finish changes to conditionally use pandas fix #35

pytaxize/__init__.py

@@ -41,41 +41,6 @@
     getfullrecordfromlsid,
     getfullrecordfromtsn,
     getgeographicdivisionsfromtsn,
-    getgeographicvalues,
-    getglobalspeciescompletenessfromtsn,
-    gethierarchydownfromtsn,
-    gethierarchyupfromtsn,
-    getitistermsfromcommonname,
-    getitisterms,
-    getitistermsfromscientificname,
-    hierarchy,
-    getjurisdictionaloriginfromtsn,
-    getjurisdictionoriginvalues,
-    getjurisdictionvalues,
-    getkingdomnamefromtsn,
-    getkingdomnames,
-    getlastchangedate,
-    getlsidfromtsn,
-    getothersourcesfromtsn,
-    getparenttsnfromtsn,
-    getpublicationsfromtsn,
-    getranknames,
-    getrecordfromlsid,
-    getreviewyearfromtsn,
-    getscientificnamefromtsn,
-    gettaxonauthorshipfromtsn,
-    gettaxonomicusagefromtsn,
-    gettsnbyvernacularlanguage,
-    gettsnfromlsid,
-    getunacceptabilityreasonfromtsn,
-    getvernacularlanguages,
-    searchbycommonname,
-    searchbycommonnamebeginswith,
-    searchbycommonnameendswith,
-    searchcommon,
-    searchbyscientificname,
-    searchforanymatch,
-    searchforanymatchpaged,
 )
-from .tax import names_list, vascan_search
+from .tax import names_list, vascan_search, scrapenames
 from .taxo import taxo_datasources, taxo_resolve

pytaxize/col/col.py

@@ -2,13 +2,17 @@
 import requests
 import datetime
 from lxml import etree
-import pandas as pd
 import re
 import json
 import pkg_resources
 from pytaxize.refactor import Refactor
 from pytaxize.utils import *
 
+try:
+    import pandas as pd
+except ImportError:
+    warnings.warn("Pandas library not installed, dataframes disabled")
+    pd = None
 
 def children(name=None, id=None, format=None, start=None, checklist=None):
     """

pytaxize/gbif/parse.py

@@ -1,16 +1,22 @@
-import pandas as pd
 import json
 from pytaxize.refactor import Refactor
 
+try:
+    import pandas as pd
+except ImportError:
+    warnings.warn("Pandas library not installed, dataframes disabled")
+    pd = None
 
-def parse(name):
+def parse(name, as_dataframe=False):
     """
     Parse taxon names using the GBIF name parser.
 
     :param name: A character vector of scientific names.
       Returns a DataFrame containing fields extracted from parsed
       taxon names. Fields returned are the union of fields extracted from
       all species names in scientificname
+    :param as_dataframe: (optional) Type: boolean. Return as pandas data frame?
+        default: False
 
     Author John Baumgartner (johnbb@student.unimelb.edu.au)
 
@@ -19,14 +25,18 @@ def parse(name):
 
     Usage::
 
-        import pytaxize
-        pytaxize.gbif_parse(name=['x Agropogon littoralis'])
+        from pytaxize import gbif
+        gbif.parse(name=['x Agropogon littoralis'])
+        names = ['x Agropogon littoralis', 'Helianthus annuus texanus']
+        gbif.parse(names)
+        gbif.parse(names, as_dataframe=True)
     """
     name = list(name)
-    url = "http://api.gbif.org/v0.9/parser/name"
+    url = "https://api.gbif.org/v0.9/parser/name"
     headers = {"content-type": "application/json"}
     tt = Refactor(url, payload={}, request="post").json(
         data=json.dumps(name), headers=headers
     )
-    res = pd.DataFrame(tt)
-    return res
+    if as_dataframe:
+        tt = pd.DataFrame(tt)
+    return tt

pytaxize/gn/gnr.py

@@ -1,16 +1,13 @@
 import sys
 import requests
-import pandas as pd
 import json
 import time
 from pytaxize.refactor import Refactor
 import os
 
-
 class NoResultException(Exception):
     pass
 
-
 def gnr_datasources():
     """
     Get data sources for the Global Names Resolver.

pytaxize/itis/__init__.py

@@ -17,39 +17,4 @@
     getfullrecordfromlsid,
     getfullrecordfromtsn,
     getgeographicdivisionsfromtsn,
-    getgeographicvalues,
-    getglobalspeciescompletenessfromtsn,
-    gethierarchydownfromtsn,
-    gethierarchyupfromtsn,
-    getitistermsfromcommonname,
-    getitisterms,
-    getitistermsfromscientificname,
-    hierarchy,
-    getjurisdictionaloriginfromtsn,
-    getjurisdictionoriginvalues,
-    getjurisdictionvalues,
-    getkingdomnamefromtsn,
-    getkingdomnames,
-    getlastchangedate,
-    getlsidfromtsn,
-    getothersourcesfromtsn,
-    getparenttsnfromtsn,
-    getpublicationsfromtsn,
-    getranknames,
-    getrecordfromlsid,
-    getreviewyearfromtsn,
-    getscientificnamefromtsn,
-    gettaxonauthorshipfromtsn,
-    gettaxonomicusagefromtsn,
-    gettsnbyvernacularlanguage,
-    gettsnfromlsid,
-    getunacceptabilityreasonfromtsn,
-    getvernacularlanguages,
-    searchbycommonname,
-    searchbycommonnamebeginswith,
-    searchbycommonnameendswith,
-    searchcommon,
-    searchbyscientificname,
-    searchforanymatch,
-    searchforanymatchpaged,
 )