Merge pull request #8 from z3rone-org/development

v0.4.1

Author: z3rone

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 160
+extend-ignore = E203, W503, E501, E722, F403, F405, E741, F811, F401

.github/patch_fisher_py.py

@@ -1,5 +1,4 @@
 import os
-import re
 import site
 import sys
 
@@ -8,14 +7,11 @@ def get_fisher_py_path():
         path = os.path.join(site_pkg, 'fisher_py')
         if os.path.exists(path):
             return path
-            
-    # Also check virtual environments where site.getsitepackages() might be missing
     for p in sys.path:
         path = os.path.join(p, 'fisher_py')
         if os.path.exists(path):
             return path
-            
-    raise RuntimeError("fisher_py not found in sys.path or site-packages")
+    raise RuntimeError("fisher_py not found")
 
 def patch_fisher_py():
     try:
@@ -25,34 +21,38 @@ def patch_fisher_py():
         with open(init_file, 'r') as f:
             content = f.read()
 
-        # Add import sys if needed
-        if "import sys" not in content:
-            content = "import sys\n" + content
-            
-        # 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))")
+        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")
+
+        import re
+        
+        # Add helper function at the top of the file after imports
+        helper = """
+def _safe_load_assembly(path):
+    try:
+        Assembly.LoadFrom(path)
+    except Exception:
+        pass
+"""
+        if "_safe_load_assembly" not in content:
+            content = content.replace("import os", "import os\n" + helper, 1)
+
+        def replacer(match):
+            original = match.group(1)
+            return f"_safe_load_assembly(os.path.realpath({original}))"
 
-        # 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"Assembly\.LoadFrom\(os\.path\.realpath\(os\.path\.join\(dll_path,\s*'([^']+)\.dll'\)\)\)",
-            r"clr.AddReference('\1')",
+            r"clr\.AddReference\((os\.path\.join\(dll_path,\s*'[^']+'\))\)",
+            replacer,
             content
         )
-        
+
         with open(init_file, 'w') as f:
             f.write(content)
 
         print(f"Successfully patched {init_file}")
     except Exception as e:
-        print(f"Failed to patch fisher_py: {e}")
+        print(f"Failed to patch: {e}")
         sys.exit(1)
 
 if __name__ == '__main__':

.github/workflows/release.yml

@@ -30,16 +30,18 @@ jobs:
       with:
         submodules: recursive
 
-    - name: Set version from tag
+    - name: Verify version matches tag
       if: startsWith(github.ref, 'refs/tags/v')
       shell: bash
       run: |
         TAG_VERSION="${GITHUB_REF#refs/tags/v}"
-        echo "Updating version in Cargo.toml to $TAG_VERSION"
-        if [[ "${{ runner.os }}" == "macOS" ]]; then
-          sed -i '' 's/^version = ".*"/version = "'$TAG_VERSION'"/' native_fisher_py/Cargo.toml
-        else
-          sed -i 's/^version = ".*"/version = "'$TAG_VERSION'"/' native_fisher_py/Cargo.toml
+        # Extract version from Cargo.toml
+        CARGO_VERSION=$(grep -m1 '^version =' native_fisher_py/Cargo.toml | cut -d '"' -f 2)
+        echo "Tag version: $TAG_VERSION"
+        echo "Cargo version: $CARGO_VERSION"
+        if [[ "$TAG_VERSION" != "$CARGO_VERSION" ]]; then
+          echo "Error: Tag version ($TAG_VERSION) does not match Cargo.toml version ($CARGO_VERSION)"
+          exit 1
         fi
 
     - name: Install NativeAOT Dependencies (Linux)
@@ -75,6 +77,9 @@ jobs:
       with:
         python-version: '3.9'
 
+    - name: Copy README
+      run: cp README.md native_fisher_py/
+
     - name: Build wheels
       uses: PyO3/maturin-action@v1
       with:

README.md

@@ -90,3 +90,22 @@ maturin develop
 This project is powered by the [**Thermo Fisher Scientific RawFileReader**](https://github.com/thermofisherlsms/RawFileReader) (copyright © 2016-2026 Thermo Fisher Scientific, Inc.). All rights reserved.
 
 The `native-fisher-py` package includes the official RawFileReader libraries, which remain the property of Thermo Fisher Scientific. By using this software, you agree to the terms specified in their [license](https://github.com/thermofisherlsms/RawFileReader/blob/main/License.doc).
+
+## Releasing a New Version
+Releases are fully automated via GitHub Actions (`release.yml`), but the workflow **requires** that the git tag strictly matches the version in `native_fisher_py/Cargo.toml`.
+
+To trigger a new release and publish to PyPI:
+
+1. Update the version in `native_fisher_py/Cargo.toml`.
+2. Commit the version bump.
+3. Create and push a matching git tag:
+
+```bash
+git tag vX.Y.Z
+git push origin vX.Y.Z
+```
+
+The GitHub Action will automatically:
+1. Verify that the git tag version matches the `Cargo.toml` version (failing otherwise).
+2. Build the native wheels across all platforms (macOS, Linux, Windows).
+3. Publish the final artifacts to PyPI.

native/.editorconfig

@@ -0,0 +1,17 @@
+root = true
+
+[*.cs]
+# Disable preserving single-line blocks and statements
+csharp_preserve_single_line_blocks = false
+csharp_preserve_single_line_statements = false
+
+# Newline settings for braces
+csharp_new_line_before_open_brace = all
+csharp_new_line_before_catch = true
+csharp_new_line_before_else = true
+csharp_new_line_before_finally = true
+
+# General formatting
+insert_final_newline = true
+indent_style = space
+indent_size = 4