snaketools 0.0.8

Small library of helper tools for setting up, graphing, and working with Snakemake rules.

Small library of helper tools for setting up, graphing, and working with Snakemake rules.

• Free software: MIT license

• Documentation: https://snaketools.readthedocs.io.

Features

• SnakeRun object to initialize and manage information common to the whole run, such as:

  • a copy of the config values from the config file provided to snakemake.

  • a place to store global variables needed throughout the run.

  • more

• SnakeRule object to manage the initialization and deployment of rule-specific information including:

  • the rule name

  • a default out directory deduced from the SnakeRun object

  • a default log file path

  • a “pretty name” for the rule to be displayed in the DAG graphs.

  • attributes that store the input, output, and params values for later use.

  • a copy of the values specific to this rule from the original configuration file.

  • more

• recode_graph function that cleans up the default output of snakemake --dag and allows the use of pretty names stored in the SnakeRule objects.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

Change Log

v0.0.8 / 2018-06-08

• stopped using pinned versions.

v0.0.7 / 2017-12-18

• change pyup check to monthly

• update reqs from PYUP

• snaketools: SnakeRule now registers with SnakeRun

• snaketools: added attr SnakeRule.extra for more params

• snaketools: added attr SnakeRun.rules

• snaketools: use __all__ for importing from file

• update makefile

• update reqs

v0.0.6 / 2017-10-26

• added rewrite_snakefile_no_rules()

• flake8

• requirements.txt: removed dev-reqs

• requirements.txt: pinned flake8

• setup.py: upgraded to read from req files

• MANIFEST.in: include req files

• upgraded Makefile

• tox.ini: set line-length etc

• setup.cfg: ignore W292

• setup.cfg: exclude lib & bin from flake8

• updated .gitignore

• added coveralls badge

• HISTORY.rst: replaced header text

v0.0.5 / 2017-10-10

• requirements_dev.txt: update and pin reqs

• flake8 fixes

• tox.ini: simplified config

• added flake8 to reqs

v0.0.4 / 2017-10-10

• added preliminary test suite

• Makefile: changed install to use pip install -e .

• added example files for testing

• requirements.txt: created with pipreqs

• snaketools.py: reorder functions

• snaketools.py: formatting

• ignore .vscode/

• pin all reqs since pyup now manages

v0.0.3 / 2017-09-15

• Configure pyup

• SnakeRun.d -> SnakeRune.interim_dir

v0.0.2 / 2017-09-06

• fixed bumpversion artifact

• errors.py: pulls metadata from top module

• updated dev reqs for doc building

• activated travis ci

• Set up flake8 configuration

• Docs build corrected

v0.0.1 / 2017-09-06

• README.rst: added prelim description of features.

• snaketools.py: fixed typo

• Initial commit