Merge 3e69505 into f298823

.travis.yml

@@ -1,5 +1,4 @@
-sudo: false
-dist: trusty
+dist: xenial
 
 git:
   depth: false
@@ -8,16 +7,15 @@ language: python
 
 python:
  - 3.6
-
-cache: pip
+ - 3.7
 
 install:
-  - pip install -r requirements.txt
+  - travis_retry pip install -r requirements.txt --progress-bar off
   # install testing requirements
-  - pip install pytest==5.2.0 pytest-cov==2.5.1 pytest-pep8 coveralls
+  - travis_retry pip install -r requirements-test.txt --progress-bar off
 
 script:
-  - python -m pytest --pep8 --cov=caliban_toolbox caliban_toolbox
+  - python -m pytest --cov=caliban_toolbox --pep8
 
 after_success:
   - coveralls

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.6
+FROM python:3.7
 
 # System maintenance
 RUN apt-get update && apt-get install -y \

caliban_toolbox/__init__.py

@@ -23,4 +23,25 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ==============================================================================
-"""Data Engineering Toolbox for DeepCell"""
+"""Data Engineering Toolbox for Caliban"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+from caliban_toolbox import pre_annotation
+# from caliban_toolbox import tracking
+from caliban_toolbox import utils
+from caliban_toolbox import aws_functions
+from caliban_toolbox import figure_eight_functions
+from caliban_toolbox import log_file
+from caliban_toolbox import relabel
+from caliban_toolbox import reshape_data
+
+from caliban_toolbox.pre_annotation import *
+# from caliban_toolbox.tracking import *
+from caliban_toolbox.utils import *
+
+del absolute_import
+del division
+del print_function

caliban_toolbox/aws_functions.py

@@ -23,18 +23,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ==============================================================================
-import sys
-import boto3
 import os
+import sys
 import threading
 import re
 
-from urllib.parse import urlencode
+import boto3
 
-import numpy as np
+from urllib.parse import urlencode
 from getpass import getpass
 
-from caliban_toolbox.utils.utils import get_img_names, list_npzs_folder
+from caliban_toolbox.utils.misc_utils import list_npzs_folder
 
 
 # Taken from AWS Documentation

caliban_toolbox/pre_annotation/__init__.py

@@ -0,0 +1,36 @@
+# Copyright 2016-2020 The Van Valen Lab at the California Institute of
+# Technology (Caltech), with support from the Paul Allen Family Foundation,
+# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
+# All rights reserved.
+#
+# Licensed under a modified Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.github.com/vanvalenlab/caliban-toolbox/LICENSE
+#
+# The Work provided may be used for non-commercial academic purposes only.
+# For any other use of the Work, including commercial use, please contact:
+# vanvalenlab@gmail.com
+#
+# Neither the name of Caltech nor the names of its contributors may be used
+# to endorse or promote products derived from this software without specific
+# prior written permission.
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+"""Caliban Toolbox Pre-Annotation Module"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+from caliban_toolbox.pre_annotation import data_loader
+
+del absolute_import
+del division
+del print_function