modularize constants and fix imports

pepkit · Nov 16, 2017 · e9ecad2 · e9ecad2
1 parent cb37516
commit e9ecad2
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Showing 5 changed files with 34 additions and 23 deletions.
diff --git a/pep/__init__.py b/pep/__init__.py
@@ -14,11 +14,6 @@
 from .models import *
 
 
-FLAGS = ["completed", "running", "failed", "waiting", "partial"]
-
-GENERIC_PROTOCOL_KEY = "*"
-SAMPLE_INDEPENDENT_PROJECT_SECTIONS = \
-        ["metadata", "derived_columns", "implied_columns", "trackhubs"]
 LOGGING_LEVEL = "INFO"
 LOGGING_LOCATIONS = (stdout, )
 

diff --git a/pep/const.py b/pep/const.py
@@ -0,0 +1,30 @@
+""" Package constants """
+
+__author__ = "Vince Reuter"
+__email__ = "vreuter@virginia.edu"
+
+__all__ = ["ALL_INPUTS_ATTR_NAME", "COL_KEY_SUFFIX", "COMPUTE_SETTINGS_VARNAME",
+           "DATA_SOURCE_COLNAME", "DATA_SOURCES_SECTION",
+           "DEFAULT_COMPUTE_RESOURCES_NAME", "FLAGS",
+           "GENERIC_PROTOCOL_KEY", "REQUIRED_INPUTS_ATTR_NAME",
+           "SAMPLE_ANNOTATIONS_KEY", "SAMPLE_EXECUTION_TOGGLE",
+           "SAMPLE_NAME_COLNAME", "SAMPLE_INDEPENDENT_PROJECT_SECTIONS",
+           "VALID_READ_TYPES"]
+
+
+COMPUTE_SETTINGS_VARNAME = "PEPENV"
+DEFAULT_COMPUTE_RESOURCES_NAME = "default"
+SAMPLE_NAME_COLNAME = "sample_name"
+DATA_SOURCE_COLNAME = "data_source"
+SAMPLE_ANNOTATIONS_KEY = "sample_annotation"
+DATA_SOURCES_SECTION = "data_sources"
+SAMPLE_EXECUTION_TOGGLE = "toggle"
+COL_KEY_SUFFIX = "_key"
+VALID_READ_TYPES = ["single", "paired"]
+REQUIRED_INPUTS_ATTR_NAME = "required_inputs_attr"
+ALL_INPUTS_ATTR_NAME = "all_inputs_attr"
+FLAGS = ["completed", "running", "failed", "waiting", "partial"]
+GENERIC_PROTOCOL_KEY = "*"
+SAMPLE_INDEPENDENT_PROJECT_SECTIONS = \
+        ["metadata", "derived_columns", "implied_columns", "trackhubs"]
+
diff --git a/pep/models.py b/pep/models.py
@@ -68,6 +68,7 @@
 import pandas as _pd
 import yaml
 
+from .const import *
 from .utils import \
     add_project_sample_constants, alpha_cased, check_bam, check_fastq, \
     expandpath, get_file_size, grab_project_data, import_from_source, \
@@ -82,18 +83,6 @@
 __all__ = __functions__ + __classes__
 
 
-COMPUTE_SETTINGS_VARNAME = "PEPENV"
-DEFAULT_COMPUTE_RESOURCES_NAME = "default"
-SAMPLE_NAME_COLNAME = "sample_name"
-DATA_SOURCE_COLNAME = "data_source"
-SAMPLE_ANNOTATIONS_KEY = "sample_annotation"
-DATA_SOURCES_SECTION = "data_sources"
-SAMPLE_EXECUTION_TOGGLE = "toggle"
-COL_KEY_SUFFIX = "_key"
-VALID_READ_TYPES = ["single", "paired"]
-REQUIRED_INPUTS_ATTR_NAME = "required_inputs_attr"
-ALL_INPUTS_ATTR_NAME = "all_inputs_attr"
-
 ATTRDICT_METADATA = {"_force_nulls": False, "_attribute_identity": False}
 
 _LOGGER = logging.getLogger(__name__)

diff --git a/pep/utils.py b/pep/utils.py
@@ -1,7 +1,6 @@
 """ Helpers without an obvious logical home. """
 
 from collections import defaultdict, Iterable
-import copy
 import contextlib
 import logging
 import os
@@ -11,9 +10,7 @@
 
 import yaml
 
-from . import \
-    GENERIC_PROTOCOL_KEY, SAMPLE_INDEPENDENT_PROJECT_SECTIONS, \
-    SAMPLE_NAME_COLNAME
+from .const import GENERIC_PROTOCOL_KEY, SAMPLE_INDEPENDENT_PROJECT_SECTIONS
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -299,7 +296,7 @@ def sample_folder(prj, sample):
     :return str: this Project's root folder for the given Sample
     """
     return os.path.join(prj.metadata.results_subdir,
-                        sample[SAMPLE_NAME_COLNAME])
+                        sample["sample_name"])
 
 
 

diff --git a/tests/test_utils.py b/tests/test_utils.py
@@ -3,7 +3,7 @@
 import copy
 import mock
 import pytest
-from pep import SAMPLE_INDEPENDENT_PROJECT_SECTIONS, SAMPLE_NAME_COLNAME
+from pep.const import SAMPLE_INDEPENDENT_PROJECT_SECTIONS, SAMPLE_NAME_COLNAME
 from pep.models import AttributeDict, Project, Sample
 from pep.utils import add_project_sample_constants, grab_project_data
 from tests.helpers import named_param, nonempty_powerset