switch from matplotlib to bokeh in metricset

Author: ptooley

pypop/__init__.py

@@ -12,8 +12,6 @@
 
 from .version import get_version
 
-__all__ = ['__version__']
+__all__ = ["__version__"]
 
 __version__ = get_version()
-
-

pypop/config.py

@@ -7,7 +7,7 @@
 
 from os.path import normpath, expanduser
 
-__all__ = ['set_paramedir_path', 'set_dimemas_path', 'set_tmpdir_path']
+__all__ = ["set_paramedir_path", "set_dimemas_path", "set_tmpdir_path"]
 
 _dimemas_path = None
 _paramedir_path = None

pypop/dimemas.py

@@ -59,9 +59,7 @@ def dimemas_idealise(tracefile, outpath=None):
 
     # Pass trace, run config and path to idealisation skeleton config and let
     # dimemas_analyze work its subtle magic(k)s
-    return dimemas_analyse(
-        tracefile, IDEAL_CONF_PATH, outpath, subs
-    )
+    return dimemas_analyse(tracefile, IDEAL_CONF_PATH, outpath, subs)
 
 
 def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
@@ -93,7 +91,7 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
 
     # Perform all work in a tempdir with predictable names,
     # this works around a series of weird dimemas bugs
-    
+
     # Make sure config._tmpdir_path exists before using it
     if config._tmpdir_path:
         try:
@@ -142,7 +140,7 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
     # Now create the dim file for dimemas
     tmp_dim = os.path.join(workdir, splitext(basename(tmp_prv))[0] + ".dim")
 
-    prv2dim_binpath = 'prv2dim'
+    prv2dim_binpath = "prv2dim"
     if config._dimemas_path:
         prv2dim_binpath = os.path.join(config._dimemas_path, prv2dim_binpath)
 
@@ -165,7 +163,7 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
     except Exception as err:
         raise RuntimeError("prv2dim execution_failed: {}".format(err))
 
-    dimemas_binpath = 'Dimemas'
+    dimemas_binpath = "Dimemas"
     if config._dimemas_path:
         dimemas_binpath = os.path.join(config._dimemas_path, dimemas_binpath)
 
@@ -228,4 +226,4 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
     shutil.rmtree(workdir, ignore_errors=True)
 
     # finally return outpath as promised
-    return os.path.join(outpath,filestem + ".sim.prv")
+    return os.path.join(outpath, filestem + ".sim.prv")

pypop/extrae.py

@@ -111,14 +111,14 @@ def chop_prv_to_roi(prv_file, outfile=None):
     if outfile:
         workdir = dirname(normpath(outfile))
     else:
-        tgtname = ".chop".join(splitext(basename(prv_file))) 
+        tgtname = ".chop".join(splitext(basename(prv_file)))
         # Make sure config._tmpdir_path exists before using it
         if config._tmpdir_path:
             try:
                 os.makedirs(config._tmpdir_path, exist_ok=True)
             except OSError as err:
                 print("FATAL: {}".format(err))
-        workdir = mkdtemp(dir=config._tmpdir_path)        
+        workdir = mkdtemp(dir=config._tmpdir_path)
         outfile = os.path.join(workdir, tgtname)
 
     roi_filter = resource_filename(__name__, ROI_FILTER_XML)
@@ -183,7 +183,8 @@ def chop_prv_to_roi(prv_file, outfile=None):
         )
 
     return outfile
-    
+
+
 def _get_roi_times(roi_prv):
     """ Extract ROi timing information from a filtered trace
 
@@ -195,20 +196,16 @@ def _get_roi_times(roi_prv):
     df = data.event
 
     # Get the first on and last off events
-    grouped = df.reset_index(level='time').groupby(level=['task','thread'])
+    grouped = df.reset_index(level="time").groupby(level=["task", "thread"])
     ons = grouped.nth(1)
-    offs = grouped.last()    
-    
+    offs = grouped.last()
+
     # Check the events have the expected values
-    if not (ons['value'] == 1).all():
-        raise ValueError(
-            "Unexpected event value: expected 40000012:1"
-        )
-    if not (offs['value'] == 0).all():
-        raise ValueError(
-            "Unexpected event value: expected 40000012:0"
-        )
-    return ons['time'].min(), 1 + offs['time'].max()
+    if not (ons["value"] == 1).all():
+        raise ValueError("Unexpected event value: expected 40000012:1")
+    if not (offs["value"] == 0).all():
+        raise ValueError("Unexpected event value: expected 40000012:0")
+    return ons["time"].min(), 1 + offs["time"].max()
 
 
 def paramedir_analyze(
@@ -381,16 +378,16 @@ def run_paramedir(tracefile, paramedir_config, outfile=None, variables=None):
     outfile: str
         Path to the output file.
     """
- 
+
     # Make sure config._tmpdir_path exists before using it
     if config._tmpdir_path:
         try:
             os.makedirs(config._tmpdir_path, exist_ok=True)
         except OSError as err:
             print("FATAL: {}".format(err))
-    
+
     tmpdir = mkdtemp(dir=config._tmpdir_path)
-        
+
     # If variables is none, still sub with empty dict
     variables = variables if variables else {}
     tmp_config = _write_substituted_config(paramedir_config, tmpdir, variables)

pypop/metrics/hybrid.py

@@ -250,6 +250,7 @@ def _calculate_metrics(self, ref_key=None, sort_keys=True):
 class MPI_OpenMP_Multiplicative_Metrics(MetricSet):
     """Proposed Hybrid MPI+OpenMP Metrics (multiplicative version).
     """
+
     _metric_list = [
         Metric("Global Efficiency", 0, desc=k_GE_desc),
         Metric("Parallel Efficiency", 1, desc=k_PE_desc),