Changelog

3.0.1 (2021-02-10)

• Pin spacy dependency above 3.x.x

• Remove support for older spacy versions

3.0.0 (2021-01-27)

Breaking Changes

• Rework of executors

  • explore is now a method on the executor object

  • Add a man-page executor

  • aclimatise.explore is now deprecated

• Replaces dataclasses with attrs throughout

New Features

• Add docker_image field to Command

• The DockerExecutor has been updated to automatically set this field based on the Docker image being used by it

• Add Janis converter (#73)

Bug Fixes

• Support / as a synonym delimiter (#67)

• Use the optional/required status of each flag appropriately in the downstream CWL/WDL (#68)

2.2.0 (2020-09-26)

• Add command.reanalyse(), which re-analyses the help text stored in the command, using the current parser

• Add command['sort'] which lets you access subcommands by name

2.1.0 (2020-09-22)

• Add bedtools random as a test case

• Use a simple metric to exclude flags unless they have a somewhat valid description text, this should result in less false-positive flags being detected

• Fixed the id field in the CWL tool definitions including some path elements (like ..)

• Use cwltool as a command-line tool instead of via the Python API (it is supposed to be more stable)

2.0.0 (2020-09-16)

• Rename the package from acclimatise to aclimatise, to be consistent with the naming elsewhere. This is a breaking change, and will require you to pip install aclimatise from now on.

• Similarly, rename the module to aclimatise. This will require you to import aclimatise

• Rename the CLI utility from acclimatise to aclimatise.

1.2.0 (2020-09-13)

User-Facing Changes

• Add output generation for CWL and WDL

Fixes

• Fix the railroad diagrams not building

Internal Changes

• Upgrade wdlgen to 3.0.0

• Delete hash.py, which was unused

• Add Command.outputs, which is a property that returns all outputs

• Add (rudimentary) prioritisation for types, ensuring we don’t always choose the type derived from the argument (this is an initial attempt at #37)

• Support more complex assertions for test cases, including the number of outputs

• Small improvements to the infer_type regexes

• Refactor test case assertions into the HelpText class

1.1.1 (2020-09-10)

• Fix the README file in PyPI

1.1.0 (2020-09-10)

User-Facing Changes

• Better distinction between description blocks and flags, allowing us to successfully parse flags of this form:

  --use_strict (enforce strict mode)
        type: bool  default: false
  --es5_readonly (activate correct semantics for inheriting readonliness)
        type: bool  default: true
  

• Support parsing multiple usage blocks, and add the UsageInstance class, which provides access to all these usage examples in the help. For example after parsing the text below, we would have 4 UsageInstance instances. The instances are provided on Command.usage:

  Usage:
    shell [options] -e string
      execute string in V8
    shell [options] file1 file2 ... filek
      run JavaScript scripts in file1, file2, ..., filek
    shell [options]
    shell [options] --shell [file1 file2 ... filek]
      run an interactive JavaScript shell
  

• Add flag and positional de-duplication, ensuring we don’t have duplicate options in the final Command

• Add the max_length parameter to parse_help: If the input text has more than this many lines, no attempt will be made to parse the file (as it’s too large, will likely take a long time, and there’s probably an underlying problem if this has happened). In this case, an empty Command will be returned

• Enforce that a Positional must have at least 2-character names, in the parser

• Enforce that a Positional must have a description, in the parser

Internal Changes

• Rewrite of both the flag and usage parser

• Added more customizable indent tokens, meaning we no longer need the customIndentedBlock

• Refactor both the usage parser and the flag parser into subclasses of IndentParserMixin, which provides useful common parsing logic that relates to indentation

• Use MatchFirst instead of MatchLongest logic in most places in the parser. This should result in more consistent behaviour.

• Add typeHLA.js text, which is derived from the bwa-kit container.

Fixes

• Always strip out newlines from the WDL description

1.0.3 (2020-08-26)

• Add a hard timeout to the DockerExecutor, even if it’s producing output, e.g. the yes command.

1.0.2 (2020-08-25)

• Ensure we never return None from the DockerExecutor

• Add initial parsing of “output inputs”. Thanks to @bernt-matthias (#15). However this information is not yet used in the converters.

1.0.1 (2020-08-22)

• Enforce timeouts for all executors, including Docker

• Restructure the executors such that the parameters are all set in the constructor, not in the execute() call

1.0.0 (2020-08-19)

Since the creation of executors is actually a breaking change, this is now a new major version

User-Facing

• Support executables that have a file extension e.g. samtools.pl

• Refactor the command execution code into a new Executor class, and add a docker executor, allowing you to aCLImatise executables in a Docker image

• Fix for usage parsing when usage is in the middle of the line

Internal

• Run CI on pull requests

• Remove cwlgen as a dependency, thanks to @illusional (#26)

• Make infer_type return None if it can’t determine a type, allowing better handling behaviour. Thanks to @bernt-matthias (#25)

0.2.2 (2020-07-22)

• Add support for Python 3.6 again

• Parse positionals by default from the CLI

• Fix bug involving name generation using different-length strings

• Add samtools bedcov test case

• Add a get_subclasses method for WrapperGenerator

0.2.1 (2020-07-04)

• Add automatic railroad diagram generation for grammar

• Add names to many of the parser elements to facilitate diagram generations

• Add genomethreader test

0.2.0 (2020-05-25)

Features

• Add parameter_meta (parameter documentation) generation back into WDL definitions

• Add acclimatise.model.Command.depth(), and :py:attribute:`acclimatise.model.Command.parent` to acclimatise.model.Command to facilitate the traversal of the command tree

• Add dinosaur and mauveAligner as test cases in test/test_data

• Convert tests into a series of test case objects that can be used to parameterize each test function

• Add the option to parallelize tests using pytest-parallel

• Better conversion of symbols to variable names, for example “/” is now “slash” rather than “solidus”

• Add logging to the high level functions like explore_command, using the acclimatise logger. This should make tracking errors and progress a tad easier.

• By default, re-use the best help command from the parent on the child. For example if we determine that samtools --help is the most accurate help command for samtools, then we use samtools sort --help without having to test out every possible flag here

• Add generated_using field to the Command class, which tracks the flag used to generate it

Changes

• Set the default command depth to 3

• aCLImatise now only supports Python >= 3.7.5, due to this bug

Fixes

• Avoid variable naming collisions using a generator-based iteration method in acclimatise.name_generation.generate_names

• Keep a global spacy instance to minimize memory footprint. This is available in :py:module:`acclimatise.nlp`

• Fix infinite loops in explore, e.g. tools like dinosaur and mauve by adding more advanced subcommand detection in acclimatise.is_subcommand

• Make cmd optional for validators

• Always run commands in a pseudo-TTY so that commands like samtools will output help

• Various other fixes

0.1.5 (2020-05-18)

• Bugfix for when we have no help text

• Add a test for a program that we know fails

0.1.4 (2020-05-18)

• Choose best command using length of help text, if everything else is equal

0.1.3 (2020-05-15)

• Command types now contain a help_text field which records the string that was used to generate them. This should enable efficient re-parsing, and can also be displayed downstream by BaseCamp

• Rewrite tests into a parametrized, consolidated end-to-end test

• Fix “OPTIONS” being considered a positional argument, when really it’s a placeholder for flags

• Remove positional arguments that precede the main command, so dotnet Pisces.dll will be removed from the entire command

0.1.2 (2020-05-15)

• Generating YAML output now produces one file for each subcommand, to match other converters

0.1.1 (2020-05-13)

• Make explore -o flag default to current working directory, for simplicity

• Updated the readme

• Add installation instructions

0.1.0 (2020-05-13)

• Fix the doubled variable names like bytesBytes

• Smarter POS-based algorithm for generating names from descriptions

• Automatically choose a description based name when we have only short named flags like -n

• Add changelog

• Add comprehensive testing for CWL and WDL generation

• Fix for variable names with symbols in them

• Use regex library for faster and more concise regex