Merge branch 'allow-timeout-as-number' into new-new-copier

hail/Makefile

@@ -181,8 +181,7 @@ $(FAST_PYTHON_JAR_EXTRA_CLASSPATH): build.gradle
 python-jar: $(PYTHON_JAR)
 
 .PHONY: pytest
-pytest: $(PYTHON_VERSION_INFO) $(INIT_SCRIPTS)
-pytest: python/README.md $(FAST_PYTHON_JAR) $(FAST_PYTHON_JAR_EXTRA_CLASSPATH)
+pytest: install-editable
 	cd python && \
           $(HAIL_PYTHON3) -m pytest \
             -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
@@ -202,8 +201,7 @@ pytest: python/README.md $(FAST_PYTHON_JAR) $(FAST_PYTHON_JAR_EXTRA_CLASSPATH)
 
 # NOTE: Look at upload-remote-test-resources target if test resources are missing
 .PHONY: pytest-inter-cloud
-pytest-inter-cloud: install-editable
-pytest-inter-cloud: upload-remote-test-resources
+pytest-inter-cloud: upload-remote-test-resources install-editable
 	cd python && \
           HAIL_TEST_STORAGE_URI=$(TEST_STORAGE_URI) \
           HAIL_TEST_GCS_BUCKET=$(HAIL_TEST_GCS_BUCKET) \
@@ -349,15 +347,20 @@ upload-artifacts: $(WHEEL)
 # NOTE: 1-day expiration of the test bucket means that this
 # target must be run at least once a day. To trigger this target to re-run,
 # > rm upload-remote-test-resources
+upload-remote-test-resources: install-editable
 upload-remote-test-resources: $(shell git ls-files src/test/resources)
 upload-remote-test-resources: $(shell git ls-files python/hail/docs/data)
 	# # If hailtop.aiotools.copy gives you trouble:
 	# gcloud storage cp -r src/test/resources/\* $(CLOUD_HAIL_TEST_RESOURCES_DIR)
 	# gcloud storage cp -r python/hail/docs/data/\* $(CLOUD_HAIL_DOCTEST_DATA_DIR)
-	python3 -m hailtop.aiotools.copy -vvv 'null' '[\
-             {"from":"src/test/resources","to":"$(CLOUD_HAIL_TEST_RESOURCES_DIR)"},\
-             {"from":"python/hail/docs/data","to":"$(CLOUD_HAIL_DOCTEST_DATA_DIR)"}\
-        ]' --timeout 600
+	python3 -m hailtop.aiotools.copy \
+            -vvv \
+            'null' \
+            "[\
+              {\"from\":\"src/test/resources\",\"to\":\"$(CLOUD_HAIL_TEST_RESOURCES_DIR)\"}, \
+              {\"from\":\"python/hail/docs/data\",\"to\":\"$(CLOUD_HAIL_DOCTEST_DATA_DIR)\"} \
+             ]" \
+            --timeout 600
 	touch $@
 
 # NOTE: 1-day expiration of the test bucket means that this

hail/python/hailtop/aiocloud/aioaws/fs.py

@@ -1,5 +1,19 @@
-from typing import Any, AsyncIterator, BinaryIO, cast, AsyncContextManager, Dict, List, Optional, Set, Tuple, Type
+from typing import (
+    Any,
+    AsyncIterator,
+    BinaryIO,
+    cast,
+    AsyncContextManager,
+    Dict,
+    List,
+    Optional,
+    Set,
+    Tuple,
+    Type,
+    Union,
+)
 from types import TracebackType
+import aiohttp
 import sys
 from concurrent.futures import ThreadPoolExecutor
 import os.path
@@ -341,12 +355,32 @@ def __init__(
         max_workers: Optional[int] = None,
         *,
         max_pool_connections: int = 10,
+        timeout: Optional[Union[int, float, aiohttp.ClientTimeout]] = None,
     ):
         if not thread_pool:
             thread_pool = ThreadPoolExecutor(max_workers=max_workers)
         self._thread_pool = thread_pool
+
+        kwargs = {}
+        if isinstance(timeout, aiohttp.ClientTimeout):
+            if timeout.sock_read:
+                kwargs['read_timeout'] = timeout.sock_read
+            elif timeout.total:
+                kwargs['read_timeout'] = timeout.total
+
+            if timeout.sock_connect:
+                kwargs['connect_timeout'] = timeout.sock_connect
+            elif timeout.connect:
+                kwargs['connect_timeout'] = timeout.connect
+            elif timeout.total:
+                kwargs['connect_timeout'] = timeout.total
+        elif isinstance(timeout, (int, float)):
+            kwargs['read_timeout'] = timeout
+            kwargs['connect_timeout'] = timeout
+
         config = botocore.config.Config(
             max_pool_connections=max_pool_connections,
+            **kwargs,
         )
         self._s3 = boto3.client('s3', config=config)
 

hail/python/hailtop/aiocloud/aioazure/fs.py

@@ -1,6 +1,7 @@
 from typing import Any, AsyncContextManager, AsyncIterator, Dict, List, Optional, Set, Tuple, Type, Union
 from types import TracebackType
 
+import aiohttp
 import abc
 import re
 import os
@@ -372,7 +373,13 @@ async def wrapped(self: 'AzureAsyncFS', url, *args, **kwargs):
 class AzureAsyncFS(AsyncFS):
     PATH_REGEX = re.compile('/(?P<container>[^/]+)(?P<name>.*)')
 
-    def __init__(self, *, credential_file: Optional[str] = None, credentials: Optional[AzureCredentials] = None):
+    def __init__(
+        self,
+        *,
+        credential_file: Optional[str] = None,
+        credentials: Optional[AzureCredentials] = None,
+        timeout: Optional[Union[int, float, aiohttp.ClientTimeout]] = None,
+    ):
         if credentials is None:
             scopes = ['https://storage.azure.com/.default']
             if credential_file is not None:
@@ -382,6 +389,16 @@ def __init__(self, *, credential_file: Optional[str] = None, credentials: Option
         elif credential_file is not None:
             raise ValueError('credential and credential_file cannot both be defined')
 
+        if isinstance(timeout, aiohttp.ClientTimeout):
+            self.read_timeout = timeout.sock_read or timeout.total or 5
+            self.connection_timeout = timeout.sock_connect or timeout.connect or timeout.total or 5
+        elif isinstance(timeout, (int, float)):
+            self.read_timeout = timeout
+            self.connection_timeout = timeout
+        else:
+            self.read_timeout = 5
+            self.connection_timeout = 5
+
         self._credential = credentials.credential
         self._blob_service_clients: Dict[Tuple[str, str, Union[AzureCredentials, str, None]], BlobServiceClient] = {}
 
@@ -482,8 +499,8 @@ def get_blob_service_client(self, account: str, container: str, token: Optional[
             self._blob_service_clients[k] = BlobServiceClient(
                 f'https://{account}.blob.core.windows.net',
                 credential=credential,  # type: ignore
-                connection_timeout=5,
-                read_timeout=5,
+                connection_timeout=self.connection_timeout,
+                read_timeout=self.read_timeout,
             )
         return self._blob_service_clients[k]
 

hail/python/hailtop/aiotools/copy.py

@@ -200,7 +200,6 @@ async def main() -> None:
     timeout = args.timeout
     if timeout:
         timeout = float(timeout)
-    print(timeout)
     gcs_kwargs = {
         'gcs_requester_pays_configuration': requester_pays_project,
         'timeout': timeout,