Feature/ipc rewrite

.github/workflows/test.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches: [ main, development ]
 
 jobs:
   test:
@@ -37,21 +37,21 @@ jobs:
         if [[ "${{ runner.os }}" == "macOS" ]]; then
           ARCH=$(uname -m)
           if [[ "$ARCH" == "arm64" ]]; then RID="osx-arm64"; else RID="osx-x64"; fi
-          LIB_FILE="ThermoNativeReader.dylib"
+          LIB_FILE="ThermoNativeReader"
         elif [[ "${{ runner.os }}" == "Linux" ]]; then
           RID="linux-x64"
-          LIB_FILE="ThermoNativeReader.so"
+          LIB_FILE="ThermoNativeReader"
         else
           RID="win-x64"
-          LIB_FILE="ThermoNativeReader.dll"
+          LIB_FILE="ThermoNativeReader.exe"
         fi
         dotnet publish -r $RID -c Release -p:PublishAot=true
         echo "DYLIB_PATH=$(pwd)/bin/Release/net8.0/$RID/publish/$LIB_FILE" >> $GITHUB_ENV
 
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.12'
 
     - name: Install Rust
       uses: dtolnay/rust-toolchain@stable
@@ -63,6 +63,13 @@ jobs:
         pip install maturin pytest numpy
         pip install fisher-py
 
+    - name: Decompress test data
+      run: gunzip -d -k test_data/*.gz
+    - name: Download test data
+      run: |
+        wget -q -P test_data ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD066718/20250411_Ast0_500SPD_EVO685_JVO_EV1107_050ng_HEK-CPR_380-980_2Th_1P5ms_OFF_05_20250413081131.raw
+        wget -q -P test_data https://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD066944/20250307_AST0_NEO5_JVO_MV50_DR_100SPD_10ng_HEK_Ref_DDA_2Th_1p5ms_10ms_v2Ref_cycle_03.raw
+
     - name: Build and test
       run: |
         source .venv/bin/activate

.gitignore

@@ -54,6 +54,9 @@ coverage.xml
 venv/
 pip-log.txt
 pip-delete-this-directory.txt
+Pipfile
+Pipfile.lock
+.python-version
 
 # Rust
 target/
@@ -66,4 +69,10 @@ publish_output*.txt
 *output*txt
 *.dylib*
 _build/
-/tmp/
+/tmp/
+venv3.11/pyvenv.cfg
+/scratch
+test_data/MS2_MS1_zoom.raw
+test_data/MS2_MS1_astral.raw
+test_data/20250411_Ast0_500SPD_EVO685_JVO_EV1107_050ng_HEK-CPR_380-980_2Th_1P5ms_OFF_05_20250413081131.raw
+test_data/20250307_AST0_NEO5_JVO_MV50_DR_100SPD_10ng_HEK_Ref_DDA_2Th_1p5ms_10ms_v2Ref_cycle_03.raw