Fix "Avoid mutable default arguments" issue

.landscape.yml

@@ -1,8 +1,9 @@
 doc-warnings: true
 test-warnings: no
-strictness: medium
+strictness: high
 autodetect: yes
 ignore-patterns:
+    - */__init__.py
     - examples/*
     - test/*
     - docs/*

pycbc/fft/fft_callback.py

@@ -199,9 +199,11 @@ def compile(source, name):
     fhash.write(str(hash(source)))
     return lib_file
 
-def get_fn_plan(callback=None, out_callback=None, name='pycbc_cufft', parameters=[]):
+def get_fn_plan(callback=None, out_callback=None, name='pycbc_cufft', parameters=None):
     """ Get the IFFT execute and plan functions
     """
+    if parameters is None:
+        parameters = []
     source = fftsrc.render(input_callback=callback, output_callback=out_callback, parameters=parameters)
     path = compile(source, name)
     lib = ctypes.cdll.LoadLibrary(path)

pycbc/io/record.py

@@ -1146,12 +1146,14 @@ def default_fields(cls, include_virtual=True, **kwargs):
         return dict(cls._staticfields.items() + add_fields.items())
 
 
-    def __new__(cls, shape, name=None, additional_fields=None, field_kwargs={},
+    def __new__(cls, shape, name=None, additional_fields=None, field_kwargs=None,
             **kwargs):
         """The ``additional_fields`` should be specified in the same way as
         ``dtype`` is normally given to FieldArray. The ``field_kwargs`` are
         passed to the class's default_fields method as keyword arguments.
         """
+        if field_kwargs is None:
+            field_kwargs = {}
         if 'names' in kwargs and 'dtype' in kwargs:
             raise ValueError("Please provide names or dtype, not both")
         default_fields = cls.default_fields(include_virtual=False,

pycbc/results/metadata.py

@@ -94,7 +94,7 @@ def load_png_metadata(filename):
                     '.html':load_html_metadata,
                    }
 
-def save_fig_with_metadata(fig, filename, fig_kwds={}, **kwds):
+def save_fig_with_metadata(fig, filename, fig_kwds=None, **kwds):
     """ Save plot to file with metadata included. Kewords translate to metadata
     that is stored directly in the plot file. Limited format types available.
 
@@ -105,6 +105,8 @@ def save_fig_with_metadata(fig, filename, fig_kwds={}, **kwds):
     filename: str
         Name of file to store the plot.
     """
+    if fig_kwds is None:
+        fig_kwds = {}
     try:
         extension = os.path.splitext(filename)[1]
         kwds['version'] = pycbc.version.git_verbose_msg

pycbc/tmpltbank/bank_output_utils.py

@@ -43,7 +43,7 @@ def return_empty_sngl():
     return sngl
 
 def return_search_summary(start_time=0, end_time=0, nevents=0,
-                          ifos=[], **kwargs):
+                          ifos=None, **kwargs):
     """
     Function to create a SearchSummary object where all columns are populated
     but all are set to values that test False (ie. strings to '', floats/ints
@@ -59,6 +59,8 @@ def return_search_summary(start_time=0, end_time=0, nevents=0,
     lsctables.SeachSummary
         The "empty" SearchSummary object.
     """
+    if ifos is None:
+        ifos = []
 
     # create an empty search summary
     search_summary = lsctables.SearchSummary()
@@ -283,7 +285,7 @@ def calculate_ethinca_metric_comps(metricParams, ethincaParams, mass1, mass2,
     return fMax_theor, gammaVals
 
 def output_sngl_inspiral_table(outputFile, tempBank, metricParams,
-                               ethincaParams, programName="", optDict = {},
+                               ethincaParams, programName="", optDict = None,
                                outdoc=None, **kwargs):
     """
     Function that converts the information produced by the various pyCBC bank
@@ -317,6 +319,8 @@ def output_sngl_inspiral_table(outputFile, tempBank, metricParams,
         All other key word arguments will be passed directly to 
         ligolw_process.register_to_xmldoc
     """
+    if optDict is None:
+        optDict = {}
     if outdoc is None:
         outdoc = ligolw.Document()
         outdoc.appendChild(ligolw.LIGO_LW())

pycbc/workflow/coincidence.py

@@ -57,7 +57,9 @@ class PyCBCFindCoincExecutable(Executable):
     """ Find coinc triggers using a folded interval method
     """
     current_retention_level = Executable.ALL_TRIGGERS
-    def create_node(self, trig_files, bank_file, veto_file, veto_name, template_str, tags=[]):
+    def create_node(self, trig_files, bank_file, veto_file, veto_name, template_str, tags=None):
+        if tags is None:
+            tags = []
         segs = trig_files.get_times_covered_by_files()
         seg = segments.segment(segs[0][0], segs[-1][1])
         node = Node(self)
@@ -75,7 +77,9 @@ class PyCBCStatMapExecutable(Executable):
     """ Calculate FAP, IFAR, etc
     """
     current_retention_level = Executable.MERGED_TRIGGERS
-    def create_node(self, coinc_files, tags=[]):
+    def create_node(self, coinc_files, tags=None):
+        if tags is None:
+            tags = []
         segs = coinc_files.get_times_covered_by_files()
         seg = segments.segment(segs[0][0], segs[-1][1])
 
@@ -89,7 +93,9 @@ class PyCBCStatMapInjExecutable(Executable):
     """ Calculate FAP, IFAR, etc
     """
     current_retention_level = Executable.MERGED_TRIGGERS
-    def create_node(self, zerolag, full_data, injfull, fullinj, tags=[]):
+    def create_node(self, zerolag, full_data, injfull, fullinj, tags=None):
+        if tags is None:
+            tags = []
         segs = zerolag.get_times_covered_by_files()
         seg = segments.segment(segs[0][0], segs[-1][1])
 
@@ -106,7 +112,9 @@ class PyCBCHDFInjFindExecutable(Executable):
     """ Find injections in the hdf files output
     """
     current_retention_level = Executable.MERGED_TRIGGERS
-    def create_node(self, inj_coinc_file, inj_xml_file, veto_file, veto_name, tags=[]):
+    def create_node(self, inj_coinc_file, inj_xml_file, veto_file, veto_name, tags=None):
+        if tags is None:
+            tags = []
         node = Node(self)        
         node.add_input_list_opt('--trigger-file', inj_coinc_file)
         node.add_input_list_opt('--injection-file', inj_xml_file)
@@ -120,7 +128,9 @@ def create_node(self, inj_coinc_file, inj_xml_file, veto_file, veto_name, tags=[
 class PyCBCDistributeBackgroundBins(Executable):
     """ Distribute coinc files amoung different background bins """
     current_retention_level = Executable.ALL_TRIGGERS
-    def create_node(self, coinc_files, bank_file, background_bins, tags=[]):
+    def create_node(self, coinc_files, bank_file, background_bins, tags=None):
+        if tags is None:
+            tags = []
         node = Node(self)
         node.add_input_list_opt('--coinc-files', coinc_files)
         node.add_input_opt('--bank-file', bank_file)
@@ -140,7 +150,9 @@ def create_node(self, coinc_files, bank_file, background_bins, tags=[]):
 
 class PyCBCCombineStatmap(Executable):
     current_retention_level = Executable.MERGED_TRIGGERS
-    def create_node(self, stat_files, tags=[]):
+    def create_node(self, stat_files, tags=None):
+        if tags is None:
+            tags = []
         node = Node(self)
         node.add_input_list_opt('--statmap-files', stat_files)
         node.new_output_file_opt(stat_files[0].segment, '.hdf', '--output-file', tags=tags)
@@ -165,7 +177,9 @@ def make_foreground_censored_veto(workflow, bg_file, veto_file, veto_name,
     workflow += node
     return node.output_files[0]
 
-def merge_single_detector_hdf_files(workflow, bank_file, trigger_files, out_dir, tags=[]):
+def merge_single_detector_hdf_files(workflow, bank_file, trigger_files, out_dir, tags=None):
+    if tags is None:
+        tags = []
     make_analysis_dir(out_dir)
     out = FileList()
     for ifo in workflow.ifos:
@@ -179,7 +193,9 @@ def merge_single_detector_hdf_files(workflow, bank_file, trigger_files, out_dir,
     return out
 
 def find_injections_in_hdf_coinc(workflow, inj_coinc_file, inj_xml_file, 
-                                 veto_file, veto_name, out_dir, tags=[]):
+                                 veto_file, veto_name, out_dir, tags=None):
+    if tags is None:
+        tags = []
     make_analysis_dir(out_dir)
     exe = PyCBCHDFInjFindExecutable(workflow.cp, 'hdfinjfind', 
                                     ifos=workflow.ifos, 
@@ -188,9 +204,11 @@ def find_injections_in_hdf_coinc(workflow, inj_coinc_file, inj_xml_file,
     workflow += node
     return node.output_files[0]     
 
-def convert_bank_to_hdf(workflow, xmlbank, out_dir, tags=[]):
+def convert_bank_to_hdf(workflow, xmlbank, out_dir, tags=None):
     """Return the template bank in hdf format
     """
+    if tags is None:
+        tags = []
     #FIXME, make me not needed
     if len(xmlbank) > 1:
         raise ValueError('Can only convert a single template bank')
@@ -204,9 +222,11 @@ def convert_bank_to_hdf(workflow, xmlbank, out_dir, tags=[]):
     workflow.add_node(bank2hdf_node)
     return bank2hdf_node.output_files
 
-def convert_trig_to_hdf(workflow, hdfbank, xml_trigger_files, out_dir, tags=[]):
+def convert_trig_to_hdf(workflow, hdfbank, xml_trigger_files, out_dir, tags=None):
     """Return the list of hdf5 trigger files outpus
     """
+    if tags is None:
+        tags = []
     #FIXME, make me not needed
     logging.info('convert single inspiral trigger files to hdf5')
     make_analysis_dir(out_dir)
@@ -325,11 +345,13 @@ def setup_background_bins_inj(workflow, coinc_files, background_file, bank_file,
     return cstat_node.output_files[0]
 
 def setup_interval_coinc_inj(workflow, hdfbank, full_data_trig_files, inj_trig_files,
-                           background_file, veto_file, veto_name, out_dir, tags=[]):
+                           background_file, veto_file, veto_name, out_dir, tags=None):
     """
     This function sets up exact match coincidence and background estimation
     using a folded interval technique.
     """
+    if tags is None:
+        tags = []
     make_analysis_dir(out_dir)
     logging.info('Setting up coincidence for injection')
 
@@ -374,11 +396,13 @@ def setup_interval_coinc_inj(workflow, hdfbank, full_data_trig_files, inj_trig_f
     return setup_statmap_inj(workflow, bg_files, background_file, hdfbank, out_dir, tags=tags)
 
 def setup_interval_coinc(workflow, hdfbank, trig_files,
-                         veto_files, veto_names, out_dir, tags=[]):
+                         veto_files, veto_names, out_dir, tags=None):
     """
     This function sets up exact match coincidence and background estimation
     using a folded interval technique.
     """
+    if tags is None:
+        tags = []
     make_analysis_dir(out_dir)
     logging.info('Setting up coincidence')
 

pycbc/workflow/configuration.py

@@ -138,7 +138,7 @@ class WorkflowConfigParser(glue.pipeline.DeepCopyableConfigParser):
     This is a sub-class of glue.pipeline.DeepCopyableConfigParser, which lets
     us add a few additional helper features that are useful in workflows.
     """
-    def __init__(self, configFiles=[], overrideTuples=[], parsedFilePath=None):
+    def __init__(self, configFiles=None, overrideTuples=None, parsedFilePath=None):
         """
         Initialize an WorkflowConfigParser. This reads the input configuration
         files, overrides values if necessary and performs the interpolation.
@@ -160,6 +160,10 @@ def __init__(self, configFiles=[], overrideTuples=[], parsedFilePath=None):
         WorkflowConfigParser
             Initialized WorkflowConfigParser instance.
         """
+        if configFiles is None:
+            configFiles = []
+        if overrideTuples is None:
+            overrideTuples = []
         glue.pipeline.DeepCopyableConfigParser.__init__(self)
 
         # Enable case sensitive options

pycbc/workflow/core.py

@@ -123,7 +123,7 @@ class Executable(pegasus_workflow.Executable):
     # file will be retained, but a warning given
     current_retention_level = KEEP_BUT_RAISE_WARNING
     def __init__(self, cp, name, 
-                       universe=None, ifos=None, out_dir=None, tags=[]):
+                       universe=None, ifos=None, out_dir=None, tags=None):
         """
         Initialize the Executable class.
 
@@ -146,6 +146,8 @@ def __init__(self, cp, name,
         tags : list of strings
             A list of strings that is used to identify this job.
         """
+        if tags is None:
+            tags = []
         tags = [tag.upper() for tag in tags]
         self.tags = tags
         if isinstance(ifos, (str, unicode)):
@@ -559,7 +561,7 @@ def get_command_line(self):
 
         return [exe_path] + arglist
 
-    def new_output_file_opt(self, valid_seg, extension, option_name, tags=[],
+    def new_output_file_opt(self, valid_seg, extension, option_name, tags=None,
                             store_file=None, use_tmp_subdirs=False):
         """
         This function will create a workflow.File object corresponding to the given
@@ -584,6 +586,8 @@ def new_output_file_opt(self, valid_seg, extension, option_name, tags=[],
             in the specified output location if True. If false file will be
             removed when no longer needed in the workflow.
         """
+        if tags is None:
+            tags = []
 
         # Changing this from set(tags) to enforce order. It might make sense
         # for all jobs to have file names with tags in the same order.
@@ -634,14 +638,16 @@ def add_multiifo_output_list_opt(self, opt, outputs):
             self._add_output(outfile)
 
     def new_multiifo_output_list_opt(self, opt, ifos, analysis_time, extension,
-                                     tags=[], store_file=None,
+                                     tags=None, store_file=None,
                                      use_tmp_subdirs=False):
         """ Add an option that determines a list of outputs from multiple
             detectors. Files will be supplied as --opt ifo1:input1 ifo2:input2
             .....
             File names are created internally from the provided extension and
             analysis time.
         """
+        if tags is None:
+            tags = []
         all_tags = copy.deepcopy(self.executable.tags)
         for tag in tags:
             if tag not in all_tags:

pycbc/workflow/gatefiles.py

@@ -36,7 +36,7 @@
 from pycbc.workflow.core import File, FileList, make_analysis_dir, resolve_url
 
 def setup_gating_workflow(workflow, science_segs, datafind_outs,
-                             output_dir=None, tags=[]):
+                             output_dir=None, tags=None):
     '''
     Setup gating section of CBC workflow. At present this only supports pregenerated
     gating files, in the future these could be created within the workflow.
@@ -61,6 +61,8 @@ def setup_gating_workflow(workflow, science_segs, datafind_outs,
     gate_files : pycbc.workflow.core.FileList
         The FileList holding the gate files, 0 or 1 per ifo
     '''
+    if tags is None:
+        tags = []
     logging.info("Entering gating module.")
     make_analysis_dir(output_dir)
     cp = workflow.cp
@@ -86,7 +88,7 @@ def setup_gating_workflow(workflow, science_segs, datafind_outs,
     return gate_files
 
 
-def setup_gate_pregenerated(workflow, tags=[]):
+def setup_gate_pregenerated(workflow, tags=None):
     '''
     Setup CBC workflow to use pregenerated gating files.
     The file given in cp.get('workflow','pregenerated-gating-file-(ifo)') will 
@@ -105,6 +107,8 @@ def setup_gate_pregenerated(workflow, tags=[]):
     gate_files : pycbc.workflow.core.FileList
         The FileList holding the gating files
     '''
+    if tags is None:
+        tags = []
     gate_files = FileList([])
 
     cp = workflow.cp

pycbc/workflow/grb_utils.py

@@ -199,7 +199,7 @@ def make_exttrig_file(cp, ifos, sci_seg, out_dir):
     return xml_file
 
 
-def get_ipn_sky_files(workflow, tags=[]):
+def get_ipn_sky_files(workflow, tags=None):
     '''
     Retreive the sky point files for searching over the IPN error box and
     populating it with injections.
@@ -219,6 +219,8 @@ def get_ipn_sky_files(workflow, tags=[]):
     ipn_files : pycbc.workflow.core.FileList
         FileList holding the details of the IPN sky point files.
     '''
+    if tags is None:
+        tags = []
     cp = workflow.cp
     ipn_search_points = cp.get("workflow-inspiral", "ipn-search-points")
     ipn_search_points = resolve_url(ipn_search_points)

pycbc/workflow/injection.py

@@ -77,7 +77,7 @@ def cut_distant_injections(workflow, inj_file, out_dir, tags=None):
 
 def setup_injection_workflow(workflow, output_dir=None,
                              inj_section_name='injections', exttrig_file=None,
-                             tags =[]):
+                             tags =None):
     """
     This function is the gateway for setting up injection-generation jobs in a
     workflow. It should be possible for this function to support a number
@@ -109,6 +109,8 @@ def setup_injection_workflow(workflow, output_dir=None,
         identify them. The FileList class contains functions to search
         based on tags.
     """
+    if tags is None:
+        tags = []
     logging.info("Entering injection module.")
     make_analysis_dir(output_dir)