New upstream version 5.5.3

      - checkout

      - restore_cache:

          keys:

            - snakemake-{{ checksum ".circleci/setup.sh" }}-{{ checksum "test-environment.yml" }}-{{ checksum ".circleci/common.sh" }}

            - snakemake-{{ .Environment.CACHE_VERSION }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum "test-environment.yml" }}-{{ checksum ".circleci/common.sh" }}

      - run:

          name: Update PATH

          command: echo 'export PATH="`pwd`/miniconda/bin:$PATH"' >> $BASH_ENV

          name: Setup Conda

          command: .circleci/setup.sh

      - save_cache:

          key: snakemake-{{ checksum ".circleci/setup.sh" }}-{{ checksum "test-environment.yml" }}-{{ checksum ".circleci/common.sh" }}

          key: snakemake-{{ .Environment.CACHE_VERSION }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum "test-environment.yml" }}-{{ checksum ".circleci/common.sh" }}

          paths:

            - miniconda

      - run:

            $GCLOUD config set project snakemake-testing

      - run:

          name: Run tests

          no_output_timeout: 30m

          no_output_timeout: 60m

          command: |

            export GCLOUD_CLUSTER=t-`uuidgen`

            export GOOGLE_APPLICATION_CREDENTIALS=${HOME}/gcloud-service-key.json

version: 2

sphinx:

  configuration: docs/conf.py

python:

  version: 3.6

  install:

    - requirements: docs/requirements.txt

[5.5.3] - 2019-07-11

====================

Changed

-------

- Various bug fixes.

- Polished reports.

[5.5.2] - 2019-06-25

====================

Changed

-------

- Various minor bug fixes in reports.

- Speed improvements when using checkpoints.

[5.5.1] - 2019-06-18

====================

Changed

-------

- Improved report interface. In particular for large files.

- Small TSV tables are automatically rendered as HTML with datatables.

- Be more permissive with Snakefile choices: allow "Snakefile", "snakefile", "workflow/Snakefile", "workflow/snakefile". 

[5.5.0] - 2019-05-31

====================

Added

-----

- Script directives now also support Julia.

Changed

-------

- Various small bug fixes.

[5.4.5] - 2019-04-12

====================

Changed

-------

- Fixed a bug with pipe output.

- Cleaned up error output.

[5.4.4] - 2019-03-22

====================

Changed

-------

- Vastly improved performance of HTML reports generated with --report, via a more efficient encoding of dara-uri based download links.

- Tighter layout, plus thumbnails and a lightbox for graphical results in HTML reports.

- Bug fix for pipe groups.

- Updated docs.

- Better error handling in DRMAA executor.

[5.4.3] - 2019-03-11

====================

Changed

-------

- More robust handling of conda environment activation that should work with all setups where the conda is available when starting snakemake.

- Fixed bugs on windows.

[5.4.2] - 2019-02-15

====================

Changed

-------

- Fixed a bug where git module cannot be imported from wrapper.

[5.4.1] - 2019-02-14

====================

Added

-----

- Warning when R script is used in combination with conda and R_LIBS environment variable is set. This can cause unexpected results and should be avoided.

Changed

-------

- Improved quoting of paths in conda commands.

- Fixed various issues with checkpoints.

- Improved error messages when combining groups with cluster config.

- Fixed bugs in group implementation.

- Fixed singularity in combination with shadow. 

[5.4.0] - 2018-12-18

====================

channels:

  - conda-forge

dependencies:

  - python >=3.5

  - datrie

  - wrapt

  - pyyaml

  - requests

  - appdirs

  - docutils

  - ratelimiter

  - configargparse

  - jsonschema

  - gitpython

  - sphinx

  - pip:

    - sphinxcontrib-napoleon

  - sphinx-argparse

  - sphinx_rtd_theme

  - docutils==0.12

  - recommonmark

  - commonmark

Internal API

============

These pages document the entire internal API of Snakemake.

.. toctree::

   :maxdepth: 4

   snakemake