Easy Update

If you support R and Python easyconfigs, this tool will automate the process of updating module versions and recursively check for dependent modules. Easy_Update is a tool for maintaining EasyBuild easyconfig files for Python and R. R-Bioconductor libararies are also supported. Easy_update rewrites easyconfig files with updated version information for each module in exts_list[]. Easy_update also checks for dependencies recursively and adds any missing dependent modules to exts_list. If you have been maintaining package lists by hand, you will notice that easy_update will reorder your exts_list based on the correct dependency hierarchy. Easy_update writes dependent packages ahead of the parent module. If dependent packages are found further within exts_list, they will will be treated as duplicates and removed. If you are running easy update for the first time I would suggest that you run it twice to ensure that the modules are in the correct order.

Usage

The main usage for easy_update is --exts-update which will update the version field of all extensions in exts_list. The output is written to a new file, with extension .update.

Options

• -h, --help show this help message and exit
• --version show program's version number and exit
• -v, --verbose Verbose; print lots of extra stuff
• --debug set log level to debug, (default: false)
• --exts-update easy_config update version info for exts_list in EasyConfig
• --exts-annotate easy_config Annotate all extensions from EasyConfig and dependencies. Output is Markdown
• --exts-dep-graph easy_config print Graph dependancies for exts
• --exts-description easy_config Output descrption for libraries in exts_list
• --exts-search-cran package_name output libray metadata from CRAN/BioConductor
• --exts-search-pypi package_name display library metadata from PyPi

Usage: ./easy_update.py --exts-update Python-2.7.12-foss-2016b.eb

Output: Python-2.7.12-foss-2016b.update

Note: When using BioConductor modules in easyconfig files the variable local_biocver or biocver must be set, otherwise BioConductor will not be searched. Example local_biocver = 3.20.

Verbose Flag

Verbose output show how each library is handled. Possible actions are: ['keep', 'update', 'processed', 'duplicate']. Modules that are added show the dependancy. R lanuage extensions who shy they are dependent: ['Depends', 'Imports', 'LinkingTo']

tidyposterior Imports tune Imports dials Imports DiceDesign

            collections : 0.3.7 Imports from EpiModel        (add) [730, 44]
                 EpiModel : 2.4.0 -> 2.5.0                (update) [730, 44]
...
               DiceDesign : 1.10 Imports from dials          (add) [730, 126]
                      sfd : 0.1.0 Imports from dials         (add) [730, 128]
                    dials : 1.4.0 Imports from tune          (add) [730, 129]
                 doFuture : 1.0.2 Imports from tune          (add) [730, 131]
                    GPfit : 1.0-8 Imports from tune          (add) [730, 133]
             sparsevctrs : 0.3.1 Imports from parsnip        (add) [730, 136]
                  parsnip : 1.3.1 Imports from tune          (add) [730, 137]
              modelenv : 0.2.0 Imports from workflows        (add) [730, 140]
                workflows : 1.2.0 Imports from tune          (add) [730, 141]
                yardstick : 1.3.2 Imports from tune          (add) [730, 143]
              tune : 1.3.0 Imports from tidyposterior        (add) [730, 144]
      workflowsets : 1.1.0 Imports from tidyposterior        (add) [730, 146]
            tidyposterior : 1.0.1                           (keep) [730, 146]

Python Notes

Making sense of Pypi metadata can be problematic. Starting with the release of 2.3.0 packaging is used to parse and evalute the requires_dist metadata from PyPi.org. requires_dist format is defined in PEP508. Added PEP550 name normilization.

TODO

Integrate with EasyBuild FrameWork. Version two of EasyUpdate has been refactored to seperate core update features from framework features. The framework.py performs: reading/parsing easyconfig files, finding easyconfig files, rewritting easyconfig files, set easyblock type, create module names from dependencies list. The new refactoring should make integration easier.