Support for version 1.9.2

.github/workflows/python-app.yml

@@ -28,7 +28,9 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py install
+        pip install poetry
+        poetry build
+        poetry install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

environment.yml

@@ -20,7 +20,6 @@ dependencies:
   - pygam
   - scipy==1.13.1
   - scikit-learn
-  - setuptools
   - pip
   - pip:
     - tensorboard

pyproject.toml

@@ -1,41 +1,64 @@
 [tool.poetry]
 name = "quantms-utils"
-version = "0.0.10"
 description = "Python scripts and helpers for the quantMS workflow"
-authors = ["Yasset Perez-Riverol", "Dai Chengxin"]
+readme = "README.md"
+license = "MIT"
+version = "0.0.13"
+authors = [
+    "Yasset Perez-Riverol <ypriverol@gmail.com>",
+    "Dai Chengxin <chengxin2024@126.com>",
+    "Julianus Pfeuffer <jule.pf@gmail.com>"
+]
+keywords = [
+    "quantms",
+    "proteomics",
+    "mass-spectrometry",
+    "data-analysis",
+    "big data"
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Development Status :: 5 - Production/Stable"
+]
 packages = [
     { include = "quantmsutils" }
 ]
 
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
 [tool.poetry.dependencies]
-click = ">=7.0"
-pydantic = ">=1.10,<2"
-python = "^3.7"
-sdrf-pipelines = ">=0.0.29"
-pyopenms = ">=2.6.0"
-pandas = ">=1.0.0"
-ms2rescore = "==3.0.3"
-deeplc = "==2.2.38"
-ms2pip = "==4.0.0.dev8"
-psm-utils = "==0.8.2"
+python = ">=3.8,<4.0"
+click = "*"
+sdrf-pipelines = ">=0.0.31"
+pyopenms = "*"
+ms2rescore = "3.0.3"
+deeplc = "2.2.38"
+ms2pip = "4.0.0.dev8"
+psm-utils = "0.8.2"
+deeplcretrainer = "*"
+pydantic = "*"
+pandas = "*"
 protobuf = ">=3.9.2,<4"
-scipy = "==1.13.1"
-
-[tool.poetry.dev-dependencies]
-pytest = "*"
+numpy = "*"
+pyarrow = "*"
+pygam = "*"
+scipy = "1.13.1"
+scikit-learn = "*"
 
-[tool.pytest.ini_options]
-minversion = "6.0"
-addopts = "-ra -q"
-testpaths = ["tests"]
-
-[tool.black]
-line-length = 88
-target-version = ['py37', 'py38', 'py39', 'py310', 'py311']
+[tool.poetry.urls]
+GitHub = "https://github.com/bigbio/quantms-utils"
+PyPi = "https://pypi.org/project/quantms-utils/"
+Quantms = "https://quantms.org"
+LICENSE = "https://github.com/bigbio/quantms-utils/blob/main/LICENSE"
 
 [tool.poetry.scripts]
 quantmsutilsc = "quantmsutils.quantmsutilsc:main"
+
+[tool.isort]
+profile = "black"
+
+[tool.black]
+line-length = 99
+target-version = ["py38"]

quantmsutils/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.12"
+__version__ = "0.0.13"

quantmsutils/diann/diann2mztab.py

@@ -362,7 +362,7 @@ def diann_version(self) -> str:
         return diann_version_id
 
     def validate_diann_version(self) -> None:
-        supported_diann_versions = ["1.8.1", "1.9.beta.1"]
+        supported_diann_versions = ["1.8.1", "1.9.beta.1", "1.9.2"]
         if self.diann_version not in supported_diann_versions:
             raise ValueError(f"Unsupported DIANN version {self.diann_version}")
 
@@ -411,7 +411,7 @@ def convert_to_mztab(
         )
 
         mtd, database = mztab_mtd(
-            index_ref, dia_params, str(self.fasta), charge, missed_cleavages
+            index_ref, dia_params, str(self.fasta), charge, missed_cleavages, self.diann_version
         )
         pg = pd.read_csv(
             self.pg_matrix,
@@ -545,7 +545,7 @@ def mtd_mod_info(fix_mod, var_mod):
     return fix_ptm, var_ptm, fix_flag, var_flag
 
 
-def mztab_mtd(index_ref, dia_params, fasta, charge, missed_cleavages):
+def mztab_mtd(index_ref, dia_params, fasta, charge, missed_cleavages, diann_version):
     """
     Construct MTD sub-table.
 
@@ -587,7 +587,7 @@ def mztab_mtd(index_ref, dia_params, fasta, charge, missed_cleavages):
     out_mztab_mtd.loc[1, "psm_search_engine_score[1]"] = (
         "[MS, MS:MS:1001869, protein-level q-value, ]"
     )
-    out_mztab_mtd.loc[1, "software[1]"] = "[MS, MS:1003253, DIA-NN, Release (v1.8.1)]"
+    out_mztab_mtd.loc[1, "software[1]"] = "[MS, MS:1003253, DIA-NN, {}]".format(diann_version)
     out_mztab_mtd.loc[1, "software[1]-setting[1]"] = fasta
     out_mztab_mtd.loc[1, "software[1]-setting[2]"] = "db_version:null"
     out_mztab_mtd.loc[1, "software[1]-setting[3]"] = (

recipe/meta.yaml

@@ -1,7 +1,7 @@
 # recipe/meta.yaml
 package:
   name: quantms-utils
-  version: "0.0.12"
+  version: "0.0.13"
 
 source:
   path: ../
@@ -19,7 +19,6 @@ requirements:
   host:
     - python >=3.8,<4.0
     - pip
-    - setuptools
   run:
     - click
     - sdrf-pipelines>=0.0.31

requirements.txt

@@ -13,5 +13,4 @@ numpy
 pyarrow
 pygam
 scipy==1.13.1
-scikit-learn
-setuptools
+scikit-learn