ms2rescore fix version for DeepLC

.github/workflows/conda-build.yml

@@ -35,8 +35,17 @@ jobs:
 
     - name: Install the built package and test
       run: |
-        mamba create --name quantmsutils quantms-utils --use-local
+        mamba create --name quantmsutils quantms-utils==0.0.14 --use-local
         conda activate quantmsutils
         conda list
         quantmsutilsc --help
-        quantmsutilsc --version
+        quantmsutilsc --version
+
+    - 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
+        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_comet.idXML
+    - name: Test percolator ms2rescore
+      run: |
+        conda activate quantmsutils
+        quantmsutilsc ms2rescore --psm_file TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --spectrum_path TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes 2 --ms2pip_model HCD2021 --feature_generators 'ms2pip,deeplc' --id_decoy_pattern ^rev --test_fdr 0.05

environment.yml

@@ -8,8 +8,9 @@ dependencies:
   - click
   - sdrf-pipelines>=0.0.31
   - pyopenms
-  - ms2rescore=3.0.3
   - pandas
   - numpy
   - pyarrow
+  - ms2rescore=3.0.3
+  - deepLC=2.2.38
   - psm-utils=0.8.3

pyproject.toml

@@ -3,7 +3,7 @@ name = "quantms-utils"
 description = "Python scripts and helpers for the quantMS workflow"
 readme = "README.md"
 license = "MIT"
-version = "0.0.13"
+version = "0.0.14"
 authors = [
     "Yasset Perez-Riverol <[email protected]>",
     "Dai Chengxin <[email protected]>",
@@ -38,6 +38,7 @@ pandas = "*"
 numpy = "*"
 pyarrow = "*"
 psm-utils = "0.8.3"
+deepLC = "2.2.38"
 
 [tool.poetry.urls]
 GitHub = "https://github.com/bigbio/quantms-utils"

quantmsutils/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.13"
+__version__ = "0.0.14"

recipe/meta.yaml

@@ -1,7 +1,7 @@
 # recipe/meta.yaml
 package:
   name: quantms-utils
-  version: "0.0.13"
+  version: "0.0.14"
 
 source:
   path: ../
@@ -25,10 +25,11 @@ requirements:
     - click
     - sdrf-pipelines>=0.0.31
     - pyopenms
-    - ms2rescore=3.0.3
     - pandas
     - numpy
     - pyarrow
+    - ms2rescore==3.0.3
+    - deepLC==2.2.38
     - psm-utils=0.8.3
 test:
   imports:

requirements.txt

@@ -5,4 +5,5 @@ ms2rescore==3.0.3
 pandas
 numpy
 pyarrow
-psm-utils==0.8.3
+deepLC==2.2.38
+psm-utils==0.8.3