v0.1.3

What's Changed

• add build-doc to makefile by @stevebachmeier in #130
• restructure docs; add README install notes to high-level index by @stevebachmeier in #131
• Sbachmei/mic 5665/jenkins py version matrix by @stevebachmeier in #132
• Add branch name to jenkins conda env by @patricktnast in #128
• Sbachmei/mic 5561/add indexes to api by @stevebachmeier in #134
• Sbachmei/mic 5561/improve docstrings cli configuration by @stevebachmeier in #133
• Sbachmei/mic 5755/improve supported py version handling by @stevebachmeier in #136
• try code-block directive by @stevebachmeier in #137
• various fixes by @stevebachmeier in #139
• remove setuptools_scm section in pyproject.toml by @stevebachmeier in #140

Full Changelog: v0.1.2...v0.1.3

v0.1.2

What's Changed

• Sbachmei/mic 5476/add optional schema arg to config constructor by @stevebachmeier in #127
• Sbachmei/mic 5643/publish docs by @stevebachmeier in #129

Full Changelog: v0.1.1...v0.1.2

v0.1.1

What's Changed

• Sbachmei/mic 5560/choice sections by @stevebachmeier in #125
• release v0.1.1 by @stevebachmeier in #126

Full Changelog: v0.1.0...v0.1.1

v0.1.0

What's Changed

• Feature/mic 4269 1.0.0 docker by @stevebachmeier in #3
• Allow for user-specified input data by @stevebachmeier in #4
• Feature/sbachmei/mic 4273 cli by @stevebachmeier in #6
• Feature/sbachmei/mic 4333 1.0.2 singularity by @stevebachmeier in #7
• Feature/sbachmei/mic 4272 1.0.2 refactors by @stevebachmeier in #8
• Feature/sbachmei/mic 4272 launch slurm jobs by @stevebachmeier in #9
• Feature/sbachmei/mic 4472 ci by @stevebachmeier in #10
• Feature/sbachmei/mic 4470 remove docker image even if fails by @stevebachmeier in #11
• Feature/sbachmei/mic 4481 create config object by @stevebachmeier in #12
• Feature/sbachmei/mic 4465 move container engine to config by @stevebachmeier in #14
• Feature/sbachmei/mic 4433 1.0.3 configurable input data by @stevebachmeier in #15
• add --output-dir option by @stevebachmeier in #16
• Feature/sbachmei/mic 4458 timestamp option by @stevebachmeier in #17
• hide run_slurm_job by @stevebachmeier in #18
• change step directory structure by @stevebachmeier in #19
• Feature/milestone1.1 rscript by @mattkappel in #20
• Treat docker and singularity equally by @mattkappel in #22
• Milestone 1.1 - Implementation with R dependencies by @mattkappel in #21
• Add spark local implementation script by @mattkappel in #23
• Implement singularity linker run for local spark step implementation by @mattkappel in #24
• Add spark cluster RT code to repo by @mattkappel in #25
• setuptools-scm by @stevebachmeier in #26
• Feature/sbachmei/mic 4691 2.0 implementation metadata by @stevebachmeier in #27
• Pipeline object by @stevebachmeier in #28
• Feature/sbachmei/mic 4698 pipeline schema and step by @stevebachmeier in #30
• add Implementation objects and refactor Pipeline for them by @stevebachmeier in #31
• Feature/sbachmei/mic 4491 test coverage by @stevebachmeier in #33
• one implementation metadata file by @stevebachmeier in #34
• Spark cluster building via linker by @mattkappel in #35
• Bugfix/sbachmei/mic 4708 singularity pwd by @stevebachmeier in #37
• Feature/sbachmei/mic 4709 validation batch logging by @stevebachmeier in #38
• Feature/sbachmei/mic 4678 2.0 two steps python pandas by @stevebachmeier in #39
• Feature/sbachmei/mic 4754 improve logging dir by @stevebachmeier in #40
• linker build spark cluster improvements by @mattkappel in #41
• Feature/sbachmei/mic 4753 milestone 2.1 implementation configuration by @stevebachmeier in #42
• Feature/mic 4592 container using spark cluster by @stevebachmeier in #43
• Input Validation by @patricktnast in #45
• Feature/sbachmei/mic 4647 connect distributed spark cluster to tool by @stevebachmeier in #44
• Fix Step Test and refactor validation to pipeline by @patricktnast in #47
• filepath change by @stevebachmeier in #48
• change log level of spark warnings from warning to debug by @stevebachmeier in #49
• add optional 'keep_alive' spark key by @stevebachmeier in #50
• Refactor schema validation into Config by @patricktnast in #51
• update tests to dummy pipeline by @stevebachmeier in #53
• runtime error if no results made by @stevebachmeier in #58
• move logic, minor renaming by @stevebachmeier in #57
• Milestone 2.2: R Implementation by @patricktnast in #59
• add defaults; refactor some attributes; add pytests by @stevebachmeier in #60
• Update CODEOWNERS by @patricktnast in #61
• move implementation-specific configuration logic to Config method by @stevebachmeier in #62
• Feature/sbachmei/mic 4723 validate config by @stevebachmeier in #64
• Feature/sbachmei/mic 4849 improve pipeline unit tests by @stevebachmeier in #65
• move validation tests into separate module by @stevebachmeier in #66
• Add missing PipelineSchema tests by @stevebachmeier in #67
• add test for Config._load_missing_computing_environment by @stevebachmeier in #68
• Feature/sbachmei/mic 4852 improve step tests by @stevebachmeier in #69
• Feature/sbachmei/mic 4853 4855 4856 improve tests data singularity general utils by @stevebachmeier in #70
• Feature/sbachmei/mic 4857 improve slurm utils tests by @stevebachmeier in #71
• Feature/sbachmei/mic 4858 spark utils unit tests by @stevebachmeier in #72
• Feature/sbachmei/mic 4846 local e2e tests by @stevebachmeier in #74
• better check for if on slurm by @stevebachmeier in #75
• Feature/sbachmei/mic 4847 ci by @stevebachmeier in #82
• remove triggers by @stevebachmeier in #83
• Snakemake Integration by @patricktnast in #86
• Milestone 2.3: Four Steps by @patricktnast in #89
• Increase FS Latency Timeout by @patricktnast in #90
• Rename repo to EasyLink by @patricktnast in #91
• Make Config a ConfigTree by @patricktnast in #92
• Refactor to Pipeline Graph by @patricktnast in #93
• Schema Graph Refactor by @patricktnast in #94
• Milestone 2.12: Add tests for (existing) hierarchical step. by @patricktnast in #95
• Re-Order Node Removal to be More Self-Contained by Level by @patricktnast in #96
• Change placement of step keys by @patricktnast in #97
• remove method to fill configuration defaults by @patricktnast in #99
• Single-Step Loops by @patricktnast in #98
• Loops 2: Step Sequences by @patricktnast in #100
• Swap Step 1 and Step 4 by @patricktnast in #101
• Milestone 2.9: Parallel Steps by @patricktnast in #102
• Fix bug with parallel validations by @patricktnast in #105
• Add DAG visualization by @patricktnast in #104
• add missing slot mappings by @patricktnast in #106
• add command to integration tests by @patricktnast in #107
• install python-graphviz with conda by @patricktnast in #109
• Set Config as step attribute by @patricktnast in #110
• Bugfix for step config by @patricktnast in #111
• Separate Pipeline Graph construction from Pipeline Schema by @patricktnast in #108
• Albrja/Mic-5240/Slack develoepr on Jenkins pipeline failure by @albrja in #113
• Reduce multiple inheritance through State design by @patricktnast in #112
• Bugfix/jenkinsfile by @albrja in #114
• add outer "steps" key by @patricktnast in #116
• Combined Implementations by @patricktnast in #117
• Set Env Var in Implementation by @patricktnast in #118
• Add Container Building docs/ scripts to Easylink by @patricktnast in #120
• Deduplicate Slots in Combined Implementations by @patricktnast in #119
• Sbachmei/mic 5570/minor cleanup by @stevebachmeier...