: "3.9"
             # PRs to the repository master branch are only ok if coming from any patch or release branch
             - name: Install mlf-core
               run: pip install mlf-core

.github/workflows/publish_docs.yml

@@ -7,13 +7,13 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install pip
               run: |
@@ -30,7 +30,7 @@ jobs:
 
             - name: Deploy
               if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'}}
-              uses: peaceiris/actions-gh-pages@v3
+              uses: peaceiris/actions-gh-pages@v4
               with:
                   github_token: ${{ secrets.GITHUB_TOKEN }}
                   publish_dir: ./docs/_build/html

.github/workflows/publish_package.yml

@@ -10,12 +10,12 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.4
+              uses: actions/checkout@v4
               with:
                   fetch-depth: 2
 
             - name: Set up Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: "3.9"
 
@@ -29,7 +29,7 @@ jobs:
                   poetry build --ansi
 
             - name: Publish package on PyPI
-              uses: pypa/gh-action-pypi-publish@v1.8.14
+              uses: pypa/gh-action-pypi-publish@v1.10.3
               with:
                   # TODO COOKIETEMPLE: Configure your PyPI Token to enable automatic deployment to PyPi on releases
                   # https://help.github.com/en/actions/configuring-and-managing-workflows/creating-and-storing-encrypted-secrets

.github/workflows/release_drafter.yml

@@ -14,6 +14,6 @@ jobs:
     update_release_draft:
         runs-on: ubuntu-latest
         steps:
-            - uses: release-drafter/release-drafter@v5
+            - uses: release-drafter/release-drafter@v6
               env:
                   GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/run_cookietemple_lint.yml

@@ -7,11 +7,11 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: 3.9
 

.github/workflows/run_tests.yml

@@ -19,47 +19,47 @@ jobs:
             matrix:
                 include:
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "pre-commit",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "safety",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "mypy",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: windows-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: macos-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "typeguard",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "xdoctest",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "docs-build",
                       }
@@ -69,10 +69,10 @@ jobs:
 
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.4
+              uses: actions/checkout@v4
 
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: ${{ matrix.python-version }}
 
@@ -116,15 +116,16 @@ jobs:
               run: nox --force-color --python=${{ matrix.python-version }}
 
             - name: Upload coverage data
-              if: always() && matrix.session == 'tests'
-              uses: actions/upload-artifact@v3
+              if: always() && matrix.session == 'tests' && matrix.os == 'ubuntu-latest'
+              uses: actions/upload-artifact@v4
               with:
+                  include-hidden-files: "true"
                   name: coverage-data
                   path: ".coverage.*"
 
             - name: Upload documentation
               if: matrix.session == 'docs-build'
-              uses: actions/upload-artifact@v3
+              uses: actions/upload-artifact@v4
               with:
                   name: docs
                   path: docs/_build
@@ -134,12 +135,12 @@ jobs:
         needs: tests
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
-            - name: Set up Python 3.8
-              uses: actions/setup-python@v5.1.0
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install Poetry
               run: |
@@ -154,7 +155,7 @@ jobs:
                   nox --version
 
             - name: Download coverage data
-              uses: actions/download-artifact@v3
+              uses: actions/download-artifact@v4
               with:
                   name: coverage-data
 
@@ -165,4 +166,4 @@ jobs:
               run: nox --force-color --session=coverage -- xml -i
 
             - name: Upload coverage report
-              uses: codecov/codecov-action@v3.1.1
+              uses: codecov/codecov-action@v4.6.0

.github/workflows/sync_project.yml

@@ -10,14 +10,14 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install cookietemple
               run: pip install cookietemple
 
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               with:
                   fetch-depth: 0
                   token: "${{ secrets.CT_SYNC_TOKEN }}"

README.rst

@@ -1,5 +1,5 @@
-spectrum_fundamentals
-===========================
+Spectrum Fundamentals
+=====================
 
 |PyPI| |Python Version| |License| |Read the Docs| |Build| |Tests| |Codecov| |pre-commit| |Black|
 
@@ -13,15 +13,15 @@ spectrum_fundamentals
    :target: https://opensource.org/licenses/MIT
    :alt: License
 .. |Read the Docs| image:: https://img.shields.io/readthedocs/spectrum_fundamentals/latest.svg?label=Read%20the%20Docs
-   :target: https://spectrum_fundamentals.readthedocs.io/
-   :alt: Read the documentation at https://spectrum_fundamentals.readthedocs.io/
+   :target: https://spectrum-fundamentals.readthedocs.io/
+   :alt: Read the documentation at https://spectrum-fundamentals.readthedocs.io/
 .. |Build| image:: https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Build%20spectrum_fundamentals%20Package/badge.svg
    :target: https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Package
    :alt: Build Package Status
 .. |Tests| image:: https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Run%20spectrum_fundamentals%20Tests/badge.svg
    :target: https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Tests
    :alt: Run Tests Status
-.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/master/graph/badge.svg
+.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals
    :alt: Codecov
 .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
@@ -31,37 +31,10 @@ spectrum_fundamentals
    :target: https://github.com/psf/black
    :alt: Black
 
+spectrum_fundamentals is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest).
 
-Features
---------
-
-* TODO
-
-
-Installation
-------------
-
-You can install *spectrum_fundamentals* via pip_ from PyPI_:
-
-.. code:: console
-
-   $ pip install spectrum_fundamentals
-
-
-Usage
------
-
-Please see the `Command-line Reference <Usage_>`_ for details.
-
-
-Credits
--------
-
-This package was created with cookietemple_ using Cookiecutter_ based on Hypermodern_Python_Cookiecutter_.
-
-.. _cookietemple: https://cookietemple.com
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _PyPI: https://pypi.org/
-.. _Hypermodern_Python_Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python
-.. _pip: https://pip.pypa.io/
-.. _Usage: https://spectrum_fundamentals.readthedocs.io/en/latest/usage.html
+It provides the following functionalities:
+ -  conversion between search engine-specific modstrings and the ProForma standard
+ -  calculation of theoretical peptide / ion masses
+ -  annotation of spectra
+ -  spectral similarity calculation with various metrics

ReadMe.md

@@ -1,35 +1,30 @@
-# Spectrum Fundamentals
-
-Spectrum Fundamentals is a package we use in our rescoring pipeline. It was created to be able to handle spectra from different files.
-
-## Features
+[![PyPI](https://img.shields.io/pypi/v/spectrum_fundamentals.svg)](https://pypi.org/project/spectrum_fundamentals/)
+[![Python Version](https://img.shields.io/pypi/pyversions/spectrum_fundamentals)](https://pypi.org/project/spectrum_fundamentals)
+[![License](https://img.shields.io/github/license/wilhelm-lab/spectrum_fundamentals)](https://opensource.org/licenses/MIT)
+[![Read the Docs](https://img.shields.io/readthedocs/spectrum_fundamentals/latest.svg?label=Read%20the%20Docs)](https://spectrum-fundamentals.readthedocs.io/)
+[![Build](https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Build%20spectrum_fundamentals%20Package/badge.svg)](https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Package)
+[![Tests](https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Run%20spectrum_fundamentals%20Tests/badge.svg)](https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Tests)
+[![Codecov](https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/main/graph/badge.svg)](https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
--   Annotate Spectra.
--   Modify peptide sequence to follow one of the recommended notations of ProForma.
--   Generate features than can be used by percoltor for rescoring (spectral angle, cosine similarity, Pearson's correlation, Spearman's correlation, etc.).
-
-## Installation
-
-Install with:
+# Spectrum Fundamentals
 
-```
-pip install git+https://github.com/wilhelm-lab/spectrum_fundamentals
-```
+spectrum_fundamentals is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest).
 
-## Usage
+It provides the following functionalities:
 
-### Annotation Pipeline
+-   conversion between search engine-specific modstrings and the ProForma standard
+-   calculation of theoretical peptide / ion masses
+-   annotation of spectra
+-   spectral similarity calculation with various metrics
 
-The annotation script can be found in the package in annotation/annotation.py.
+## Documentation
 
--   Install and import the function:
+The official documentation can be found at https://spectrum-fundamentals.readthedocs.io
 
-```
-from spectrum_fundamentals.annotation.annotation import annotate_spectra
-```
+## How to cite
 
--   Apply the function on any given dataframe with peptides meta data, raw intensities and mz:
+Please always cite the main publication:
 
-```
-annotate_spectra(dataframe)
-```
+[Oktoberfest] Picciani M, Gabriel W, Giurcoiu VG et al. (2023), _Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit_, [Proteomics](https://doi.org/10.1002/pmic.202300112)