From 93bb5f59c4015d516fa3e6d9e0e92e999a683f14 Mon Sep 17 00:00:00 2001
From: dennisbrookner <debrookner@gmail.com>
Date: Fri, 13 Oct 2023 17:21:15 -0400
Subject: [PATCH] starting to include typing

---
 src/matchmaps/_compute_realspace_diff.py | 32 ++++++++++++------------
 src/matchmaps/_utils.py                  |  5 ++--
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/src/matchmaps/_compute_realspace_diff.py b/src/matchmaps/_compute_realspace_diff.py
index 8fd4e89..cf9d3e3 100755
--- a/src/matchmaps/_compute_realspace_diff.py
+++ b/src/matchmaps/_compute_realspace_diff.py
@@ -28,24 +28,24 @@
 
 
 def compute_realspace_difference_map(
-    pdboff,
-    mtzoff,
-    mtzon,
-    Foff,
-    SigFoff,
-    Fon,
-    SigFon,
-    ligands=None,
-    dmin=None,
-    spacing=0.5,
-    on_as_stationary=False,
+    pdboff : Path,
+    mtzoff : Path,
+    mtzon : Path,
+    Foff : str,
+    SigFoff : str,
+    Fon : str,
+    SigFon : str,
+    ligands : list = None,
+    dmin : int = None,
+    spacing = 0.5,
+    on_as_stationary : bool = False,
     input_dir=Path("."),
     output_dir=Path("."),
     verbose=False,
-    rbr_selections=None,
-    eff=None,
-    keep_temp_files=None,
-    radius=5,
+    rbr_selections : list[str] = None,
+    eff : str = None,
+    keep_temp_files : str = None,
+    radius : int = 5,
 ):
     """
     Compute a real-space difference map from mtzs.
@@ -89,7 +89,7 @@ def compute_realspace_difference_map(
         Name of a file containing a template .eff parameter file for phenix.refine.
         If omitted, the sensible built-in .eff template is used. If you need to change something,
         I recommend copying the template from the source code and editing that.
-    keep_temp_files : bool, optional
+    keep_temp_files : str, optional
         If not None, the name of a subdirectory of the output_dir into which intermediate matchmaps files are moved upon program completion.
     radius : float, optional
         Maximum distance away from protein model to include voxels. Only applies to the "unmasked" difference map output.
diff --git a/src/matchmaps/_utils.py b/src/matchmaps/_utils.py
index 4e63f00..36fccf3 100644
--- a/src/matchmaps/_utils.py
+++ b/src/matchmaps/_utils.py
@@ -854,11 +854,12 @@ def _quicknorm(array):
     return (array - array.mean()) / array.std()
 
 def _validate_inputs(
-    input_dir,
-    output_dir,
+    input_dir : Path,
+    output_dir : Path,
     ligands,
     *files,
 ):
+
     # use pathlib to validate input files and directories
     output_dir = Path(output_dir)
     output_dir.mkdir(parents=True, exist_ok=True)