From dfc02cfa42d85bfb5e538d1270c626bb411482fe Mon Sep 17 00:00:00 2001
From: Alejo Rossia <alejo.r94@gmail.com>
Date: Tue, 24 Feb 2026 16:17:16 +0100
Subject: [PATCH 1/2] Windows-compatible reports

Changes required to make the report function work on Windows too. The should still run as usual on Linux/Mac but requires verification.
---
 src/smefit/analyze/__init__.py    | 17 ++++++++++-------
 src/smefit/analyze/html_utils.py  | 12 ++++++++----
 src/smefit/analyze/latex_tools.py |  5 ++++-
 3 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/src/smefit/analyze/__init__.py b/src/smefit/analyze/__init__.py
index 8b76c9e1..b039dfd8 100644
--- a/src/smefit/analyze/__init__.py
+++ b/src/smefit/analyze/__init__.py
@@ -2,7 +2,7 @@
 import pathlib
 import shutil
 import subprocess
-
+import sys
 import yaml
 from matplotlib import rc, use
 
@@ -69,14 +69,17 @@ def run_report(report_card_file):
     # Move all files to a meta folder
     meta_path = pathlib.Path(f"{report_folder}/meta").absolute()
     meta_path.mkdir()
-    subprocess.call(f"mv {report_folder}/*.* {meta_path}", shell=True)
+    for f in report_folder.glob("*.*"):
+        shutil.move(str(f), meta_path)
 
     # Combine PDF files together into raw pdf report
-    subprocess.call(
-        f"gs -q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite \
-                -sOutputFile={report_folder}/report_{report_name}.pdf `ls -rt {meta_path}/*.pdf`",
-        shell=True,
-    )
+    pdf_files = sorted(meta_path.glob("*.pdf"), key=os.path.getmtime)
+    gs_cmd = "gswin64c" if sys.platform == "win32" else "gs"
+    subprocess.call([
+        gs_cmd, "-q", "-dNOPAUSE", "-dBATCH", "-sDEVICE=pdfwrite",
+        f"-sOutputFile={report_folder}/report_{report_name}.pdf",
+        *[str(f) for f in pdf_files],
+        ])
 
     # dump html index
     dump_html_index(
diff --git a/src/smefit/analyze/html_utils.py b/src/smefit/analyze/html_utils.py
index 7dcd7c82..85b5ac45 100644
--- a/src/smefit/analyze/html_utils.py
+++ b/src/smefit/analyze/html_utils.py
@@ -106,10 +106,14 @@ def run_htlatex(report_path, tex_file):
     new_style = report_path.joinpath("style.css")
     shutil.copyfile(style_css, new_style)
     # title = tex_file.stem.replace("_", " ")
-    subprocess.call(
-        f"pandoc {tex_file} --standalone --mathjax --output {tex_file.with_suffix('.html')} --metadata title=' ' -c {new_style.stem}.css",
-        shell=True,
-    )
+    subprocess.call([
+    "pandoc", str(tex_file),
+    "--standalone",
+    "--mathjax",
+    "--output", str(tex_file.with_suffix('.html')),
+    "--metadata", "title= ",
+    "-c", f"{new_style.stem}.css",
+    ])
 
 
 def dump_html_index(html_report, html_index, report_path, report_title):
diff --git a/src/smefit/analyze/latex_tools.py b/src/smefit/analyze/latex_tools.py
index 4b9e9c42..41457086 100644
--- a/src/smefit/analyze/latex_tools.py
+++ b/src/smefit/analyze/latex_tools.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+import os
 import pathlib
 import subprocess
 
@@ -84,7 +85,9 @@ def run_pdflatex(report, filename):
         f"pdflatex -halt-on-error -output-directory {report} {filename}.tex > {report}/pdflatex.log",
         shell=True,
     )
-    subprocess.call(f"rm {report}/*.log {report}/*.aux {report}/*.out", shell=True)
+    for ext in ["*.log", "*.aux", "*.out"]:
+        for f in report.glob(ext):
+            os.remove(f)
 
 
 def compile_tex(report, L, filename):

From 68bf6fa42395cce02273c188f33b2a0c0caaa3aa Mon Sep 17 00:00:00 2001
From: Alejo Rossia <alejo.r94@gmail.com>
Date: Tue, 24 Feb 2026 16:28:27 +0100
Subject: [PATCH 2/2] Added os in __init__.py

---
 src/smefit/analyze/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/smefit/analyze/__init__.py b/src/smefit/analyze/__init__.py
index b039dfd8..55bd92b3 100644
--- a/src/smefit/analyze/__init__.py
+++ b/src/smefit/analyze/__init__.py
@@ -3,6 +3,7 @@
 import shutil
 import subprocess
 import sys
+import os
 import yaml
 from matplotlib import rc, use