Showing 1 of 1 files from the diff.

@@ -87,11 +87,11 @@
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87 87
    a_out = 0
88 88
    while smirks.find('$(') != -1:
89 89
        # Find first atom
90 -
        atom, a_in, a_out = _find_embedded_brackets(smirks, '\[', '\]')
90 +
        atom, a_in, a_out = _find_embedded_brackets(smirks, r'\[', r'\]')
91 91
        d = atom.find('$(')
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        # Find atom with the $ string embedded
93 93
        while d == -1:
94 -
            atom, temp_in, temp_out = _find_embedded_brackets(smirks[a_out+1:], '\[', '\]')
94 +
            atom, temp_in, temp_out = _find_embedded_brackets(smirks[a_out+1:], r'\[', r'\]')
95 95
            a_in = a_out + temp_in + 1
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            a_out += temp_out + 1
97 97
            d = atom.find('$(')
@@ -109,11 +109,11 @@
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109 109
        else:
110 110
            ring_out = ''
111 111
112 -
        embedded, p_in, p_out = _find_embedded_brackets(atom, '\(', '\)')
112 +
        embedded, p_in, p_out = _find_embedded_brackets(atom, r'\(', r'\)')
113 113
        # two forms of embedded strings $(*~stuff) or $([..]~stuff)
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        # in the latter case the first atom refers the current atom
115 115
        if embedded[1] == '[':
116 -
            first, f_in, f_out = _find_embedded_brackets(embedded, '\[','\]')
116 +
            first, f_in, f_out = _find_embedded_brackets(embedded, r'\[',r'\]')
117 117
            first = _convert_embedded_SMIRKS(first)
118 118
            new_atom = atom[:d]+first[1:-1]+atom[p_out+1:]
119 119
            embedded = embedded[f_out+1:]
@@ -285,7 +285,7 @@
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285 285
286 286
            # Add label to the end of SMARTS
287 287
            else:
288 -
                sub_string, start, end = _find_embedded_brackets(smirks, '\[','\]')
288 +
                sub_string, start, end = _find_embedded_brackets(smirks, r'\[',r'\]')
289 289
                if self.ring is not None:
290 290
                    return sub_string[:-1] + ':' + str(self.index) + ']'+str(self.ring)
291 291
                else:
@@ -470,7 +470,8 @@
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470 470
        # Generate RegEx string for decorators:
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        self.no_bracket_atom_reg = r'('+'|'.join([element_sym, aro_sym, replace_str])+')'
472 472
        self.atom_reg = '|'.join([element_num, aro_ali, needs_int,
473 -
            optional_int, chirality, replace_str, element_sym, aro_sym])
473 +
                                  optional_int, chirality, replace_str,
474 +
                                  element_sym, aro_sym])
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        self.atom_reg = r'('+self.atom_reg+')'
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476 477
        # Define bond regular expression options below in order:
@@ -573,7 +574,7 @@
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573 574
        store = list() # to store indices while branching
574 575
        bondingTo = idx # which atom are we going to bond to
575 576
576 -
        atom_string, start, end = _find_embedded_brackets(smirks, '\[', '\]')
577 +
        atom_string, start, end = _find_embedded_brackets(smirks, r'\[', r'\]')
577 578
578 579
        if start != 0: # first atom is not in square brackets
579 580
            if start != -1:
@@ -625,7 +626,7 @@
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625 626
                continue
626 627
627 628
            # find beginning and end of next [atom]
628 -
            atom_string, start, end = _find_embedded_brackets(leftover, '\[', '\]')
629 +
            atom_string, start, end = _find_embedded_brackets(leftover, r'\[', r'\]')
629 630
630 631
            if start != -1: # no more square brackets
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                bond_string = leftover[:start]
Files Coverage
chemper 89.40%
Project Totals (11 files) 89.40%
578.3
TRAVIS_OS_NAME=linux
578.6
TRAVIS_PYTHON_VERSION=3.6
TRAVIS_OS_NAME=linux
578.2
TRAVIS_OS_NAME=osx
578.4
TRAVIS_PYTHON_VERSION=3.6
TRAVIS_OS_NAME=linux
rmb2c3lug7acw77g
578.1
TRAVIS_OS_NAME=osx
578.5
TRAVIS_OS_NAME=osx
578.7
TRAVIS_PYTHON_VERSION=3.6
TRAVIS_OS_NAME=linux
8vas7q3ivl3bh6x9
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coverage:
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    - test/.*
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    - compare/.*
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    - test_helper.py
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    - setup.py
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comment:
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Sunburst
The inner-most circle is the entire project, moving away from the center are folders then, finally, a single file. The size and color of each slice is representing the number of statements and the coverage, respectively.
Icicle
The top section represents the entire project. Proceeding with folders and finally individual files. The size and color of each slice is representing the number of statements and the coverage, respectively.
Grid
Each block represents a single file in the project. The size and color of each block is represented by the number of statements and the coverage, respectively.
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