From 974db1f435ea0b314b5135aba9c9ae6674f3944d Mon Sep 17 00:00:00 2001
From: thoffman <thoffman@embl.de>
Date: Fri, 24 May 2024 16:00:22 +0200
Subject: [PATCH 1/2] add executable parameter

---
 lil_aretomo/aretomo.py | 6 ++++--
 lil_aretomo/utils.py   | 9 +++++----
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/lil_aretomo/aretomo.py b/lil_aretomo/aretomo.py
index 6f275ee..1bdfcbe 100644
--- a/lil_aretomo/aretomo.py
+++ b/lil_aretomo/aretomo.py
@@ -22,7 +22,8 @@ def align_tilt_series(
         nominal_rotation_angle: Optional[float] = None,
         correct_tilt_angle_offset: bool = False,
         gpu_ids: Optional[Sequence[int]] = None,
-        skip_if_completed: bool = False
+        skip_if_completed: bool = False,
+        executable: Optional[str]='AreTomo'
 ) -> AreTomoOutput:
     """Align a single-axis tilt-series using AreTomo.
 
@@ -43,7 +44,7 @@ def align_tilt_series(
     gpu_ids: integer ids for GPUs on the system (zero indexed).
     skip_if_completed: skip alignment if previous results found.
     """
-    if check_aretomo_on_path() is False:
+    if check_aretomo_on_path(executable) is False:
         raise RuntimeError("AreTomo executable was not found. \
         Put 'AreTomo' on the PATH to proceed.")
     if do_local_alignments is True and n_patches_xy is None:
@@ -68,6 +69,7 @@ def align_tilt_series(
         do_local_alignments=do_local_alignments,
         n_patches_xy=n_patches_xy,
         gpu_ids=gpu_ids,
+        executable=executable
     )
     aretomo_output = AreTomoOutput(tilt_series_file=tilt_series_file, reconstruction_file=reconstruction_file)
     if aretomo_output.contains_alignment_results is False or skip_if_completed is False:
diff --git a/lil_aretomo/utils.py b/lil_aretomo/utils.py
index 5994258..a26db38 100644
--- a/lil_aretomo/utils.py
+++ b/lil_aretomo/utils.py
@@ -47,11 +47,12 @@ def get_aretomo_command(
         nominal_tilt_axis_angle: Optional[float] = None,
         do_local_alignments: bool = True,
         n_patches_xy: Optional[Tuple[int, int]] = None,
-        gpu_ids: Optional[Sequence[int]] = None
+        gpu_ids: Optional[Sequence[int]] = None,
+        executable: Optional[str] = 'AreTomo',
 ) -> List[str]:
     """Generate a command which can be used to run AreTomo."""
     command = [
-        'AreTomo',
+        executable,
         '-InMrc', f'{tilt_series_file}',
         '-OutMrc', f'{reconstruction_file}',
         '-OutBin', f'{binning_factor:.3f}',
@@ -71,9 +72,9 @@ def get_aretomo_command(
     return command
 
 
-def check_aretomo_on_path():
+def check_aretomo_on_path(executable: Optional[str] = 'AreTomo'):
     """Check the PATH for AreTomo."""
-    return shutil.which('AreTomo') is not None
+    return shutil.which(executable) is not None
 
 
 def read_aln(filename: os.PathLike) -> pd.DataFrame:

From 09901ccd2e5ce2aa1e6f229a5fab0d1cbd1a501f Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Fri, 24 May 2024 16:28:57 +0200
Subject: [PATCH 2/2] Update utils.py

---
 lil_aretomo/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lil_aretomo/utils.py b/lil_aretomo/utils.py
index a26db38..97f006b 100644
--- a/lil_aretomo/utils.py
+++ b/lil_aretomo/utils.py
@@ -52,7 +52,7 @@ def get_aretomo_command(
 ) -> List[str]:
     """Generate a command which can be used to run AreTomo."""
     command = [
-        executable,
+        f'{executable}',
         '-InMrc', f'{tilt_series_file}',
         '-OutMrc', f'{reconstruction_file}',
         '-OutBin', f'{binning_factor:.3f}',