Issue54 fix - stage1 in notebook

scousepy/scouse.py

@@ -21,6 +21,8 @@
 import time
 import pyspeckit
 import random
+import asyncio
+
 warnings.simplefilter('ignore', wcs.FITSFixedWarning)
 
 from .stage_3 import *
@@ -349,22 +351,43 @@ def stage_1(config='', interactive=True):
             coverageobject=ScouseCoverage(scouseobject=self,verbose=self.verbose,
                                             interactive=interactive)
             if interactive:
-                 coverageobject.show()
-            if coverageobject.config_file is None or len(coverageobject.config_file) == 0:
-                raise ValueError("Coverage configuration was set to be 'interactive', but the "
-                        "interactive plot window did not wait for input. If you are running in "
-                        "Jupyter notebooks or Spyder then try running scouse as a script instead. "
-                        "Alternatively set interactive=False and manually update coverage.config.")
+                coverageobject.show()
+                if not coverageobject.coverage_is_complete:
+                    # we are in a notebook and need asyncio
+                    async def wait_on_interactive():
+                        while coverageobject.config_file is None:
+                            await asyncio.sleep(1)
+                        self.save_coverage(coverageobject, old_log)
+                        self.run_coverage(coverageobject)
+                        plt.close(coverageobject.fig.number)
+
+                    loop = asyncio.get_event_loop()
+                    loop.create_task(wait_on_interactive())
+            else:
+                self.save_coverage(coverageobject, old_log)
+                self.run_coverage(coverageobject)
+
+        return self
+
+    def save_coverage(self, coverageobject, old_log):
+        from .io import import_from_config
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore')
 
             # write out the config file for the coverage
-            self.coverage_config_file_path=os.path.join(self.outputdirectory,self.filename,'config_files','coverage.config')
+            self.coverage_config_file_path=os.path.join(self.outputdirectory,
+                    self.filename, 'config_files', 'coverage.config')
             with open(self.coverage_config_file_path, 'w') as file:
                 for line in coverageobject.config_file:
                     file.write(line)
             # set the parameters
             import_from_config(self, self.coverage_config_file_path)
             log.setLevel(old_log)
 
+    def run_coverage(self, coverageobject):
+        from .stage_1 import generate_SAAs, plot_coverage, compute_noise, get_x_axis
+        from .verbose_output import print_to_terminal
+
         # start the time once the coverage has been generated
         starttime = time.time()
 

scousepy/scousecoverage.py

@@ -29,6 +29,8 @@ class ScouseCoverage(object):
     """
     def __init__(self, scouseobject=None, create_config_file=True, verbose=True, interactive=True):
 
+        self.coverage_is_complete = False
+
         # For moments
         self.scouseobject=scouseobject
         self.verbose=verbose
@@ -388,6 +390,9 @@ def __init__(self, scouseobject=None, create_config_file=True, verbose=True, int
             self.run_coverage(None)
             # complete the coverage task
             self.coverage_complete(None)
+        else:
+            self.fig.canvas.flush_events()
+            self.fig.canvas.draw_idle()
 
 
     def show(self):
@@ -432,6 +437,8 @@ def coverage_complete(self, event):
                 self.samplesize=0.0
             self.config_file=make_config_file(self)
 
+        self.coverage_is_complete = True
+
         # close the window
         self.close_window()
 

scousepy/stage_1.py

@@ -155,7 +155,7 @@ def generate_SAAs(scouseobject, coverageobject):
         if scouseobject.njobs > 1:
             # if __name__ == 'scousepy.stage_1':
             #     print(__name__)
-                results = parallel_map(create_saa, inputlist, numcores=scouseobject.njobs)
+                results = list(parallel_map(create_saa, inputlist, numcores=scouseobject.njobs))
         else:
             if scouseobject.verbose:
                 results=[create_saa(input) for input in tqdm(inputlist)]