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Release 0.11.1
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,233 +1,149 @@ | ||
| # Changelog | ||
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| This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. | ||
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| - **Unreleased** | ||
| ## [Unreleased] | ||
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| ## [0.11.1] - 2019-04-17 | ||
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| - **v0.11 (*2019-04-17*)** | ||
| ### Changed | ||
| - Improved documentation | ||
| - Improved interaction with `peppy` and `divvy` dependencies | ||
|
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||
| - Added | ||
| ## [0.11] - 2019-04-17 | ||
|
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| - Implemented `looper rerun` command. | ||
| ### Added | ||
| - Implemented `looper rerun` command. | ||
| - Support use of custom `resources` in pipeline's `compute` section | ||
| - Listen for itemized compute resource specification on command-line with `--resources` | ||
| - Support pointing to `Project` config file with folder path rather than full filepath | ||
| - Add `selector-attribute` parameter for more generic sample selection. | ||
|
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||
| - Support use of custom `resources` in pipeline's `compute` section | ||
|
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| - Listen for itemized compute resource specification on command-line with `--resources` | ||
|
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| - Support pointing to `Project` config file with folder path rather than full filepath | ||
|
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||
| - Changed | ||
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||
| - Switched to a Jinja-style templating system for summary output | ||
|
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||
| - Made various UI changes to adapt to `caravel` use. | ||
|
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||
| - Using `attmap` for "attribute-style key-vale store" implementation | ||
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| - Removed Python 3.4 support. | ||
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| - UI: change parameter names `in/exclude-samples` to `selector-in/exclude`. | ||
|
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||
| - New: | ||
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| - Add `selector-attribute` parameter for more generic sample selection. | ||
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||
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| - **v0.10.0 (*2018-12-20*)** | ||
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| - Changed | ||
|
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| - ``PipelineInterface`` now derives from ``peppy.AttributeDict``. | ||
|
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||
| - On ``PipelineInterface``, iteration over pipelines now is with ``iterpipes``. | ||
|
|
||
| - Rename ``parse_arguments`` to ``build_parser``, which returns ``argparse.ArgumentParser`` object | ||
|
|
||
| - Integers in HTML reports are made more human-readable by including commas. | ||
|
|
||
| - Column headers in HTML reports are now stricly for sorting; there's a separate list for plottable columns. | ||
|
|
||
| - More informative error messages | ||
|
|
||
| - Fixed | ||
|
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||
| - HTML samples list is fully populated. | ||
|
|
||
| - Existence of an object lacking an anchor image is no longer problematic for ``summarize``. | ||
|
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||
| - Basic package test in Python 3 now succeeds: ``python3 setup.py test``. | ||
|
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| - **v0.9.2** (*2018-11-12*): | ||
|
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| - Fixed | ||
|
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||
| - Fixed bugs with ``looper summarize`` when no summarizers were present | ||
|
|
||
| - Added CLI flag to force ``looper destroy`` for programmatic access | ||
|
|
||
| - Fixed a bug for samples with duplicate names | ||
|
|
||
| - Added new display features (graphs, table display) for HTML summary output. | ||
|
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||
|
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| - **v0.9.1** (*2018-06-30*): | ||
|
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||
| - Fixed | ||
|
|
||
| - Fixed several bugs with ``looper summarize`` that caused failure on edge cases. | ||
|
|
||
|
|
||
| - **v0.9.0** (*2018-06-25*): | ||
|
|
||
| - New | ||
|
|
||
| - Support for custom summarizers | ||
|
|
||
| - Add ``allow-duplicate-names`` command-line options | ||
|
|
||
| - Allow any variables in environment config files or other ``compute`` sections to be used in submission templates. This allows looper to be used with containers. | ||
|
|
||
| - Add nice universal project-level HTML reporting | ||
|
|
||
|
|
||
| - **v0.8.1** (*2018-04-02*): | ||
|
|
||
| - Changed | ||
|
|
||
| - Minor documentation and packaging updates for first Pypi release. | ||
|
|
||
| - Fix a bug that incorrectly mapped protocols due to case sensitive issues | ||
|
|
||
| - Fix a bug with ``report_figure`` that made it output pandas code | ||
|
|
||
|
|
||
| - **v0.8.0** (*2018-01-19*): | ||
|
|
||
| - Changed | ||
|
|
||
| - Use independent `peppy` package, replacing ``models`` module for core data types. | ||
|
|
||
| - Integrate ``ProtocolInterface`` functionality into ``PipelineInterface``. | ||
|
|
||
| - **v0.7.2** (*2017-11-16*): | ||
|
|
||
| - Fixed | ||
| ### Changed | ||
| - Switched to a Jinja-style templating system for summary output | ||
| - Made various UI changes to adapt to `caravel` use. | ||
| - Using `attmap` for "attribute-style key-vale store" implementation | ||
| - Removed Python 3.4 support. | ||
| - UI: change parameter names `in/exclude-samples` to `selector-in/exclude`. | ||
|
|
||
| - Correctly count successful command submissions when not using `--dry-run`. | ||
| ## [0.10.0] - 2018-12-20 | ||
|
|
||
| - **v0.7.1** (*2017-11-15*): | ||
| ### Changed | ||
| - `PipelineInterface` now derives from `peppy.AttributeDict`. | ||
| - On `PipelineInterface`, iteration over pipelines now is with `iterpipes`. | ||
| - Rename `parse_arguments` to `build_parser`, which returns `argparse.ArgumentParser` object | ||
| - Integers in HTML reports are made more human-readable by including commas. | ||
| - Column headers in HTML reports are now stricly for sorting; there's a separate list for plottable columns. | ||
| - More informative error messages | ||
| - HTML samples list is fully populated. | ||
| - Existence of an object lacking an anchor image is no longer problematic for `summarize`. | ||
| - Basic package test in Python 3 now succeeds: `python3 setup.py test`. | ||
|
|
||
| - Fixed | ||
|
|
||
| - No longer falsely display that there's a submission failure. | ||
|
|
||
| - Allow non-string values to be unquoted in the ``pipeline_args`` section. | ||
| ## [v0.9.2] - 2018-11-12 | ||
|
|
||
| - **v0.7** (*2017-11-15*): | ||
| ### Changed | ||
| - Fixed bugs with `looper summarize` when no summarizers were present | ||
| - Added CLI flag to force `looper destroy` for programmatic access | ||
| - Fixed a bug for samples with duplicate names | ||
| - Added new display features (graphs, table display) for HTML summary output. | ||
|
|
||
| - New | ||
|
|
||
| - Add ``--lump`` and ``--lumpn`` options | ||
|
|
||
| - Catch submission errors from cluster resource managers | ||
|
|
||
| - Implied columns can now be derived | ||
|
|
||
| - Now protocols can be specified on the command-line `--include-protocols` | ||
|
|
||
| - Add rudimentary figure summaries | ||
|
|
||
| - Simplifies command-line help display | ||
|
|
||
| - Allow wildcard protocol_mapping for catch-all pipeline assignment | ||
|
|
||
| - Improve user messages | ||
|
|
||
| - New sample_subtypes section in pipeline_interface | ||
|
|
||
| - Changed | ||
|
|
||
| - Sample child classes are now defined explicitly in the pipeline interface. Previously, they were guessed based on presence of a class extending Sample in a pipeline script. | ||
|
|
||
| - Changed 'library' key sample attribute to 'protocol' | ||
|
|
||
| - **v0.6** (*2017-07-21*): | ||
| ## [0.9.1] - 2018-06-30 | ||
|
|
||
| - New | ||
| ### Changed | ||
| - Fixed several bugs with `looper summarize` that caused failure on edge cases. | ||
|
|
||
| - Add support for implied_column section of the project config file | ||
|
|
||
| - Add support for Python 3 | ||
|
|
||
| - Merges pipeline interface and protocol mappings. This means we now allow direct pointers to ``pipeline_interface.yaml`` files, increasing flexibility, so this relaxes the specified folder structure that was previously used for ``pipelines_dir`` (with ``config`` subfolder). | ||
|
|
||
| - Allow URLs as paths to sample sheets. | ||
|
|
||
| - Allow tsv format for sample sheets. | ||
|
|
||
| - Checks that the path to a pipeline actually exists before writing the submission script. | ||
| ## [0.9.0] - 2018-06-25 | ||
|
|
||
| - Changed | ||
| ### Added | ||
| - Support for custom summarizers | ||
| - Add `allow-duplicate-names` command-line options | ||
| - Allow any variables in environment config files or other `compute` sections to be used in submission templates. This allows looper to be used with containers. | ||
| - Add nice universal project-level HTML reporting | ||
|
|
||
| - Changed LOOPERENV environment variable to PEPENV, generalizing it to generic models | ||
| ## [0.8.1] - 2018-04-02 | ||
|
|
||
| - Changed name of ``pipelines_dir`` to ``pipeline_interfaces`` (but maintained backwards compatibility for now). | ||
| ### Changed | ||
| - Minor documentation and packaging updates for first Pypi release. | ||
| - Fix a bug that incorrectly mapped protocols due to case sensitive issues | ||
| - Fix a bug with `report_figure` that made it output pandas code | ||
|
|
||
| - Changed name of ``run`` column to ``toggle``, since ``run`` can also refer to a sequencing run. | ||
|
|
||
| - Relaxes many constraints (like resources sections, pipelines_dir columns), making project configuration files useful outside looper. This moves us closer to dividing models from looper, and improves flexibility. | ||
| ## [0.8.0] - 2018-01-19 | ||
|
|
||
| - Various small bug fixes and dev improvements. | ||
| ### Changed | ||
| - Use independent `peppy` package, replacing `models` module for core data types. | ||
| - Integrate `ProtocolInterface` functionality into `PipelineInterface`. | ||
|
|
||
| - Require `setuptools` for installation, and `pandas 0.20.2`. If `numexpr` is installed, version `2.6.2` is required. | ||
| ## [0.7.2] - 2017-11-16 | ||
| ### Changed | ||
| - Correctly count successful command submissions when not using `--dry-run`. | ||
|
|
||
| - Allows tilde in ``pipeline_interfaces`` | ||
| ## [0.7.1] - 2017-11-15 | ||
|
|
||
| - **v0.5** (*2017-03-01*): | ||
| ### Changed | ||
| - No longer falsely display that there's a submission failure. | ||
| - Allow non-string values to be unquoted in the `pipeline_args` section. | ||
|
|
||
| - New | ||
|
|
||
| - Add new looper version tracking, with `--version` and `-V` options and printing version at runtime | ||
|
|
||
| - Add support for asterisks in file paths | ||
|
|
||
| - Add support for multiple pipeline directories in priority order | ||
|
|
||
| - Revamp of messages make more intuitive output | ||
|
|
||
| - Colorize output | ||
|
|
||
| - Complete rehaul of logging and test infrastructure, using logging and pytest packages | ||
|
|
||
| - Changed | ||
|
|
||
| - Removes pipelines_dir requirement for models, making it useful outside looper | ||
|
|
||
| - Small bug fixes related to `all_input_files` and `required_input_files` attributes | ||
| ## [0.7] - 2017-11-15 | ||
| ### Added | ||
| - Add `--lump` and `--lumpn` options | ||
| - Catch submission errors from cluster resource managers | ||
| - Implied columns can now be derived | ||
| - Now protocols can be specified on the command-line `--include-protocols` | ||
| - Add rudimentary figure summaries | ||
| - Simplifies command-line help display | ||
| - Allow wildcard protocol_mapping for catch-all pipeline assignment | ||
| - Improve user messages | ||
| - New sample_subtypes section in pipeline_interface | ||
|
|
||
| - More robust installation and more explicit requirement of Python 2.7 | ||
|
|
||
|
|
||
| - **v0.4** (*2017-01-12*): | ||
|
|
||
| - New | ||
|
|
||
| - New command-line interface (CLI) based on sub-commands | ||
|
|
||
| - New subcommand (``looper summarize``) replacing the ``summarizePipelineStats.R`` script | ||
|
|
||
| - New subcommand (``looper check``) replacing the ``flagCheck.sh`` script | ||
|
|
||
| - New command (``looper destroy``) to remove all output of a project | ||
|
|
||
| - New command (``looper clean``) to remove intermediate files of a project flagged for deletion | ||
|
|
||
| - Support for portable and pipeline-independent allocation of computing resources with Looperenv. | ||
|
|
||
| - Changed | ||
|
|
||
| - Removed requirement to have ``pipelines`` repository installed in order to extend base Sample objects | ||
|
|
||
| - Maintenance of sample attributes as provided by user by means of reading them in as strings (to be improved further) | ||
|
|
||
| - Improved serialization of Sample objects | ||
| ### Changed | ||
| - Sample child classes are now defined explicitly in the pipeline interface. Previously, they were guessed based on presence of a class extending Sample in a pipeline script. | ||
| - Changed 'library' key sample attribute to 'protocol' | ||
|
|
||
| ## [0.6] - 2017-07-21 | ||
| ### Added | ||
| - Add support for implied_column section of the project config file | ||
| - Add support for Python 3 | ||
| - Merges pipeline interface and protocol mappings. This means we now allow direct pointers to `pipeline_interface.yaml` files, increasing flexibility, so this relaxes the specified folder structure that was previously used for `pipelines_dir` (with `config` subfolder). | ||
| - Allow URLs as paths to sample sheets. | ||
| - Allow tsv format for sample sheets. | ||
| - Checks that the path to a pipeline actually exists before writing the submission script. | ||
|
|
||
| ### Changed | ||
| - Changed LOOPERENV environment variable to PEPENV, generalizing it to generic models | ||
| - Changed name of `pipelines_dir` to `pipeline_interfaces` (but maintained backwards compatibility for now). | ||
| - Changed name of `run` column to `toggle`, since `run` can also refer to a sequencing run. | ||
| - Relaxes many constraints (like resources sections, pipelines_dir columns), making project configuration files useful outside looper. This moves us closer to dividing models from looper, and improves flexibility. | ||
| - Various small bug fixes and dev improvements. | ||
| - Require `setuptools` for installation, and `pandas 0.20.2`. If `numexpr` is installed, version `2.6.2` is required. | ||
| - Allows tilde in `pipeline_interfaces` | ||
|
|
||
| ## [0.5] - 2017-03-01 | ||
| ### Added | ||
| - Add new looper version tracking, with `--version` and `-V` options and printing version at runtime | ||
| - Add support for asterisks in file paths | ||
| - Add support for multiple pipeline directories in priority order | ||
| - Revamp of messages make more intuitive output | ||
| - Colorize output | ||
| - Complete rehaul of logging and test infrastructure, using logging and pytest packages | ||
|
|
||
| ### Changed | ||
| - Removes pipelines_dir requirement for models, making it useful outside looper | ||
| - Small bug fixes related to `all_input_files` and `required_input_files` attributes | ||
| - More robust installation and more explicit requirement of Python 2.7 | ||
|
|
||
|
|
||
| ## [0.4] - 2017-01-12 | ||
| ### Added | ||
| - New command-line interface (CLI) based on sub-commands | ||
| - New subcommand (`looper summarize`) replacing the `summarizePipelineStats.R` script | ||
| - New subcommand (`looper check`) replacing the `flagCheck.sh` script | ||
| - New command (`looper destroy`) to remove all output of a project | ||
| - New command (`looper clean`) to remove intermediate files of a project flagged for deletion | ||
| - Support for portable and pipeline-independent allocation of computing resources with Looperenv. | ||
|
|
||
| ### Changed | ||
| - Removed requirement to have `pipelines` repository installed in order to extend base Sample objects | ||
| - Maintenance of sample attributes as provided by user by means of reading them in as strings (to be improved further) | ||
| - Improved serialization of Sample objects |
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