Enable tox testing and make flake8 compliant

dicom-standard/extract_attributes.py → dicom_standard/extract_attributes.py

@@ -3,13 +3,14 @@
 '''
 import sys
 
-import parse_lib as pl
-import parse_relations as pr
-from table_utils import table_to_dict
+from . import parse_lib as pl
+from . import parse_relations as pr
+from .table_utils import table_to_dict
 
 COLUMN_TITLES = ['tag', 'name', 'keyword', 'valueRepresentation', 'valueMultiplicity', 'retired']
 ATTR_TABLE_ID = 'table_6-1'
 
+
 def get_attribute_table(standard):
     all_tables = standard.find_all('div', class_='table')
     html_table = pl.find_tdiv_by_id(all_tables, ATTR_TABLE_ID)

dicom-standard/extract_ciod_module_data.py → dicom_standard/extract_ciod_module_data.py

@@ -6,14 +6,15 @@
 import sys
 import re
 
-import parse_lib as pl
-import parse_relations as pr
-from table_utils import expand_spans, table_to_dict, stringify_table, tdiv_to_table_list
+from . import parse_lib as pl
+from . import parse_relations as pr
+from .table_utils import expand_spans, table_to_dict, stringify_table, tdiv_to_table_list
 
 CHAPTER_ID = 'chapter_A'
 TABLE_SUFFIX = re.compile(".*IOD Modules$")
 COLUMN_TITLES = ['informationEntity', 'module', 'reference_fragment', 'usage']
 
+
 def get_ciod_tables(standard):
     chapter_A_table_divs = pl.all_tdivs_in_chapter(standard, CHAPTER_ID)
     ciod_table_divs = list(filter(is_valid_ciod_table, chapter_A_table_divs))
@@ -61,6 +62,7 @@ def get_ciod_description(tdiv):
     except AttributeError:
         return None
 
+
 if __name__ == "__main__":
     standard = pl.parse_html_file(sys.argv[1])
     tables, tdivs = get_ciod_tables(standard)

dicom-standard/extract_macros.py → dicom_standard/extract_macros.py

@@ -9,10 +9,10 @@
 
 from bs4 import BeautifulSoup, Tag
 
-import parse_lib as pl
-import parse_relations as pr
-from table_utils import expand_spans, stringify_table, tdiv_to_table_list, TableListType
-from macro_utils import get_id_from_link, MetadataTableType
+from . import parse_lib as pl
+from . import parse_relations as pr
+from .table_utils import expand_spans, stringify_table, tdiv_to_table_list, TableListType
+from .macro_utils import get_id_from_link, MetadataTableType
 
 # Macros and modules require the same metadata and formatting,
 # so they can share these two functions.

dicom-standard/extract_modules_with_attributes.py → dicom_standard/extract_modules_with_attributes.py

@@ -6,15 +6,16 @@
 import sys
 import re
 
-import parse_lib as pl
-import parse_relations as pr
+from . import parse_lib as pl
+from . import parse_relations as pr
 from table_utils import expand_spans, table_to_dict, stringify_table, tdiv_to_table_list
 
 CHAPTER_ID = 'chapter_C'
 TABLE_SUFFIX = re.compile("(.*Module Attributes$)|(.*Module Table$)")
 COLUMN_TITLES_WITH_TYPE = ['name', 'tag', 'type', 'description']
 COLUMN_TITLES_NO_TYPE = ['name', 'tag', 'description']
 
+
 def get_module_tables(standard):
     chapter_C_table_divs = pl.all_tdivs_in_chapter(standard, CHAPTER_ID)
     module_table_divs = list(filter(is_valid_module_table, chapter_C_table_divs))
@@ -64,6 +65,7 @@ def clean_table_description(description):
         table_link.string = 'This module '
     return description
 
+
 if __name__ == '__main__':
     standard = pl.parse_html_file(sys.argv[1])
     tables, tdivs = get_module_tables(standard)

dicom-standard/extract_sections.py → dicom_standard/extract_sections.py

@@ -1,9 +1,8 @@
 import sys
 import re
 import os
-from bs4 import BeautifulSoup
 
-from parse_lib import parse_html_file, write_pretty_json
+from .parse_lib import parse_html_file, write_pretty_json
 
 REFERENCED_IDS_RE = re.compile(r'(sect.*)|(figure.*)|(biblio.*)|(table.*)|(note.*)')
 

dicom-standard/hierarchy_utils.py → dicom_standard/hierarchy_utils.py

@@ -7,7 +7,8 @@
 
 from bs4 import Tag
 
-import parse_lib as pl
+from . import parse_lib as pl
+
 
 def get_hierarchy_markers(name: str) -> str:
     clean_name = name.strip().replace('\n', '')

dicom-standard/macro_utils.py → dicom_standard/macro_utils.py

@@ -8,12 +8,12 @@
 
 from bs4 import BeautifulSoup, Tag
 
-import parse_lib as pl
-from hierarchy_utils import get_hierarchy_markers
+from .hierarchy_utils import get_hierarchy_markers
 
 MetadataTableType = Dict[str, Any]
 MacrosType = Dict[str, MetadataTableType]
 
+
 def expand_macro_rows(table: Tag, macros: MacrosType) -> List[Dict[str, str]]:
     # This variable is used to stop an infinite macro reference
     # loop in the standard at the SR Document Content module.
@@ -62,7 +62,7 @@ def flatten_one_layer(nested_element_list: List[List[Any]]) -> List[Any]:
 def referenced_macro_id_from_include_statement(macro_reference_html: str) -> str:
     parsed_reference = BeautifulSoup(macro_reference_html, 'html.parser')
     id_anchor = parsed_reference.find('a', class_='xref')
-    return id_anchor.get('href')[1:] # Remove the first '#' character
+    return id_anchor.get('href')[1:]  # Remove the first '#' character
 
 
 def get_macros_by_id(macro_id: str, macros: MacrosType, hierarchy_marker: str) -> MetadataTableType:

dicom-standard/parse_lib.py → dicom_standard/parse_lib.py

@@ -10,14 +10,15 @@
 
 from bs4 import BeautifulSoup, NavigableString, Tag
 
-import parse_relations as pr
+from . import parse_relations as pr
 
 BASE_DICOM_URL = "http://dicom.nema.org/medical/dicom/current/output/html/"
 BASE_SHORT_DICOM_SECTION_URL = "http://dicom.nema.org/medical/dicom/current/output/chtml/"
 SHORT_DICOM_URL_PREFIX = "http://dicom.nema.org/medical/dicom/current/output/chtml/part03/"
 
 allowed_attributes = ["href", "src", "type", "data", "colspan", "rowspan"]
 
+
 def parse_html_file(filepath: str) -> BeautifulSoup:
     with open(filepath, 'r') as html_file:
         return BeautifulSoup(html_file, 'html.parser')

dicom-standard/parse_relations.py → dicom_standard/parse_relations.py

@@ -6,6 +6,7 @@
 from typing import List
 from bs4 import Tag
 
+
 def table_rows(table_div: Tag) -> List[Tag]:
     return table_div.find('tbody').find_all('tr')
 

dicom-standard/postprocess_mark_references.py → dicom_standard/postprocess_mark_references.py

@@ -7,14 +7,14 @@
 
 from bs4 import BeautifulSoup
 
-import parse_lib as pl
+from . import parse_lib as pl
 
-IGNORED_REFERENCES_RE = re.compile(r'(.*ftp.*)|(.*http.*)|(.*part05.*)|(.*chapter.*)|(.*PS3.*)|(.*DCM.*)|(.*glossentry.*)')
+IGNORED_REFS_RE = re.compile(r'(.*ftp.*)|(.*http.*)|(.*part05.*)|(.*chapter.*)|(.*PS3.*)|(.*DCM.*)|(.*glossentry.*)')
 
 
 def get_valid_reference_anchors(parsed_html):
     anchor_tags = parsed_html.find_all('a', href=True)
-    return [a for a in anchor_tags if not re.match(IGNORED_REFERENCES_RE, a['href'])]
+    return [a for a in anchor_tags if not re.match(IGNORED_REFS_RE, a['href'])]
 
 
 def record_references_inside_pairs(module_attr_pairs):
@@ -37,6 +37,7 @@ def record_reference_in_pair(pair):
 def finalize_descriptions(pair):
     pair['description'] = pl.clean_html(pair['description'])
 
+
 def reference_structure_from_anchor(reference):
     return {
         "sourceUrl": reference.get('href'),

dicom-standard/postprocess_save_references.py → dicom_standard/postprocess_save_references.py

@@ -6,8 +6,7 @@
 
 from bs4 import BeautifulSoup
 
-import parse_lib as pl
-from macro_utils import flatten_one_layer
+from . import parse_lib as pl
 
 
 def find_reference_html_in_sections(pairs, section_listing):

dicom-standard/postprocess_update_reference_links.py → dicom_standard/postprocess_update_reference_links.py

@@ -1,6 +1,7 @@
 import sys
 
-import parse_lib as pl
+from . import parse_lib as pl
+
 
 def update_sourceurls(module_attr_pairs, references):
     for pair in module_attr_pairs:

dicom-standard/preprocess_modules_with_attributes.py → dicom_standard/preprocess_modules_with_attributes.py

@@ -8,11 +8,10 @@
 '''
 import sys
 
-from bs4 import BeautifulSoup
+from . import parse_lib as pl
+from .macro_utils import expand_macro_rows
+from .hierarchy_utils import record_hierarchy_for_module
 
-import parse_lib as pl
-from macro_utils import expand_macro_rows
-from hierarchy_utils import record_hierarchy_for_module
 
 def expand_all_macros(module_attr_tables, macros):
     expanded_attribute_lists = [expand_macro_rows(table, macros)
@@ -46,7 +45,6 @@ def preprocess_attribute(attr):
     return cleaned_attribute
 
 
-
 def expand_hierarchy(tables):
     return [record_hierarchy_for_module(table) for table in tables]
 

dicom-standard/process_ciod_module_relationship.py → dicom_standard/process_ciod_module_relationship.py

@@ -4,14 +4,16 @@
 '''
 import sys
 
-import parse_lib as pl
+from . import parse_lib as pl
+
 
 def define_all_relationships(ciod_module_list):
     all_relationships = []
     for table in ciod_module_list:
         ciod = table['name']
         modules = table['modules']
-        all_relationships.extend([define_ciod_module_relationship(ciod, module) for module in modules])
+        all_relationships.extend([define_ciod_module_relationship(ciod, module)
+                                  for module in modules])
     return all_relationships
 
 

dicom-standard/process_ciods.py → dicom_standard/process_ciods.py

@@ -4,7 +4,8 @@
 '''
 import sys
 
-import parse_lib as pl
+from . import parse_lib as pl
+
 
 def ciods_from_extracted_list(ciod_module_list):
     ciods = {}

dicom-standard/process_module_attribute_relationship.py → dicom_standard/process_module_attribute_relationship.py

@@ -1,6 +1,7 @@
 import sys
 
-import parse_lib as pl
+from . import parse_lib as pl
+
 
 def module_attr_relationship_table(module_attr_relationship_list):
     entries = []

dicom-standard/process_modules.py → dicom_standard/process_modules.py

@@ -4,7 +4,8 @@
 '''
 import sys
 
-import parse_lib as pl
+from . import parse_lib as pl
+
 
 def modules_from_tables(tables):
     modules = {}

dicom-standard/table_utils.py → dicom_standard/table_utils.py

@@ -6,10 +6,11 @@
 from copy import copy
 from bs4 import Tag
 
-import parse_relations as pr
+from . import parse_relations as pr
 
 TableListType = List[List[Tag]]
 
+
 def table_to_dict(table: TableListType, row_names: List[str]) -> List[Dict[str, List[Tag]]]:
     return [dict(zip(row_names, row)) for row in table]
 
@@ -37,7 +38,7 @@ def expand_rows(table: TableListType) -> TableListType:
     communicated between each row (the rowspan information).
     '''
     extended_table = []
-    row_expansion = [] # Format: [(bs_html_object, row_index)]
+    row_expansion = []  # Format: [(bs_html_object, row_index)]
     for row in table:
         expanded_row, row_expansion = expand_rowspans(row, row_expansion)
         extended_table.append(expanded_row)
@@ -71,7 +72,7 @@ def slide_down(start_idx: int, row: List[Tag], num_slides: int = 1) -> List[Tag]
     '''
     try:
         sliding_rows = row[start_idx:len(row)]
-        new_row = row[0:len(row)-len(sliding_rows)]
+        new_row = row[0:len(row) - len(sliding_rows)]
         for i in range(num_slides):
             new_row.append(None)
         new_row.extend(sliding_rows)
@@ -105,7 +106,7 @@ def is_new_rowspan_cell(cell: Tag, idx: int, row_expansion: List[Tuple[Tag, int]
 
 
 def remove_completed_rowspans(row_expansion: List[Tuple[Tag, int]]) -> List[Tuple[Tag, int]]:
-    return [(cell,idx) for (cell, idx) in row_expansion
+    return [(cell, idx) for (cell, idx) in row_expansion
             if has_rowspans_to_expand(cell)]
 
 
@@ -126,6 +127,6 @@ def expand_cell_colspan(cell: Tag) -> Tag:
     if colspan_count is not None:
         colspans = int(colspan_count)
         cell['colspan'] = 1
-        for i in range(colspans-1):
+        for i in range(colspans - 1):
             expanded_cell.append(None)
     return expanded_cell

setup.py

@@ -43,7 +43,7 @@
     ],
 
     extras_require={
-        'dev': [],
+        'dev': ['check-manifest'],
         'test': ['pytest'],
     },