Merge branch 'dev' of github.com:USGS-Astrogeology/ISIS3 into stats (8c2d0ccc) · Commits · aflab / astrogeology / ISIS3

Jenkinsfile

+140 −59

Original line number	Diff line number	Diff line
		pipeline {
		agent none
		environment {
		ISISROOT="${workspace}" + "/build/"
		ISIS3TESTDATA="/usgs/cpkgs/isis3/testData/"
		ISIS3DATA="/usgs/cpkgs/isis3/data/"
		}
		stages {
		stage('Build') {
		parallel {
		stage('Fedora25') {
		agent {
		label 'isis-fedora-25'
		}
		steps {
		sh """
		conda env create -n isis3 -f environment.yml
		source activate isis3
		mkdir -p ./install ./build && cd build
		source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF -DCMAKE_INSTALL_PREFIX=../install -Disis3Data=/usgs/cpkgs/isis3/data -Disis3TestData=/usgs/cpkgs/isis3/testData ../isis
		set +e
		ninja -j8 && ninja install
		source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		ctest -V -R _unit_ --timeout 500
		ctest -V -R _app_ --timeout 500
		ctest -V -R _module_ --timeout 500
		"""
		}
		}
		stage('CentOS7') {
		agent {
		label 'isis-centos-7'
		}
		steps {
		sh """
		conda env create -n isis3 -f environment.yml
		source activate isis3
		cd build
		set +e
		source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		ctest -V -R _unit_ --timeout 500
		ctest -V -R _app_ --timeout 500
		ctest -V -R _module_ --timeout 500
		"""
		}
		}
		}
		}
		}
		// post {
		// success {
		// sh 'pwd && ls'
		// archiveArtifacts artifacts: "build/objects/*.o"
		// }
		// always {
		// mail to: 'ccombs@usgs.gov',
		// subject: "Build Finished: ${currentBuild.fullDisplayName}",
		// body: "Link: ${env.BUILD_URL}"
		// sh "rm -rf build/* && rm -rf install/*"
		// cleanWs()
		// }
		// }
		properties([pipelineTriggers([githubPush()])])

		def nodes = [:]

		nodes["isis-fedora-25"] = {
		node("isis-fedora-25") {
		withEnv(["ISISROOT=" + "${workspace}" + "/build/", "ISIS3TESTDATA=/usgs/cpkgs/isis3/testData/", "ISIS3DATA=/usgs/cpkgs/isis3/data/"]) {
		stage ("Fedora 25") {
		git branch: 'dev', url: 'https://github.com/USGS-Astrogeology/ISIS3.git'
		// sh """
		// git clone https://github.com/abseil/googletest.git gtest
		// conda config --set channel_alias http://astro-bin.wr.usgs.gov/conda
		// conda config --prepend channels anaconda
		// conda config --append channels conda-forge
		// conda config --append channels usgs-astrogeology
		// conda config --prepend default_channels anaconda
		// conda env create -n isis3 -f environment.yml
		// source activate isis3
		// mkdir -p ./install ./build && cd build
		// cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF -DCMAKE_INSTALL_PREFIX=../install -Disis3Data=/usgs/cpkgs/isis3/data -Disis3TestData=/usgs/cpkgs/isis3/testData ../isis
		// set +e
		// ninja -j8 && ninja install
		// source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		// ctest -V -R _unit_ --timeout 500
		// ctest -V -R _app_ --timeout 500
		// ctest -V -R _module_ --timeout 500
		// """
		}
		}
		}
		}

		nodes["isis-centos-7"] = {
		node("isis-centos-7") {
		withEnv(["ISISROOT=" + "${workspace}" + "/build/", "ISIS3TESTDATA=/usgs/cpkgs/isis3/testData/", "ISIS3DATA=/usgs/cpkgs/isis3/data/"]) {
		stage ("CentOS 7") {
		git branch: 'dev', url: 'https://github.com/USGS-Astrogeology/ISIS3.git'
		// sh """
		// git clone https://github.com/abseil/googletest.git gtest
		// conda config --set channel_alias http://astro-bin.wr.usgs.gov/conda
		// conda config --prepend channels anaconda
		// conda config --append channels conda-forge
		// conda config --append channels usgs-astrogeology
		// conda config --prepend default_channels anaconda
		// conda env create -n isis3 -f environment.yml
		// source activate isis3
		// mkdir -p ./install ./build && cd build
		// cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF -DCMAKE_INSTALL_PREFIX=../install -Disis3Data=/usgs/cpkgs/isis3/data -Disis3TestData=/usgs/cpkgs/isis3/testData ../isis
		// set +e
		// ninja -j8 && ninja install
		// source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		// ctest -V -R _unit_ --timeout 500
		// ctest -V -R _app_ --timeout 500
		// ctest -V -R _module_ --timeout 500
		// """
		}
		}
		}
		}

		nodes["isis-debian-9"] = {
		node("isis-debian-9") {
		withEnv(["ISISROOT=" + "${workspace}" + "/build/", "ISIS3TESTDATA=/usgs/cpkgs/isis3/testData/", "ISIS3DATA=/usgs/cpkgs/isis3/data/"]) {
		stage ("Debian 9") {
		git branch: 'dev', url: 'https://github.com/USGS-Astrogeology/ISIS3.git'
		// sh """
		// git clone https://github.com/abseil/googletest.git gtest
		// conda config --set channel_alias http://astro-bin.wr.usgs.gov/conda
		// conda config --prepend channels anaconda
		// conda config --append channels conda-forge
		// conda config --append channels usgs-astrogeology
		// conda config --prepend default_channels anaconda
		// conda env create -n isis3 -f environment.yml
		// source activate isis3
		// mkdir -p ./install ./build && cd build
		// cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF -DCMAKE_INSTALL_PREFIX=../install -Disis3Data=/usgs/cpkgs/isis3/data -Disis3TestData=/usgs/cpkgs/isis3/testData ../isis
		// set +e
		// ninja -j8 && ninja install
		// source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		// ctest -V -R _unit_ --timeout 500
		// ctest -V -R _app_ --timeout 500
		// ctest -V -R _module_ --timeout 500
		// """
		}
		}
		}
		}

		nodes["isis-ubuntu-1804"] = {
		node("isis-ubuntu-1804") {
		withEnv(["ISISROOT=" + "${workspace}" + "/build/", "ISIS3TESTDATA=/usgs/cpkgs/isis3/testData/", "ISIS3DATA=/usgs/cpkgs/isis3/data/"]) {
		stage ("Ubuntu 18.04") {
		git branch: 'dev', url: 'https://github.com/USGS-Astrogeology/ISIS3.git'
		// sh """
		// git clone https://github.com/abseil/googletest.git gtest
		// conda config --set channel_alias http://astro-bin.wr.usgs.gov/conda
		// conda config --prepend channels anaconda
		// conda config --append channels conda-forge
		// conda config --append channels usgs-astrogeology
		// conda config --prepend default_channels anaconda
		// conda env create -n isis3 -f environment.yml
		// source activate isis3
		// mkdir -p ./install ./build && cd build
		// cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF -DCMAKE_INSTALL_PREFIX=../install -Disis3Data=/usgs/cpkgs/isis3/data -Disis3TestData=/usgs/cpkgs/isis3/testData ../isis
		// set +e
		// ninja -j8 && ninja install
		// source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		// ctest -V -R _unit_ --timeout 500
		// ctest -V -R _app_ --timeout 500
		// ctest -V -R _module_ --timeout 500
		// """
		}
		}
		}
		}

		nodes["mac1013"] = {
		node("mac1013") {
		withEnv(["ISISROOT=" + "${workspace}" + "/build/", "ISIS3TESTDATA=/usgs/cpkgs/isis3/testData/", "ISIS3DATA=/usgs/cpkgs/isis3/data/"]) {
		stage ("MacOS 10.13 (High Sierra)") {
		git branch: 'dev', url: 'https://github.com/USGS-Astrogeology/ISIS3.git'
		// sh """
		// git clone https://github.com/abseil/googletest.git gtest
		// conda config --set channel_alias http://astro-bin.wr.usgs.gov/conda
		// conda config --prepend channels anaconda
		// conda config --append channels conda-forge
		// conda config --append channels usgs-astrogeology
		// conda config --prepend default_channels anaconda
		// conda env create -n isis3 -f environment.yml
		// source activate isis3
		// mkdir -p ./install ./build && cd build
		// cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF -DCMAKE_INSTALL_PREFIX=../install -Disis3Data=/usgs/cpkgs/isis3/data -Disis3TestData=/usgs/cpkgs/isis3/testData ../isis
		// set +e
		// ninja -j8 && ninja install
		// source /usgs/cpkgs/isis3/isis3mgr_scripts/initIsisCmake.sh .
		// ctest -V -R _unit_ --timeout 500
		// ctest -V -R _app_ --timeout 500
		// ctest -V -R _module_ --timeout 500
		// """
		}
		}
		}
		}

		parallel nodes

isis/src/base/apps/cubeit/cubeit.xml

+3 −0

Original line number	Diff line number	Diff line
		@@ -79,6 +79,9 @@
		Modified Makefile of badinputs app test to truncate paths before data directory. Allows tests
		to pass when not using the default data area. Fixes #4783.
		</change>
		<change name="Stuart Sides" date="2018-11-19">
		Removed the tracking label group if it exists in the output cube. Fixes #5533.
		</change>
		</history>

		<groups>

isis/src/base/apps/cubeit/main.cpp

+7 −0

Original line number	Diff line number	Diff line
		@@ -183,6 +183,13 @@ void IsisMain() {
		ocube->deleteBlob("Table", "InputImages");
		}

		// Delete the Tracking group if it exists (3.6.0 and up)
		// The tracking group could be transfered from the first input cube, but it does not
		// represent the images used in any other band after cubeit.
		if(ocube->hasGroup("Tracking")) {
		ocube->deleteGroup("Tracking");
		}

		p2.EndProcess();

		// Now loop and mosaic in each cube

isis/src/docsys/documents/InstallGuide/InstallGuide.xml

+54 −50

Original line number	Diff line number	Diff line
		@@ -34,20 +34,31 @@ you must <em>not</em> upgrade the ISIS Data Files!!!
		<ol>
		<li>Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large:
		<a href="https://www.anaconda.com/download">Anaconda installer</a>, <a href="https://conda.io/miniconda.html">Miniconda installer</a></li>
		<li>If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment.</li>

		<li>If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment.
		<pre>
		<strong>chmod +x Anaconda3-5.2.0-Linux-x86_64.sh</strong>
		<strong>./Anaconda3-5.2.0-Linux-x86_64.sh</strong>
		</pre>

		This will start the Anaconda installer which will guide you through the installation process.
		<li>After the installation has finished, open up a bash prompt in your terminal window.</li>
		This will start the Anaconda installer which will guide you through the installation process.</li>

		<li>If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86_64.pkg) will be downloaded. Double-click on the file to start the installation process.</li>
		<li>Again from within a terminal window, create a new environment for your ISIS3 installation:

		<li>After the installation has finished, open up a bash prompt in your terminal window.</li>

		<li>Next setup your Anaconda environment for ISIS3. In the bash prompt, run the following commands:
		<pre>
		<em>#Add the following channels to the Anaconda installation</em>
		<strong>conda config --add channels conda-forge</strong>
		<strong>conda config --add channels usgs-astrogeology</strong>
		<em>#Create a new conda environment to install ISIS3 in</em>
		<strong>conda create -n isis3 python=3.6</strong>

		<em>#Activate the environment</em>
		<em>#Depending on your OS, you may need to use conda activate isis3 instead</em>
		<strong>source activate isis3</strong>

		<em>#Add the following channels to the environment</em>
		<strong>conda config --env --add channels conda-forge</strong>
		<strong>conda config --env --add channels usgs-astrogeology</strong>

		#Verify you have the correct channels:
		<strong>conda config --show channels</strong>
		@@ -61,51 +72,41 @@ you must <em>not</em> upgrade the ISIS Data Files!!!

		<em>#The order is important. If conda-forge is before usgs-astrogeology, you will need to run:</em>

		<strong>conda config --add channels usgs-astrogeology</strong>
		<strong>conda config --env --add channels usgs-astrogeology</strong>
		</pre></li>


		<em>#Create a new conda environment to install ISIS3 in.</em>
		<strong>conda create -n isis3</strong>

		<em>#Activate the environment</em>
		<strong>source activate isis3</strong>

		<em>#Download the ISIS3 version</em>
		<li>The environment is now ready to download ISIS3 and its dependencies:
		<pre>
		<strong>conda install -c usgs-astrogeology isis3</strong>
		</pre></li>

		<li>Finally, setup the environment variables:
		<pre>
		<em>#Execute the ISIS3 variable initialization script with default arguments.</em>
		<em>#This script prepares default values for: $ISISROOT/$ISIS3DATA/$ISIS3TESTDATA</em>

		<strong>python $CONDA_PREFIX/scripts/isis3VarInit.py</strong>
		</pre>

		Executing this script with no arguments will result in $ISIS3DATA=$CONDA_PREFIX/data,
		and $ISIS3TESTDATA=$CONDA_PREFIX/testdata. The user can specify different directories
		for both of these optional values:

		<strong>./$CONDA_PREFIX/scripts/isis3VarInit --data-dir=[path to data directory] --test-dir=[path to test data directory]</strong>

		<pre>
		<strong>python $CONDA_PREFIX/scripts/isis3VarInit.py --data-dir=[path to data directory] --test-dir=[path to test data directory]</strong>
		</pre>

		Directions for running rsync to download ISIS3 data can be found <a href="#ISIS3DataDownload">here.</a>


		<em>#Run the source activate command a second time to process the changes:</em>

		<strong>source activate isis3</strong>

		To avoid having to do this every time you open a new terminal window, we suggest adding the following lines to the end of your .bashrc file
		(if running a variant of Linux) to ensure that conda is in your PATH variable. If you are running Mac OS X, these lines would be appended
		to the end of your .bash_profile file:


		<strong>source activate isis3</strong>
		<strong>python $CONDA_PREFIX/scripts/isis3VarInit.py</strong>
		Now everytime the isis3 environment is activated, $ISISROOT, $ISIS3DATA, and $ISIS3TESTDATA
		will be set to the values passed to isis3VarInit.py. This does not happen retroactively,
		re-activate the isis3 envionment with the following command:
		<pre>
		<em>#Depending on your OS, you may need to use conda activate isis3 instead</em>
		<strong>source activate isis3</strong>
		</pre></li>
		</ol>



		</pre>
		</li>
		</ol>
		<h3>Operating System Requirements</h3>
		<p>ISIS3 runs on many UNIX variants. ISIS does not run natively on MS Windows,
		although it has been successfully run on Windows 10 using the Windows
		@@ -117,12 +118,15 @@ you must <em>not</em> upgrade the ISIS Data Files!!!
		<li>Ubuntu 18.04 LTS</li>
		<li>Mac OS X 10.13.6 High Sierra</li>
		<li>Fedora 28</li>
		<li>CentOS 7.2</li>
		</ul>

		<p>
		ISIS3 may be run on other Linux or macOS operating systems then those listed above,
		but it has not been tested and is not supported.
		</p>


		<h3>Hardware Requirements</h3>
		<p>Here are the minimum hardware requirements</p>
		<ul>