Merge pull request #31 from cioos-siooc/add_match_taxa

add match_taxa wrap, fix env.yml

environment.yml

@@ -5,6 +5,7 @@ dependencies:
 - geopandas
 - pyworms
 - ckanapi
+- httpx
 - plotly
 - async
 - requests

pyobistools/taxa.py

@@ -11,6 +11,9 @@
 
 from pyobistools.utils import removesuffix
 
+from pyobistools.validation import check_scientificname_and_ids as check_names
+
+
 STANDARD_SPECIES_COLUMNS = {
     'taxon_id': np.nan,
     'url': '',
@@ -94,6 +97,20 @@ def add_suffix(name: str) -> t.List[str]:
     return [name.strip() + s for s in suffixes]
 
 
+def match_taxa(names, ask=True, itis_usage=False):
+    """
+    Wrap the existing functionality in validation in the expected name for this function as per R's iobis/obistools.
+
+    @param names    List of scientific names to check against
+    @param ask      Do we ask the user to resolve multi-match or ambiguous names?
+    @param itis_usage   Pass through the ITIS check setting for the client function to handle
+
+    @return structure with appended lsids where WoRMS (or ITIS can resolve them)
+    """
+
+    return check_names.check_scientificname_and_ids(names, value='names', itis_usage=itis_usage)
+
+
 def search_worms(names: t.List[str],
                  kwargs: t.Dict[str, t.Any] = {}) -> pd.DataFrame:
     """