Get the tour model generation code to work again (#788)

* Get the tour model generation code to work again

The big changes were to move the visualization imports, notably
matplotlib, into the individual visualization functions.
It is terrible practice to mix computation and viz, not the least because
the dependencies for the computation are unnecessarily bloated by viz modules

other changes:

- remove invalid and unused reference to edb directly
- change print -> print() to support python3
- remove erroneous close paranthesis
- add pykov to the computation environment

Testing done:

Without the fixes:
```
(emission) kshankar-35069s:e-mission-server kshankar$ ./e-mission-py.bash emission/pipeline/model_stage.py
storage not configured, falling back to sample, default configuration
Connecting to database URL localhost
Traceback (most recent call last):
  File "emission/pipeline/model_stage.py", line 13, in <module>
    import emission.storage.decorations.tour_model_queries as esdtmq
  File "/Users/kshankar/e-mission/e-mission-server/emission/storage/decorations/tour_model_queries.py", line 12, in <module>
    import emission.storage.decorations.common_place_queries as esdcpq
  File "/Users/kshankar/e-mission/e-mission-server/emission/storage/decorations/common_place_queries.py", line 16, in <module>
    import pykov as pk
ModuleNotFoundError: No module named 'pykov'
```

and multiple other errors

With the fixes:

```
 Cleanedplace({'source': 'DwellSegmentationTimeFilter', 'enter_ts': 1610812590, 'enter_local_dt': {'year': 2021, 'month': 1, 'day': 16, 'hour': 8, 'minute': 56, 'second': 30, 'weekday': 5, 'timezone': 'America/Denver'}, 'enter_fmt_time': '2021-01-16T08:56:30-07:00', 'location': {'type': 'Point', 'coordinates': [-104.891193, 39.7660244]}, 'raw_places': [ObjectId('60031cc37dc9bcbfa487c31e'), ObjectId('60031cc37dc9bcbfa487c31e')], 'ending_trip': ObjectId('60031cc47dc9bcbfa487c327'), 'starting_trip': ObjectId('60039b632fb2ebf61146462a'), 'exit_ts': 1610843452.733473, 'exit_fmt_time': '2021-01-16T17:30:52.733473-07:00', 'exit_local_dt': {'year': 2021, 'month': 1, 'day': 16, 'hour': 17, 'minute': 30, 'second': 52, 'weekday': 5, 'timezone': 'America/Denver'}, 'duration': 30862.733473062515})], 'end': 0, 'start': 1, 'start_coords': [-104.90605494323428, 39.764846852552445], 'end_coords': [-104.89127443959791, 39.765978419090914]}
2021-01-24 15:07:42,885:DEBUG:After creating map, number of places is 2
2021-01-24 15:07:42,885:DEBUG:Adding 55 places for this place
2021-01-24 15:07:42,889:DEBUG:Adding 55 places for this place
```

* Revert changes to the webserver conf and the notebook additions

Which should really go into a different PR

emission/analysis/modelling/tour_model/featurization.py

@@ -11,7 +11,6 @@
 from builtins import object
 from past.utils import old_div
 import logging
-import matplotlib.pyplot as plt
 import numpy
 from sklearn.cluster import KMeans
 from sklearn import metrics
@@ -142,6 +141,7 @@ def check_clusters(self):
     #map the clusters
     #TODO - move this to a file in emission.analysis.plotting to map clusters from the database
     def map_clusters(self):
+        import matplotlib.pyplot as plt
         from matplotlib import colors as matcol
         colormap = plt.cm.get_cmap()
 

emission/analysis/modelling/tour_model/similarity.py

@@ -11,9 +11,6 @@
 from past.utils import old_div
 import logging
 import math
-import matplotlib
-matplotlib.use('Agg')
-import matplotlib.pyplot as plt
 import numpy
 from sklearn import metrics
 from numpy.linalg import norm
@@ -147,6 +144,9 @@ def match(self,a,bin):
 
     #create the histogram
     def graph(self):
+        import matplotlib
+        matplotlib.use('Agg')
+        import matplotlib.pyplot as plt
         bars = [0] * len(self.bins)
         for i in range(len(self.bins)):
             bars[i] = len(self.bins[i])

emission/pipeline/model_stage.py

@@ -11,7 +11,6 @@
 import emission.net.usercache.abstract_usercache as enua
 import emission.storage.timeseries.abstract_timeseries as esta
 import emission.storage.decorations.tour_model_queries as esdtmq
-from emission.core.get_database import get_db, get_mode_db, get_section_db
 
 import emission.analysis.intake.cleaning.filter_accuracy as eaicf
 import emission.analysis.intake.segmentation.trip_segmentation as eaist
@@ -59,7 +58,7 @@ def run_model_pipeline(process_number, uuid_list):
 		try: 
 			run_model_pipeline_for_user(uuid)
 		except Exception as e:
-			print "dang flabbit failed on error %s" % e
+			print("dang flabbit failed on error %s" % e)
 
 
 def run_mode_inference_pipeline_for_user(uuid):
@@ -107,7 +106,7 @@ def run_mode_pipeline_for_user(MIP, uuid):
 
 	timerange = get_time_range_for_mode_inference(uuid)
 	MIP.runPipelineModelStage(uuid, timerange)
-	mark_mode_inference_done_for_user(uuid, MIP.getLastTimestamp})
+	mark_mode_inference_done_for_user(uuid, MIP.getLastTimestamp)
 
 
 if __name__ == '__main__':

setup/environment36.yml

@@ -24,4 +24,5 @@ dependencies:
   - pyfcm==1.4.7
   - pygeocoder==1.2.5
   - pymongo==3.11.0
+  - pykov==0.1
 prefix: /Users/shankari/OSS/anaconda/envs/emission