Metadata-Version: 2.1
Name: cwlgen
Version: 0.4.2
Summary: Generation of CWL programmatically. Available types: Workflow, CommandLineTool and Requirements
Home-page: UNKNOWN
Author: Kenzo-Hugo Hillion and Herve Menager
Author-email: kehillio@pasteur.fr
License: MIT
Description: # python-cwlgen (deprecated)
        
        ## Deprecated
        
        `python-cwlgen` is now deprecated, please use [`cwl-utils >= 0.4`](https://github.com/common-workflow-language/cwl-utils).
        
        ```sh
        from cwl_utils import parser_v1_0
        
        # You could alias this as cwlgen to simplify the migration
        from cwl_utils import parser_v1_0 as cwlgen
        ```
        
        Migration notes:
        
        - Method changes
          - `get_dict() → save()` 
          - `parse_cwl(cwlfile)` → `load_document(cwlfile)`
          - `parse_dict` → No super clear analogue, but loaded through `_RecordLoader(CommandLineTool)` || `_UnionLoader((CommandLineToolLoader, ...workflow + other loaders)`
        
        - Field names:
          - Uses `camelCase` instead of `snake_case`
          - No more special field names, eg:
            - `tool_id` | `workflow_id` | `input_id` | etc → `id`
            - `StepInput`: `inputs` → `in_`
            
        - Other notes:
          - Classes aren't nested anymore, ie: `cwlgen.InitialWorkDirRequirement.Dirent` → `cwl_utils.parser_v1_0.Dirent`.
          - Take care if you're migrating to a newer spec, as some classes might have changed names (notably: `InputParameter` -> `WorkflowInputParameter`)
          - Don't forget to catch all references of cwlgen, as missing one (or using mismatch versions of the parser) will cause:
          
            ```python
            raise RepresenterError('cannot represent an object: %s' % (data,))
            ruamel.yaml.representer.RepresenterError: cannot represent an object: 
            <cwlgen.common.CommandInputArraySchema object at 0x1100a5780>
            ```
            
        If you have issues with the migration, please see [this thread](https://github.com/common-workflow-language/python-cwlgen/issues/27) or raise an issue on CWLUtils.
            
        ---
        
        ## Original README
        
        [![Build Status](https://travis-ci.org/common-workflow-language/python-cwlgen.svg?branch=master)](https://travis-ci.org/common-workflow-language/python-cwlgen)
        [![codecov](https://codecov.io/gh/common-workflow-language/python-cwlgen/branch/master/graph/badge.svg)](https://codecov.io/gh/common-workflow-language/python-cwlgen)
        [![Documentation Status](https://readthedocs.org/projects/python-cwlgen/badge/?version=latest)](http://python-cwlgen.readthedocs.io/en/latest/?badge=latest)
        [![PyPI version](https://badge.fury.io/py/cwlgen.svg)](https://badge.fury.io/py/cwlgen)
        
        Python-cwlgen is a python library for the generation of CWL programmatically.
        It supports the generation of CommandLineTool, Workflow and DockerRequirement.
        The library works for both Python 2.7.12+ and 3.6.0.
        
        ------------------------
        
        
        ## Common Workflow Language
        
        [Common Workflow Language (CWL)](https://www.commonwl.org/v1.0/index.html) is a language to describe workflows. 
        The [user guide](http://www.commonwl.org/user_guide/01-introduction/index.html)
         gives a gentle explanation of what its goals are, but broadly:
         
         1. Stop writing bash scripts for long complex jobs.
         2. Take pipelines anywhere (portability).
         3. Enforce reproducibility guidelines.
         
        This python repository is a python wrapper for _most_ of the classes (work in progress), 
        allowing you to build the structure of the workflow in Python and have this module generate and export CWL for you.
        
        **Nb:** This doesn't check the logic of Workflows or CommandLineTools for you.  
        [CWLTool](https://github.com/common-workflow-language/cwltool) has a `--validate` mode that you can use.
        
        ## Quick-start guide
        
        You can install python-cwlgen through pip with the following command:
        
        ```bash
        pip install cwlgen
        ```
        
        ### How it works?
        
        This repository contains a number of python classes that mirror the CWL specifications ([Workflow](https://www.commonwl.org/v1.0/Workflow.html)| 
        [CommandLineTool](https://www.commonwl.org/v1.0/CommandLineTool.html)). In essence, each class's initializer has all 
        of the properties it expects, which may be another object. The classes include the relevant docstrings to give you 
        context of classes and their properties.
        
        The `examples/` folder contains some simple examples, however in essence you simply initialize the class you're 
        trying to build. An initializer for a class has all of the properties it expects which may be another object.
        
        
        _Creating a CommandLineTool_
        ```python
        import cwlgen
        
        tool_object = cwlgen.CommandLineTool(tool_id="echo-tool", base_command="echo", label=None, doc=None,
                         cwl_version="v1.0", stdin=None, stderr=None, stdout=None, path=None)
        tool_object.inputs.append(
            cwlgen.CommandInputParameter("myParamId", param_type="string", label=None, secondary_files=None, param_format=None,
                         streamable=None, doc=None, input_binding=None, default=None)
        )
        
        # to get the dictionary representation:
        dict_to_export = tool_object.get_dict()
        
        # to get the string representation (YAML)
        yaml_export = tool_object.export_string()
        
        # print to console
        tool_object.export()
        
        # print to file
        tool_object.export("echotool.cwl")
        ```
        
        ## References
        
        CWL is developed by an informal, multi-vendor working group consisting of organizations and individuals 
        aiming to enable scientists to share data analysis workflows. 
        The [CWL project is on Github](https://github.com/common-workflow-language/common-workflow-language).
        
        
        ## Known issues
        
        - `SchemaDefRequirement` doesn't parse the `types` subfield into the specific types 
        (`InputRecordSchema | InputEnumSchema |  InputArraySchema`), but leaves them as a simple dictionary.
Keywords: cwl
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Environment :: Console
Description-Content-Type: text/markdown
