Merge a67212f into 9e25f6f

.github/workflows/release-workflow.yml

@@ -101,7 +101,7 @@ jobs:
     - name: Install conda environment py310
       uses: conda-incubator/setup-miniconda@v2
       with:
-        activate-environment: py39
+        activate-environment: py310
         environment-file: environment.ubuntu.singularity.yml
         auto-activate-base: false
     - name: Install dependencies

kipoi_containers/zenodoclient.py

@@ -2,6 +2,8 @@
 import os
 from pathlib import Path
 import requests
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry
 from typing import Dict, Tuple, Union
 
 
@@ -15,11 +17,21 @@ def __init__(self) -> None:
         self.params = {
             "access_token": os.environ.get("ZENODO_ACCESS_TOKEN", "")
         }
+        retry_strategy = Retry(
+            total=3,
+            backoff_factor=1,
+            status_forcelist=[429, 500, 502, 503, 504],
+            allowed_methods=["GET", "PUT", "DELETE"],
+        )
+        adapter = HTTPAdapter(max_retries=retry_strategy)
+        self.session = requests.Session()
+        self.session.mount("https://", adapter)
+        self.session.mount("http://", adapter)
 
     def get_content(self, url: str, **kwargs) -> Dict:
         """Performs GET request to an url and returns the
         response body"""
-        response = requests.get(url, params=self.params | kwargs)
+        response = self.session.get(url, params=self.params | kwargs)
         response.raise_for_status()
         return response.json()
 
@@ -28,11 +40,11 @@ def put_content(self, url: str, data: Union[Path, Dict], **kwargs) -> Dict:
         or a dict and returns the response body"""
         if isinstance(data, Path):
             with open(data, "rb") as file_handle:
-                response = requests.put(
+                response = self.session.put(
                     url, data=file_handle, params=(self.params | kwargs)
                 )
         else:
-            response = requests.put(
+            response = self.session.put(
                 url,
                 data=json.dumps(data),
                 params=(self.params | kwargs),
@@ -51,7 +63,7 @@ def post_content(self, url: str, **kwargs) -> Tuple[int, Dict]:
     def delete_content(self, url: str, **kwargs) -> None:
         # Assumption: There will always be one file associated with each version
         """Performs DELETE request to an url"""
-        response = requests.delete(
+        response = self.session.delete(
             url,
             params=(self.params | kwargs),
         )

setup.py

@@ -15,6 +15,7 @@
     "spython",
     "pre-commit",
     "click",
+    "kipoi",
 ]
 setup_requirements = []
 
@@ -38,10 +39,7 @@
             "update_all_singularity=kipoi_containers.update_all_singularity_images:run_update",
         ],
     },
-    install_requires=[
-        requirements,
-        "kipoi @ https://github.com/kipoi/kipoi/archive/master.tar.gz",
-    ],
+    install_requires=requirements,
     license="MIT license",
     include_package_data=True,
     keywords="kipoi_containers",