Merge branch 'main' into development

MannLabs · Jan 5, 2025 · c4694e6 · c4694e6
2 parents 9973121 + 485717b
commit c4694e6
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Showing 20 changed files with 38 additions and 27 deletions.
diff --git a/.github/workflows/_run_tests.yml b/.github/workflows/_run_tests.yml
@@ -1,5 +1,5 @@
 # reusable workflow to run tests on different installation types and OS
-name: run-tests
+name: Run unit tests
 
 on:
   workflow_call:
@@ -17,7 +17,8 @@ on:
         required: true
         type: string
 jobs:
-  run-unit-tests-stable-ubuntu:
+  run-unit-tests:
+    name: Unit tests [${{ inputs.os }}]
     runs-on: ${{ inputs.os }}
     steps:
     - uses: actions/checkout@v4
@@ -35,17 +36,17 @@ jobs:
       shell: bash -l {0}
       run: conda info
     - name: Install mono
+      if: ${{ !contains(inputs.os, 'windows') }}
       shell: bash -l {0}
       run: |
         conda install mono
-
     - name: Perform pip installation with all stable dependencies
       shell: bash -l {0}
       run: |
         cd misc
-        . ./${{ inputs.install-script }} alphadia ${{ inputs.python-version }}
+        . ./${{ inputs.install-script }} alphadia ${{ inputs.python-version }} ${{ !contains(inputs.os, 'windows') }}
     - name: Run tests
       shell: bash -l {0}
       run: |
         cd tests
-        . ./${{ inputs.test-script }} alphadia ${{ inputs.python-version }}
+        . ./${{ inputs.test-script }} alphadia ${{ inputs.python-version }} ${{ !contains(inputs.os, 'windows') }}
diff --git a/.github/workflows/branch-checks.yaml b/.github/workflows/branch-checks.yaml
@@ -15,8 +15,9 @@ jobs:
 
   # For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
   run-tests-stable:
-    name: Test stable pip installation on ubuntu-latest
+    name: Test 'stable' on ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest]
         python-version: ["3.10", "3.11", "3.12"]

diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
@@ -21,7 +21,7 @@ concurrency:
 
 jobs:
   run-unit-tests-stable:
-    name: Test stable pip installation on 3 OS
+    name: Test 'stable' on ${{ matrix.os }}
     strategy:
       matrix:
         os:  [ubuntu-latest, macos-13, windows-latest]
@@ -34,7 +34,7 @@ jobs:
       test-script: ./run_unit_tests.sh
 
   run-unit-tests-loose:
-    name: Test loose pip installation on 3 OS
+    name: Test 'loose' on ${{ matrix.os }}
     strategy:
       matrix:
         os: [ ubuntu-latest, macos-13, windows-latest ]

diff --git a/alphadia/__init__.py b/alphadia/__init__.py
@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.9.1"
+__version__ = "1.9.2"
diff --git a/alphadia/outputaccumulator.py b/alphadia/outputaccumulator.py
@@ -585,8 +585,8 @@ def ms2_quality_control(
         # use the precursor for MS2 learning if the median correlation is above the cutoff
         use_for_ms2[i] = median_correlation > precursor_correlation_cutoff
 
-        # Fix: Use loc to modify the original DataFrame instead of the view
-        spec_lib_base.fragment_intensity_df.loc[start_idx:stop_idx] = (
+        # Fix: Use iloc to modify the original DataFrame instead of the view
+        spec_lib_base.fragment_intensity_df.iloc[start_idx:stop_idx] = (
             fragment_intensity_view.values
             * (
                 fragment_correlation_view

diff --git a/alphadia/transferlearning/train.py b/alphadia/transferlearning/train.py
@@ -5,6 +5,7 @@
 import torch
 from alphabase.peptide.fragment import remove_unused_fragments
 from alphabase.peptide.mobility import ccs_to_mobility_for_df, mobility_to_ccs_for_df
+from alphabase.peptide.precursor import refine_precursor_df
 from peptdeep.model.charge import ChargeModelForModAASeq
 from peptdeep.model.model_interface import CallbackHandler, LR_SchedulerInterface
 from peptdeep.pretrained_models import ModelManager
@@ -564,13 +565,14 @@ def finetune_ms2(
         test_intensity_df = test_intensity_df[0]
 
         # Prepare order for peptdeep prediction
-
+        val_psm_df = refine_precursor_df(val_psm_df)
         reordered_val_psm_df = self._reset_frag_idx(val_psm_df)
         reordered_val_intensity_df = self._order_intensities(
             reordered_precursor_df=reordered_val_psm_df,
             unordered_precursor_df=val_psm_df,
             unordered_frag_df=val_intensity_df,
         )
+        test_psm_df = refine_precursor_df(test_psm_df)
         reordered_test_psm_df = self._reset_frag_idx(test_psm_df)
         reordered_test_intensity_df = self._order_intensities(
             reordered_precursor_df=reordered_test_psm_df,

diff --git a/gui/package.json b/gui/package.json
@@ -1,7 +1,7 @@
 {
   "name": "alphadia",
   "productName": "alphadia-gui",
-  "version": "1.9.1",
+  "version": "1.9.2",
   "description": "Graphical user interface for DIA data analysis",
   "main": "dist/electron.js",
   "homepage": "./",

diff --git a/gui/src/main/modules/profile.js b/gui/src/main/modules/profile.js
@@ -3,7 +3,7 @@ const path = require("path")
 const { app, shell, BrowserWindow} = require("electron")
 const { dialog } = require('electron')
 
-const VERSION = "1.9.1"
+const VERSION = "1.9.2"
 
 const Profile = class {
 

diff --git a/misc/.bumpversion.cfg b/misc/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.9.1
+current_version = 1.9.2
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git a/misc/pip_install.sh b/misc/pip_install.sh
@@ -3,8 +3,13 @@ set -e -u
 INSTALL_TYPE=$1 # stable, loose, etc..
 ENV_NAME=${2:-alphadia}
 PYTHON_VERSION=${3:-3.11}
+INSTALL_MONO=${4:-false}
 
-conda create -n $ENV_NAME python=$PYTHON_VERSION mono -y
+if [ "$INSTALL_MONO" = "true" ]; then
+  conda create -n $ENV_NAME python=$PYTHON_VERSION mono -y
+else
+  conda create -n $ENV_NAME python=$PYTHON_VERSION -y
+fi
 
 if [ "$INSTALL_TYPE" = "loose" ]; then
   INSTALL_STRING=""

diff --git a/release/linux/build_installer_linux.sh b/release/linux/build_installer_linux.sh
@@ -10,7 +10,7 @@ rm -rf dist build *.egg-info
 rm -rf dist_pyinstaller build_pyinstaller
 
 python -m build
-pip install "dist/alphadia-1.9.1-py3-none-any.whl[stable]"
+pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
 
 if [ "${CPU_OR_GPU}" != "GPU" ]; then
     pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu

diff --git a/release/linux/control b/release/linux/control
@@ -1,5 +1,5 @@
 Package: alphadia
-Version: 1.9.1
+Version: 1.9.2
 Architecture: all
 Maintainer: Mann Labs <[email protected]>
 Description: alphadia

diff --git a/release/macos/build_installer_macos.sh b/release/macos/build_installer_macos.sh
@@ -10,7 +10,7 @@ rm -rf dist_pyinstaller build_pyinstaller
 export EAGER_IMPORT=true  # TODO check if this can be removed with newset peptdeep version w/out transformer dependenc
 
 python -m build
-pip install "dist/alphadia-1.9.1-py3-none-any.whl[stable]"
+pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pyinstaller release/pyinstaller/alphadia.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y
diff --git a/release/macos/build_package_macos.sh b/release/macos/build_package_macos.sh
@@ -7,10 +7,10 @@ set -e -u
 # Set up package name and version
 PACKAGE_NAME="alphadia"
 APP_NAME="alphadia"
-PACKAGE_VERSION="1.9.1"
+PACKAGE_VERSION="1.9.2"
 PKG_FOLDER="dist/$APP_NAME.app"
 
-# BUILD_NAME is taken from environment variables, e.g. alphadia-1.9.1-macos-darwin-arm64 or alphadia-1.9.1-macos-darwin-x64
+# BUILD_NAME is taken from environment variables, e.g. alphadia-1.9.2-macos-darwin-arm64 or alphadia-1.9.2-macos-darwin-x64
 rm -rf ${BUILD_NAME}.pkg
 
 # Cleanup the package folder

diff --git a/release/macos/distribution.xml b/release/macos/distribution.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>AlphaDIA 1.9.1</title>
+    <title>AlphaDIA 1.9.2</title>
     <background mime-type="image/png" file="alphadia.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

diff --git a/release/macos/info.plist b/release/macos/info.plist
@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alphadia.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphadia.1.9.1</string>
+	<string>alphadia.1.9.2</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.9.1</string>
+	<string>1.9.2</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

diff --git a/release/windows/alphadia_innoinstaller.iss b/release/windows/alphadia_innoinstaller.iss
@@ -5,7 +5,7 @@
 ; so all paths are given relative to the location of this .iss file.
 
 #define MyAppName "AlphaDIA"
-#define MyAppVersion "1.9.1"
+#define MyAppVersion "1.9.2"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphadia"
 #define MyAppExeName "alphadia-gui.exe"
@@ -29,7 +29,7 @@ PrivilegesRequired=lowest
 PrivilegesRequiredOverridesAllowed=dialog
 ; release workflow expects artifact at root of repository
 OutputDir=..\..\
-; example for BUILD_NAME: alphadia-1.9.1-win-x64
+; example for BUILD_NAME: alphadia-1.9.2-win-x64
 OutputBaseFilename={#GetEnv('BUILD_NAME')}
 SetupIconFile=..\logos\alphadia.ico
 Compression=lzma

diff --git a/release/windows/build_installer_windows.ps1 b/release/windows/build_installer_windows.ps1
@@ -5,7 +5,7 @@ Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./build
 Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist
 
 python -m build
-pip install "dist/alphadia-1.9.1-py3-none-any.whl[stable]"
+pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install tbb==2021.13.1

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
@@ -17,6 +17,7 @@ transformers==4.40.2
 directlfq==0.2.19
 pythonnet==3.0.3
 zstandard==0.22.0
+dask==2024.11.2
 # not direct dependencies but we have to restrict the versions
 numpy<2 # test: tolerate_version avoid the breaking change in numpy >= 2
 scipy==1.12.0
diff --git a/requirements/requirements_loose.txt b/requirements/requirements_loose.txt
@@ -6,6 +6,7 @@ alpharaw>=0.3.1  # test: tolerate_version
 alphatims
 alphabase>=1.4.0 # test: tolerate_version
 peptdeep>=1.3.0 # test: tolerate_version
+dask==2024.11.2 # test: tolerate_version
 progressbar
 neptune
 seaborn