Fix 2 bugs, rename tilde.sh to tilde, refactor

Author: blokhin

README.md

@@ -25,27 +25,27 @@ Run ```pip install -r requirements.txt``` to install Python dependencies.
 Finally, ensure if the framework is ready:
 
 ```shell
-./utils/tilde.sh -x
+./utils/tilde -x
 ```
 
 Additionally, installation is covered in [this blog post](https://blog.tilde.pro/simple-ab-initio-materials-data-mining-tutorial-6127c777dabc).
 
 ## Usage
 
 ```shell
-./utils/tilde.sh --help
+./utils/tilde --help
 ```
 
 For example, to scan folder(s) recursively (**-r**), with terse print (**-t**), showing information on calculation metadata (**-i**) and convergence (**-v**) and adding results to a database (**-a**):
 
 ```shell
-./utils/tilde.sh /home/user/work1 /home/work2 -r -t -v -a -i
+./utils/tilde /home/user/work1 /home/work2 -r -t -v -a -i
 ```
 
 Other example: for the perovskite structures (shipped with Tilde), extract the distortion of the MO6-octahedra wrt cubic phase (in Euler angles). Here the **-m** switch invokes **perovskite_tilting** module (see **apps** folder):
 
 ```shell
-./utils/tilde.sh tilde/tests/apps/perovskite_tilting/outputs -m perovskite_tilting
+./utils/tilde tilde/tests/apps/perovskite_tilting/outputs -m perovskite_tilting
 ```
 
 ## GUI

setup.py

@@ -66,12 +66,12 @@
     'futures',
     'httplib2',
     'quantum_esperanto',
-    'pycrystal'
+    'pycrystal >= 1.0.2'
 ]
 
 setup(
     name='tilde',
-    version='0.9.2',
+    version='0.9.3',
     description='Materials informatics framework for ab initio data repositories',
     long_description=long_description,
     url='https://github.com/tilde-lab/tilde',
@@ -87,10 +87,10 @@
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7'
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8'
     ],
     keywords='CRYSTAL Quantum-ESPRESSO VASP ab-initio materials informatics first-principles',
     packages=packages,
@@ -99,7 +99,8 @@
     tests_require= ['nose',],
     test_suite='nose.collector',
     scripts=[
-        "utils/tilde.sh",
-        "utils/entry.py"
+        "utils/tilde",
+        "utils/entry.py",
+        "utils/gui_server.py"
     ]
 )

tilde/core/common.py

@@ -117,6 +117,7 @@ def cmp_e_conv(vals):
 
 def generate_cif(structure, comment=None, symops=['+x,+y,+z']):
     parameters = cell_to_cellpar(structure.cell)
+
     cif_data = "# " + comment + "\n\n" if comment else ''
     cif_data += 'data_tilde_project\n'
     cif_data += '_cell_length_a    ' + "%2.6f" % parameters[0] + "\n"
@@ -125,19 +126,21 @@ def generate_cif(structure, comment=None, symops=['+x,+y,+z']):
     cif_data += '_cell_angle_alpha ' + "%2.6f" % parameters[3] + "\n"
     cif_data += '_cell_angle_beta  ' + "%2.6f" % parameters[4] + "\n"
     cif_data += '_cell_angle_gamma ' + "%2.6f" % parameters[5] + "\n"
-    cif_data += "_symmetry_space_group_name_H-M 'P1'" + "\n"
+    cif_data += "_symmetry_space_group_name_H-M 'P1'" + "\n\n"
     cif_data += 'loop_' + "\n"
     cif_data += '_symmetry_equiv_pos_as_xyz' + "\n"
     for i in symops:
         cif_data += i + "\n"
-    cif_data += 'loop_' + "\n"
+
+    cif_data += '\nloop_' + "\n"
+    cif_data += '_atom_site_label' + "\n"
     cif_data += '_atom_site_type_symbol' + "\n"
     cif_data += '_atom_site_fract_x' + "\n"
     cif_data += '_atom_site_fract_y' + "\n"
     cif_data += '_atom_site_fract_z' + "\n"
     pos = structure.get_scaled_positions()
     for n, i in enumerate(structure):
-        cif_data += "%s   % 1.8f   % 1.8f   % 1.8f\n" % (i.symbol, pos[n][0], pos[n][1], pos[n][2])
+        cif_data += "%s   %s   % 1.8f   % 1.8f   % 1.8f\n" % (i.symbol, i.symbol, pos[n][0], pos[n][1], pos[n][2])
     return cif_data
 
 def generate_xyz(atoms):

tilde/core/settings.py

@@ -101,7 +101,7 @@ def connect_database(settings, named=None, no_pooling=False, default_actions=Tru
                 sys.exit(INIT_DATA + ' not found!')
 
             f = open(INIT_DATA)
-            statements = filter(None, f.read().splitlines())
+            statements = list(filter(None, f.read().splitlines()))
             f.close()
 
             nlines = 0

tilde/parsers/CRYSTAL/CRYSTAL.py

@@ -41,7 +41,8 @@ def __init__(self, filename):
         elif filename.endswith('.out'):
             check_files = [filename.replace('.out', '') + '.d12', filename.replace('.out', '') + '.gui']
         for check in check_files:
-            if os.path.exists(os.path.join(cur_folder, check)): self.related_files.append(os.path.join(cur_folder, check))
+            if os.path.exists(os.path.join(cur_folder, check)):
+                self.related_files.append(os.path.join(cur_folder, check))
 
     @staticmethod
     def fingerprints(test_string):

utils/entry.py

@@ -71,14 +71,17 @@
 if args.path or args.targetlist:
     finalized = 'YES' if settings['skip_unfinished'] else 'NO'
     notests = 'YES' if settings['skip_notenergy'] else 'NO'
-    print("Only finalized: %s; only with total energy: %s; skip paths if they start/end with any of: %s" % (finalized, notests, settings['skip_if_path']))
+    print("Only finalized: %s; only with total energy: %s; skip paths if they start/end with any of: %s" %
+        (finalized, notests, settings['skip_if_path'])
+    )
 
     if args.path and args.targetlist:
         args.targetlist = None
     if args.path:
         target_source = args.path
     if args.targetlist:
-        if not os.path.exists(args.targetlist): sys.exit("Incorrect file: %s" % args.targetlist)
+        if not os.path.exists(args.targetlist):
+            sys.exit("Incorrect file: %s" % args.targetlist)
         target_source = (ln.strip() for ln in open(args.targetlist))
 
 # -x option
@@ -100,7 +103,8 @@
             output_lines, add_msg = '', ''
 
             if error:
-                if args.terse and 'was read' in error: continue
+                if args.terse and 'was read' in error:
+                    continue
                 print(task, error)
                 logging.info("%s %s" % (task, error))
                 continue
@@ -119,16 +123,23 @@
                 found_topics = []
                 skip_topics = ['location', 'elements', 'nelem', 'natom', 'spg']
                 for n, entity in enumerate(work.hierarchy):
-                    if entity['cid'] > 1999 or entity['source'] in skip_topics: continue # apps hierarchy
+                    if entity['cid'] > 1999 or entity['source'] in skip_topics:
+                        continue # apps hierarchy
 
                     if entity['multiple']:
-                        try: found_topics.append(
-                            [entity['category']] + [num2name(x, entity, work.hierarchy_values) for x in calc.info[ entity['source'] ]]
-                        )
-                        except KeyError: pass
+                        try:
+                            found_topics.append(
+                                [entity['category']] + [num2name(x, entity, work.hierarchy_values) for x in calc.info[ entity['source'] ]]
+                            )
+                        except KeyError:
+                            pass
                     else:
-                        try: found_topics.append( [entity['category'], num2name(calc.info.get(entity['source']), entity, work.hierarchy_values)] )
-                        except KeyError: pass
+                        try:
+                            found_topics.append(
+                                [entity['category'], num2name(calc.info.get(entity['source']), entity, work.hierarchy_values)]
+                            )
+                        except KeyError:
+                            pass
 
                 j, out = 0, ''
                 for t in found_topics:
@@ -143,9 +154,16 @@
                     output_lines += str(calc.convergence) + "\n"
                 if calc.tresholds:
                     for i in range(len(calc.tresholds)):
-                        try: ncycles = calc.ncycles[i]
-                        except IndexError: ncycles = ""
-                        output_lines += "%1.2e" % calc.tresholds[i][0] + " "*2 + "%1.5f" % calc.tresholds[i][1] + " "*2 + "%1.4f" % calc.tresholds[i][2] + " "*2 + "%1.4f" % calc.tresholds[i][3] + " "*2 + "E=" + "%1.4f" % calc.tresholds[i][4] + " eV" + " "*2 + "(%s)" % ncycles + "\n"
+                        try:
+                            ncycles = calc.ncycles[i]
+                        except IndexError:
+                            ncycles = "^"
+                        output_lines += "%1.2e" % calc.tresholds[i][0] + " " * 2 + \
+                                        "%1.5f" % calc.tresholds[i][1] + " " * 2 + \
+                                        "%1.4f" % calc.tresholds[i][2] + " " * 2 + \
+                                        "%1.4f" % calc.tresholds[i][3] + " " * 2 + \
+                                        "E=" + ("%1.4f" % calc.tresholds[i][4] if calc.tresholds[i][4] else "^") + " eV" + " " * 2 + \
+                                        "(%s)" % ncycles + "\n"
 
             # -s option
             if args.structures:
@@ -160,8 +178,10 @@
 
             # -c option
             if args.cif:
-                try: calc.structures[ args.cif ]
-                except IndexError: output_lines += "Warning! Structure "+args.cif+" not found!" + "\n"
+                try:
+                    calc.structures[args.cif]
+                except IndexError:
+                    output_lines += "Warning! Structure " + args.cif + " not found!" + "\n"
                 else:
                     N = args.cif if args.cif > 0 else len(calc.structures) + 1 + args.cif
                     comment = calc.info['formula'] + " extracted from " + task + " (structure N " + str(N) + ")"
@@ -173,7 +193,7 @@
 
             # -m option
             if args.module:
-                if args.module == True:
+                if args.module is True:
                     calc = work.postprocess(calc, dry_run=True)
                     output_lines += "Modules to be invoked: " + str([i for i in calc.apps]) + "\n"
                 else: