Make CIViCpy Python >=3.5 compatible

civicpy/__version__.py

@@ -5,10 +5,10 @@
 __minor__ = '0'
 __patch__ = '1'
 __meta_label__ = ''
-__short_version__ = f"{__major__}.{__minor__}"
-__version__ = f"{__short_version__}.{__patch__}"
+__short_version__ = "{}.{}".format(__major__, __minor__)
+__version__ = "{}.{}".format(__short_version__, __patch__)
 if __meta_label__:
-    __version__ += f"-{__meta_label__}"
+    __version__ += "-{}".format(__meta_label__)
 __authors__ = ['Alex H. Wagner', 'Susanna Kiwala']
 __author_email__ = 'help@civicpy.org'
 __license__ = 'MIT'

civicpy/civic.py

@@ -1,7 +1,6 @@
 import requests
 import importlib
 import logging
-import datetime
 import pandas as pd
 import pickle
 import os
@@ -10,6 +9,9 @@
 from civicpy import REMOTE_CACHE_URL, LOCAL_CACHE_PATH, CACHE_TIMEOUT_DAYS
 import requests
 from civicpy.exports import VCFWriter
+from datetime import datetime, timedelta
+from backports.datetime_fromisoformat import MonkeyPatch
+MonkeyPatch.patch_fromisoformat()
 
 
 CACHE = dict()
@@ -21,7 +23,7 @@
 
 HPO_TERMS = dict()
 
-FRESH_DELTA = datetime.timedelta(days=CACHE_TIMEOUT_DAYS)
+FRESH_DELTA = timedelta(days=CACHE_TIMEOUT_DAYS)
 
 MODULE = importlib.import_module('civicpy.civic')
 
@@ -36,7 +38,8 @@
 }
 
 
-_CoordinateQuery = namedtuple('CoordinateQuery', ['chr', 'start', 'stop', 'alt', 'ref', 'build', 'key'], defaults=(None, None, "GRCh37", None))
+_CoordinateQuery = namedtuple('CoordinateQuery', ['chr', 'start', 'stop', 'alt', 'ref', 'build', 'key'])
+_CoordinateQuery.__new__.__defaults__ = (None, None, "GRCh37", None)
 
 
 class CoordinateQuery(_CoordinateQuery):  # Wrapping for documentation
@@ -57,7 +60,7 @@ class CoordinateQuery(_CoordinateQuery):  # Wrapping for documentation
 
 def pluralize(string):
     if string in UNMARKED_PLURALS:
-        return f'{string}_items'
+        return '{}_items'.format(string)
     if string.endswith('s'):
         return string
     return string + 's'
@@ -269,7 +272,7 @@ def update_cache(from_remote_cache=True, remote_cache_url=REMOTE_CACHE_URL,
                 v.update()
         _get_elements_by_ids('assertion', allow_cached=False, get_all=True)
         _get_elements_by_ids('variant_group', allow_cached=False, get_all=True)
-        CACHE['full_cached'] = datetime.datetime.now()
+        CACHE['full_cached'] = datetime.now()
         _build_coordinate_table(variants)
         save_cache(local_cache_path=local_cache_path)
 
@@ -316,7 +319,7 @@ def __init__(self, partial=False, **kwargs):
                     if (partial and field not in CivicRecord._SIMPLE_FIELDS) or field in self._OPTIONAL_FIELDS:
                         self._incomplete.add(field)     # Allow for incomplete data when partial flag set
                     else:
-                        raise AttributeError(f'Expected {field} attribute for {self.type}, none found.')
+                        raise AttributeError('Expected {} attribute for {}, none found.'.format(field, self.type))
 
         for field in self._COMPLEX_FIELDS:
             try:
@@ -328,7 +331,7 @@ def __init__(self, partial=False, **kwargs):
                     self._incomplete.add(field)
                     continue
                 else:
-                    raise AttributeError(f'Expected {field} attribute for {self.type}, none found.')
+                    raise AttributeError('Expected {} attribute for {}, none found.'.format(field, self.type))
             is_compound = isinstance(v, list)
             cls = get_class(field)
             if is_compound:
@@ -358,15 +361,15 @@ def __dir__(self):
         return [attribute for attribute in super().__dir__() if not attribute.startswith('_')]
 
     def __repr__(self):
-        return f'<CIViC {self.type} {self.id}>'
+        return '<CIViC {} {}>'.format(self.type, self.id)
 
     def __getattr__(self, item):
         if self._partial and item in self._incomplete:
             self.update()
         return object.__getattribute__(self, item)
 
     def __hash__(self):
-        return hash(f'{self.type}:{self.id}')
+        return hash('{}:{}'.format(self.type, self.id))
 
     def __eq__(self, other):
         return hash(self) == hash(other)
@@ -394,7 +397,7 @@ def update(self, allow_partial=True, force=False, **kwargs):
                 v = getattr(cached, field)
                 setattr(self, field, v)
             self._partial = False
-            logging.info(f'Loading {str(self)} from cache')
+            logging.info('Loading {} from cache'.format(str(self)))
             return True
         resp_dict = element_lookup_by_id(self.type, self.id)
         self.__init__(partial=False, **resp_dict)
@@ -833,7 +836,7 @@ def __init__(self, **kwargs):
     @property
     def created_at(self):
         assert self._created_at[-1] == 'Z'
-        return datetime.datetime.fromisoformat(self._created_at[:-1])
+        return datetime.fromisoformat(self._created_at[:-1])
 
     @created_at.setter
     def created_at(self, value):
@@ -862,9 +865,9 @@ def __repr__(self):
         try:
             _id = self.id
         except AttributeError:
-            return f'<CIViC Attribute {self.type}>'
+            return '<CIViC Attribute {}>'.format(self.type)
         else:
-            return f'<CIViC Attribute {self.type} {self.id}>'
+            return '<CIViC Attribute {} {}>'.format(self.type, self.id)
 
     def __init__(self, **kwargs):
         kwargs['partial'] = False
@@ -927,7 +930,7 @@ def __init__(self, **kwargs):
     @property
     def timestamp(self):
         assert self._timestamp[-1] == 'Z'
-        return datetime.datetime.fromisoformat(self._timestamp[:-1])
+        return datetime.fromisoformat(self._timestamp[:-1])
 
     @timestamp.setter
     def timestamp(self, value):
@@ -959,7 +962,7 @@ def get_cached(element_type, element_id):
 def _has_full_cached_fresh(delta=FRESH_DELTA):
     s = 'full_cached'
     if CACHE.get(s, False):
-        return CACHE[s] + delta > datetime.datetime.now()
+        return CACHE[s] + delta > datetime.now()
     return False
 
 
@@ -970,11 +973,11 @@ def _get_elements_by_ids(element, id_list=[], allow_cached=True, get_all=False):
         if not get_all:
             cached = [get_cached(element, element_id) for element_id in id_list]
             if all(cached):
-                logging.info(f'Loading {pluralize(element)} from cache')
+                logging.info('Loading {} from cache'.format(pluralize(element)))
                 return cached
         else:
             cached = [get_cached(element, element_id) for element_id in CACHE['{}_all_ids'.format(pluralize(element))]]
-            logging.info(f'Loading {pluralize(element)} from cache')
+            logging.info('Loading {} from cache'.format(pluralize(element)))
             return cached
     if id_list and get_all:
         raise ValueError('Please pass list of ids or use the get_all flag, not both.')
@@ -1411,7 +1414,7 @@ def get_all_variant_ids():
 
 
 def _get_all_element_ids(element):
-    url = f'https://civicdb.org/api/{element}?count=100000'
+    url = 'https://civicdb.org/api/{}?count=100000'.format(element)
     resp = requests.get(url)
     resp.raise_for_status()
     return [x['id'] for x in resp.json()['records']]

civicpy/cli.py

@@ -20,7 +20,7 @@ def cli():
               help='Hard-update from live API (slow) or \
               soft-update from daily precache (fast; default)')
 @click.option('--cache-save-path',
-              help=f'Filepath to save cache to. Default: {LOCAL_CACHE_PATH}',
+              help='Filepath to save cache to. Default: {}'.format(LOCAL_CACHE_PATH),
               default=LOCAL_CACHE_PATH)
 def update(soft, cache_save_path):
     """Updates CIViC content from server and stores to local cache file"""

civicpy/exports.py

@@ -204,21 +204,21 @@ def writerecords(self, with_header=True):
                     assert ';' not in v
                     assert '=' not in v
                 if v:
-                    out.append(f'{field}={v}')
+                    out.append('{}={}'.format(field, v))
             out_dict['INFO'] = ';'.join(out)
 
             super().writerow(out_dict)
             rows.append(out_dict)
         return rows
 
     def _write_meta_file_lines(self):
-        self._f.write(f'##fileformat=VCFv{self.version}\n')
+        self._f.write('##fileformat=VCFv{}\n'.format(self.version))
         self._f.write('##fileDate={}\n'.format(
             datetime.date.today().strftime('%Y%m%d')
         ))
         self._f.write('##reference=ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/GRCh37-lite.fa.gz\n')
-        self._f.write(f'##source=CIViCpy_v{__version__}\n')
-        self._f.write(f'##aboutURL=https://civicdb.org/help/evidence/overview\n')
+        self._f.write('##source=CIViCpy_v{}\n'.format(__version__))
+        self._f.write('##aboutURL=https://civicdb.org/help/evidence/overview\n')
 
     def _write_meta_info_lines(self):
         # Gene
@@ -232,10 +232,10 @@ def _write_meta_info_line(self, id_, number, type_, description, **kwargs):
         assert id_ not in self.meta_info_fields
         assert id_ not in self.VCF_RESERVED_FIELDS
         self.meta_info_fields.append(id_)
-        s = [f'ID={id_},Number={number},Type={type_},Description="{description}"']
-        s.extend([f'{k}={v}' for k, v in kwargs])
+        s = ['ID={},Number={},Type={},Description="{}"'.format(id_, number, type_, description)]
+        s.extend(['{}={}'.format(k, v) for k, v in kwargs])
         out = ','.join(s)
-        self._f.write(f'##INFO=<{out}>\n')
+        self._f.write('##INFO=<{}>\n'.format(out))
 
     def _add_variant_record(self, variant_record):
         self.variant_records.add(variant_record)

setup.py

@@ -25,7 +25,8 @@
         'pandas',
         'Click',
         'vcfpy',
-        'pysam'
+        'pysam',
+        'backports-datetime-fromisoformat',
     ],
     extras_require={
         'test': [
@@ -40,7 +41,7 @@
             'sphinxcontrib.programoutput'
         ]
     },
-    python_requires='>=3.7',
+    python_requires='>=3.5',
     entry_points={
         'console_scripts': [
             'civicpy=civicpy.cli:cli'