refactor process and bump version (#30)

a Hail Mary-commit, counting on it working, we need CI!

Author: cjayb

setup.py

@@ -20,13 +20,13 @@ def run(self):
 
 setup(
     name = "stormdb",
-    version = "0.4b",
+    version = "0.5",
     author = "Christopher Bailey",
     author_email = "[email protected]",
-    description = ("Access to StormDb @ CFIN"),
+    description = ("Tools for accessing StormDb @ CFIN"),
     license = "BSD",
     keywords = "code",
-    url = "https://github.com/cfin-tools/stormdb.git",
+    url = "https://github.com/meeg-cfin/stormdb-python.git",
     packages=['stormdb'],
     scripts=['bin/submit_to_cluster'],
     long_description=read('README.md'),

stormdb/__init__.py

@@ -1,7 +1,5 @@
 """
-STORM database access
+STORM database access and cluster processing tools.
 """
 
-__VERSION__= '0.3git'
-
-#import .access
+__VERSION__ = '0.5'

stormdb/process/__init__.py

@@ -0,0 +1,9 @@
+"""Tools for processing data on hyades-cluster."""
+
+# Authors:  Christopher Bailey <[email protected]>
+#           Mads Jensen <[email protected]>
+#
+# License: BSD (3-clause)
+
+from .maxfilter import Maxfilter
+from .mne_python import MNEPython

stormdb/process/base.py

@@ -0,0 +1,27 @@
+"""
+=========================
+Helpers for process-tools.
+=========================
+"""
+
+import os
+
+
+def check_destination_writable(dest):
+    try:
+        open(dest, 'w')
+    except IOError:
+        return False
+    else:
+        os.remove(dest)
+        return True
+
+
+def check_source_readable(source):
+    try:
+        fid = open(source, 'r')
+    except IOError:
+        return False
+    else:
+        fid.close()
+        return True

stormdb/process.py stormdb/process/maxfilter.pystormdb/process.py renamed to stormdb/process/maxfilter.py

@@ -1,6 +1,6 @@
 """
 =========================
-Classes to process data on hyades cluster
+Classes related to Maxfilter
 
 Credits:
     Several functions are modified versions from those in mne-python
@@ -11,54 +11,14 @@
 # Author: Chris Bailey <[email protected]>
 #
 # License: BSD (3-clause)
-import os
 import warnings
-import inspect
 import numpy as np
 
 from mne.io import Raw
 from mne.bem import fit_sphere_to_headshape
 
-from .cluster import ClusterBatch
-
-
-class MNEPython(ClusterBatch):
-    """ Foo
-    """
-    def __init__(self, proj_name, bad=[], verbose=True):
-        super(MNEPython, self).__init__(proj_name)
-
-        self.info = dict(bad=bad, io_mapping=[])
-
-    def parse_arguments(self, func):
-        # argspec = inspect.getargspec(Raw.filter)
-        argspec = inspect.getargspec(func)
-        n_pos = len(argspec.args) - len(argspec.defaults)
-        args = argspec.args[1:n_pos]  # drop self
-        kwargs = {key: val for key, val in zip(argspec.args[n_pos:],
-                                               argspec.defaults)}
-        return(args, kwargs)
-
-    def raw_filter(self, in_fname, out_fname, l_freq, h_freq, **kwargs):
-        if not check_source_readable(in_fname):
-            raise IOError('Input file {0} not readable!'.format(in_fname))
-        if not check_destination_writable(out_fname):
-            raise IOError('Output file {0} not writable!'.format(out_fname))
-
-        script = ("from mne.io import read_raw_fif;"
-                  "raw = read_raw_fif('{in_fname:s}', preload=True);"
-                  "raw.filter({l_freq}, {h_freq}{kwargs:});"
-                  "raw.save('{out_fname:s}')")
-        filtargs = ', '.join("{!s}={!r}".format(key, val) for
-                             (key, val) in kwargs.items())
-        filtargs = ', ' + filtargs if len(kwargs) > 0 else filtargs
-        cmd = "python -c \""
-        cmd += script.format(in_fname=in_fname, out_fname=out_fname,
-                             l_freq=l_freq, h_freq=h_freq, kwargs=filtargs)
-        cmd += "\""
-
-        self.add_job(cmd, n_threads=1, job_name='mne.raw.filter')
-        self.info['io_mapping'] += [dict(input=in_fname, output=out_fname)]
+from .base import check_destination_writable, check_source_readable
+from ..cluster import ClusterBatch
 
 
 class Maxfilter(ClusterBatch):
@@ -360,23 +320,3 @@ def __init__(self, proj_name, bad=[], verbose=True):
     #         uniq_bads = [b for b in new_bads if b not in self.bad]
     #         self.info['bad'] = uniq_bads
     #         self.logger.info('Maxfilter object bad channel list updated')
-
-
-def check_destination_writable(dest):
-    try:
-        open(dest, 'w')
-    except IOError:
-        return False
-    else:
-        os.remove(dest)
-        return True
-
-
-def check_source_readable(source):
-    try:
-        fid = open(source, 'r')
-    except IOError:
-        return False
-    else:
-        fid.close()
-        return True

stormdb/process/mne_python.py

@@ -0,0 +1,43 @@
+import inspect
+
+from .base import check_destination_writable, check_source_readable
+from ..cluster import ClusterBatch
+
+
+class MNEPython(ClusterBatch):
+    """Clusterised mne-python commands.
+    """
+    def __init__(self, proj_name, bad=[], verbose=True):
+        super(MNEPython, self).__init__(proj_name)
+
+        self.info = dict(bad=bad, io_mapping=[])
+
+    def parse_arguments(self, func):
+        # argspec = inspect.getargspec(Raw.filter)
+        argspec = inspect.getargspec(func)
+        n_pos = len(argspec.args) - len(argspec.defaults)
+        args = argspec.args[1:n_pos]  # drop self
+        kwargs = {key: val for key, val in zip(argspec.args[n_pos:],
+                                               argspec.defaults)}
+        return(args, kwargs)
+
+    def raw_filter(self, in_fname, out_fname, l_freq, h_freq, **kwargs):
+        if not check_source_readable(in_fname):
+            raise IOError('Input file {0} not readable!'.format(in_fname))
+        if not check_destination_writable(out_fname):
+            raise IOError('Output file {0} not writable!'.format(out_fname))
+
+        script = ("from mne.io import read_raw_fif;"
+                  "raw = read_raw_fif('{in_fname:s}', preload=True);"
+                  "raw.filter({l_freq}, {h_freq}{kwargs:});"
+                  "raw.save('{out_fname:s}')")
+        filtargs = ', '.join("{!s}={!r}".format(key, val) for
+                             (key, val) in kwargs.items())
+        filtargs = ', ' + filtargs if len(kwargs) > 0 else filtargs
+        cmd = "python -c \""
+        cmd += script.format(in_fname=in_fname, out_fname=out_fname,
+                             l_freq=l_freq, h_freq=h_freq, kwargs=filtargs)
+        cmd += "\""
+
+        self.add_job(cmd, n_threads=1, job_name='mne.raw.filter')
+        self.info['io_mapping'] += [dict(input=in_fname, output=out_fname)]