Repository: scverse/scanpy

Issue:
`NameError: name 'logg' is not defined` when using `sc.queries.mitochondrial_genes`
I just tried
```python
import scanpy.api as sc
sc.queries.mitochondrial_genes('www.ensembl.org', 'strange_organism')
```
I would expect scanpy complains that it does not know `'strange_organism'`, but I get the error 
```python
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-13-6a41b361ab41> in <module>()
      1 import scanpy.api as sc
----> 2 sc.queries.mitochondrial_genes('www.ensembl.org', 'drerio')

~/software/scanpy/scanpy/queries/__init__.py in mitochondrial_genes(host, org)
     34         s.add_attribute_to_xml('mgi_symbol')
     35     else:
---> 36         logg.msg('organism ', str(org), ' is unavailable', v=4, no_indent=True)
     37         return None
     38     s.add_attribute_to_xml('chromosome_name')

NameError: name 'logg' is not defined
```
It seems to me like `queries/__init__.py` misses an `from .. import logging as logg` statement.

Would maybe also make sense to show the the message that an organism is not available at verbosity level 1 instead of 4?


Discussion:

Resolving patch:
diff --git a/scanpy/queries/__init__.py b/scanpy/queries/__init__.py
--- a/scanpy/queries/__init__.py
+++ b/scanpy/queries/__init__.py
@@ -1,4 +1,5 @@
 import pandas as pd
+from .. import logging as logg
 
 
 def mitochondrial_genes(host, org):
@@ -8,9 +9,9 @@ def mitochondrial_genes(host, org):
     ----------
     host : {{'www.ensembl.org', ...}}
         A valid BioMart host URL.
-    org : {{'hsapiens', 'mmusculus'}}
-        Organism to query. Currently available are human ('hsapiens') and mouse
-        ('mmusculus').
+    org : {{'hsapiens', 'mmusculus', 'drerio'}}
+        Organism to query. Currently available are human ('hsapiens'), mouse
+        ('mmusculus') and zebrafish ('drerio').
 
     Returns
     -------
@@ -32,6 +33,9 @@ def mitochondrial_genes(host, org):
     elif org == 'mmusculus':
         s.add_dataset_to_xml('mmusculus_gene_ensembl')
         s.add_attribute_to_xml('mgi_symbol')
+    elif org == 'drerio':
+        s.add_dataset_to_xml('drerio_gene_ensembl')
+        s.add_attribute_to_xml('zfin_id_symbol')
     else:
         logg.msg('organism ', str(org), ' is unavailable', v=4, no_indent=True)
         return None
@@ -55,9 +59,9 @@ def gene_coordinates(host, org, gene, chr_exclude=[]):
     ----------
     host : {{'www.ensembl.org', ...}}
         A valid BioMart host URL. Can be used to control genome build.
-    org : {{'hsapiens', 'mmusculus'}}
-        Organism to query. Currently available are human ('hsapiens') and mouse
-        ('mmusculus').
+    org : {{'hsapiens', 'mmusculus', 'drerio'}}
+        Organism to query. Currently available are human ('hsapiens'), mouse
+        ('mmusculus') and zebrafish ('drerio').
     gene :
         The gene symbol (e.g. 'hgnc_symbol' for human) for which to retrieve
         coordinates.
@@ -83,6 +87,9 @@ def gene_coordinates(host, org, gene, chr_exclude=[]):
     elif org == 'mmusculus':
         s.add_dataset_to_xml('mmusculus_gene_ensembl')
         s.add_attribute_to_xml('mgi_symbol')
+    elif org == 'drerio':
+        s.add_dataset_to_xml('drerio_gene_ensembl')
+        s.add_attribute_to_xml('zfin_id_symbol')
     else:
         logg.msg('organism ', str(org), ' is unavailable', v=4, no_indent=True)
         return None


Test patch: