Merge pull request #154 from prjemian/LGTM-153

fixes #153 : LGTM code review recommendations

conda-recipe/run_test.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
-import os, sys, unittest
-import spec2nexus
+# import spec2nexus
 
 # TODO: test something
 print("test not implemented yet")

create_release_notes.py

@@ -8,7 +8,7 @@
 
 from __future__ import print_function
 from datetime import datetime
-import os, sys
+import os
 import github       # pip install pygithub or conda install -c conda-forge pygithub
 import collections
 import argparse

setup.py

@@ -11,9 +11,8 @@
 # The full license is in the file LICENSE, distributed with this software.
 #-----------------------------------------------------------------------------
 
-from setuptools import setup, find_packages
+from setuptools import setup
 import os
-import re
 import sys
 
 import versioneer
@@ -44,7 +43,6 @@
     install_requires = spec2nexus.__install_requires__,
     package_dir      = {'': 'src'},
     packages         = ['spec2nexus', 'spec2nexus.plugins', ],
-    #packages=find_packages(),
     package_data     = {
          'spec2nexus': [
             'data/02_03_setup_fly/*',

src/spec2nexus/_version.py

@@ -495,7 +495,7 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split('/'):
+        for _i in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
         return {"version": "0+unknown", "full-revisionid": None,

src/spec2nexus/dev_datafile.py

@@ -14,11 +14,11 @@
 if __name__ == '__main__':
     pwd = os.path.abspath(os.getcwd())
     prefix = os.path.abspath(os.path.join(pwd, 'data', 'APS_spec_data'))
-    file1 = prefix + '.dat'
+    # file1 = prefix + '.dat'
     hfile = prefix + '.hdf5'
-    # lmn40.spe has two header sections, 2nd is just before "#S 8"
-    prefix = os.path.abspath(os.path.join(pwd, 'data', 'lmn40'))
-    file1 = prefix + '.spe'
+    # # lmn40.spe has two header sections, 2nd is just before "#S 8"
+    # prefix = os.path.abspath(os.path.join(pwd, 'data', 'lmn40'))
+    # file1 = prefix + '.spe'
 
     # CdOsO has four header sections and two #S 1 scans
     prefix = os.path.abspath(os.path.join(pwd, 'data', 'CdOsO'))

src/spec2nexus/dev_extractSpecScan.py

@@ -22,7 +22,7 @@
 #args = 'data/APS_spec_data.dat -s 1 6   -c mr USAXS_PD I0 seconds'
 #args = 'data/33id_spec.dat     -s 1 6   -c H K L signal elastic I0 seconds'
 #args = 'data/CdOsO     -s 1 1.1 48   -c HerixE H K L T_control_LS340  T_sample_LS340 ICO-C  PIN-D  PIN-C Seconds'
-args = 'data/02_03_setup.dat     -s 46  1-3   -c ar  ay  dy  Epoch  seconds  I0  USAXS_PD'
+# args = 'data/02_03_setup.dat     -s 46  1-3   -c ar  ay  dy  Epoch  seconds  I0  USAXS_PD'
 # args = 'data/02_03_setup.dat     -s 47   -c mr seconds  I0  USAXS_PD'
 args = 'data/xpcs_plugin_sample.spec  -s 7   -c img_n  Epoch  ccdc'
 

src/spec2nexus/nexus.py

@@ -18,9 +18,8 @@
 
 __url__ = 'http://spec2nexus.readthedocs.org/en/latest/spec2nexus.html'
 
-import os                           #@UnusedImport
-import sys                          #@UnusedImport
-import numpy as np                  #@UnusedImport
+import os
+import sys
 
 if __name__ == "__main__":
     # put us on the path for developers

src/spec2nexus/plugin.py

@@ -44,13 +44,10 @@
 """
 
 
-import os                           #@UnusedImport
-import sys                          #@UnusedImport
-import imp                          #@UnusedImport
-import inspect                      #@UnusedImport
-import pprint                       #@UnusedImport
-import re                           #@UnusedImport
-from spec2nexus.utils import strip_first_word #@UnusedImport
+import os
+import imp
+import inspect
+import re
 
 
 PLUGIN_SEARCH_PATH_ENVIRONMENT_VARIABLE = 'SPEC2NEXUS_PLUGIN_PATH'

src/spec2nexus/plugins/XPCS_spec2nexus.py

@@ -10,10 +10,10 @@
 SPEC data file control lines unique to the APS XPCS instrument
 """
 
-from spec2nexus.plugin import ControlLineHandler, strip_first_word
+from spec2nexus.plugin import ControlLineHandler
 from spec2nexus.eznx import makeGroup
-from spec2nexus.spec import SpecDataFileHeader
-from spec2nexus.spec import SpecDataFileScan
+from spec2nexus.spec import SpecDataFileHeader, SpecDataFileScan
+from spec2nexus.utils import strip_first_word
 
 class XPCS_VA(ControlLineHandler):
     """**#VA**"""

src/spec2nexus/plugins/spec_common_spec2nexus.py

@@ -21,8 +21,6 @@
 
 from collections import OrderedDict
 import datetime
-import re
-import time
 
 from spec2nexus.eznx import write_dataset, makeGroup, openGroup
 from spec2nexus.plugin import ControlLineHandler

src/spec2nexus/scanf.py

@@ -136,7 +136,8 @@ def scanf(fmt, s=None):
     or None if the format does not match.
     """
 
-    if s == None: s = sys.stdin
+    if s is None:
+        s = sys.stdin
     if hasattr(s, "readline"): 
         s = s.readline()
 

src/spec2nexus/spec.py

@@ -114,10 +114,7 @@
 """
 
 from collections import OrderedDict
-import datetime
-import os       #@UnusedImport
-import re       #@UnusedImport
-import sys      #@UnusedImport
+import os
 import time
 from spec2nexus.utils import get_all_plugins
 

src/spec2nexus/specplot.py

@@ -680,7 +680,7 @@ def retrieve_plot_data(self):
         axis1 = self.scan.data.get(label1)
         axis2 = self.scan.data.get(label2)
         intervals1, intervals2 = map(int, (intervals1, intervals2))
-        start1, end1, start2, end2, time = map(float, (start1, end1, start2, end2, time))
+        # unused: start1, end1, start2, end2, time = map(float, (start1, end1, start2, end2, time))
 
         if len(axis1) < intervals1 and min(axis2) == max(axis2):
             # stopped scan before second row started, 1-D plot is better (issue #82)

src/spec2nexus/specplot_gallery.py

@@ -65,6 +65,12 @@
 from spec2nexus import spec
 from spec2nexus import specplot
 
+try:
+    FileNotFoundError
+except NameError:
+    FileNotFoundError = IOError     # py27 compatibility
+
+
 MTIME_CACHE_FILE = 'mtime_cache.txt'
 HTML_INDEX_FILE = 'index.html'
 DOC_URL = 'http://spec2nexus.readthedocs.io/en/latest/specplot_gallery.html'
@@ -139,7 +145,7 @@ def plot_all_scans(self, specFile):
             logger('    mtime_specFile: ' + str(mtime_specFile))
             logger('    mtime_pngdir:   ' + str(mtime_pngdir))
             sd = specplot.openSpecFile(specFile)
-        except:
+        except FileNotFoundError:
             return    # could not open file, be silent about it
         if len(sd.headers) == 0:    # no scan header found, again, silence
             return

src/spec2nexus/uxml/uxml_spec2nexus.py

@@ -82,8 +82,7 @@ class Dataset(object):
 
     def __init__(self, xml_node):
         self.name = xml_node.get('name')
-        ds = eznx.makeDataset(None, self.name, 'test')
-        pass
+        eznx.makeDataset(None, self.name, 'test')
 
 
 class Group(object):
@@ -97,7 +96,6 @@ def __init__(self, xml_node):
 #         group = h5py.Group()
 #         group.create_group(self.name)
         #openGroup(None, self.name, self.NX_class)
-        pass
 
 
 class Hardlink(object):
@@ -156,11 +154,11 @@ def postprocess(self, scan, *args, **kws):
 
     def writer(self, h5parent, writer, scan, *args, **kws):
         """Describe how to store this data in an HDF5 NeXus file"""
-        desc = 'UXML metadata'
+        #desc = 'UXML metadata'
         #eznx.write_dataset(h5parent, "counting_basis", desc)
         #eznx.write_dataset(h5parent, "T", float(scan.T), units='s', description = desc)
         # TODO: parse the XML and store
         selector = dict(dataset=Dataset, group=Group, hardlink=Hardlink)
         for item in scan.UXML_root:
-            obj = selector[item.tag](item)
-            #print item.tag, item.get('name'), obj, obj.name
+            _obj = selector[item.tag](item)
+            #print item.tag, item.get('name'), _obj, obj.name

src/spec2nexus/writer.py

@@ -135,7 +135,7 @@ def root_attributes(self):
             c = header0.comments[0]
             user = c[c.find('User = '):].split('=')[1].strip()
             dd['SPEC_user'] = user
-        except:
+        except Exception:
             pass
         return dd
 
@@ -162,16 +162,19 @@ def save_data(self, nxdata, scan):
         """*internal*: store the scan data"""
         scan_type = scan.scanCmd.split()[0]
 
-        signal, axes = '', ['',]
         if scan_type in ('mesh', 'hklmesh'):
             # hklmesh  H 1.9 2.1 100  K 1.9 2.1 100  -800000
             signal, axes = self.mesh(nxdata, scan)
         elif scan_type in ('hscan', 'kscan', 'lscan', 'hklscan'):
             # hklscan  1.00133 1.00133  1.00133 1.00133  2.85 3.05  200 -400000
             h_0, h_N, k_0, k_N, l_0, l_N = scan.scanCmd.split()[1:7]
-            if   h_0 != h_N: axes = ['H',]
-            elif k_0 != k_N: axes = ['K',]
-            elif l_0 != l_N: axes = ['L',]
+            # TODO: why bother defining axes here?  Not used.  issue #155
+            if h_0 != h_N: 
+                axes = ['H',]
+            elif k_0 != k_N: 
+                axes = ['K',]
+            elif l_0 != l_N: 
+                axes = ['L',]
             signal, axes = self.oneD(nxdata, scan)
         else:
             signal, axes = self.oneD(nxdata, scan)
@@ -234,6 +237,7 @@ def mca_spectra(self, nxdata, scan, primary_axis_label):
                 channels = np.arange(1, len(spectrum[0])+1, dtype=int)
                 _mca_x_ = a + channels * (b + channels * c)
                 self.write_ds(nxdata, ds_name + 'channel_', channels, units = 'channel')
+                self.write_ds(nxdata, ds_name + 'channel_scaled_x', _mca_x_, units = '')
 
     def mesh(self, nxdata, scan):
         """*internal*: data parser for 2-D mesh and hklmesh"""
@@ -245,7 +249,6 @@ def mesh(self, nxdata, scan):
         #  hklmesh Q1 start1 end1 intervals1 Q2 start2 end2 intervals2 time
         # mesh:    data/33id_spec.dat  scan 22
         # hklmesh: data/33bm_spec.dat  scan 17
-        signal, axes = '', ['',]
 
         label1, start1, end1, intervals1, label2, start2, end2, intervals2, time = scan.scanCmd.split()[1:]
         if label1 not in scan.data:
@@ -255,7 +258,7 @@ def mesh(self, nxdata, scan):
         axis1 = scan.data.get(label1)
         axis2 = scan.data.get(label2)
         intervals1, intervals2 = map(int, (intervals1, intervals2))
-        start1, end1, start2, end2, time = map(float, (start1, end1, start2, end2, time))
+        # unused: start1, end1, start2, end2, time = map(float, (start1, end1, start2, end2, time))
         if len(axis1) < intervals1:     # stopped scan before second row started
             signal, axes = self.oneD(nxdata, scan)        # fallback support
         else: