Update for v0.2.

Author: pichuan

README.md

@@ -47,8 +47,7 @@ cd deepconsensus
 source install.sh
 ```
 
-If you have GPU, run `source install-gpu.sh` instead, which will use
-`requirements-gpu.txt` instead of `requirements.txt`. Currently the only
+If you have GPU, run `source install-gpu.sh` instead. Currently the only
 difference is that the GPU version installs `tensorflow-gpu` instead of
 `intel-tensorflow`.
 

install-gpu.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+# Copyright (c) 2021, Google Inc.
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+# 
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# 3. Neither the name of Google Inc. nor the names of its contributors
+#    may be used to endorse or promote products derived from this software without
+#    specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# Usage:  source install.sh
+#
+# This script installs all the packages required to build DeepConsensus.
+#
+# This script will run as-is on Ubuntu 20.04.
+#
+# We also assume that apt-get is already installed and available.
+
+function note_build_stage {
+  echo "========== [$(date)] Stage '${1}' starting"
+}
+
+# Update package list
+################################################################################
+note_build_stage "Update package list"
+sudo -H apt-get -qq -y update
+
+# Install pip
+################################################################################
+note_build_stage "Update pip"
+sudo -H apt-get -y install python3-dev python3-pip
+sudo -H apt-get -y update
+python3 -m pip install --upgrade pip
+
+# Update PATH so that newly installed pip is the one we actually use.
+export PATH="$HOME/.local/bin:$PATH"
+echo "$(pip --version)"
+
+# Install python packages used by DeepConsensus.
+################################################################################
+python3 -m pip install --user -r requirements.txt
+python3 -m pip install --user "tensorflow-gpu>=2.4.0,<=2.7.0"

install.sh

@@ -57,3 +57,4 @@ echo "$(pip --version)"
 # Install python packages used by DeepConsensus.
 ################################################################################
 python3 -m pip install --user -r requirements.txt
+python3 -m pip install --user "intel-tensorflow>=2.4.0,<=2.7.0"

run_all_tests.sh

@@ -27,23 +27,23 @@
 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 # Script to test DeepConsensus.
-# Tested with Python3.6.
+# Tested with Python3.8.
 # Before running this, run:
 #   source install.sh
 
 set -euo pipefail
 
+python3 -m deepconsensus.inference.quick_inference_test
 python3 -m deepconsensus.models.data_providers_test
 python3 -m deepconsensus.models.losses_and_metrics_test
-python3 -m deepconsensus.models.model_inference_test
 python3 -m deepconsensus.models.model_inference_transforms_test
-python3 -m deepconsensus.models.model_train_custom_loop_test
-python3 -m deepconsensus.models.model_utils_test
 python3 -m deepconsensus.models.networks_test
 python3 -m deepconsensus.postprocess.stitch_utils_test
-python3 -m deepconsensus.preprocess.generate_input_test
-python3 -m deepconsensus.preprocess.generate_input_transforms_test
-python3 -m deepconsensus.preprocess.merge_datasets_test
-python3 -m deepconsensus.preprocess.merge_datasets_transforms_test
-python3 -m deepconsensus.preprocess.preprocess_utils_test
+python3 -m deepconsensus.preprocess.preprocess_test
+python3 -m deepconsensus.preprocess.utils_test
 python3 -m deepconsensus.utils.utils_test
+
+# These tests take longer to run.
+python3 -m deepconsensus.models.model_inference_test
+python3 -m deepconsensus.models.model_train_custom_loop_test
+python3 -m deepconsensus.models.model_utils_test