orto 1.0.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.0.0'
+__version__ = '1.0.1'

orto/cli.py

@@ -1,23 +1,21 @@
 import argparse
 import xyz_py as xyzp
-import xyz_py.atomic as atomic
-import matplotlib.pyplot as plt
-import matplotlib as mpl
+from xyz_py.atomic import elements as atomic_elements
 import sys
 import pathlib
 import os
 import copy
 import subprocess
-import pandas as pd
+from pandas import read_csv
 import scipy.constants as constants
 import numpy as np
-import extto
-import docx
+from extto import DataNotFoundError
 import re
-import mmap
-import shutil
+from mmap import mmap, ACCESS_READ
+from shutil import move as shutilmove
 
 
+from docx import Document
 from docx.enum.text import WD_ALIGN_PARAGRAPH
 from docx.enum.table import WD_ALIGN_VERTICAL
 from docx.shared import Pt
@@ -28,17 +26,6 @@ from . import job
 from . import utils as ut
 from . import input as inp
 
-# Change matplotlib font size to be larger
-mpl.rcParams.update({'font.size': 12})
-
-# Set user specified font name
-if os.getenv('orto_fontname'):
-    try:
-        plt.rcParams['font.family'] = os.getenv('orto_fontname')
-    except ValueError:
-        ut.cprint('Error in orto_fontname environment variable', 'red')
-        sys.exit(1)
-
 _SHOW_CONV = {
     'on': True,
     'save': False,
@@ -126,7 +113,7 @@ def extract_sf_energies_func(uargs):
         title = 'Spin-Free energies'
 
         # Create document
-        doc = docx.Document()
+        doc = Document()
 
         doc.add_heading(title, 0)
 
@@ -261,7 +248,7 @@ def extract_gmatrix_func(uargs, save=True):
         title = titles[uargs.type]
 
         # Create document
-        doc = docx.Document()
+        doc = Document()
 
         doc.add_heading(title, 0)
 
@@ -357,12 +344,12 @@ def gen_trunc_molden_func(uargs):
     # occurrences of 'Occup='
     _patt = re.compile(b'Sym=')
     with open(uargs.input_file, mode="r") as file_obj:
-        with mmap.mmap(file_obj.fileno(), length=0, access=mmap.ACCESS_READ) as mmap_obj: # noqa
+        with mmap(file_obj.fileno(), length=0, access=ACCESS_READ) as mmap_obj:
             n_MO = len(_patt.findall(mmap_obj))
 
     _patt = re.compile(b'Occup= 0.000000')
     with open(uargs.input_file, mode="r") as file_obj:
-        with mmap.mmap(file_obj.fileno(), length=0, access=mmap.ACCESS_READ) as mmap_obj: # noqa
+        with mmap(file_obj.fileno(), length=0, access=ACCESS_READ) as mmap_obj:
             n_virt = len(_patt.findall(mmap_obj))
 
     ut.cprint(
@@ -399,7 +386,7 @@ def gen_trunc_molden_func(uargs):
     # If no output file given
     if uargs.output_file == '.tmp.molden':
         # Copy new file to original name
-        shutil.move(uargs.output_file, uargs.input_file)
+        shutilmove(uargs.output_file, uargs.input_file)
         uargs.output_file = uargs.input_file
 
     ut.cprint(f'New molden file written to {uargs.output_file}', 'cyan')
@@ -554,6 +541,19 @@ def plot_abs_func(uargs):
     -------
     None
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+
+    # Set user specified font name
+    if os.getenv('orto_fontname'):
+        try:
+            plt.rcParams['font.family'] = os.getenv('orto_fontname')
+        except ValueError:
+            ut.cprint('Error in orto_fontname environment variable', 'red')
+            sys.exit(1)
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     version = oe.OrcaVersionExtractor.extract(uargs.output_file)
 
@@ -744,7 +744,7 @@ def extract_orbs_func(uargs, save=True) -> None:
         # Disable spin if not present in file
         if mult == 1:
             uargs.spin = None
-    except extto.DataNotFoundError:
+    except DataNotFoundError:
         pass
 
     extractors = {
@@ -772,7 +772,7 @@ def extract_orbs_func(uargs, save=True) -> None:
                 )
                 uargs.flavour = name
                 break
-            except extto.DataNotFoundError:
+            except DataNotFoundError:
                 failed += 1
         if failed == len(extractors):
             ut.red_exit(
@@ -783,7 +783,7 @@ def extract_orbs_func(uargs, save=True) -> None:
             data = extractors[uargs.flavour](
                 uargs.output_file
             )
-        except extto.DataNotFoundError as dne:
+        except DataNotFoundError as dne:
             ut.red_exit(str(dne))
 
     # Unpack data
@@ -955,7 +955,7 @@ def extract_pop_func(uargs, save=True) -> None:
             data = oe.MullikenPopulationExtractorDensities.extract(
                 uargs.output_file
             )
-        except extto.DataNotFoundError:
+        except DataNotFoundError:
             data = oe.MullikenPopulationExtractorPopulations.extract(
                 uargs.output_file
             )
@@ -1018,6 +1018,11 @@ def plot_susc_func(uargs) -> None:
         None
 
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     # Extract data from file
     data = oe.SusceptibilityExtractor.extract(uargs.output_file)
@@ -1039,7 +1044,7 @@ def plot_susc_func(uargs) -> None:
 
     # Load experimental data if provided
     if uargs.exp_file is not None:
-        exp_data = pd.read_csv(
+        exp_data = read_csv(
             uargs.exp_file,
             comment='#',
             skipinitialspace=True
@@ -1113,6 +1118,11 @@ def plot_ailft_func(uargs) -> None:
     -------
         None
     '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
 
     # Create extractor
     data = oe.AILFTOrbEnergyExtractor.extract(uargs.output_file)
@@ -1940,7 +1950,7 @@ def read_args(arg_list=None):
         '-e',
         '--elements',
         type=str,
-        default=atomic.elements,
+        default=atomic_elements,
         nargs='+',
         help='Only print contributions from specified element(s) e.g. Ni'
     )

{orto-1.0.0.dist-info → orto-1.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.0.0
+Version: 1.0.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.0.0.dist-info → orto-1.0.1.dist-info}/RECORD

@@ -1,13 +1,13 @@
 orto/__init__.py,sha256=iSR4TAfpJn1_mwTnnncgwmWBz3q_ImdmhnOORKcOvE0,63
-orto/__version__.py,sha256=RsZjRjMprNcDm97wqRRSk6rTLgTX8N0GyicZyZ8OsBQ,22
-orto/cli.py,sha256=4W6KgUjmdI8wYo3n5Dp74YgH8a4q7-IsxBf7fhWl6P4,59396
+orto/__version__.py,sha256=3KXfAcA5rzzQXMtfwpHphgbJNZdA0XWaW96kdWVSZJw,22
+orto/cli.py,sha256=xRcJw_65gQmpBsmruRe46r2gd7fBdLpoh9Z0oPLPcM8,59795
 orto/extractor.py,sha256=kJnVI_Zwz7yorbojWdgxN-NSspJIY9pKoDb1RD2dHUg,67488
 orto/input.py,sha256=UMYNPGeqOCNKvPYJVfVS2JU7Ost_xM1ZG28t5f9-Er0,7084
 orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
 orto/plotter.py,sha256=ICrO03T_HGe-H1XKZ2qzsKYdPY44E0PKiXqIQQawd7I,15633
 orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
-orto-1.0.0.dist-info/METADATA,sha256=P-6wCgp-dPyw8b8N0d8m4Et-C8MXJGBySV75lL9Y2JQ,1140
-orto-1.0.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.0.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.0.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.0.0.dist-info/RECORD,,
+orto-1.0.1.dist-info/METADATA,sha256=tkPj-dCGN-DhaYdlyGkXVysH-4STdCAf4kPr-hXYbfU,1140
+orto-1.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.0.1.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.0.1.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.0.1.dist-info/RECORD,,