Update to handle multiple bundles

Author: adelavega

neuroscout_cli/cli.py

@@ -2,30 +2,29 @@
 neuroscout
 
 Usage:
-    neuroscout run <bundle_id> [-dn -o <out_dir> -i <install_dir> --n-cpus=<n> --work-dir=<dir> --dataset-name=<name>]
-    neuroscout install <bundle_id> [-dn -i <install_dir>]
+    neuroscout run <outdir> <bundle_id>... [options]
+    neuroscout install <bundle_id>... [-n -i <install_dir>]
     neuroscout ls <bundle_id>
     neuroscout -h | --help
     neuroscout --version
 
 Options:
     -i <install_dir>        Directory to download dataset and bundle [default: .]
-    -o <out_dir>            Output directory [default: bundle_dir]
     --work-dir=<dir>        Working directory
     --n-cpus=<n>            Maximum number of threads across all processes [default: 1]
     -n, --no-download       Dont download dataset (if available locally)
     --dataset-name=<name>   Manually specify dataset name
     -h --help               Show this screen
     -v, --version           Show version
-    -d, --debug             Debug mode
 
 Commands:
     run                     Runs a first level, group level, or full analysis.
     install                 Installs a bundle and/or dataset.
     ls                      Lists the available files in a bundle's dataset.
 
 Examples:
-    neuroscout run 5xh -n
+    neuroscout run 5xhaS /out -n
+    neuroscout run 5xhaS 38fdx /out
 
 Help:
     For help using this tool, please open an issue on the Github
@@ -36,20 +35,22 @@
 
 from docopt import docopt
 from . import __version__ as VERSION
-import logging
 import sys
 
 def main():
     # CLI entry point
     import neuroscout_cli.commands
     args = docopt(__doc__, version=VERSION)
 
-    if args.get('--debug'):
-        logging.basicConfig(level=logging.DEBUG)
-
     for (k, v) in args.items():
         if hasattr(neuroscout_cli.commands, k) and v:
             k = k[0].upper() + k[1:]
             command = getattr(neuroscout_cli.commands, k)
-            command(args).run()
+            if k in ['Run', 'Install']:
+                bundles = args.pop('<bundle_id>')
+                # Loop over bundles
+                for b in bundles:
+                    print("Running bundle {}".format(b))
+                    args['<bundle_id>'] = b
+                    command(args).run()
             sys.exit(0)

neuroscout_cli/commands/install.py

@@ -97,7 +97,7 @@ def run(self):
                 return self.bundle_dir.absolute()
             else:
                 raise ValueError(
-                    "Manually specified dastaset directory does not contain",
+                    "Manually specified dataset directory does not contain",
                     "analysis bundle. Try again, or re-download bundle.")
         else:
             return self.download_data()

neuroscout_cli/commands/run.py

@@ -5,6 +5,9 @@
 import shutil
 from pathlib import Path
 
+# Options not to be passed onto fitlins
+INVALID = ['--no-download', '--version', '--help', '-i', 'run', '<bundle_id>', '--dataset-name']
+
 class Run(Command):
     ''' Command for running neuroscout workflows. '''
 
@@ -13,12 +16,7 @@ def run(self):
         install_command = Install(self.options.copy())
         bundle_path = install_command.run()
 
-        out_dir = self.options.pop('-o')
-        if out_dir == "bundle_dir":
-            out_dir = (install_command.bundle_dir).absolute()
-        else:
-            out_dir = Path(out_dir)
-
+        out_dir = Path(self.options.pop('<outdir>'))
         tmp_out = mkdtemp()
 
         dataset_dir = install_command.dataset_dir.absolute()
@@ -33,8 +31,7 @@ def run(self):
         ]
 
         # Fitlins invalid keys
-        invalid = ['--no-download', '--version', '--help', '-i', 'run', '<bundle_id>', '--dataset-name']
-        for k in invalid:
+        for k in INVALID:
             self.options.pop(k, None)
 
         # Add remaining optional arguments
@@ -51,4 +48,4 @@ def run(self):
         # Call fitlins as if CLI
         run_fitlins(fitlins_args)
         # Copy to out_dir (doing this because of Windows volume)
-        shutil.copytree(Path(tmp_out) / 'fitlins', out_dir / 'fitlins')
+        shutil.copytree(Path(tmp_out) / 'fitlins', out_dir / self.bundle_id)