Merge branch 'master' of github.com:saezlab/pypath

pypath/formats/sdf.py

@@ -660,7 +660,7 @@ def index_info(self):
         Prints number of records indexed and name of the source file.
         """
 
-        msg = f'Indexed {len(self.names['id'])} records from `{self.fname}`.'
+        msg = f"Indexed {len(self.names['id'])} records from `{self.fname}`."
 
         if not self.silent:
 

pypath/inputs/ramp/__init__.py

@@ -24,3 +24,5 @@
 """
 
 from ._sqlite import *
+from ._rest import *
+from ._mapping import *

pypath/inputs/ramp/_mapping.py

@@ -19,6 +19,12 @@
 
 from __future__ import annotations
 
+import pandas as pd
+
+from ._sqlite import ramp_raw
+
+__all__ = ['ramp_mapping']
+
 
 def ramp_mapping(
         id_type_a: str,

pypath/inputs/ramp/_rest.py

@@ -24,6 +24,9 @@
 import pypath.resources.urls as urls
 import pypath.share.curl as curl
 
+__all__ = ['ramp_id_types']
+
+
 def ramp_id_types(
         entity_type: Literal['gene', 'compound'] | None = None,
     ) -> set[str]:

pypath/inputs/ramp/_sqlite.py

@@ -19,7 +19,8 @@
 
 from __future__ import annotations
 
-from collections.abc import Generator, Any
+from collections.abc import Generator
+from typing import Any
 import os
 import sqlite3
 

pypath/inputs/uniprot.py

@@ -651,6 +651,7 @@ def __iter__(self):
             silent = False,
             large = True,
             compr = 'gz',
+            slow = True,
         )
         result = c.result if c.result or self.fail_on_empty else [0].__iter__()
         _ = next(result)

pypath/utils/mapping.py

@@ -126,7 +126,7 @@
         dict(
             **{
                 it: it
-                for it in ramp_input.ramp_id_types_2('compound')
+                for it in ramp_input.ramp_id_types('compound')
             },
             **input_formats.RAMP_MAPPING,
         ),