Add new release workflow

.github/workflows/create_release.yml

@@ -0,0 +1,23 @@
+# Create a draft release and build and upload all installers to it.
+
+on:
+  workflow_dispatch:
+    inputs:
+      commit_to_release:
+        description: 'Enter commit hash to release (example: ef4037cb571f99cb4919b520fde7174972aae473)'
+        type: string
+        required: true
+      tag_to_release:
+        description: 'Enter tag to release (example: v1.5.5)'
+        type: string
+        required: true
+
+jobs:
+  create-release:
+    uses: MannLabs/alphashared/.github/workflows/create-release.yml@v1
+    with:
+      package_name: peptdeep
+      build_nodejs_ui: false
+      commit_to_release: ${{ inputs.commit_to_release }}
+      tag_to_release: ${{ inputs.tag_to_release }}
+    secrets: inherit

.github/workflows/pip_installation.yml

@@ -21,7 +21,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-13, windows-latest]
         # macOS-latest and macos-latest-xlarge use Arm64, resulting in MPS OOM error in peptdeep
-        # os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
+        # os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}
@@ -34,7 +34,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-13, windows-latest]
-        # os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
+        # os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}

.gitignore

@@ -1,3 +1,11 @@
+# User defined:
+peptdeep/logs
+*.DS_Store
+*sandbox*
+*installed_models*
+*.last_checked*
+*mono_crash.*.blob
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -128,19 +136,3 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
-
-# User defined:
-peptdeep/logs
-*.DS_Store
-*sandbox*
-*installed_models*
-*.last_checked*
-
-# nbdev2
-*.gitattributes
-_docs*
-# *_quarto.yml
-# *sidebar.yml
-*_proc*
-# .gitconfig is now autogenerated
-.gitconfig

.pre-commit-config.yaml

@@ -7,10 +7,10 @@ repos:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
-# - repo: https://github.com/astral-sh/ruff-pre-commit
-#   rev: v0.4.0
-#   hooks:
-#     - id: ruff-format
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.0
+  hooks:
+    - id: ruff-format
 #     - id: ruff
 
 exclude: .bumpversion.cfg

README.md

@@ -381,12 +381,12 @@ common:
   user_defined_modifications: {}
   # For example,
   # user_defined_modifications:
-  #   "Dimethyl2@Any N-term":
+  #   "Dimethyl2@Any_N-term":
   #     composition: "H(2)2H(2)C(2)"
   #     modloss_composition: "H(0)" # can be without if no modloss
   #   "Dimethyl2@K":
   #     composition: "H(2)2H(2)C(2)"
-  #   "Dimethyl6@Any N-term":
+  #   "Dimethyl6@Any_N-term":
   #     composition: "2H(4)13C(2)"
   #   "Dimethyl6@K":
   #     composition: "2H(4)13C(2)"
@@ -496,16 +496,16 @@ library:
   fix_mods:
   - Carbamidomethyl@C
   var_mods:
-  - Acetyl@Protein N-term
+  - Acetyl@Protein_N-term
   - Oxidation@M
   special_mods: [] # normally for Phospho or GlyGly@K
   special_mods_cannot_modify_pep_n_term: False
   special_mods_cannot_modify_pep_c_term: False
   labeling_channels: {}
   # For example,
   # labeling_channels:
-  #   0: ['Dimethyl@Any N-term','Dimethyl@K']
-  #   4: ['Dimethyl:2H(2)@Any N-term','Dimethyl:2H(2)@K']
+  #   0: ['Dimethyl@Any_N-term','Dimethyl@K']
+  #   4: ['Dimethyl:2H(2)@Any_N-term','Dimethyl:2H(2)@K']
   #   8: [...]
   min_var_mod_num: 0
   max_var_mod_num: 2
@@ -565,7 +565,7 @@ See examples:
 import pandas as pd
 df = pd.DataFrame({
     'sequence': ['ACDEFGHIK','LMNPQRSTVK','WYVSTR'],
-    'mods': ['Carbamidomethyl@C','Acetyl@Protein N-term;Phospho@S',''],
+    'mods': ['Carbamidomethyl@C','Acetyl@Protein_N-term;Phospho@S',''],
     'mod_sites': ['2','0;7',''],
     'charge': [2,3,1],
 })
@@ -593,7 +593,7 @@ df[['sequence','mods','mod_sites']]
 |  | sequence | mods | mod_sites |
 | --- | --- | --- | --- |
 | 0 | ACDEFGHIK | Carbamidomethyl@C | 2 |
-| 1 | LMNPQRSTVK | Acetyl@Protein N-term;Phospho@S | 0;7 |
+| 1 | LMNPQRSTVK | Acetyl@Protein_N-term;Phospho@S | 0;7 |
 | 2 | WYVSTR | | |
 
 ##### precursor_table
@@ -605,7 +605,7 @@ df
 |  | sequence | mods | mod_sites | charge |
 | --- | --- | --- | --- | --- |
 | 0 | ACDEFGHIK | Carbamidomethyl@C | 2 | 2 |
-| 1 | LMNPQRSTVK | Acetyl@Protein N-term;Phospho@S | 0;7 | 3 |
+| 1 | LMNPQRSTVK | Acetyl@Protein_N-term;Phospho@S | 0;7 | 3 |
 | 2 | WYVSTR | | | 1 |
 
 > Columns of `proteins` and `genes` are optional for these txt/tsv/csv
@@ -686,7 +686,7 @@ model_mgr:
     # alphabase modification to modifications of other search engines
     # For example,
     # psm_modification_mapping:
-    #   Dimethyl@Any N-term:
+    #   Dimethyl@Any_N-term:
     #     - _(Dimethyl-n-0)
     #     - _(Dimethyl)
     #   Dimethyl:2H(2)@K:
@@ -942,8 +942,21 @@ clone the repository and create a [pull
 request](https://github.com/MannLabs/alphapeptdeep/pulls) with a new
 branch. For an even more interactive participation, check out the
 [discussions](https://github.com/MannLabs/alphapeptdeep/discussions) and
-the [the Contributors License Agreement](misc/CLA.md).
+the [Contributors License Agreement](misc/CLA.md).
 
+### Notes for developers
+#### pre-commit hooks
+It is highly recommended to use the provided pre-commit hooks, as the CI pipeline enforces all checks therein to
+pass in order to merge a branch.
+
+The hooks need to be installed once by
+```bash
+pre-commit install
+```
+You can run the checks yourself using:
+```bash
+pre-commit run --all-files
+```
 ------------------------------------------------------------------------
 
 ## Changelog

docs/conf.py

@@ -14,14 +14,15 @@
 import sys
 import importlib
 import inspect
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'peptdeep'
-copyright = '2022, Mann Labs, MPIB'
-author = 'Mann Labs, MPIB'
+project = "peptdeep"
+copyright = "2022, Mann Labs, MPIB"
+author = "Mann Labs, MPIB"
 
 release = "1.2.1"
 
@@ -31,34 +32,33 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.napoleon',
+    "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "sphinx.ext.linkcode",
-    'sphinx.ext.viewcode',
-    'autodocsumm',
-    'nbsphinx',
-    'myst_parser',
+    "sphinx.ext.viewcode",
+    "autodocsumm",
+    "nbsphinx",
+    "myst_parser",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = [
-    '_build', 'Thumbs.db', '.DS_Store',
-    '_modidx,py'
-]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "_modidx,py"]
 
 code_url = f"https://github.com/mannlabs/alphapeptdeep/blob/main"
 
+
 def linkcode_resolve(domain, info):
     # Non-linkable objects from the starter kit in the tutorial.
     if domain == "js" or info["module"] == "connect4":
         return
 
-    if domain != "py": return
+    if domain != "py":
+        return
 
     mod = importlib.import_module(info["module"])
     if "." in info["fullname"]:
@@ -93,16 +93,16 @@ def linkcode_resolve(domain, info):
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'furo'
-html_logo = '_static/peptdeep.png'
-html_favicon = '_static/peptdeep.png'
+html_theme = "furo"
+html_logo = "_static/peptdeep.png"
+html_favicon = "_static/peptdeep.png"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 autodoc_default_options = {
-    'autosummary': True,
-    'special-members': '__init__',  # Include __init__ methods.
+    "autosummary": True,
+    "special-members": "__init__",  # Include __init__ methods.
 }

docs/notebooks.rst

@@ -6,10 +6,10 @@ Tutorials and notebooks about how to use AlphaPeptDeep
 .. toctree::
    :maxdepth: 1
 
+   tutorials/tutorial_immunopeptidomics
    nbs/tutorial_models_from_scratch
    nbs/tutorial_speclib_from_fasta
    nbs/alphapeptdeep_hdf_to_tsv
-   nbs/tutorial_HLA_prediction
    nbs/tutorial_model_manager
    nbs/tutorial_building_rt_model
    nbs/tutorial_building_ccs_model

docs/tutorials/example.fasta

@@ -0,0 +1,9 @@
+>tr|A0A024R161|A0A024R161_HUMAN Guanine nucleotide-binding protein subunit gamma OS=Homo sapiens GN=DNAJC25-GNG10 PE=3 SV=1
+MGAPLLSPGWGAGAAGRRWWMLLAPLLPALLLVRPAGALVEGLYCGTRDCYEVLGVSRSA
+GKAEIARAYRQLARRYHPDRYRPQPGDEGPGRTPQSAEEAFLLVATAYETLKVSQAAAEL
+QQYCMQNACKDALLVGVPAGSNPFREPRSCALL
+>tr|A0A024RAP8|A0A024RAP8_HUMAN HCG2009644, isoform CRA_b OS=Homo sapiens GN=KLRC4-KLRK1 PE=4 SV=1
+MGWIRGRRSRHSWEMSEFHNYNLDLKKSDFSTRWQKQRCPVVKSKCRENASPFFFCCFIA
+VAMGIRFIIMVTIWSAVFLNSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNW
+YESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLT
+IIEMQKGDCALYASSFKGYIENCSTPNTYICMQRTV