Patch release with jpype1 moved to the extra dependencies (#365)

The `jpype1` dependency is not default anymore, and is included in the `cern` and `test` extras.
The package itself is now mock-imported  in the `timber_extract` module.

Author: fsoubelet

omc3/__init__.py

@@ -11,7 +11,7 @@
 __title__ = "omc3"
 __description__ = "An accelerator physics tools package for the OMC team at CERN."
 __url__ = "https://github.com/pylhc/omc3"
-__version__ = "0.2.3"
+__version__ = "0.2.4"
 __author__ = "pylhc"
 __author_email__ = "[email protected]"
 __license__ = "MIT"

omc3/tune_analysis/timber_extract.py

@@ -19,8 +19,8 @@
 
 import numpy as np
 import tfs
-from jpype import JException, java
 
+# from jpype import JException, java
 from omc3.tune_analysis import constants as const
 from omc3.utils import logging_tools
 from omc3.utils.mock import cern_network_import
@@ -32,6 +32,7 @@
 
 LOG = logging_tools.get_logger(__name__)
 pytimber = cern_network_import("pytimber")
+jpype = cern_network_import("jpype")
 
 MAX_RETRIES = 10  # number of retries on retryable exception
 AcceptableTimeStamp = NewType("AcceptableTimeStamp", Union[CERNDatetime, int, float])
@@ -60,7 +61,7 @@ def extract_between_times(
     t_start: AcceptableTimeStamp,
     t_end: AcceptableTimeStamp,
     keys: Sequence[str] = None,
-    names: Dict[str, str] = None
+    names: Dict[str, str] = None,
 ) -> tfs.TfsDataFrame:
     """
     Extracts data for keys between ``t_start`` and ``t_end`` from ``Timber``.
@@ -90,13 +91,15 @@ def extract_between_times(
         try:
             # We use timestamps to avoid any confusion with local time
             extract_dict = db.get(keys, t_start.timestamp(), t_end.timestamp())
-        except java.lang.IllegalStateException as e:
-            raise IOError("Could not get data from Timber, user probably has no access to NXCALS") from e
-        except JException as e:  # Might be a case for retries
-            if "RetryableException" in str(e) and (tries + 1) < MAX_RETRIES:
+        except jpype.java.lang.IllegalStateException as java_state_error:
+            raise IOError(
+                "Could not get data from Timber, user probably has no access to NXCALS"
+            ) from java_state_error
+        except jpype.JException as java_exception:  # Might be a case for retries
+            if "RetryableException" in str(java_exception) and (tries + 1) < MAX_RETRIES:
                 LOG.warning(f"Could not get data from Timber! Trial no {tries + 1} / {MAX_RETRIES}")
                 continue  # will go to the next iteratoin of the loop, so retry
-            raise IOError("Could not get data from timber!") from e
+            raise IOError("Could not get data from timber!") from java_exception
         else:
             break
 

omc3/utils/mock.py

@@ -20,6 +20,7 @@ class CERNNetworkMockPackage:
     actually installed. Designed for packages installable only from inside the CERN network,
     that are declared as ``cern`` extra. See module documentation.
     """
+
     def __init__(self, name: str):
         self.name = name
 

setup.py

@@ -2,7 +2,6 @@
 
 import setuptools
 
-
 # The directory containing this file
 TOPLEVEL_DIR = pathlib.Path(__file__).parent.absolute()
 ABOUT_FILE = TOPLEVEL_DIR / "omc3" / "__init__.py"
@@ -32,29 +31,30 @@
     "uncertainties>=3.1.4",
     "optics-functions>=0.1.0",
     "turn_by_turn>=0.2.0",
-    "jpype1>=1.3.0",
 ]
 
 # Extra dependencies
 EXTRA_DEPENDENCIES = {
     "cern": [
+        "jpype1>=1.3.0",
         "pytimber>=2.8.0",
     ],
     "test": [
         "pytest>=5.2",
         "pytest-cov>=2.7",
         "pytest-timeout>=1.4",
         "hypothesis>=5.0.0",
+        "jpype1>=1.3.0",
         "attrs>=19.2.0",
     ],
     "doc": [
         "sphinx",
         "travis-sphinx",
-        "sphinx_rtd_theme"
+        "sphinx_rtd_theme",
     ],
 }
 EXTRA_DEPENDENCIES.update(
-    {'all': [elem for list_ in EXTRA_DEPENDENCIES.values() for elem in list_]}
+    {"all": [elem for list_ in EXTRA_DEPENDENCIES.values() for elem in list_]}
 )
 
 
@@ -85,6 +85,6 @@
         "Topic :: Scientific/Engineering :: Visualization",
     ],
     install_requires=DEPENDENCIES,
-    tests_require=EXTRA_DEPENDENCIES['test'],
+    tests_require=EXTRA_DEPENDENCIES["test"],
     extras_require=EXTRA_DEPENDENCIES,
 )