small changes

pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
     "pandas",
     "rich",
     "topaz-em",
+    "sh",
 ]
 
 # extras

src/waretomo/_aretomo.py

@@ -9,7 +9,7 @@
 import GPUtil
 from rich import print
 
-from .threaded import run_threaded
+from ._threaded import run_threaded
 
 
 @contextmanager

src/waretomo/_fix.py

@@ -4,7 +4,7 @@
 
 from rich import print
 
-from .threaded import run_threaded
+from ._threaded import run_threaded
 
 
 def _ccderaser(

src/waretomo/_fix_mdoc.py

@@ -1,21 +1,22 @@
 import pandas as pd
-from mdocfile.mdoc import Mdoc
+from mdocfile.data_models import Mdoc
 
-from .threaded import run_threaded
+from ._threaded import run_threaded
 
 
 def _tilt_mdoc(
     mdoc_file, tlt_file, skipped_tilts, verbose=False, dry_run=False, overwrite=False
 ):
-    if verbose:
-        print(f"Tilting mdoc: {mdoc_file}")
-        print(f"using: {tlt_file}")
-
     output = mdoc_file.parent / "mdoc_tilted" / mdoc_file.name
 
     if not overwrite and output.exists():
         raise FileExistsError(output)
 
+    if verbose:
+        print(f"Tilting mdoc: {mdoc_file}")
+        print(f"using: {tlt_file}")
+        print(f"saving to {output}")
+
     if not dry_run:
         mdoc = Mdoc.from_file(mdoc_file)
         new_angles = iter(pd.read_csv(tlt_file, header=None)[0])

src/waretomo/_stack.py

@@ -4,7 +4,7 @@
 
 from rich import print
 
-from .threaded import run_threaded
+from ._threaded import run_threaded
 
 
 def _stack(

src/waretomo/main.py

@@ -164,7 +164,7 @@ def cli(
     from rich.panel import Panel
     from rich.progress import Progress
 
-    from .parse import parse_data
+    from ._parse import parse_data
 
     if gpus is not None:
         gpus = [int(gpu) for gpu in gpus.split(",")]
@@ -174,7 +174,7 @@ def cli(
         mdoc_dir = warp_dir
     mdoc_dir = Path(mdoc_dir)
     if output_dir is None:
-        output_dir = warp_dir / "stemia"
+        output_dir = warp_dir / "waretomo_processing"
     output_dir = Path(output_dir)
     output_dir.mkdir(parents=True, exist_ok=True)
 
@@ -223,16 +223,18 @@ def cli(
 
         nl = "\n"
 
-        not_ready = "".join(f'{nl}{" " * 12}- {ts}' for ts in tilt_series_unprocessed)
-        ready = "".join(f'{nl}{" " * 12}- {ts["name"]}' for ts in tilt_series)
+        not_ready_log = "".join(
+            f'{nl}{" " * 12}- {ts}' for ts in tilt_series_unprocessed
+        )
+        ready_log = "".join(f'{nl}{" " * 12}- {ts["name"]}' for ts in tilt_series)
         excluded = "".join(f'{nl}{" " * 12}- {ts}' for ts in tilt_series_excluded)
-        steps = "".join(
+        steps_log = "".join(
             f'{nl}{" " * 12}- '
-            '[{"green" if v else "red"}]{k}[/{"green" if v else "red"}] '
+            f'[{"green" if v else "red"}]{k}[/{"green" if v else "red"}] '
             for k, v in steps.items()
         )
-        opts = "".join(f'{nl}{" " * 12}- {k}: {v}' for k, v in meta_kwargs.items())
-        aretomo_opts = "".join(
+        opts_log = "".join(f'{nl}{" " * 12}- {k}: {v}' for k, v in meta_kwargs.items())
+        aretomo_opts_log = "".join(
             f'{nl}{" " * 12}- {k}: {v}' for k, v in aretomo_kwargs.items()
         )
 
@@ -242,12 +244,12 @@ def cli(
                     f"""
             [bold]Warp directory[/bold]: {warp_dir}
             [bold]Mdoc directory[/bold]: {mdoc_dir}
-            [bold]Tilt series - NOT READY[/bold]: {not_ready}
-            [bold]Tilt series - READY[/bold]: {ready}
+            [bold]Tilt series - NOT READY[/bold]: {not_ready_log}
+            [bold]Tilt series - READY[/bold]: {ready_log}
             [bold]Tilt series - EXCLUDED[/bold]: {excluded}
-            [bold]Processing steps[/bold]: {steps}
-            [bold]Run options[/bold]: {opts}
-            [bold]AreTomo options[/bold]: {aretomo_opts}
+            [bold]Processing steps[/bold]: {steps_log}
+            [bold]Run options[/bold]: {opts_log}
+            [bold]AreTomo options[/bold]: {aretomo_opts_log}
         """
                 )
             )