Merge pull request #179 from cgat-developers/AC-aws

included S3 decorators

Author: Acribbs

.gitignore

@@ -59,3 +59,5 @@ _test_commandline.yaml
 # sample workflow
 means.txt
 sample*
+
+.idea

all-tests.sh

@@ -17,3 +17,4 @@ pytest -v tests/test_pipeline_execution.py
 pytest -v tests/test_pipeline_cli.py
 pytest -v tests/test_pipeline_actions.py
 pytest -v tests/test_execution_cleanup.py
+pytest -v tests/test_s3_decorators.py

cgatcore/__init__.py

@@ -0,0 +1,28 @@
+# cgatcore/__init__.py
+
+
+class CgatCore:
+    """Main class to encapsulate CGAT core functionality with lazy loading."""
+
+    def __init__(self):
+        self._pipeline = None
+        self._remote = None
+
+    @property
+    def pipeline(self):
+        """Lazy load the pipeline module."""
+        if self._pipeline is None:
+            from cgatcore import pipeline
+            self._pipeline = pipeline
+        return self._pipeline
+
+    def get_remote(self):
+        """Dynamically load and return the remote module when explicitly called."""
+        if self._remote is None:
+            from cgatcore import remote
+            self._remote = remote
+        return self._remote
+
+
+# Create a global instance of the CgatCore class
+cgatcore = CgatCore()

cgatcore/experiment.py

@@ -297,13 +297,13 @@ class method (:func:`cached_method`) calls.
 import functools
 import gzip
 import warnings
-import pipes
 import optparse
 import argparse
 import textwrap
 import random
 import uuid
 import yaml
+import shlex as pipes  # Use shlex as a replacement for pipes
 # import convenience functions from logging
 import logging
 import logging.config