Merge remote-tracking branch 'origin/refactor_multistep_search' into …

…rename_plan

# Conflicts:
#	.github/workflows/_run_tests.yml
#	misc/pip_install.sh

.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') }}

.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"]

.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 ]

README.md

@@ -77,8 +77,13 @@ AlphaDIA can be installed on Windows, macOS and Linux. Please choose the preferr
 Currently available for **MacOS** and **Windows**.
 You can download the latest release of alphaDIA [here](https://github.com/Mannlabs/alphadia/releases/latest).
 
-* **Windows:** Download the latest `win-x64` build. Save it and double click it to install. If you receive a warning during installation click *Run anyway*.
-* **MacOS:** Download the latest `darwin-arm64` build. Please note that alphaDIA currently requires an ARM based M1/2/3 processor for the one-click installer. Save the installer and open the parent folder in Finder. Right-click and select *open*. If you receive a warning during installation click *Open*. If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+* **Windows:** Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
+* **MacOS:** Download the latest build suitable for your chip architecture
+(can be looked up by clicking on the Apple Symbol > *About this Mac* > *Chip* ("M1", "M2", "M3" -> `arm64`, "Intel" -> `x64`),
+`alphadia-X.Y.Z-macos-darwin-arm64.pkg` or `alphadia-X.Y.Z-macos-darwin-x64.pkg`. Open the parent folder of the downloaded file in Finder,
+right-click and select *open*. If you receive a warning during installation click *Open*. If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+* **Linux:** Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+
 
 As of now, **Linux** users need follow the steps for the
 [developer installation](docs/installation.md#developer-installation) in order to use the GUI.
@@ -122,7 +127,10 @@ Make sure you have installed the GUI using the one-click installer. To verify yo
 
 ### 2. Test data
 
-For the first search we will be using a spectral library to search 60SPD bulk HeLa samples on the Orbitrap Astral. Download the test samples and save them: [HeLa library](https://datashare.biochem.mpg.de/s/Uw2yfNSbApfPpTk), [RAW files].(https://datashare.biochem.mpg.de/s/339jg5HtGrwLwDN)
+For the first search we will be using a spectral library to search 60SPD bulk HeLa samples on the Orbitrap Astral.
+Download the test samples and save them:
+[HeLa library](https://datashare.biochem.mpg.de/s/Uw2yfNSbApfPpTk),
+[RAW files](https://datashare.biochem.mpg.de/s/339jg5HtGrwLwDN)
 
 ### 3. Search settings
 
@@ -153,7 +161,10 @@ In case of issues, check out the following:
 ---
 ## Citations
 
-A manuscript has been submitted to bioRxiv.
+A manuscript has been submitted to bioRxiv:
+> **AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics**
+> Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Tim Heymann, Xie-Xuan Zhou, Magnus Schwörer, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Wen-Feng Zeng, Matthias Mann
+> bioRxiv 2024.05.28.596182; doi: https://doi.org/10.1101/2024.05.28.596182
 
 ---
 ## How to contribute

alphadia/__init__.py

@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.9.1"
+__version__ = "1.9.2"