Support for version 1.9.2

.github/workflows/conda-build.yml

@@ -5,54 +5,44 @@ on: [push, pull_request]
 jobs:
   build:
     runs-on: ubuntu-latest
-
+    defaults:
+      run:
+        shell: bash -el {0}
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4  # Update to latest version
 
     - name: Set up Miniconda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        auto-update-conda: true
-        python-version: 3.8
-        channels: conda-forge,defaults,bioconda
-
-    - name: Create conda environment
-      run: conda env create -f environment.yml
-
-    - name: Install mamba, boa and conda-build
+        mamba-version: "*"
+        channels: conda-forge,bioconda
+        cache-downloads: true
+        auto-update-conda: false
+        activate-environment: test
+        python-version: 3.11
+
+    - name: Setup conda-build and anaconda-client
       run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate quantmsutils
-        conda install conda-forge::mamba
-        conda install conda-forge::boa
-        mamba install conda-build anaconda-client
-      shell: bash -l {0}
-
-    - name: Activate conda environment and build package
+         mamba install -q conda-build anaconda-client conda-verify
+
+    - name: Build package
       run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate quantmsutils
-        conda mambabuild recipe
-      shell: bash -l {0}
+        conda build purge-all
+        conda config --set solver libmamba
+        conda config --set channel_priority strict
+        conda build recipe --suppress-variables --override-channels --channel conda-forge --channel bioconda --no-anaconda-upload
 
     - name: Install the built package
       run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate quantmsutils
         mamba install --use-local quantms-utils
-      shell: bash -l {0}
 
     - name: Output package info
       run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate quantmsutils
         conda list
-      shell: bash -l {0}
 
     - name: Test the installed package
       run: |
-        conda activate quantmsutils
+        # this will fail. you need to create a quantmsutil env first
         quantmsutilsc --help
         quantmsutilsc --version
-      shell: bash -l {0}

.github/workflows/python-app.yml

@@ -26,9 +26,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
+        python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py install
+        pip install poetry
+        poetry build
+        pip install dist/*.whl
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -37,7 +39,7 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        poetry run pytest
     - name: Download test data
       run: |
         wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML

environment.yml

@@ -3,24 +3,15 @@ name: quantmsutils
 channels:
   - bioconda
   - conda-forge
+  - defaults
 dependencies:
   - 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=1.10.14
   - pandas
-  - protobuf>=3.9.2,<4  # Ensure compatibility with tensorboard
   - numpy
   - pyarrow
-  - pygam
-  - scipy==1.13.1
-  - scikit-learn
-  - setuptools
-  - pip
-  - pip:
-    - tensorboard
+  - psm-utils=0.8.3
+  - ms2pip>=4.0.0-dev8
+  - deeplc>=2.2

pyproject.toml

@@ -1,41 +1,62 @@
 [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"
-protobuf = ">=3.9.2,<4"
-scipy = "==1.13.1"
+python = ">=3.8,<3.12"
+click = "*"
+sdrf-pipelines = ">=0.0.31"
+pyopenms = "*"
+ms2rescore = "3.0.3"
+pandas = "*"
+numpy = "*"
+pyarrow = "*"
+psm-utils = "0.8.3"
+ms2pip = ">=4.0.0-dev8"
+deeplc = ">=2.2"
 
-[tool.poetry.dev-dependencies]
-pytest = "*"
+[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.pytest.ini_options]
-minversion = "6.0"
-addopts = "-ra -q"
-testpaths = ["tests"]
+[tool.poetry.scripts]
+quantmsutilsc = "quantmsutils.quantmsutilsc:main"
+
+[tool.isort]
+profile = "black"
 
 [tool.black]
-line-length = 88
-target-version = ['py37', 'py38', 'py39', 'py310', 'py311']
+line-length = 99
+target-version = ["py39"]
 
-[tool.poetry.scripts]
-quantmsutilsc = "quantmsutils.quantmsutilsc:main"
+[build-system]
+requires = ["poetry-core>=1.2.0"]
+build-backend = "poetry.core.masonry.api"

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/conda_build_config.yaml

@@ -0,0 +1,2 @@
+python:
+    - 3.11

recipe/meta.yaml

@@ -1,7 +1,7 @@
 # recipe/meta.yaml
 package:
   name: quantms-utils
-  version: "0.0.12"
+  version: "0.0.13"
 
 source:
   path: ../
@@ -12,31 +12,26 @@ build:
   noarch: python
   run_exports:
     - {{ pin_subpackage('quantms-utils', max_pin="x.x") }}
-  script: "{{ PYTHON }} -m pip install . --no-deps -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   number: 0
 
 requirements:
   host:
-    - python >=3.8,<4.0
+    - python
     - pip
-    - setuptools
+    - poetry-core >=1.2.0
   run:
+    - python
     - 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=1.10.14
     - pandas
-    - protobuf>=3.9.2,<4  # Ensure compatibility with tensorboard
     - numpy
     - pyarrow
-    - pygam
-    - scipy==1.13.1
-    - scikit-learn
+    - psm-utils=0.8.3
+    - ms2pip>=4.0.0-dev8
+    - deeplc>=2.2
 
 test:
   imports:
@@ -55,4 +50,4 @@ about:
 
 extra:
   recipe-maintainers:
-    - ypriverol
+    - ypriverol

requirements.txt

@@ -2,16 +2,9 @@ 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==1.10.14
 pandas
-protobuf>=3.9.2,<4  # Ensure compatibility with tensorboard
 numpy
 pyarrow
-pygam
-scipy==1.13.1
-scikit-learn
-setuptools
+psm-utils==0.8.3
+ms2pip>=4.0.0-dev8
+deeplc >=2.2