aiondata - pypi Package Compare versions

Comparing version 0.4.4 to 0.4.5

aiondata/bindingdb.py

 import io
-from typing import Optional, Generator, Union
+from typing import Optional, Generator, Union, Tuple
 import urllib.request
@@ -41,7 +41,7 @@ from rdkit import Chem
             if cached_sdf.exists():
-                self.fd = self.from_compressed_file(cached_sdf)
+                self.outer_fd, self.fd = self.from_compressed_file(cached_sdf)
             else:
-                self.fd = self.from_url(self.SOURCE)
+                self.outer_fd, self.fd = self.from_url(self.SOURCE)
         else:
-            self.fd = fd
+            self.outer_fd, self.fd = fd
 
@@ -77,3 +77,3 @@ def _convert_to_numeric(
     @staticmethod
-    def from_url(url: str) -> io.BufferedReader:
+    def from_url(url: str) -> Tuple[zipfile.ZipFile, io.BufferedReader]:
         """
@@ -86,13 +86,11 @@ Creates a BindingDB instance from a URL containing a compressed SDF file, using streaming.
         Returns:
-            A BufferedReader instance containing the content of the SDF file.
+            A tuple containing the ZipFile instance and a BufferedReader instance containing the content of the SDF file.
         """
-        with urllib.request.urlopen(url) as response:
-            with zipfile.ZipFile(io.BytesIO(response.read())) as z:
-                sdf_name = z.namelist()[0]
-                with z.open(sdf_name) as sdf_file:
-                    sdf_content = io.BufferedReader(sdf_file)
-        return sdf_content
+        response = urllib.request.urlopen(url)
+        return BindingDB.from_compressed_file(io.BytesIO(response.read()))
 
     @staticmethod
-    def from_compressed_file(file_path: str) -> io.BufferedReader:
+    def from_compressed_file(
+        file_path: str,
+    ) -> Tuple[zipfile.ZipFile, io.BufferedReader]:
         """
@@ -105,9 +103,9 @@ Creates a BindingDB instance from a compressed SDF file.
         Returns:
-            A BufferedReader instance containing the content of the SDF file.
+            A tuple containing the ZipFile instance and a BufferedReader instance containing the content of the SDF file.
         """
-        with zipfile.ZipFile(file_path) as z:
-            sdf_name = z.namelist()[0]
-            with z.open(sdf_name) as sdf_file:
-                sdf_content = io.BufferedReader(sdf_file)
-        return sdf_content
+        zip_file = zipfile.ZipFile(file_path)
+        sdf_name = zip_file.namelist()[0]
+        sdf_file = zip_file.open(sdf_name)
+        sdf_content = io.BufferedReader(sdf_file)
+        return zip_file, sdf_content
 
@@ -125,3 +123,3 @@ @staticmethod
         """
-        return open(file_path, "rb")
+        return None, open(file_path, "rb")
 
@@ -165,4 +163,8 @@ def to_generator(self, progress_bar: bool = True) -> Generator[dict, None, None]:
 
+        self.fd.close()
+        if self.outer_fd is not None:
+            self.outer_fd.close()
+
         # Re-enable logging
         RDLogger.EnableLog("rdApp.error")
         RDLogger.EnableLog("rdApp.warning")

PKG-INFO

 Metadata-Version: 2.1
 Name: aiondata
-Version: 0.4.4
+Version: 0.4.5
 Summary: A common data access layer for AI-driven drug discovery.
@@ -5,0 +5,0 @@ Home-page: https://www.github.com/aion-labs/aiondata

pyproject.toml

 [tool.poetry]
 name = "aiondata"
-version = "0.4.4"
+version = "0.4.5"
 description = "A common data access layer for AI-driven drug discovery."
@@ -5,0 +5,0 @@ authors = ["JJ Ben-Joseph <[e-mail]>"]

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Improved metrics

Total package byte prevSize

50622

0.25%

Lines of code

580

0.17%