Add optional cli argument for spind path

pyzebra/app/cli.py

@@ -38,10 +38,11 @@ def main():
     )
 
     parser.add_argument(
-        "--anatric-path",
+        "--anatric-path", type=str, default=None, help="path to anatric executable",
-        type=str,
+    )
-        default=None,
+
-        help="path to anatric executable",
+    parser.add_argument(
+        "--spind-path", type=str, default=None, help="path to spind scripts folder",
     )
 
     parser.add_argument(
@@ -55,7 +56,7 @@ def main():
 
     logger.info(app_path)
 
-    pyzebra_handler = PyzebraHandler(args.anatric_path)
+    pyzebra_handler = PyzebraHandler(args.anatric_path, args.spind_path)
     handler = ScriptHandler(filename=app_path, argv=args.args)
     server = Server(
         {"/": Application(pyzebra_handler, handler)},

pyzebra/app/handler.py

@@ -5,7 +5,7 @@ class PyzebraHandler(Handler):
     """Provides a mechanism for generic bokeh applications to build up new streamvis documents.
     """
 
-    def __init__(self, anatric_path):
+    def __init__(self, anatric_path, spind_path):
         """Initialize a pyzebra handler for bokeh applications.
 
         Args:
@@ -14,6 +14,7 @@ class PyzebraHandler(Handler):
         super().__init__()  # no-op
 
         self.anatric_path = anatric_path
+        self.spind_path = spind_path
 
     def modify_document(self, doc):
         """Modify an application document with pyzebra specific features.
@@ -26,5 +27,6 @@ class PyzebraHandler(Handler):
         """
         doc.title = "pyzebra"
         doc.anatric_path = self.anatric_path
+        doc.spind_path = self.spind_path
 
         return doc

pyzebra/app/panel_spind.py

@@ -5,6 +5,7 @@ import subprocess
 import tempfile
 
 import numpy as np
+from bokeh.io import curdoc
 from bokeh.layouts import column, row
 from bokeh.models import (
     Button,
@@ -22,6 +23,8 @@ import pyzebra
 
 
 def create():
+    doc = curdoc()
+
     path_prefix_textinput = TextInput(title="Path prefix:", value="")
     selection_list = TextAreaInput(title="ROIs:", rows=7)
     lattice_const_textinput = TextInput(
@@ -54,7 +57,7 @@ def create():
                     "-n",
                     "2",
                     "python",
-                    os.path.expanduser("~/spind/gen_hkl_table.py"),
+                    os.path.join(doc.spind_path, "gen_hkl_table.py"),
                     lattice_const_textinput.value,
                     "--max-res",
                     str(max_res_spinner.value),
@@ -81,7 +84,7 @@ def create():
                     "-n",
                     "2",
                     "python",
-                    os.path.expanduser("~/spind/SPIND.py"),
+                    os.path.join(doc.spind_path, "SPIND.py"),
                     temp_peak_list_dir,
                     temp_hkl_file,
                     "-o",
@@ -136,6 +139,9 @@ def create():
     process_button = Button(label="Process", button_type="primary")
     process_button.on_click(process_button_callback)
 
+    if doc.spind_path is None:
+        process_button.disabled = True
+
     ub_matrix_textareainput = TextAreaInput(title="UB matrix:", rows=7, width=400)
     hkl_textareainput = TextAreaInput(title="hkl values:", rows=7, width=400)
 

scripts/pyzebra-start.sh

@@ -1,4 +1,4 @@
 source /home/pyzebra/miniconda3/etc/profile.d/conda.sh
 
 conda activate prod
-pyzebra --port=80 --allow-websocket-origin=pyzebra.psi.ch:80
+pyzebra --port=80 --allow-websocket-origin=pyzebra.psi.ch:80 --spind-path=/home/pyzebra/spind

scripts/pyzebra-test-start.sh

@@ -1,4 +1,4 @@
 source /home/pyzebra/miniconda3/etc/profile.d/conda.sh
 
 conda activate test
-python ~/pyzebra/pyzebra/app/cli.py --allow-websocket-origin=pyzebra.psi.ch:5006
+python ~/pyzebra/pyzebra/app/cli.py --allow-websocket-origin=pyzebra.psi.ch:5006 --spind-path=/home/pyzebra/spind