Merge branch 'slurmoverssh'

containers/tramway-notebook

@@ -58,27 +58,17 @@ The container OS is Ubuntu Xenial and can run on top of old OSes like CentOS6.
 
     #pip3.6 install --upgrade pip
     pip3.6 uninstall -qy tramway || true
-    pip3.6 install . -r requirements.txt
+    #pip3.6 install . -r requirements.txt
     pip3.6 install .[animate,roi,webui]
 
     pip3.6 install scikit-learn
     pip3.6 install paramiko
     pip3.6 install notebook
-
-    #apt-get install -y --no-install-recommends \
-    #    firefox firefox-geckodriver
+    pip3.6 install colorcet
 
     mkdir -p /pasteur
 
 %runscript
 
-    #cmd="tramway"
-    #python="python3.6"
-    #if [ -n "$1" -a "$1" = "-s" ]; then
-    #   cmd="${python} -s -m tramway"
-    #   shift
-    #fi
-    #exec $cmd $@
-
     exec jupyter notebook $@
 

scripts/tramway-browse

@@ -4,7 +4,7 @@ import tempfile as tmp
 import sys
 import subprocess
 
-def browse(files=[], browser='Firefox'):
+def browse(files=[], browser='Firefox', colormap=None):
     if not files:
         import glob
         filepattern = '*.rwa'
@@ -25,8 +25,10 @@ from selenium import webdriver
 a = RWAnalyzer()
 a.spt_data.from_rwa_files(['{}'])
 a.env.script = '{}'
-a.browser.show_maps(webdriver=webdriver.{})
-""".format("', '".join(files), script.name, browser)
+{}a.browser.show_maps(webdriver=webdriver.{})
+""".format("', '".join(files), script.name,
+        '' if colormap is None else "a.browser.colormap = '{}'\n".format(colormap),
+        browser)
     script.write(source)
     script.flush()
     try:
@@ -43,6 +45,7 @@ def main():
         description='Browse TRamWAy-generated .rwa files')
     parser.add_argument('files', nargs='*', help='for example: *.rwa or */*.rwa')
     parser.add_argument('--browser', default='Firefox', choices=['Firefox','Chrome','Edge','Ie','Opera','Safari','WebKitGTK'])
+    parser.add_argument('--colormap', help="Matplotlib colormap name")
     print(browse(**parser.parse_args().__dict__))
 
 if __name__ == '__main__':

tramway/analyzer/browser/__init__.py

@@ -52,11 +52,26 @@ class Browser(AnalyzerNode):
     The showed parameter values can also be exported with the side panel.
     Note that all features are exported together with the spatial bin center coordinates.
     """
+    __slots__ = ('_colormap',)
+    @property
+    def colormap(self):
+        """ Colormap for inferred parameter maps.
+
+        See also :func:`~tramway.plot.bokeh.map.scalar_map_2d`."""
+        return self._colormap
+    @colormap.setter
+    def colormap(self, cm):
+        self._colormap = cm
+    def __init__(self, analyzer):
+        AnalyzerNode.__init__(self, parent=analyzer)
+        self._colormap = None
     def show_maps(self, **kwargs):
         """ see also :func:`~tramway.plot.bokeh.analyzer.browse_maps`. """
         from tramway.plot.bokeh.analyzer import browse_maps
         browse_maps(self._eldest_parent, **kwargs)
 
+Attribute.register(Browser)
+
 
 __all__ = ['Browser']
 

tramway/analyzer/env/environments.py

@@ -1029,19 +1029,32 @@ def wait_for_job_completion(self):
                     self.logger.error(err.rstrip())
                 elif out:
                     # parse and print progress info
-                    out = out.splitlines()
-                    try:
-                        start, stop = out[0].split()[0].split('-')
-                    except ValueError:
-                        raise RuntimeError('unexpected squeue message: \n'+'\n'.join(out))
-                    stop = stop.split('%')[0]
-                    start, stop = int(start), int(stop)
+                    start, _out = None, []
+                    _continue = False
+                    for line in out.splitlines():
+                        parts = line.split()
+                        if '-' in parts[0]:
+                            if start is None:
+                                try:
+                                    start, stop = parts[0].split('-')
+                                except ValueError:
+                                    self.logger.debug('squeue output parsing failed: \n'+out)
+                                    _continue = True; break
+                                else:
+                                    stop = stop.split('%')[0]
+                                    start, stop = int(start), int(stop)
+                            else:
+                                self.logger.debug('squeue output parsing failed: \n'+out)
+                                _continue = True; break
+                        else:
+                           _out.append(parts)
+                    if _continue:
+                        continue
                     total = stop
                     pending = stop - start
                     running = 0
                     other = 0
-                    for out in out[1:]:
-                        out = out.split()
+                    for out in _out:
                         array_ix, status, time_used = int(out[0]), out[1], out[2]
                         reason = ' '.join(out[3:])
                         if status == 'R':