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Implementation of Dynamic Statistical Comparisons

Project description

PyPI Version Travis Status

The project wiki is the main source of documentation for both developers and users of the DSC project. If you are new to the concept of DSC, it may worth reading this blog post to understand the motivation behind this project.

This work is supported by the the Gordon and Betty Moore Foundation via an Investigator Award to Matthew Stephens, Grant GBMF4559, as part of the Data-Driven Discovery program. If you have any questions or want to share some information with the developer / user community, please open a github issue.

Developer notes

Upgrading DSC to latest development version

For most users, we recommend installing the most recent stable release. If you would like to upgrade your existing installation of DSC to the most recent (unstable) development version, follow these steps.

DSC is closely developed in parallel with SoS. Therefore, the development version of DSC (maintained in the master branch of the GitHub repository) typically requires the development version of SoS.

Install the latest SoS

git clone https://github.com/vatlab/SoS.git
cd SoS
pip install .

Install DSC from source

git clone https://github.com/stephenslab/dsc.git
cd dsc
pip install .

Or, if you have cloned the repository before,

cd dsc
git pull
pip install .

Install dscrutils from source

Assuming the working directory in your R environment is the dsc repository, run the following code in R to install the latest development version of the dscrutils R package:

getwd() # Should be ... /dsc
install.packages("dscrutils",repos = NULL,type = "source")

Project maintenance

Although relatively stable and usable in practice, DSC is still actively being developed. Occasionally upgrades to the most recent version will lead to changes of file signatures that triggers rerun of existing benchmark even if they have not been changed. When this happens we will indicate in bold in our release note below that “a file signature clean up is recommended” (see release note 0.2.7.7 for example). That means after such DSC upgrades you should rerun your benchmark with --touch option to update file signatures. If possible, it is recommended that you rerun your benchmark from scratch (if resources can afford) with -s none instead of --touch to skip all existing files. We apologize for the inconveniences it incurs.

Change Log

Upcoming release

Goal for 0.4.0

  • Support for multiple output per modules.
  • Improve scripts command options.

0.3.x

0.3.10

  • Issue #154
  • Add a remote job option nodes_per_job and provide such mechanism to run on multiple nodes.
  • SoS bumped to version 0.20.2

0.3.9

  • Issue #179
  • Issue #182
  • Issue #183
  • SoS bumped to version 0.19.11 for additional improvements in cluster job submission.

0.3.8

  • Issue #171 is partially improved.

0.3.7

  • dscquery now properly handles NULL module output variables.
  • Some performance improvements on I/O database.
  • SoS bumped to version 0.19.7 for various bug fixes on cluster job submitter.

0.3.6

  • Now SQLite keywords can be used as module names: no error message will be triggered.
  • Introduce an explicit syntax for base module: a module without executable is considered base module.
  • Bump rpy2 version requirment version 3.0.0+ for benchmark with R and Python modules.
  • SoS bumped to version 0.19.5 for improved memory usage on job submitter and improved Python module version check.

0.3.5

Major improvements to dscrquery

  • Performance improvement #168
  • Output format improvement #174

0.3.4

  • Reimplement dsc-query and dscrquery for improved handling of missing value #145.
  • Reimplement dscrquery’s condition statement to make it more R-user friendly.
  • Add unknown command argument #162.
  • [minor] Introduce DSC::run::default, for the behavior of running the script without targets.
  • [minor] #161
  • SoS bumped to version 0.19.1 for improved sockets management and improved R library auto-installation.

0.3.3

  • [minor] #160
  • SoS bumped to version 0.18.4 for performance optimizations.

0.3.2

  • Various improvements for remote job submission and execution (mostly on SoS).
  • SoS bumped to version 0.18.1 to support these changes.

0.3.1

  • Improved database I/O performance to cope with file system latency.
  • Improved Python to R data flow.
  • Paralleled data extraction in dscquery.
  • SoS bumped to version 0.17.4 to support a new implementation of job queues.

0.3.0

  • SoS bumped to version 0.16.9 to support a new implementation of signatures.
  • [minor] Bug fix #147.

0.2.x

0.2.9.1

  • Stop moving library imports to the front of scripts, due to various side effect.

0.2.9.0

  • SoS bumped to version 0.9.16.0 for optimized remote task file management.
  • [minor] Bug fixes.

A file signature clean up is required after this upgrade.

0.2.8.6

  • Change in query behavior #145

0.2.8.5

  • Bug fixes for cluster execution #142, #143, #144.
  • Add -d option to output DAG #141.
  • Removed -p option because it triggers rerun and cannot be easily implemented otherwise.
  • SoS bumped to version 0.9.14.10 for many of the fixes above.

A file signature clean up is recommended after this upgrade.

0.2.8.4

  • Fix running Python 3 based modules on Mac computer with homebrew installed Python #140.

0.2.8.3

  • dsc-io can now convert CSV to HTML with pop-up figures.
  • Add groups and load.pkl options to dscrutils::dscquery.
  • [minor] Bug fixes.

0.2.8.2

  • Add -p option to print stdout and stderr to screen.
  • SoS bumped to version 0.9.14.1 for
  • Improved parallel slot management.
  • Improved messaging on executed steps (use -v 3 to display in DSC).

0.2.8.1

  • Minor file check performance optimization.
  • Force overwrite converted pkl to rds in dscutils::dscquery, as a save default.

0.2.8

Input string parameter behavior has changed since this version. Now un-quoted strings will be treated input script code; string parameters will have to be quoted. A new DSC configuration parser has been implemented to overcome pyYAML restrictions. Please submit a bug report if the new parser misbehaves.

A file signature clean up is recommended after this upgrade.

0.2.7.11

  • [minor] More stringent check on improper module names ending with _{digits}.

0.2.7.10

  • Stop adding script hash to default seed #136.
  • [minor] SoS bumped to version 0.9.13.8 a bug fix release.

A file signature clean up is recommended after this upgrade.

0.2.7.9

Minor touches on 0.2.7.8 – just a celebration of the 1,000-th commit to the DSC repo on github, after 2 years and 3 months into this project.

0.2.7.8

  • Implement a preliminary %include feature to provide alternative code organization style.
  • Allow for ! operator in List() and Dict().
  • SoS bumped to version 0.9.13.7 for improved remote job support.
  • [minor] Various bug fixes.

0.2.7.7

  • Improvements for module with shell executables and command options.
  • Improvements for remote execution #131.
  • Improved logging.
  • Bug fixes #126, #127.
  • SoS bumped to version 0.9.13.4 for #128 and related.

A file signature clean up is recommended after this upgrade.

0.2.7.6

  • Add new feature dscrutils::shiny_plot to display simple benchmark results.
  • [minor] Display unused modules with -h option.

0.2.7.5

  • Add R / Python packages and version display with -h option.
  • Add .gitignore for cache folder when a git environment is detected.
  • SoS bumped to 0.9.13.3 that now bundles the pbs module.

0.2.7.4

  • Improved R’s sessionInfo format.
  • Bug fixes #119, #121, #122
  • [minor] Error message improvements.

0.2.7.3

  • More stringent R library and command executable check.
  • [minor] Fix a regression bug on path due to 0.2.7.2.

0.2.7.2

  • Improved Windows path support.
  • [minor] Fix a bug with nested tuple with raw().

0.2.7.1

  • Dump individual data object with scripts using dsc-query *.pkl and dsc-query *.rds.
  • [minor] Improve behavior for length 1 vector in R’s list with R() operator.
  • [minor] Various bug fixes.

0.2.7

  • #92 paired parameter input convention.
  • #90 and #93 use Rmd files as module executables.
  • #94 and #95 added DSC::replicate and command option --replicate.
  • Enhance R() operator due to use of dscrutils package. This packages is now required to parse DSC file when R modules are involved.
  • Add, by default, a variable DSC_DEBUG to output files that saves various runtime info.
  • SoS bumped to 0.9.13.2
    • Support R github package force install when version mismatches.
    • Force use pip to install local development version.
    • #97 Improved error logging and reporting behavior.
  • [minor] Revert from ruamel.yaml to yaml for better performance.
  • [minor] [#96](https://github.com/stephenslab/dsc/issues/96)
  • [minor] [#98](https://github.com/stephenslab/dsc/issues/98)
  • [minor] Various bug fixes.

0.2.6.5

  • Bring back partial mixed languages support. Piplines with mixed R and Python code can communicate data of limited types (recursively support array, matrix, dataframe), via ``rpy2`` as in versions prior to 0.2.5.x. Support for additional languages will be implemented on need basis with HDF5 format #86.

0.2.6.4

  • Add a dsc-io command to convert between python pickle and R RDS files – an internal command for data conversion and a test for rpy2 configuration.

0.2.6.3

  • Inline module executable via language interpreters (eg. R(), Python()).

0.2.6.2

  • [minor] Ignore leading . in file(): file(.txt) and file(txt) are equivalent.
  • [minor] Disallow derivation of modules from ensemble.
  • [minor] Various bug fixes.

0.2.6.1

  • Internally replace RDS format with HDF5 format for Python routines. Pipeline with mixed languages is now officially broken at this point until the next major release that supports ``HDF5`` in R.
  • SoS required version bumped to 0.9.12.7 for relevant upstream bug fixes for remote host computing.
  • [minor] Various bug fixes.

0.2.6

  • Bring back --host option; add a companion option --to-host to facilicate sending resources to remote computer.
  • Add --truncate switch.
  • SoS required version bumped to 0.9.12.3 for relevant upstream bug fixes.
  • [minor] Improved command interface.

0.2.5.2

  • SoS required version bumped to 0.9.12.2 for relevant upstream bug fixes.

0.2.5.1

  • Change in seed behavior: since this release seed will no longer be a DSC keyword. Users are responsible to set seeds on their own.
  • [minor] Allow for both lower case and capitalized operator names File/file, List/list, Dict/dict.

0.2.5

  • New syntax release, compatible with SoS 0.9.12.1.
  • Removed --host option due to upstream changes.

0.1.x

0.1.0

  • First release, compatible with SoS 0.6.4.

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