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OpenMS support #105

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OpenMS support #105

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4c756cb
initiate OpenMS support
Arslan-Siraj Apr 30, 2024
a28a888
file add
Arslan-Siraj Apr 30, 2024
53e8241
add in __init__
Arslan-Siraj May 2, 2024
578023c
label as bool
Arslan-Siraj May 2, 2024
3c27d03
Merge remote-tracking branch 'origin' into OpenMS_support
victorgiurcoiu Nov 22, 2024
8fa8def
Fixed mypy
victorgiurcoiu Nov 22, 2024
6170efa
Added unit tests for openms
victorgiurcoiu Nov 25, 2024
499c0c4
Added example test openms file
victorgiurcoiu Nov 26, 2024
8636843
fixed code, tests, annotations, added pyopenms
picciama Dec 6, 2024
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1,340 changes: 692 additions & 648 deletions poetry.lock
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3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -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"
Expand All @@ -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,<3.3,!=3.2.0.1"

[tool.poetry.dev-dependencies]
pytest = ">=6.2.3"
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67 changes: 34 additions & 33 deletions requirements.txt
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@@ -1,11 +1,11 @@
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"
anyio==4.7.0 ; 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"
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"
Expand All @@ -14,24 +14,24 @@ charset-normalizer==3.4.0 ; python_version >= "3.9" and python_full_version < "3
click==8.1.7 ; 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"
coverage[toml]==7.6.8 ; 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"
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"
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==24.10.31 ; 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==4.55.2 ; 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==2.6.3 ; 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"
Expand All @@ -42,59 +42,60 @@ 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==3.23.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
matplotlib==3.9.3 ; 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"
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"
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"
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"
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"
pydantic-core==2.27.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
pydantic==2.10.3 ; 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"
pymzml==2.5.10 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
pyopenms==3.2.0 ; 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"
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"
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"
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==75.6.0 ; 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"
Expand All @@ -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"
Expand All @@ -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==0.41.3 ; 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"
uvicorn==0.32.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
virtualenv==20.28.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
watchfiles==1.0.0 ; 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"
1 change: 1 addition & 0 deletions spectrum_io/search_result/__init__.py
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Expand Up @@ -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
1 change: 0 additions & 1 deletion spectrum_io/search_result/msfragger.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
},
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