Merge pull request #5 from z3rone-org/development

## Architecture & Core
* Refactored C#, Rust, and Python layers to use a handle-based architecture, enabling support for simultaneous open files.
* Implemented centroid streaming in C# and Rust, including logic to safely skip excessively large raw data payloads.

## Python Bindings
* Propagated file handles to all objects in `classes.py` and `raw_file.py` to ensure proper routing for native `get_*` calls.
* Added `gradient.py` to parse Vanquish Neo pump gradients from instrument method texts.

## Testing & CI
* Added test suite covering centroid streaming, collision energy extraction, gradient parsing, and metadata.
* Added compressed `.raw.gz` test data and a `conftest.py` fixture.
* Patched CI scripts (`patch_fisher_py.py` and `test.yml`) to resolve `AssemblyLoadContext` loading errors during parity testing.

## Build System & Dependencies
* Bundled required Thermo `.dll` files directly into the Python package for Maturin builds.
* Updated `build.sh`, `pyproject.toml`, and `.gitignore` configurations.

Author: z3rone

.github/patch_fisher_py.py

@@ -25,15 +25,25 @@ def patch_fisher_py():
         with open(init_file, 'r') as f:
             content = f.read()
 
-        # Add import System.Reflection if needed
-        if "from System.Reflection import Assembly" not in content:
-            content = content.replace("from System import Environment", "from System import Environment\nfrom System.Reflection import Assembly")
+        # Add import sys if needed
+        if "import sys" not in content:
+            content = "import sys\n" + content
 
-        # Replace clr.AddReference(os.path.join(dll_path, '...')) 
-        # with Assembly.LoadFrom(os.path.realpath(os.path.join(dll_path, '...')))
+        # Ensure sys.path.append(dll_path) is added
+        if "sys.path.append(os.path.realpath(dll_path))" not in content:
+            content = content.replace("clr.AddReference('mscorlib')", "clr.AddReference('mscorlib')\nsys.path.append(os.path.realpath(dll_path))")
+
+        # Replace clr.AddReference(os.path.join(dll_path, 'AssemblyName.dll'))
+        # with clr.AddReference('AssemblyName')
+        content = re.sub(
+            r"clr\.AddReference\((?:os\.path\.join\()?dll_path,\s*'([^']+)\.dll'(?:\))?\)",
+            r"clr.AddReference('\1')",
+            content
+        )
+        # Also clean up any lingering Assembly.LoadFrom from previous patches just in case
         content = re.sub(
-            r"clr\.AddReference\((os\.path\.join\(dll_path, '[^']+'\))\)",
-            r"Assembly.LoadFrom(os.path.realpath(\1))",
+            r"Assembly\.LoadFrom\(os\.path\.realpath\(os\.path\.join\(dll_path,\s*'([^']+)\.dll'\)\)\)",
+            r"clr.AddReference('\1')",
             content
         )
 

.github/workflows/test.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches: [ main, development ]
 
 jobs:
   test:
@@ -51,7 +51,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
 
     - name: Install Rust
       uses: dtolnay/rust-toolchain@stable
@@ -63,6 +63,9 @@ jobs:
         pip install maturin pytest numpy
         pip install fisher-py
 
+    - name: Decompress test data
+      run: gunzip -d -k test_data/*.gz
+
     - name: Build and test
       run: |
         source .venv/bin/activate
@@ -72,7 +75,10 @@ jobs:
         cp ${{ env.DYLIB_PATH }} native_fisher_py/python/native_fisher_py/
         
         # Install the package
-        pip install ./native_fisher_py
+        cp README.md native_fisher_py/
+        cd native_fisher_py
+        maturin develop
+        cd ..
         
         # Parity tests will automatically fall back to ground_truth.json if fisher-py fails
         python -m pytest tests

.gitignore

@@ -54,6 +54,9 @@ coverage.xml
 venv/
 pip-log.txt
 pip-delete-this-directory.txt
+Pipfile
+Pipfile.lock
+.python-version
 
 # Rust
 target/
@@ -68,3 +71,7 @@ publish_output*.txt
 _build/
 /tmp/
 venv3.11/pyvenv.cfg
+/scratch
+
+# Downloadable test data
+test_data/*.raw

build.sh

@@ -28,12 +28,14 @@ cd ../..
 # Copy the built library into the python package directory
 # This allows maturin to include it in the wheel
 cp $DYLIB_PATH native_fisher_py/python/native_fisher_py/
+cp vendor/RawFileReader/Libs/NetCore/Net8/Assemblies/*.dll native_fisher_py/python/native_fisher_py/
 
 # 2. Build Python Package
 cd native_fisher_py
 export THERMO_NATIVE_LIB=$(pwd)/python/native_fisher_py/$LIB_NAME
 
 # Check for maturin
+cp ../README.md README.md
 if command -v maturin >/dev/null 2>&1; then
     maturin develop
 elif command -v pipenv >/dev/null 2>&1 && pipenv run maturin --version >/dev/null 2>&1; then