Merge pull request #27 from pepkit/dev

Dev

divvy/_version.py

@@ -1,2 +1,2 @@
-__version__ = "0.2"
+__version__ = "0.2.1"
 

divvy/compute.py

@@ -6,7 +6,7 @@
 from sys import stdout
 import yaml
 
-from attmap import AttMap
+from attmap import PathExAttMap
 from .const import \
     COMPUTE_SETTINGS_VARNAME, \
     DEFAULT_COMPUTE_RESOURCES_NAME
@@ -16,7 +16,7 @@
 _LOGGER = logging.getLogger(__name__)
 
 
-class ComputingConfiguration(AttMap):
+class ComputingConfiguration(PathExAttMap):
     """
     Represents computing configuration objects.
 
@@ -147,7 +147,7 @@ def activate_package(self, package_name):
             # Augment compute, creating it if needed.
             if self.compute is None:
                 _LOGGER.debug("Creating Project compute")
-                self.compute = AttMap()
+                self.compute = PathExAttMap()
                 _LOGGER.debug("Adding entries for package_name '%s'", package_name)
             self.compute.add_entries(self.compute_packages[package_name])
 
@@ -186,7 +186,7 @@ def get_active_package(self):
         """
         Returns settings for the currently active compute package
 
-        :return AttMap: data defining the active compute package
+        :return PathExAttMap: data defining the active compute package
         """
         return self.compute
 
@@ -204,7 +204,7 @@ def reset_active_settings(self):
         
         :return bool: success flag
         """
-        self.compute = AttMap()
+        self.compute = PathExAttMap()
         return True
 
     def update_packages(self, config_file):
@@ -241,7 +241,7 @@ def update_packages(self, config_file):
                                     loaded_packages[key][key2])
 
             if self.compute_packages is None:
-                self.compute_packages = AttMap(loaded_packages)
+                self.compute_packages = PathExAttMap(loaded_packages)
             else:
                 self.compute_packages.add_entries(loaded_packages)
         _LOGGER.info("Available packages: {}".format(', '.join(self.list_compute_packages())))

divvy/utils.py

@@ -351,7 +351,7 @@ def sample_folder(prj, sample):
     """
     Get the path to this Project's root folder for the given Sample.
 
-    :param AttMap | Project prj: project with which sample is associated
+    :param PathExAttMap | Project prj: project with which sample is associated
     :param Mapping sample: Sample or sample data for which to get root output
         folder path.
     :return str: this Project's root folder for the given Sample
@@ -430,18 +430,14 @@ class CommandChecker(object):
     """
     Validate PATH availability of executables referenced by a config file.
 
-    :param path_conf_file: path to configuration file with
+    :param str path_conf_file: path to configuration file with
         sections detailing executable tools to validate
-    :type path_conf_file: str
-    :param sections_to_check: names of
+    :param Iterable[str] sections_to_check: names of
         sections of the given configuration file that are relevant;
         optional, will default to all sections if not given, but some
         may be excluded via another optional parameter
-    :type sections_to_check: Iterable[str]
-    :param sections_to_skip: analogous to
+    :param Iterable[str] sections_to_skip: analogous to
         the check names parameter, but for specific sections to skip.
-    :type sections_to_skip: Iterable[str]
-
     """
 
 

docs/changelog.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## divvy [0.2.1] - 2019-03-19
+
+### Changed
+- For environment variable population, use updated version of `attmap`
+
 ## divvy [0.2] - 2019-03-13
 
 ### Added

requirements/requirements-all.txt

@@ -1,4 +1,5 @@
 pandas>=0.20.2
 pyyaml>=3.12
 nbsphinx
-attmap>=0.2
+attmap>=0.4
+

tests/divvy_tests/test_divvy.py

@@ -1,5 +1,5 @@
 import pytest
-from attmap import AttMap
+from attmap import PathExAttMap
 from tests.conftest import DCC_ATTRIBUTES, FILES
 
 class DefaultDCCTests:
@@ -51,9 +51,9 @@ class GettingActivePackageTests:
     """ Test for the get_active_package method"""
 
     def test_settings_nonempty(self, dcc):
-        """ Test if get_active_package produces a nonempty AttMap object """
+        """ Test if get_active_package produces a nonempty PathExAttMap object """
         settings = dcc.get_active_package()
-        assert settings != AttMap()
+        assert settings != PathExAttMap()
 
 
 class ListingPackagesTests:
@@ -88,7 +88,7 @@ class UpdatingPackagesTests:
     def test_update_packages(self, dcc, config_file):
         """ Test updating does not produce empty compute packages """
         dcc.update_packages(config_file)
-        assert dcc.compute_packages != AttMap()
+        assert dcc.compute_packages != PathExAttMap()