v2.1.0

Highlights

Environment variables are now properly compatible with Galaxy's job conf and support both lists and dicts (#79):

 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/.*:
   gpus: 1
   env:
     - name: MY_ADDITIONAL_FLAG
       value: "arthur"
     - file: /galaxy/tools/hisat2.env
 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7:
   inherits: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/.*:
   env:
     MY_ADDITIONAL_FLAG: "zaphod"

What's Changed

• Automatically convert envs to string, but make sure params are preserved by @nuwang in #73
• Fix indentation by @bernt-matthias in #76
• Convert env to a list compatible with Galaxy job conf by @natefoo in #79
• Fix missing app.config.is_set() in mock config for dry-run by @natefoo in #80
• Refactor and fix dryrun by @nuwang in #82
• Add initializer to handle empty sequence when reducing by @nuwang in #84

New Contributors

• @bernt-matthias made their first contribution in #76

Full Changelog: v2.0.1...v2.1.0

v2.0.1

What's Changed

• create missing init.py in tpv core test folder which was causing tpv lint to fail by @bgruening in #70

Full Changelog: v2.0.0...v2.01

v2.0.0

TPV v2.0.0 includes some breaking changes and requires some straightforward migration steps to preserve old behaviour. Please refer to the migration guide for more details.

What's Changed

• Add a tpv dry-run subcommand by @natefoo in #52
• Simplify TPV by disambiguating terms by @nuwang in #58
• Additional context params by @nuwang in #62
• Use only TPV defined destinations, ignoring job_conf by @nuwang in #63
• Add support for abstract entities by @nuwang in #64
• Add destination min accepted by @nuwang in #67
• Shared rules inheritance test by @cat-bro in #68
• Update github actions by @nuwang in #69

Full Changelog: v1.4.1...v2.0.0

v1.4.1

What's Changed

• Add PyPI deploy action from bioblend by @bgruening in #43
• Use ruamel.yaml in tpv.core.util since PyYAML is not a dependency by @natefoo in #51
• Avoid deepcopying loader when cloning entities by @nuwang in #54

New Contributors

• @natefoo made their first contribution in #51

Full Changelog: v1.4.0...v1.4.1

v1.4.0

What's Changed

• Added support for the execute block to change entity properties
• Added link to TPV shared database.

Full Changelog: v1.3.0...v1.4.0

v1.3.0

What's Changed

• Added tpv format command for prettying and ordering tpv tool lists
• Support for overriding destination name
• Fixed some bugs in context variable handling
• Misc. bug fixes and refactoring

New Contributors

• @bgruening made their first contribution in #31

Full Changelog: v1.2.0...v1.3.0

v1.2.0

• vortex package and cli renamed to tpv for consistency.
• All matching entity regexes are applied, not just the first. Order of application is in the order of definition.
• When a particular entity type is matched, its definitions are cached, so that future lookups are O(1).
• Support for job resubmission handling, with integration tests for Galaxy,
• Allow destinations to be treated as regular entities, with support for rules and expressions.
• Support for global and local context variables that can be referenced in expressions.
• Improved support for complex jobs param types like dicts and lists, which are now recursively evaluated.
• Improved documentation.

v1.1.0

• The "match" clause has been deprecated and renamed "if", for easier readability of rules.
• When no default mapping for a tool exists, choose the first available destination for a simpler initial experience.
• A sample config file has been added to provide a starting point for new TPV users.

v1.0.0

• Initial PyPi release of total-perspective-vortex.
• Basic usage docs and examples.
• 94% test coverage.
• In production in Galaxy Australia.