Saravanan666/pypi-org huggingface dataset:
Package: cw-download-chess-com-games
DescriptionDownload allchess.comgames at once.
All games PGN file will be stored current or specified directory.Raw source JSON files with extra information will be stored inoutput/cachepath.Installpip install cw-download-chess-com-gamesUsageGet helpcw_download_chess_com_games -hGet gamescw_download_chess_com_games --user_name your_chess_com_nameGet games into custom path/directorycw_download_chess_com_games --user_name your_chess_com_name --output_path .Update recent gamesDeleteoutput/cacheto allow fresh download.LicenseCopyright 2022 by Cezary K. Wagner. Licensed underAttribution-NonCommercial-NoDerivatives 4.0 International.
Package: cwe
CWE Common weakness enumeration library for Pythonhttps://cwe.mitre.org/index.htmlInstallationpipinstallcweUsageGet a CWE by ID:>>>fromcweimportDatabase>>>db=Database()>>>db.get(15)Weakness(cwe_id=15, name=External Control of System or Configuration Setting)Access attributes of the Weakness using dot notation>>>weakness=db.get(15)>>>weakness.description'One or more system settings or configuration elements can be externally controlled by a user.'Or use the weaknessgetmethod>>>weakness.get("status",None)'Incomplete'Get a dictionary of the weakness (Truncated for this example)>>>weakness.to_dict(){'cwe_id': '15', 'name': 'External Control of System or Configuration Setting', 'weakness_abstraction': 'Base'}Get the top 25 weaknesses>>>fromcweimportDatabase>>>db=Database()>>>db.get_top_25()Weakness attributesThe following weakness object attributes can accessed:cwe_idnameweakness_abstractionstatusdescriptionextended_descriptionrelated_weaknessesweakness_ordinalitiesapplicable_platformsbackground_detailsalternate_termsmodes_of_introductionexploitation_factorslikelihood_of_exploitcommon_consequencesdetection_methodspotential_mitigationsobserved_examplesfunctional_areasaffected_resourcestaxonomy_mappingsrelated_attack_patternsnotesTestsThere's a smallunittesttest suite in thetestsdirectory
Package: cweather
This is a really simple script that gives you a pretty and colorful display of
the weather on your command line. Presumably, it would be useful to put in your
login script or MOTD so that you can see the weather when you log into a
terminal.Author:Jack RosenthalRequires:Python 3.4 or greater, RequestsLicense:MITContributing:SeeCONTRIBUTING.rstInstallationInstall usingpip:pip install cweatherNotePass the--userflag topipif you would like to install for your
local user.Usagecweather[-h][--api-keyAPI_KEY][--timeoutTIMEOUT][--no-color][location]-h,--helpshow this help message and exit--api-keyAPI_KEYWunderground API key, defaults toWUNDERGROUND_API_KEYin your environment, or some random one that might work if
unset--timeoutTIMEOUTTimeout for connection--no-colorNo colors, default ifTERMisvt100locationspecifies a named location (e.g.,Golden, CO) or a postal
code, and will default to theLOCATIONenvironment variable, or 80401
(Golden, CO) if unset.
Package: cwinput
CWInputSimple Windows-oriented library to read raw input from console using multithreading.InstallationYou can get this package fromPyPipipinstallcwinputExampledeflistener(key:Key):print(f"Got{key}from keyboard")keyboard=CWInput()keyboard.subscribe(listener)# Add new listenerkeyboard.run()# Run CWInput in a new threadkeyboard.join()# Joins CWInput thread to parent thread, inherited from Thread class
Package: cwl-airflow
CWL-AirflowPython package to extendApache-Airflow 2.1.4functionality withCWL v1.1supportCite asMichael Kotliar, Andrey V Kartashov, Artem Barski, CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language, GigaScience, Volume 8, Issue 7, July 2019, giz084,https://doi.org/10.1093/gigascience/giz084Get the latest versionpip install cwl-airflowLatest versiondocumentationGet published versionpip install cwl-airflow==1.0.18Published versiondocumentationNotesNotes for developers can be found inDEV README
Package: cwl-airflow-parser
cwl-airflow-parserAboutExtendsApache-AirflowwithCWL v1.0support.Installationpip3.6install-Ucwl-airflow-parserRequirementsPackage has been tested on Ubuntu 16.04.3 and Mac OS X Sierra/ High Sierra. Make sure your system satisfies the following criteria:python 3.6dockernodejsUsagefromcwl_airflow_parserimportCWLDAG,CWLJobDispatcher,CWLJobGathererfromdatetimeimporttimedeltadefcwl_workflow(workflow_file):dag=CWLDAG(default_args={'owner':'airflow','email':['my@email.com'],'email_on_failure':False,'email_on_retry':False,'retries':20,'retry_exponential_backoff':True,'retry_delay':timedelta(minutes=30),'max_retry_delay':timedelta(minutes=60*4)},cwl_workflow=workflow_file)dag.create()dag.add(CWLJobDispatcher(dag=dag),to='top')dag.add(CWLJobGatherer(dag=dag),to='bottom')returndagcwl_workflow("/path/to/my/workflow.cwl")
Package: cwlbrowser
#cwlbrowser##cwlbrowseris a python library that allows you to open, browse and compare scientific workflows written in CWL on a Jupyter notebook### Installationpip install cwlbrowser### Documentation
Detailed documentation of usage can be found [here:](https://gitlab.cs.man.ac.uk/mbaxasp7/cwlbrowser/blob/master/doc/documentation.md)
Package: cwldep
# Common Workflow Language dependency managerThis tool helps you to import tools and workflows from other sources for use in your own workflow.# SetupIt is highly recommended to setup virtual environment before installing `cwldep`:```virtualenv -p python2 venv   # Create a virtual environment, can use `python3` as wellsource venv/bin/activate     # Activate environment before installing `cwldep````Install from source:```git clone https://github.com/common-workflow-language/cwldep.git # clone cwldep repocd cwldep         # Switch to source directorypython setup.py installcwldep -h  # Check if the installation works correctly```# Adding file dependencies```cwldep add myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl```This will download the CWL file *and its dependencies* to `raw.githubusercontent.com/common-workflow-language/workflows/master/tools`Include it in your workflow as a relative file reference:```steps:step1:in: ...out: ...run: raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl```# Changing the install target```cwldep add --install-to samtools myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl```# Using archivesYou can also import archives (.tar.gz, .tar.bz2, and .zip):```cwldep add myfile.cwl https://github.com/common-workflow-language/workflows/archive/draft2.tar.gz```This will download and extract to the local directory `github.com/common-workflow-language/workflows/archive`# Using git upstreamYou can also import git repositories:```cwldep add myfile.cwl https://github.com/common-workflow-language/workflows```This will clone into the local directory `github.com/common-workflow-language/workflows````cwldep add --set-version=draft-2 myfile.cwl https://github.com/common-workflow-language/workflows```# Installing dependenciesThis will install any dependencies listed in `myfile.cwl````cwldep install myfile.cwl```# Checking if upstream dependencies have changedThis will report if the upstream dependencies listed in `myfile.cwl` have changed```cwldep check myfile.cwl```# Updating dependenciesThis will install updated dependencies:```cwldep update myfile.cwl```# Deleting unreferenced dependenciesThis will delete any dependencies listed in the ".dep.lock" file that are not referenced by `myfile.cwl`.```cwldep clean myfile.cwl```
Package: cwlformat
CWL FormatCWL Format is a specification and a reference implementation for
a very opinionated CWL code formatter.It outputs CWL in a standardized YAML format. It has no settings or
options because you have better things to do with your time. And because
CWL Format is always correct.This repository lists the formatting rules and also contains a Python
implementation of the formatter.pip install cwlformat
cwl-format unformatted.cwl > formatted.cwlIf you don't have a > py3.6 environment, you can usepipx:pip install pipx  # from your < py3.6 environment
pipx ensurepath # ensures CLI application directory is on your $PATH
pipx install cwlformat --python python3.7 #tells pipx to set up a Py3.7 env for this appUse programmatically in Python by doingfromcwlformat.formatterimportcwl_formatformatted_text=cwl_format(unformatted_text)orfromcwlformat.formatterimportstringify_dictas_dict=load_yaml(unformatted_text)formatted_str=stringify_dict(as_dict)RulesOnly comment lines at the top of the file, including blank lines,
before the actual CWL code are preserved. All other comments are lost.Do not use this if all comments in the YAML are important to you.If the first line does not start with#!/usr/bin/envthe line#!/usr/bin/env cwl-runneris added to the top of the file.All CWL fields are ordered systematically. The field order for specific
fields have a defined precedence ("pinned fields"). Any fields not
present in this file ("free fields") are printed after the pinned fields
and ordered alphabetically.A single blank line is added before the following fields if the parent
structure is a process.inputsoutputsstepsrequirementshintsbaseCommandThe pinned fields are defined inthis YAML file.Specific pinned field orderings are available for CommandLineTool,
ExpressionTool and Workflow processes. All other types follow a generic
pinned field list.All strings that fit within 80 columns are expressed in flow style.
Longer strings or strings with new lines are expressed in block style.All lists and maps are expressed in block styleThe ordering of all lists are preservedIndentation is 2 spaces, including for listsConformance testsA series of documents are found in thetestsdirectory that can be used
to check correctness of a formatter. The files namedoriginal-*are the input files
and the files namedformatted-*are the corresponding formatted documents. There
are a mixture of YAML and JSON input files. Formatted files are always YAML.CWL ExploderThis takes as input a packed workflow (workflow with all steps in lined) and splits it
recursively into parts.cwl-explode formatted-atac-seq-pipeline.cwl expected-exploded-atac-seq.cwlResults in theexploded parent workflowand52 sub-components
Package: cwlgen-kclhi
python-cwlgenPython-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 LanguageCommon Workflow Language (CWL)is a language to describe workflows.
Theuser guidegives a gentle explanation of what its goals are, but broadly:Stop writing bash scripts for long complex jobs.Take pipelines anywhere (portability).Enforce reproducibility guidelines.This python repository is a python wrapper formostof 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.CWLToolhas a--validatemode that you can use.Quick-start guideYou can install python-cwlgen through pip with the following command:pipinstallcwlgenHow it works?This repository contains a number of python classes that mirror the CWL specifications (Workflow|CommandLineTool). 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.Theexamples/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 CommandLineToolimportcwlgentool_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 consoletool_object.export()# print to filetool_object.export("echotool.cwl")ReferencesCWL is developed by an informal, multi-vendor working group consisting of organizations and individuals
aiming to enable scientists to share data analysis workflows.
TheCWL project is on Github.Known issuesSchemaDefRequirementdoesn't parse thetypessubfield into the specific types
(InputRecordSchema | InputEnumSchema |  InputArraySchema), but leaves them as a simple dictionary.
Package: cwl-inputs-parser
cwl-inputs-parserA library for parsing the inputs field of Common Workflow Language (CWL) document.
This library aims to use it as a CWL parser to generate a web form to execute the Workflow Execution Service (WES).As a simple example, if you inputtests/all_input.cwl,tests/all_input.jsonwill be output.The schema of the parsed results iscwl-inputs-parser-schema.json.We are testing using the CWL v1.2 conformance test.
The list of test IDs that will not pass istests/cwl_conformance_test/failed_test_ids.txt.InstallationRequires Python 3.6+To install from PyPI:$pipinstallcwl-inputs-parser
$cwl-inputs-parser--helpTo install from source:$gitclonehttps://github.com/suecharo/cwl-inputs-parser.git
$cdcwl-inputs-parser
$pipinstall.
$cwl-inputs-parser--helpTo install with docker:$dockerrun-t--rmghcr.io/suecharo/cwl-inputs-parser:latestcwl-inputs-parser--helpUsageIt is deployed athttps://cwl-inputs-parser.azurewebsites.netThe easiest way to use:$curl-XPOSThttps://cwl-inputs-parser.azurewebsites.net\-d'{"wf_location": "https://raw.githubusercontent.com/suecharo/cwl-inputs-parser/main/tests/cwl_conformance_test/v1.2/wc-tool.cwl"}'[{"array":false,"default":null,"doc":null,"id":"file1","label":null,"required":true,"secondaryFiles":null,"type":"File"}]As command line toolUse as a command line tool:$cwl-inputs-parser/path/to/cwl_document(localfilepath|remoteURL)As REST API serverStart the server:$cwl-inputs-parser--server--host0.0.0.0--port8080*ServingFlaskapp'cwl_inputs_parser.server'(lazyloading)*Environment:production*Debugmode:off*Runningonhttp://172.26.0.2:8080/(PressCTRL+Ctoquit)Request withcurl:$curl-Xgetlocalhost:8080/health{"status":"ok"}# {"wf_location": "https://path/to/workflow"}$curl-XPOSTlocalhost:8080-d@tests/curl_data_location.json
...# {"wf_content": "serialized CWL contents..."}$curl-XPOSTlocalhost:8080-d@tests/curl_data_content.json
...

$curl-XPOST\localhost:8080\-d'{"wf_location": "https://raw.githubusercontent.com/suecharo/cwl-inputs-parser/main/tests/cwl_conformance_test/v1.2/wc-tool.cwl"}'[{"array":false,"default":null,"doc":null,"id":"file1","label":null,"required":true,"secondaryFiles":null,"type":"File"}]Do cwltool's--make-template:$curl-XPOSTlocalhost:8080/make-template-d@tests/curl_data_location.json"file1:  # type \"File\"\n    class: File\n    path: a/file/path\n"$curl-XPOSTlocalhost:8080/make-template-d@tests/curl_data_content.json"file1:  # type \"File\"\n    class: File\n    path: a/file/path\n"As python libraryUse as a python library:$python3
Python3.8.12(default,Oct132021,13:56:21)[GCC7.5.0]onlinux
Type"help","copyright","credits"or"license"formoreinformation.
>>>fromcwl_inputs_parser.utilsimportwf_location_to_inputs
>>>inputs=wf_location_to_inputs("./tests/cwl_conformance_test/v1.2/wc-tool.cwl")>>>inputs.as_dict()[{'default':None,'doc':None,'id':'file1','label':None,'type':'File','array':False,'required':True,'secondaryFiles':None}]Developmentdevelopment environment:docker-compose-fdocker-compose.dev.ymlup-d--build
docker-compose-fdocker-compose.dev.ymlexecappbashtesting:pytest.LicenseApache-2.0.
See theLICENSE.
Package: cwlkernel
Jupyter Notebook Kernel for Common Workflow LanguageThis is a jupyter notebook kernel which enables running Common Workflow Language. It usescwltoolas the execution engine. The goal of the kernel is to
improve the human-in-the-loop interaction. The goal of the kernel is to improve human-in-the-loop by improving the
following:Documenting the workflowEnable the developer to execute a workflow with multiple steps splited in multiple JN cellsEnable the user to execute multiple workflows stitched togetherEnsembl workflowsRun the same workflow many times over different datasets or with different settings over the same data setsRun different workflows over the same datasetsCurrently windows are not supportedExamplesIn examples directory there are many examples which illustrate how to use the kernel.How to contributeIf you are a CWL developer and you would like to contribute feel free to open an issue and ask for new features you
would like to see.
Package: cwl-subworkflows
cwl_subworkflowsA list of subworkflows used for MSK-ACCESS data processing.Free software: Apache Software License 2.0Documentation:https://cwl-subworkflows.readthedocs.io.FeaturesTODOCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.1.0 (2019-08-14)First release on PyPI.
Package: cwl-tes
GA4GH CWL Task Executioncwl-tessubmits your tasks to a TES server. Task submission is parallelized when possible.Funnelis an implementation of theGA4GH task execution API. It runs your dockerized tasks on slurm, htcondor, google compute engine, aws batch, etc.RequirementsPython 2.7 / 3.5 / 3.6DockerFunnelQuickstartStart the task serverfunnel server runRun your CWL tool/workflowcwl-tes --tes http://localhost:8000 tests/hashsplitter-workflow.cwl.yml --input tests/resources/test.txtInstallI strongly recommend using avirtualenvfor installation sincecwl-tesdepends on a specific version ofcwltool.Install from pip:pip install cwl-tesInstall from source:python setup.py installRun the v1.0 conformance testsTo start a funnel server instance automatically and run all of the tests, installtoxand run it$ pip install tox
$ toxFor running only the conformance tests in python 2.7:$ tox -e py27-unitIn a similar way they can be run on any supported python interpreter.A more manual approach:Download the conformance tests:git submodule update --init --recursiveStart the funnel server.funnel server --config /path/to/config.yamlMake sure that TMPDIR is specified in the AllowedDirs of your Local storage configuration.To run all the tests:./tests/run_conformance.shTo run a specifc test:./tests/run_conformance.sh 10
Package: cwltest
PyPI:Conda:This is a testing tool for checking the output of Tools and Workflows described
with the Common Workflow Language.  Among other uses, it is used to run the CWL
conformance tests.This is written and tested for Python 3.8, 3.9, 3.10, 3.11, and 3.12.Table of ContentsInstallRun on the command lineGenerate conformance badges using cwltestInstallInstalling the official package from PyPipipinstallcwltestOr from biocondacondainstall-cbiocondacwltestOr from sourcegitclonehttps://github.com/common-workflow-language/cwltest.gitcdcwltest&&pipinstall.Run on the command lineSimple command:cwltest --test test-descriptions.yml --tool cwl-runnerGenerate conformance badges using cwltestTo make badges that show the results of the conformance test,
you can generate JSON files forhttps://badgen.netby using –badgedir optionTo generate JSON files:cwltest --test test-descriptions.yml --tool cwl-runner --badgedir badges
...
$ cat badges/command_line_tool.json | jq .
{
  "subject": "command_line_tool",
  "status": "100%",
  "color": "green"
}Once you upload JSON file to a server, you make a badge by using a link likehttps://badgen.net/https/path/to/generated/jsonorhttps://flat.badgen.net/https/path/to/generated/json(for flat badges).Here is an example of markdown to add a badge:![test result](https://flat.badgen.net/https/path/to/generated/json?icon=commonwl)
Package: cwltool-ucsc
==================================================================Common workflow language tool description reference implementation==================================================================CWL Conformance test: |Build Status|This is the reference implementation of the Common Workflow Language.  It isintended to be feature complete and provide comprehensive validation of CWLfiles as well as provide other tools related to working with CWL.This is written and tested for Python 2.7.The reference implementation consists of two packages.  The "cwltool" packageis the primary Python module containing the reference implementation in the"cwltool" module and console executable by the same name.The "cwlref-runner" package is optional and provides an additional entry pointunder the alias "cwl-runner", which is the implementation-agnostic name for thedefault CWL interpreter installed on a host.Install-------Installing the official package from PyPi (will install "cwltool" package aswell)::pip install cwlref-runnerIf installling alongside another CWL implementation then::pip instal cwltoolTo install from source::git clone https://github.com/common-workflow-language/cwltool.gitcd cwltool && python setup.py installcd cwlref-runner && python setup.py install  # co-installing? skip thisRemember, if co-installing multiple CWL implementations then you need tomaintain which implementation ``cwl-runner`` points to via a symbolic filesystem link or [another facility](https://wiki.debian.org/DebianAlternatives).Run on the command line-----------------------Simple command::cwl-runner [tool-or-workflow-description] [input-job-settings]Or if you have multiple CWL implementations installed and you want to overridethe default cwl-runner use::cwltool [tool-or-workflow-description] [input-job-settings]Import as a module----------------Add::import cwltoolto your script.Use with boot2docker--------------------boot2docker is running docker inside a virtual machine and it only mounts ``Users``on it. The default behavoir of CWL is to create temporary directories under e.g.``/Var`` which is not accessible to Docker containers.To run CWL successfully with boot2docker you need to set the ``--tmpdir-prefix``and ``--tmp-outdir-prefix`` to somewhere under ``/Users``::$ cwl-runner --tmp-outdir-prefix=/Users/username/project --tmpdir-prefix=/Users/username/project wc-tool.cwl wc-job.json.. |Build Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance:target: https://ci.commonwl.org/job/cwltool-conformance/Tool or workflow loading from remote or local locations-------------------------------------------------------``cwltool`` can run tool and workflow descriptions on both local and remotesystems via its support for HTTP[S] URLs.Input job files and Workflow steps (via the `run` directive) can reference CWLdocuments using absolute or relative local filesytem paths. If a relative pathis referenced and that document isn't found in the current directory then thefollowing locations will be searched:http://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem
Package: cwl-upgrader
This is a standalone upgrader for Common Workflow Language documents from
versiondraft-3,v1.0, andv1.1tov1.2.Seehttps://github.com/sbg/sevenbridges-cwl-draft2-upgraderfor upgrading fromsbg:draft-2.It does not check for correctness of the input document, for that one can usethe CWL reference implementation(cwltool--validate).This is written and tested for Python 3.8, 3.9, 3.10, 3.11, and 3.12.InstallInstalling the official package from PyPI:pip install cwl-upgraderOr from source:git clone https://github.com/common-workflow-language/cwl-upgrader.git
pip install ./cwl-upgrader/Run on the command linecwl-upgrader path-to-cwl-document [another-path-to-cwl-document ...]