[pre-commit.ci] auto fixes from pre-commit.com hooks

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aiida_fleur/cmdline/launch/launch.py

@@ -155,7 +155,7 @@ def launch_fleur(fleurinp, fleur, parent_folder, settings, daemon, max_num_machi
 
 
 @click.command('scf')
-@options.STRUCTURE_OR_FILE(default="inp.xml", show_default=True)
+@options.STRUCTURE_OR_FILE(default='inp.xml', show_default=True)
 @options.INPGEN()
 @options.CALC_PARAMETERS()
 @options.SETTINGS()
@@ -171,13 +171,13 @@ def launch_scf(structure, inpgen, calc_parameters, fleurinp, fleur, wf_parameter
     """
     Launch a scf workchain
     """
-    fleurinp=None
-    
+    fleurinp = None
+
     if isinstance(structure, FleurinpData):
-        fleurinp=structure
-        structure=None
-        inpgen=None
-    
+        fleurinp = structure
+        structure = None
+        inpgen = None
+
     workchain_class = WorkflowFactory('fleur.scf')
     inputs = {
         'inpgen': inpgen,
@@ -194,26 +194,27 @@ def launch_scf(structure, inpgen, calc_parameters, fleurinp, fleur, wf_parameter
     inputs = clean_nones(inputs)
     builder = workchain_class.get_builder()
     builder.update(inputs)
-    pk=utils.launch_process(builder, daemon)
+    pk = utils.launch_process(builder, daemon)
 
     #Now create output files
     if fleurinp and not daemon:
         from aiida.orm import load_node
-        wf=load_node(pk)
-        scf_output=wf.outputs.output_scf_wc_para.get_dict()
+        wf = load_node(pk)
+        scf_output = wf.outputs.output_scf_wc_para.get_dict()
         #json with dict
         import json
-        with open("scf.json","w") as file:
-            json.dump(scf_output,file,indent=2)
+        with open('scf.json', 'w') as file:
+            json.dump(scf_output, file, indent=2)
         #plot
         from aiida_fleur.tools.plot.fleur import plot_fleur
-        plot_fleur(wf,save=True,show=False)
+        plot_fleur(wf, save=True, show=False)
 
         #store files
-        for file in ["out.xml","cdn1","cdn_last.hdf"]:
+        for file in ['out.xml', 'cdn1', 'cdn_last.hdf']:
             if file in wf.outputs.last_calc.retrieved.list_object_names():
-                with open(file,"wb") as f:
-                    f.write(wf.outputs.last_calc.retrieved.get_object_content(file,"rb"))
+                with open(file, 'wb') as f:
+                    f.write(wf.outputs.last_calc.retrieved.get_object_content(file, 'rb'))
+
 
 @click.command('relax')
 @options.STRUCTURE_OR_FILE(default=defaults.get_si_bulk_structure, show_default=True)
@@ -251,7 +252,7 @@ def launch_relax(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_p
 
 
 @click.command('eos')
-@options.STRUCTURE_OR_FILE(default="inp.xml", show_default=True)
+@options.STRUCTURE_OR_FILE(default='inp.xml', show_default=True)
 @options.INPGEN()
 @options.CALC_PARAMETERS()
 @options.FLEUR()
@@ -266,13 +267,13 @@ def launch_eos(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_par
     """
 
     workchain_class = WorkflowFactory('fleur.eos')
-    
-    fleurinp=None
-    
+
+    fleurinp = None
+
     if isinstance(structure, FleurinpData):
-        fleurinp=structure
-        structure=None
-        
+        fleurinp = structure
+        structure = None
+
     inputs = {
         'scf': {
             'wf_parameters': scf_parameters,
@@ -288,34 +289,34 @@ def launch_eos(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_par
     inputs = clean_nones(inputs)
     builder = workchain_class.get_builder()
     builder.update(inputs)
-    pk=utils.launch_process(builder, daemon)
+    pk = utils.launch_process(builder, daemon)
 
     #Now create output files
     if fleurinp and not daemon:
         from aiida.orm import load_node
-        wf=load_node(pk)
-        eos_output=wf.outputs.output_eos_wc_para.get_dict()
+        wf = load_node(pk)
+        eos_output = wf.outputs.output_eos_wc_para.get_dict()
         #json with dict
         import json
-        with open("eos.json","w") as file:
-            json.dump(eos_output,file,indent=2)
+        with open('eos.json', 'w') as file:
+            json.dump(eos_output, file, indent=2)
         #cif file
-        if "output_eos_wc_structure" in wf.outputs:
+        if 'output_eos_wc_structure' in wf.outputs:
             import os.path
-            if os.path.isfile("opt_struct.cif"): os.remove("opt_struct.cif")    
-            cif_struct=wf.outputs.output_eos_wc_structure.get_cif()
-            cif_struct.export("opt_struct.cif")
+            if os.path.isfile('opt_struct.cif'):
+                os.remove('opt_struct.cif')
+            cif_struct = wf.outputs.output_eos_wc_structure.get_cif()
+            cif_struct.export('opt_struct.cif')
         #plot
-        if eos_output["volume_gs"] >0 :
+        if eos_output['volume_gs'] > 0:
             from aiida_fleur.tools.plot.fleur import plot_fleur
-            plot_fleur(wf,save=True,show=False)
-
-        for i,uuid in enumerate(eos_output["calculations"]):
-            scf=load_node(uuid)
-            scale=eos_output["scaling"][i]
-            with open(f"out_{scale}.xml","w") as f:
-                f.write(scf.outputs.last_calc.retrieved.get_object_content("out.xml"))
+            plot_fleur(wf, save=True, show=False)
 
+        for i, uuid in enumerate(eos_output['calculations']):
+            scf = load_node(uuid)
+            scale = eos_output['scaling'][i]
+            with open(f"out_{scale}.xml", 'w') as f:
+                f.write(scf.outputs.last_calc.retrieved.get_object_content('out.xml'))
 
 
 @click.command('banddos')

aiida_fleur/cmdline/util/types.py

@@ -37,11 +37,11 @@ def convert(self, value, param, ctx):
         # aiida allows also for shorten uuids
         from aiida.orm import StructureData, QueryBuilder
 
-        if value in ["inp.xml",".",'./']:
+        if value in ['inp.xml', '.', './']:
             from aiida_fleur.data.fleurinp import FleurinpData
-            inp_files=["inp.xml"]
+            inp_files = ['inp.xml']
             #check if there are included files in this dir
-            for file in ["kpts.xml","sym.xml","relax.xml"]:
+            for file in ['kpts.xml', 'sym.xml', 'relax.xml']:
                 import os.path
                 if os.path.isfile(file):
                     inp_files.append(file)

aiida_fleur/cmdline/util/utils.py

@@ -63,4 +63,4 @@ def launch_process(process, daemon, **inputs):
         _, node = launch.run_get_node(process, **inputs)
         echo_process_results(node)
 
-    return node.pk    
+    return node.pk

aiida_fleur/cmdline/workflows/__init__.py

@@ -28,8 +28,9 @@ def cmd_workflow():
 
 
 @cmd_workflow.command('res')
-@arguments.PROCESS('process', type=ProcessParamType()
-                   )  #, type=WorkflowParamType(sub_classes=('aiida.node:process.workflow.workchain',)))
+@arguments.PROCESS(
+    'process',
+    type=ProcessParamType())  #, type=WorkflowParamType(sub_classes=('aiida.node:process.workflow.workchain',)))
 @click.option('--info/--no-info', default=False, help='Print an info header above each node.')
 @click.option('-l', '--label', 'label', type=str, help='Print only output dicts with a certain link_label.')
 @options_fl.SHOW()
@@ -69,8 +70,9 @@ def workchain_res(process, info, label, show, keys, fmt):
 
 
 @cmd_workflow.command('inputdict')
-@arguments.PROCESS('process', type=ProcessParamType()
-                   )  #, type=WorkflowParamType(sub_classes=('aiida.node:process.workflow.workchain',)))
+@arguments.PROCESS(
+    'process',
+    type=ProcessParamType())  #, type=WorkflowParamType(sub_classes=('aiida.node:process.workflow.workchain',)))
 @click.option('--info/--no-info', default=False, help='Print an info header above each node.')
 @click.option('-l', '--label', 'label', type=str, help='Print only output dicts with a certain link_label.')
 @options_fl.SHOW()

aiida_fleur/parsers/fleur.py

@@ -131,23 +131,23 @@ def parse(self, **kwargs):
 
         # Open log-file as well
         try:
-            run_was_successful="finished successfully" in error_file_lines
+            run_was_successful = 'finished successfully' in error_file_lines
         except:
-            run_was_successful=False    
+            run_was_successful = False
         if FleurCalculation._LOG_FILE_NAME in list_of_files:
             logfile = FleurCalculation._LOG_FILE_NAME
             # read
             import json
             try:
                 with output_folder.open(logfile, 'r') as efile:
                     log_file_entries = json.load(efile)
-                    run_was_successful="Success" in log_file_entries[-1]
+                    run_was_successful = 'Success' in log_file_entries[-1]
             except OSError:
                 self.logger.error(f'Failed to open log file: {logfile}.')
                 return self.exit_codes.ERROR_OPENING_OUTPUTS
             except json.JSONDecodeError:
-                self.logger.error("logfile not correctly formatted")
-                
+                self.logger.error('logfile not correctly formatted')
+
         #Now check for different kind of errors
         if not run_was_successful:
             self.logger.warning('The following was written into std error and piped to {}'
@@ -159,8 +159,7 @@ def parse(self, **kwargs):
 
             kb_used = 0.0
             if has_xml_outfile:
-                with output_folder.open(FleurCalculation._OUTXML_FILE_NAME,
-                                        'r') as out_file:  # lazy out.xml parsing
+                with output_folder.open(FleurCalculation._OUTXML_FILE_NAME, 'r') as out_file:  # lazy out.xml parsing
                     outlines = out_file.read()
                     try:
                         line_avail = re.findall(r'<mem memoryPerNode="\d+', outlines)[0]

aiida_fleur/tools/StructureData_util.py

@@ -1674,7 +1674,7 @@ def request_average_bond_length(first_bin, second_bin, user_api_key, ignore_seco
     from collections import defaultdict
     from copy import deepcopy
 
-    bond_data = defaultdict(lambda: defaultdict(lambda: 0.0))
+    bond_data = defaultdict(lambda: defaultdict(float))
     if ignore_second_bin:
         symbols = first_bin
         second_bin_calculate = first_bin