Fixes for report, GUI, and PyInstaller

.github/workflows/test.yml

@@ -45,6 +45,8 @@ jobs:
         run: uv run ms2rescore --help
 
   test-windows-installer:
+    # Only run on push to main (e.g., after PR merge)
+    if: ${{ github.ref == 'refs/heads/main' }}
     runs-on: windows-latest
     steps:
       - uses: actions/checkout@v4

ms2rescore.spec

@@ -45,7 +45,13 @@ while requirements:
     checked.add(requirement)
     module_version = importlib.metadata.version(re.match(r"^[\w\-]+", requirement)[0])
     try:
-        datas_, binaries_, hidden_imports_ = collect_all(requirement, include_py_files=True)
+        # Use filter to exclude problematic xgboost.testing module
+        filter_func = lambda name: not name.startswith("xgboost.testing") if requirement == "xgboost" else True
+        datas_, binaries_, hidden_imports_ = collect_all(
+            requirement,
+            include_py_files=True,
+            filter_submodules=filter_func
+        )
     except (ImportError, RuntimeError) as e:
         # Skip packages that fail to collect (e.g., xgboost.testing requires hypothesis)
         print(f"Warning: Failed to collect {requirement}: {e}")
@@ -61,6 +67,18 @@ while requirements:
 
 hidden_imports = sorted([h for h in hidden_imports if "tests" not in h.split(".")])
 hidden_imports = [h for h in hidden_imports if "__pycache__" not in h]
+
+# Add hdf5plugin imports to fix runtime import issues
+hidden_imports.extend([
+    "hdf5plugin.plugins.bshuf",
+    "hdf5plugin.plugins.blosc",
+    "hdf5plugin.plugins.blosc2",
+    "hdf5plugin.plugins.lz4",
+    "hdf5plugin.plugins.fcidecomp",
+    "hdf5plugin.plugins.zfp",
+    "hdf5plugin.plugins.zstd",
+])
+
 datas = [
     d
     for d in datas

ms2rescore/gui/__main__.py

@@ -2,17 +2,23 @@
 
 import multiprocessing
 import os
-import contextlib
+import sys
 
 from ms2rescore.gui.app import app
 
 
 def main():
     """Entrypoint for MS²Rescore GUI."""
     multiprocessing.freeze_support()
-    # Redirect stdout when running GUI (packaged app might not have console attached)
-    with contextlib.redirect_stdout(open(os.devnull, "w")):
-        app()
+
+    # Fix for PyInstaller windowed mode: sys.stdout/stderr can be None
+    # This causes issues with libraries that try to write to stdout (e.g., Keras progress bars)
+    if sys.stdout is None:
+        sys.stdout = open(os.devnull, "w")
+    if sys.stderr is None:
+        sys.stderr = open(os.devnull, "w")
+
+    app()
 
 
 if __name__ == "__main__":

ms2rescore/gui/app.py

@@ -859,6 +859,23 @@ def _check_updates_sync(root):
         pass
 
 
+def _setup_logging(log_level: str, log_file: str):
+    """Setup file logging for GUI."""
+    log_level_map = {
+        "critical": logging.CRITICAL,
+        "error": logging.ERROR,
+        "warning": logging.WARNING,
+        "info": logging.INFO,
+        "debug": logging.DEBUG,
+    }
+    file_handler = logging.FileHandler(log_file, mode="w", encoding="utf-8")
+    file_handler.setFormatter(
+        logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+    )
+    file_handler.setLevel(log_level_map.get(log_level, logging.INFO))
+    logging.getLogger().addHandler(file_handler)
+
+
 def function(config):
     """Function to be executed in a separate process."""
     config = config.copy()
@@ -867,6 +884,12 @@ def function(config):
     else:
         config_list = [config]
     config = parse_configurations(config_list)
+
+    # Set up file logging for GUI
+    _setup_logging(
+        config["ms2rescore"]["log_level"], config["ms2rescore"]["output_path"] + ".log.txt"
+    )
+
     rescore(configuration=config)
     if config["ms2rescore"]["write_report"]:
         webbrowser.open_new_tab(config["ms2rescore"]["output_path"] + ".report.html")

ms2rescore/report/generate.py

@@ -12,6 +12,7 @@
 import plotly.express as px
 import psm_utils.io
 from jinja2 import Environment, FileSystemLoader
+from plotly.offline import get_plotlyjs_version
 from psm_utils.psm_list import PSMList
 
 try:
@@ -93,6 +94,7 @@ def generate_report(
     log_context = _get_log_context(files)
 
     context = {
+        "plotlyjs_version": get_plotlyjs_version(),
         "metadata": {
             "generated_on": datetime.now().strftime("%d/%m/%Y %H:%M:%S"),
             "ms2rescore_version": ms2rescore.__version__,  # TODO: Write during run?
@@ -418,8 +420,10 @@ def _render_and_write(output_path_prefix: str, **context):
     """Render template with context and write to HTML file."""
     report_path = Path(output_path_prefix + ".report.html").resolve()
     logger.info("Writing report to %s", report_path.as_posix())
-    template_dir = Path(__file__).parent / "templates"
-    env = Environment(loader=FileSystemLoader(template_dir, encoding="utf-8"))
+
+    # Use importlib.resources for PyInstaller compatibility
+    template_dir = importlib.resources.files(templates)
+    env = Environment(loader=FileSystemLoader(str(template_dir), encoding="utf-8"))
     template = env.get_template("base.html")
     with open(report_path, "w", encoding="utf-8") as f:
         f.write(template.render(**context))

ms2rescore/report/templates/base.html

@@ -11,7 +11,7 @@
     <link href="https://fonts.googleapis.com/css2?family=Lato:wght@300;400&family=Oswald:wght@400;500;600;700&display=swap" rel="stylesheet" />
     <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/font-awesome@4.7.0/css/font-awesome.min.css" />
     <script type="text/javascript" id="MathJax-script" async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
-    <script type="text/javascript" src="https://cdn.plot.ly/plotly-2.25.2.min.js" charset="utf-8"></script>
+    <script type="text/javascript" src="https://cdn.plot.ly/plotly-{{ plotlyjs_version }}.min.js" charset="utf-8"></script>
     {% include 'style.html' %}
   </head>
   <body>