use Path types everywhere (#30)

* use Path types everywhere

* refactor soft edge generation into a function (#31)

* soft edge written as a function (refactored)

* make soft edge function work on copy of the original array and returning and output instead of changing 'in place'

* restructure cli imports (#29)

* restructure cli imports

* refactor soft edge generation into a function (#31)

* soft edge written as a function (refactored)

* make soft edge function work on copy of the original array and returning and output instead of changing 'in place'

* restructure cli imports

* remove redundant imports

---------

Co-authored-by: milesagraham <[email protected]>

* use Path types everywhere

---------

Co-authored-by: milesagraham <[email protected]>

src/ttmask/_cli.py

@@ -1,3 +1,3 @@
 import typer
 
-cli = typer.Typer(name="ttmask")
+cli = typer.Typer(name="ttmask")

src/ttmask/cone.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import numpy as np
 import einops
 import typer
@@ -14,7 +16,7 @@ def cone(
     cone_base_diameter: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(...),
-    output: str = typer.Option("cone.mrc"),
+    output: Path = typer.Option(Path("cone.mrc"))
 ):
     c = sidelength // 2
     center = np.array([c, c, c])

src/ttmask/cube.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import numpy as np
 import einops
 import typer
@@ -13,7 +15,7 @@ def cube(
     cube_sidelength: float = typer.Option(...),
     soft_edge_width: float = typer.Option(0),
     pixel_size: float = typer.Option(...),
-    output: str = typer.Option("cube.mrc"),
+    output: Path = typer.Option(Path("cube.mrc")),
     wall_thickness: float = typer.Option(0),
 ):
     c = sidelength // 2

src/ttmask/cuboid.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import numpy as np
 import einops
 import typer
@@ -17,7 +19,7 @@ def cuboid(
     cuboid_sidelengths: Annotated[Tuple[float, float, float], typer.Option()] = (None, None, None),
     soft_edge_width: float = typer.Option(0),
     pixel_size: float = typer.Option(...),
-    output: str = typer.Option("cuboid.mrc"),
+    output: str = typer.Option(Path("cuboid.mrc")),
     wall_thickness: float = typer.Option(0),
 ):
     c = sidelength // 2

src/ttmask/cylinder.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import numpy as np
 import einops
 import typer
@@ -15,7 +17,7 @@ def cylinder(
     wall_thickness: float = typer.Option(0),
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(...),
-    output: str = typer.Option("cylinder.mrc")
+    output: Path = typer.Option(Path("cylinder.mrc"))
 ):
     cylinder_radius = cylinder_diameter / 2
 

src/ttmask/ellipsoid.py

@@ -1,11 +1,11 @@
+from pathlib import Path
+
 import numpy as np
 import einops
 import typer
 import mrcfile
-from .soft_edge import add_soft_edge
-
-from ._cli import cli
 
+from .soft_edge import add_soft_edge
 from ._cli import cli
 
 
@@ -17,7 +17,7 @@ def ellipsoid(
     depth: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(...),
-    output: str = typer.Option("ellipsoid.mrc"),
+    output: Path = typer.Option(Path("ellipsoid.mrc")),
     wall_thickness: float = typer.Option(0),
 ):
     c = sidelength // 2

src/ttmask/sphere.py

@@ -1,3 +1,6 @@
+from pathlib import Path
+
+from ._cli import cli
 import numpy as np
 import einops
 import typer
@@ -13,7 +16,7 @@ def sphere(
     sphere_diameter: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
     pixel_size: float = typer.Option(...),
-    output: str = typer.Option("sphere.mrc"),
+    output: Path = typer.Option(Path("sphere.mrc")),
     wall_thickness: float = typer.Option(0),
 ):
     sphere_radius = sphere_diameter / 2