.appveyor.yml
.coveragerc
.gitignore
.gitmodules
.nojekyll
.travis.yml
LICENSE
MANIFEST.in
README.md
setup.py
.idea/vcs.xml
development/release
development/update_docker.sh
development/update_ec2_docker.sh
development/docker-base/Dockerfile
development/docker-base/README.md
development/docker-demo/Dockerfile
development/docker-demo/examples/DEG_list.xlsx
development/docker-demo/examples/HomePage_Example_1.ipynb
development/docker-demo/examples/HomePage_Example_2.ipynb
development/docker-demo/examples/HomePage_Example_3.ipynb
development/docker-demo/examples/Video-Input-Group.ipynb
development/docker-demo/examples/Video-Overview-of-SoS-Notebook.ipynb
development/docker-demo/examples/Video-Overview-of-SoS-Workflow-Engine.ipynb
development/docker-demo/examples/Video-Script-Format-of-Function-Calls.ipynb
development/docker-demo/examples/Video-Step-Output.ipynb
development/docker-demo/examples/count_reads
development/docker-demo/examples/JupyterCon18/1_Expand_and_Capture.ipynb
development/docker-demo/examples/JupyterCon18/2_Data_Exchange.ipynb
development/docker-demo/examples/JupyterCon18/3_SoS_Magics.ipynb
development/docker-demo/examples/JupyterCon18/4_Notebook_to_Workflow.ipynb
development/docker-demo/examples/JupyterCon18/5_Workflow_features.ipynb
development/docker-demo/examples/JupyterCon18/6_Task.ipynb
development/docker-demo/examples/JupyterCon18/7_Docker.ipynb
development/docker-demo/examples/JupyterCon18/data/DEG.xlsx
development/docker-demo/examples/JupyterCon18/data/S20_R1.fastq
development/docker-demo/examples/JupyterCon18/data/S20_R2.fastq
development/docker-demo/examples/WP_2019_SoS_Manuscript/WP2019_Mixed_Style.ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/WP2019_Mixed_Style_Data_Flow.ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/WP2019_Outcome_Oriented.ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/WP2019_Outcome_Oriented_Modular.ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/WP2019_Outcome_Oriented_Step_Targets.ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/WP2019_Process_Oriented.ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/WP2019_Process_Oriented_Modular.ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/sos2ipynb
development/docker-demo/examples/WP_2019_SoS_Manuscript/regression_modules/evaluate.R
development/docker-demo/examples/WP_2019_SoS_Manuscript/regression_modules/lasso.py
development/docker-demo/examples/WP_2019_SoS_Manuscript/regression_modules/ridge.R
development/docker-demo/examples/WP_2019_SoS_Manuscript/regression_modules/simulate.R
development/docker-notebook/Dockerfile
development/docker-notebook/README.md
docs/index.html
misc/celery/sos_task.py
misc/ipython/Using_SoS_Interactively.ipynb
misc/ipython/Using_SoS_with_IPython.ipynb
misc/ipython/ipython_magic.py
misc/ipython/sos_ipython_profile.py
misc/spyder/Using_SoS_with_Spyder.ipynb
misc/spyder/patch_spyder.py
misc/spyder/spyder_kernel.py
misc/vim-ipython/ipy.vim
misc/vim-ipython/vim_ipython.py
src/sos/__init__.py
src/sos/__main__.py
src/sos/_version.py
src/sos/actions.py
src/sos/actions_bash.py
src/sos/actions_javascript.py
src/sos/actions_julia.py
src/sos/actions_matlab.py
src/sos/actions_python.py
src/sos/actions_r.py
src/sos/actions_ruby.py
src/sos/controller.py
src/sos/converter.py
src/sos/dag.py
src/sos/eval.py
src/sos/executor_utils.py
src/sos/hosts.py
src/sos/install.py
src/sos/messages.py
src/sos/monitor.py
src/sos/parser.py
src/sos/pattern.py
src/sos/preview.py
src/sos/remote.py
src/sos/runtime.py
src/sos/section_analyzer.py
src/sos/signatures.py
src/sos/step_executor.py
src/sos/substep_executor.py
src/sos/syntax.py
src/sos/targets.py
src/sos/targets_python.py
src/sos/targets_r.py
src/sos/task_engines.py
src/sos/task_executor.py
src/sos/tasks.py
src/sos/utils.py
src/sos/visualize.py
src/sos/workers.py
src/sos/workflow_executor.py
src/sos/workflow_report.py
src/sos.egg-info/PKG-INFO
src/sos.egg-info/SOURCES.txt
src/sos.egg-info/dependency_links.txt
src/sos.egg-info/entry_points.txt
src/sos.egg-info/requires.txt
src/sos.egg-info/top_level.txt
src/sos/docker/__init__.py
src/sos/docker/actions.py
src/sos/docker/client.py
src/sos/singularity/__init__.py
src/sos/singularity/actions.py
src/sos/singularity/client.py
src/sos/templates/sos_script.tpl
src/sos/templates/workflow_report.tpl
src/sos/templates/parts/hover_doc.tpl
src/sos/templates/parts/sos-mode.js
src/sos/templates/parts/sos_report.css
src/sos/vim/sos-detect.vim
src/sos/vim/sos.vim
test/build_test_docker.sh
test/check_zombie.py
test/sample_workflow.ipynb
test/test_actions.py
test/test_bash_actions.py
test/test_config.py
test/test_convert.py
test/test_dag.py
test/test_docker_actions.py
test/test_execute.py
test/test_julia_action.py
test/test_matlab_action.py
test/test_nested.py
test/test_node_actions.py
test/test_octave_action.py
test/test_outcome.py
test/test_pack.py
test/test_parser.py
test/test_python2_actions.py
test/test_python3_actions.py
test/test_python3_target.py
test/test_r_actions.py
test/test_r_targets.py
test/test_remote.py
test/test_remove.py
test/test_ruby_actions.py
test/test_signature.py
test/test_singularity.py
test/test_target.py
test/test_task.py
test/test_utils.py
test/data/S20_R1.fastq
test/data/S20_R2.fastq