Merge pull request #105 from Arslan-Siraj/OpenMS_support

OpenMS support

.github/workflows/run_tests.yml

@@ -79,6 +79,7 @@ jobs:
             - name: Install Poetry
               run: |
                   pipx install poetry
+                  pipx inject poetry poetry-plugin-export
                   poetry --version
 
             - name: Install nox nox-poetry rich
@@ -145,6 +146,7 @@ jobs:
             - name: Install Poetry
               run: |
                   pipx install poetry
+                  pipx inject poetry poetry-plugin-export
                   poetry --version
 
             - name: Install nox nox-poetry rich

.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
             entry: end-of-file-fixer
             language: system
             types: [text]
-            stages: [commit, push, manual]
+            stages: [pre-commit, pre-push, manual]
             exclude: docs/
           - id: flake8
             name: flake8
@@ -46,7 +46,7 @@ repos:
             entry: trailing-whitespace-fixer
             language: system
             types: [text]
-            stages: [commit, push, manual]
+            stages: [pre-commit, pre-push, manual]
     - repo: https://github.com/pre-commit/mirrors-prettier
       rev: v2.5.1
       hooks:

pyproject.toml

@@ -22,7 +22,7 @@ python = ">=3.9.0,<3.11.0"
 click = ">=8.0.0"
 rich = ">=10.3.0"
 PyYAML = ">=5.4.1"
-numpy = "^1.18.1"
+numpy = ">=1.18.1"
 pandas = ">=1.3,<3.0"
 h5py = "^3.1.0"
 pyarrow = ">=16.0.0"
@@ -32,6 +32,7 @@ lxml= '>=4.5.2,<6.0.0'
 spectrum-fundamentals = ">=0.7.8,<0.8.0"
 alphatims = "^1.0.8"
 sortedcontainers = "^2.4.0"
+pyopenms = "==3.0.0"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6.2.3"

requirements.txt

@@ -1,100 +1,101 @@
 alabaster==0.7.16 ; python_version >= "3.9" and python_full_version < "3.11.0"
 alphatims==1.0.8 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 annotated-types==0.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-anyio==4.6.2.post1 ; python_version >= "3.9" and python_full_version < "3.11.0"
-attrs==24.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-authlib==1.3.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+anyio==4.8.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+attrs==24.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+authlib==1.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 babel==2.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-bandit==1.7.10 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+bandit==1.8.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 black==24.10.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-certifi==2024.8.30 ; python_version >= "3.9" and python_full_version < "3.11.0"
-cffi==1.17.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" and platform_python_implementation != "PyPy"
+certifi==2024.12.14 ; python_version >= "3.9" and python_full_version < "3.11.0"
+cffi==1.17.1 ; python_version >= "3.9" and python_full_version < "3.11.0" and platform_python_implementation != "PyPy"
 cfgv==3.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-charset-normalizer==3.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-click==8.1.7 ; python_version >= "3.9" and python_full_version < "3.11.0"
+charset-normalizer==3.4.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+click==8.1.8 ; python_version >= "3.9" and python_full_version < "3.11.0"
 colorama==0.4.6 ; python_version >= "3.9" and python_full_version < "3.11.0"
 contourpy==1.3.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-coverage[toml]==7.6.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
-cryptography==43.0.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+coverage[toml]==7.6.10 ; python_version >= "3.9" and python_full_version < "3.11.0"
+cryptography==43.0.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
 cycler==0.12.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 darglint==1.8.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 distlib==0.3.9 ; python_version >= "3.9" and python_full_version < "3.11.0"
 docutils==0.21.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
-dparse==0.6.4b0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+dparse==0.6.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 exceptiongroup==1.2.2 ; python_version >= "3.9" and python_version < "3.11"
-filelock==3.12.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
+filelock==3.16.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 flake8-bandit==4.1.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-flake8-bugbear==24.8.19 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+flake8-bugbear==24.12.12 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 flake8-docstrings==1.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 flake8-rst-docstrings==0.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 flake8==7.1.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-fonttools==4.54.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+fonttools==4.55.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
 h11==0.14.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 h5py==3.12.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
-identify==2.6.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+identify==2.6.5 ; python_version >= "3.9" and python_full_version < "3.11.0"
 idna==3.10 ; python_version >= "3.9" and python_full_version < "3.11.0"
 imagesize==1.4.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 importlib-metadata==8.5.0 ; python_version >= "3.9" and python_version < "3.10"
-importlib-resources==6.4.5 ; python_version >= "3.9" and python_version < "3.10"
+importlib-resources==6.5.2 ; python_version >= "3.9" and python_version < "3.10"
 iniconfig==2.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-jinja2==3.1.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
+jinja2==3.1.5 ; python_version >= "3.9" and python_full_version < "3.11.0"
 joblib==1.4.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
 kiwisolver==1.4.7 ; python_version >= "3.9" and python_full_version < "3.11.0"
 llvmlite==0.43.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 lxml==5.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-markdown-it-py==3.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+markdown-it-py==3.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 markupsafe==3.0.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
-marshmallow==3.23.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-matplotlib==3.9.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+marshmallow==3.24.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+matplotlib==3.9.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
 mccabe==0.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-mdurl==0.1.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+mdurl==0.1.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
 moepy==1.1.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 mypy-extensions==1.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-mypy==1.13.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+mypy==1.14.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 nodeenv==1.9.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 numba==0.60.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 numpy==1.24.4 ; python_version >= "3.9" and python_version < "3.11"
-packaging==24.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+packaging==24.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pandas==2.2.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pathspec==0.12.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
-pbr==6.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pbr==6.1.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pep8-naming==0.14.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-pillow==11.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pillow==11.1.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 platformdirs==4.3.6 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pluggy==1.5.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 pre-commit-hooks==5.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 pre-commit==4.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
-psutil==6.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-pyarrow==17.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+psutil==6.1.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pyarrow==18.1.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pycodestyle==2.12.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-pycparser==2.22 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" and platform_python_implementation != "PyPy"
+pycparser==2.22 ; python_version >= "3.9" and python_full_version < "3.11.0" and platform_python_implementation != "PyPy"
 pydantic-core==2.23.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 pydantic==2.9.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 pydocstyle==6.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 pyflakes==3.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-pygments==2.18.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pygments==2.19.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pymzml==2.5.10 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-pyparsing==3.2.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyopenms==3.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pyparsing==3.2.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pyteomics==4.7.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-pytest==8.3.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pytest==8.3.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pytz==2024.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
-pyupgrade==3.19.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyupgrade==3.19.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pyyaml==6.0.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
 pyzstd==0.16.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-regex==2024.9.11 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+regex==2024.11.6 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 requests==2.32.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
 restructuredtext-lint==1.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-rich==13.9.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+rich==13.9.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
 ruamel-yaml-clib==0.2.12 ; platform_python_implementation == "CPython" and python_full_version < "3.11.0" and python_version >= "3.9"
-ruamel-yaml==0.18.6 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-safety-schemas==0.0.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-safety==3.2.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-scikit-learn==1.5.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+ruamel-yaml==0.18.10 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+safety-schemas==0.0.10 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+safety==3.2.14 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+scikit-learn==1.6.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 scipy==1.13.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
-setuptools==75.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+setuptools==75.8.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 shellingham==1.5.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-six==1.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+six==1.17.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 sniffio==1.3.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 snowballstemmer==2.2.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 sortedcontainers==2.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
@@ -103,7 +104,7 @@ sphinx-autobuild==2024.10.3 ; python_version >= "3.9" and python_full_version <
 sphinx-autodoc-typehints==2.3.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 sphinx-click==6.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 sphinx-rtd-dark-mode==1.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-sphinx-rtd-theme==3.0.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+sphinx-rtd-theme==3.0.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 sphinx==7.4.7 ; python_version >= "3.9" and python_full_version < "3.11.0"
 sphinxcontrib-applehelp==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 sphinxcontrib-devhelp==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
@@ -112,23 +113,23 @@ sphinxcontrib-jquery==4.1 ; python_full_version >= "3.9.0" and python_full_versi
 sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 sphinxcontrib-qthelp==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 sphinxcontrib-serializinghtml==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-starlette==0.41.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-stevedore==5.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+starlette==0.45.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+stevedore==5.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 threadpoolctl==3.5.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
 tokenize-rt==6.1.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-tomli==2.0.2 ; python_version >= "3.9" and python_version < "3.11"
-tqdm==4.66.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-typeguard==4.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-typer==0.12.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+tomli==2.2.1 ; python_version >= "3.9" and python_version < "3.11"
+tqdm==4.67.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+typeguard==4.4.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+typer==0.15.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 types-attrs==19.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 types-pkg-resources==0.1.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 types-requests==2.32.0.20241016 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
 typing-extensions==4.12.2 ; python_version >= "3.9" and python_version < "3.11"
 tzdata==2024.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
-urllib3==2.2.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
-uvicorn==0.32.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-virtualenv==20.27.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-watchfiles==0.24.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
-websockets==13.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+urllib3==2.3.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+uvicorn==0.34.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+virtualenv==20.28.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+watchfiles==1.0.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
+websockets==14.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
 xdoctest[colors]==1.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
-zipp==3.20.2 ; python_version >= "3.9" and python_version < "3.10"
+zipp==3.21.0 ; python_version >= "3.9" and python_version < "3.10"

spectrum_io/search_result/__init__.py

@@ -4,6 +4,7 @@
 from .maxquant import MaxQuant
 from .msamanda import MSAmanda
 from .msfragger import MSFragger
+from .openms import OpenMS
 from .sage import Sage
 from .scout import Scout
 from .xisearch import Xisearch

spectrum_io/search_result/msfragger.py

@@ -136,7 +136,6 @@ def convert_to_internal(self, mods: dict[str, str], ptm_unimod_id: int | None, p
                 "hyperscore": "SCORE",
                 "modified_peptide": "MODIFIED_SEQUENCE",
                 "protein": "PROTEINS",
-                "peptide": "SEQUENCE",
                 "precursor_neutral_mass": "MASS",
                 "spectrum": "RAW_FILE",
             },