Merge pull request #138 from bourque/reorganize-repository

Reorganize repository
spacetelescope · Sep 11, 2018 · 2eb383c · 2eb383c
2 parents a159c66 + 56c61ae
commit 2eb383c
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Showing 34 changed files with 59 additions and 75 deletions.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -20,14 +20,9 @@ API documentation
    :caption: Contents:
 
    database.rst
-   logging.rst
-   monitor_filesystem.rst
-   monitor_mast.rst
-   permissions.rst
-   preview_image.rst
+   jwql_monitors.rst
    utils.rst
    tests.rst
-   monitor_filesystem.rst
 
 
 Indices and tables

diff --git a/docs/source/jwql_monitors.rst b/docs/source/jwql_monitors.rst
@@ -0,0 +1,15 @@
+*************
+jwql_monitors
+*************
+
+.. automodule:: jwql.jwql_monitors.monitor_filesystem
+    :members:
+    :undoc-members:
+
+.. automodule:: jwql.jwql_monitors.generate_preview_images
+    :members:
+    :undoc-members:
+
+.. automodule:: jwql.jwql_monitors.monitor_mast
+    :members:
+    :undoc-members:
diff --git a/docs/source/logging.rst b/docs/source/logging.rst
diff --git a/docs/source/monitor_filesystem.rst b/docs/source/monitor_filesystem.rst
diff --git a/docs/source/monitor_mast.rst b/docs/source/monitor_mast.rst
diff --git a/docs/source/permissions.rst b/docs/source/permissions.rst
diff --git a/docs/source/preview_image.rst b/docs/source/preview_image.rst
diff --git a/docs/source/tests.rst b/docs/source/tests.rst
@@ -4,12 +4,16 @@ tests
 
 .. automodule:: jwql.tests.test_monitor_mast
     :members:
+    :undoc-members:
 
 .. automodule:: jwql.tests.test_permissions
     :members:
+    :undoc-members:
 
-.. automodule:: jwql.tests.test_utils
+.. automodule:: jwql.tests.test_preview_image
     :members:
+    :undoc-members:
 
-.. automodule:: jwql.tests.test_preview_image
+.. automodule:: jwql.tests.test_utils
     :members:
+    :undoc-members:
diff --git a/docs/source/utils.rst b/docs/source/utils.rst
@@ -2,5 +2,18 @@
 utils
 *****
 
+.. automodule:: jwql.utils.logging_functions
+    :members:
+    :undoc-members:
+
+.. automodule:: jwql.utils.permissions
+    :members:
+    :undoc-members:
+
+.. automodule:: jwql.utils.preview_image
+    :members:
+    :undoc-members:
+
 .. automodule:: jwql.utils.utils
     :members:
+    :undoc-members:
diff --git a/jwql/__init__.py b/jwql/__init__.py
@@ -1 +0,0 @@
-from . import monitor_mast

diff --git a/jwql/database/database_interface.py b/jwql/database/database_interface.py
@@ -38,7 +38,7 @@
 from sqlalchemy.orm import sessionmaker
 from sqlalchemy.orm.query import Query
 
-from ..utils import utils
+from jwql.utils import utils
 
 
 SETTINGS = utils.get_config()

diff --git a/jwql/logging/__init__.py → jwql/instrument_monitors/__init__.py b/jwql/logging/__init__.py → jwql/instrument_monitors/__init__.py
diff --git a/jwql/monitor_filesystem/__init__.py → ...ment_monitors/common_monitors/__init__.py b/jwql/monitor_filesystem/__init__.py → ...ment_monitors/common_monitors/__init__.py
diff --git a/jwql/monitor_mast/__init__.py → ...trument_monitors/fgs_monitors/__init__.py b/jwql/monitor_mast/__init__.py → ...trument_monitors/fgs_monitors/__init__.py
diff --git a/jwql/permissions/__init__.py → ...rument_monitors/miri_monitors/__init__.py b/jwql/permissions/__init__.py → ...rument_monitors/miri_monitors/__init__.py
diff --git a/jwql/preview_image/__init__.py → ...ment_monitors/nircam_monitors/__init__.py b/jwql/preview_image/__init__.py → ...ment_monitors/nircam_monitors/__init__.py
diff --git a/jwql/instrument_monitors/niriss_monitors/__init__.py b/jwql/instrument_monitors/niriss_monitors/__init__.py
diff --git a/jwql/instrument_monitors/nirspec_monitors/__init__.py b/jwql/instrument_monitors/nirspec_monitors/__init__.py
diff --git a/jwql/jwql_monitors/__init__.py b/jwql/jwql_monitors/__init__.py
diff --git a/.../preview_image/generate_preview_images.py → .../jwql_monitors/generate_preview_images.py b/.../preview_image/generate_preview_images.py → .../jwql_monitors/generate_preview_images.py
@@ -33,11 +33,11 @@
 
 import numpy as np
 
-from jwql.logging.logging_functions import configure_logging
-from jwql.logging.logging_functions import log_info
-from jwql.logging.logging_functions import log_fail
-from jwql.permissions import permissions
-from jwql.preview_image.preview_image import PreviewImage
+from jwql.utils import permissions
+from jwql.utils.logging_functions import configure_logging
+from jwql.utils.logging_functions import log_info
+from jwql.utils.logging_functions import log_fail
+from jwql.utils.preview_image import PreviewImage
 from jwql.utils.utils import get_config
 from jwql.utils.utils import filename_parser
 from jwql.utils.utils import NIRCAM_LONGWAVE_DETECTORS
@@ -60,10 +60,10 @@ def array_coordinates(channelmod, detector_list, lowerleft_list):
     channelmod : str
         Indicator of the NIRCam channel/module of the data.
         Options are:
-            ``LW`` - for longwave channel data
-            ``SWA`` - for shortwave A module only (4 detectors) data
-            ``SWB`` - for shortwave B module only (4 detectors) data
-            ``SW`` - for shortwave both module data (8 detectors)
+        ``LW`` - for longwave channel data
+        ``SWA`` - for shortwave A module only (4 detectors) data
+        ``SWB`` - for shortwave B module only (4 detectors) data
+        ``SW`` - for shortwave both module data (8 detectors)
 
     detector_list : list
         List of detectors used in data to be simulated

diff --git a/.../monitor_filesystem/monitor_filesystem.py → jwql/jwql_monitors/monitor_filesystem.py b/.../monitor_filesystem/monitor_filesystem.py → jwql/jwql_monitors/monitor_filesystem.py
@@ -70,8 +70,8 @@
 from bokeh.layouts import gridplot
 from bokeh.plotting import figure, output_file, save
 
-from jwql.logging.logging_functions import configure_logging, log_info, log_fail
-from jwql.permissions.permissions import set_permissions
+from jwql.utils.logging_functions import configure_logging, log_info, log_fail
+from jwql.utils.permissions import set_permissions
 from jwql.utils.utils import filename_parser
 from jwql.utils.utils import get_config
 

diff --git a/jwql/monitor_mast/monitor_mast.py → jwql/jwql_monitors/monitor_mast.py b/jwql/monitor_mast/monitor_mast.py → jwql/jwql_monitors/monitor_mast.py
@@ -24,8 +24,8 @@
 from bokeh.embed import components
 import pandas as pd
 
-from jwql.logging.logging_functions import configure_logging, log_info, log_fail
-from jwql.permissions.permissions import set_permissions
+from jwql.utils.logging_functions import configure_logging, log_info, log_fail
+from jwql.utils.permissions import set_permissions
 from jwql.utils.utils import get_config, JWST_DATAPRODUCTS, JWST_INSTRUMENTS
 
 

diff --git a/jwql/tests/test_monitor_mast.py b/jwql/tests/test_monitor_mast.py
@@ -17,8 +17,8 @@
         pytest -s test_monitor_mast.py
 """
 
-from ..monitor_mast import monitor_mast as mm
-from ..utils.utils import JWST_INSTRUMENTS
+from jwql.jwql_monitors import monitor_mast as mm
+from jwql.utils.utils import JWST_INSTRUMENTS
 
 
 def test_caom_instrument_keywords():

diff --git a/jwql/tests/test_permissions.py b/jwql/tests/test_permissions.py
@@ -23,7 +23,7 @@
 import os
 import pytest
 
-from jwql.permissions.permissions import set_permissions, has_permissions, \
+from jwql.utils.permissions import set_permissions, has_permissions, \
     get_owner_string, get_group_string
 
 # directory to be created and populated during tests running

diff --git a/jwql/tests/test_preview_image.py b/jwql/tests/test_preview_image.py
@@ -25,14 +25,15 @@
 
 from astropy.io import fits
 
-from jwql.preview_image.preview_image import PreviewImage
+from jwql.utils.preview_image import PreviewImage
 
 # directory to be created and populated during tests running
 TEST_DIRECTORY = os.path.join(os.environ['HOME'], 'preview_image_test')
 
 # directory that contains sample images
 TEST_DATA_DIRECTORY = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'test_data')
 
+
 @pytest.fixture(scope="module")
 def test_directory(test_dir=TEST_DIRECTORY):
     """Create a test directory for preview image.

diff --git a/jwql/logging/logging_functions.py → jwql/utils/logging_functions.py b/jwql/logging/logging_functions.py → jwql/utils/logging_functions.py
@@ -65,7 +65,7 @@ def my_main_function():
 
 from functools import wraps
 
-from jwql.permissions.permissions import set_permissions
+from jwql.utils.permissions import set_permissions
 from jwql.utils.utils import get_config, ensure_dir_exists
 
 LOG_FILE_LOC = ''

diff --git a/jwql/permissions/permissions.py → jwql/utils/permissions.py b/jwql/permissions/permissions.py → jwql/utils/permissions.py
diff --git a/jwql/preview_image/preview_image.py → jwql/utils/preview_image.py b/jwql/preview_image/preview_image.py → jwql/utils/preview_image.py
@@ -41,7 +41,7 @@
 from jwst.datamodels import dqflags
 import numpy as np
 
-from jwql.permissions import permissions
+from jwql.utils import permissions
 
 # Use the 'Agg' backend to avoid invoking $DISPLAY
 import matplotlib

diff --git a/jwql/utils/utils.py b/jwql/utils/utils.py
@@ -25,7 +25,7 @@
 import os
 import re
 
-from ..permissions import permissions
+from jwql.utils import permissions
 
 __location__ = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__)))
 
@@ -52,7 +52,6 @@
 NIRCAM_LONGWAVE_DETECTORS = ['NRCA5', 'NRCB5']
 
 
-
 def ensure_dir_exists(fullpath):
     """Creates dirs from ``fullpath`` if they do not already exist.
     """

diff --git a/jwql/website/apps/jwql/data_containers.py b/jwql/website/apps/jwql/data_containers.py
@@ -27,14 +27,15 @@
 from astropy.io import fits
 import numpy as np
 
-from jwql.preview_image.preview_image import PreviewImage
+from jwql.utils.preview_image import PreviewImage
 from jwql.utils.utils import get_config, filename_parser, MONITORS
 
 __location__ = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__)))
 FILESYSTEM_DIR = os.path.join(get_config()['jwql_dir'], 'filesystem')
 PACKAGE_DIR = os.path.dirname(__location__.split('website')[0])
 REPO_DIR = os.path.split(PACKAGE_DIR)[0]
 
+
 def get_acknowledgements():
     """Returns a list of individuals who are acknowledged on the
     ``about`` page.

diff --git a/typing_demo/typing_demo_1.py → style_guide/typing_demo/typing_demo_1.py b/typing_demo/typing_demo_1.py → style_guide/typing_demo/typing_demo_1.py
diff --git a/typing_demo/typing_demo_2.py → style_guide/typing_demo/typing_demo_2.py b/typing_demo/typing_demo_2.py → style_guide/typing_demo/typing_demo_2.py
diff --git a/typing_demo/typing_demo_3.py → style_guide/typing_demo/typing_demo_3.py b/typing_demo/typing_demo_3.py → style_guide/typing_demo/typing_demo_3.py
diff --git a/typing_demo/typing_demo_4.py → style_guide/typing_demo/typing_demo_4.py b/typing_demo/typing_demo_4.py → style_guide/typing_demo/typing_demo_4.py