Saravanan666/pypi-org huggingface dataset:
Package: ghga-message-schemas
GHGA Message SchemasA package that collects schemas used for messaging between GHGA service.Quick StartInstallationThis package is available at PyPI:https://pypi.org/project/ghga-message-schemasYou can install it from there using:pip install ghga-message-schemasThereby, you may specify following extra(s):dev: dependencies needed for development and testingDevelopmentFor setting up the development environment, we rely on thedevcontainer featureof vscode
in combination with Docker Compose.To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers" extension (ms-vscode-remote.remote-containers) installed.
Then open this repository in vscode and run the commandRemote-Containers: Reopen in Containerfrom the vscode "Command Palette".This will give you a full-fledged, pre-configured development environment including:infrastructural dependencies (databases, etc.)all relevant vscode extensions pre-installedpre-configured linting and auto-formatinga pre-configured debuggerautomatic license-header insertionMoreover, inside the devcontainer, there if following convenience commands available
(please type it in the integrated terminal of vscode):dev_install- installs the package with all development dependencies and installs pre-commit
(please run that if you are starting the devcontainer for the first time
or if you added any python dependencies to the./setup.cfg)If you prefer not to use vscode, you could get a similar setup (without the editor specific features)
by running the following commands:# Execute in the repo's root dir:cd./.devcontainer# build and run the environment with docker-composedocker-composeup# attach to the main container:# (you can open multiple shell sessions like this)dockerexec-itdevcontainer_app_1/bin/bashLicenseThis repository is free to use and modify according to theApache 2.0 License.
Package: ghga-metadata-utils
GHGA Metadata UtilsThe GHGA Metadata Utils is a package that provides all things related to
the GHGA Metadata Schema.The repository is structured to encourage,reuse of custom generatorsmanage validation pluginsDocumentation:An extensive documentation can be foundhere(coming soon).Quick StartInstallation# Execute in the repo's root dir:pipinstall.DevelopmentFor setting up the development environment, we rely on thedevcontainer featureof vscode
in combination with Docker Compose.To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers" extension (ms-vscode-remote.remote-containers) installed.
Then open this repository in vscode and run the commandRemote-Containers: Reopen in Containerfrom the vscode "Command Palette".This will give you a full-fledged, pre-configured development environment including:infrastructural dependencies of the service (databases, etc.)all relevant vscode extensions pre-installedpre-configured linting and auto-formatinga pre-configured debuggerautomatic license-header insertionMoreover, inside the devcontainer, there are two convenience commands available
(please type them in the integrated terminal of vscode):dev_install- install the service with all development dependencies,
installs pre-commit, and applies any migration scripts to the test database
(please run that if you are starting the devcontainer for the first time
or if you added any python dependencies to the./setup.cfg)If you prefer not to use vscode, you could get a similar setup (without the editor specific features)
by running the following commands:# Execute in the repo's root dir:cd./.devcontainer# build and run the environment with docker-composedocker-composeup# attach to the main container:# (you can open multiple shell sessions like this)dockerexec-itdevcontainer_app_1/bin/bashLicenseThis repository is free to use and modify according to theApache 2.0 License.
Package: ghga-service-chassis-lib
ghga-service-chassis-libThis python library serves as chassis for the microservices developed at
German Human Genome-Phenome Archive (GHGA).It collects boilerplate code for common functionalities such as config
parameter parsing and API server setup.This library is primarily intended for internal use at GHGA and should
not be seen as a general-purpose microservice chassis.
However, if this library matches your specific needs as well,
please feel free to use it. It is open source.InstallationThis package is available at PyPI:https://pypi.org/project/ghga_service_chassis_libYou can install it from there using:pip install ghga_service_chassis_libThereby, you may specify following extra(s):api: dependencies needed to use the API server functionalitiesdev: dependencies needed for development and testingDevelopmentFor setting up the development environment, we rely on thedevcontainer featureof vscode.To use it, you have to have Docker as well as vscode with its "Remote - Containers" extension (ms-vscode-remote.remote-containers) extension installed.
Then, you just have to open this repo in vscode and run the commandRemote-Containers: Reopen in Containerfrom the vscode "Command Palette".This will give you a full-fledged, pre-configured development environment including:infrastructural dependencies of the service (databases, etc.)all relevant vscode extensions pre-installedpre-configured linting and auto-formatinga pre-configured debuggerautomatic license-header insertionMoreover, inside the devcontainer, there is follwing convenience command available
(please type it in the integrated terminal of vscode):dev_install- install the lib with all development dependencies and pre-commit hooks
(please run that if you are starting the devcontainer for the first time
or if added any python dependencies to the./setup.cfg)If you prefer not to use vscode, you could get a similar setup (without the editor specific features)
by running the following commands:# Execute in the repo's root dir:cd./.devcontainer# build and run the environment with docker-composedockerbuild-tghga-service-chassis-lib.
dockerrun-itghga-service-chassis-lib/bin/bashLicenseThis repository is free to use and modify according to theApache 2.0 License.
Package: ghga-service-commons
ghga-service-commonsThis Python library serves as a collection of common utilities used by
the microservices developed at German Human Genome-Phenome Archive (GHGA).It collects boilerplate code for common functionalities such as API server setup,
authentication and authorization.This library is primarily intended for internal use at GHGA and should
not be seen as a general-purpose microservice chassis.
However, if this library matches your specific needs as well,
please feel free to use it. It is open source.InstallationThis package is available at PyPI:https://pypi.org/project/ghga_service_commonsYou can install it from there using:pip install ghga_service_commonsThereby, you may specify following extra(s):api: dependencies needed to use the API server functionalitiesauth: dependencies needed for dealing with authentication and authorizationDevelopmentFor setting up the development environment, we rely on thedevcontainer featureof vscode.To use it, you have to have Docker as well as vscode with its "Remote - Containers" extension (ms-vscode-remote.remote-containers) extension installed.
Then, you just have to open this repo in vscode and run the commandRemote-Containers: Reopen in Containerfrom the vscode "Command Palette".This will give you a full-fledged, pre-configured development environment including:infrastructural dependencies of the service (databases, etc.)all relevant vscode extensions pre-installedpre-configured linting and auto-formattinga pre-configured debuggerautomatic license-header insertionMoreover, inside the devcontainer, there is following convenience command available
(please type it in the integrated terminal of vscode):dev_install- install the lib with all development dependencies and pre-commit hooks
(please run that if you are starting the devcontainer for the first time
or if added any python dependencies to the./setup.cfg)If you prefer not to use vscode, you could get a similar setup (without the editor specific features)
by running the following commands:# Execute in the repo's root dir:cd./.devcontainer# build and run the environment with docker-composedockerbuild-tghga-service-commons.
dockerrun-itghga-service-commons/bin/bashLicenseThis repository is free to use and modify according to theApache 2.0 License.
Package: ghga-transpiler
Ghga TranspilerGHGA-Transpiler - excel to JSON converterDescriptionThe GHGA Transpiler is a Python library and command line utility to transpile the official GHGA metadata XLSX workbooks to JSON. Please note that the GHGA Transpiler does not validate that the provided metadata is compliant with theGHGA Metadata Schema. This can be achieved by running theGHGA Validatoron the JSON data generated by the GHGA Transpiler.InstallationWe recommend installing the latest version of the GHGA transpiler using pippip install ghga-transpilerUsage:Usage: ghga-transpiler [OPTIONS] SPREAD_SHEET [OUTPUT_FILE]

  ghga-transpiler is a command line utility to transpile the official GHGA
  metadata XLSX workbooks to JSON. Please note that ghga-transpiler does not
  validate that the provided metadata is compliant with the GHGA Metadata
  Schema. This can be achieved by running ghga-validator on the JSON data
  generated by the ghga-transpiler.

Arguments:
  SPREAD_SHEET   The path to input file (XLSX)  [required]
  [OUTPUT_FILE]  The path to output file (JSON).

Options:
  -f, --force                     Override output file if it exists.
  --install-completion [bash|zsh|fish|powershell|pwsh]
                                  Install completion for the specified shell.
  --show-completion [bash|zsh|fish|powershell|pwsh]
                                  Show completion for the specified shell, to
                                  copy it or customize the installation.
  --help                          Show this message and exit.DevelopmentFor setting up the development environment, we rely on thedevcontainer featureof vscode
in combination with Docker Compose.To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers"
extension (ms-vscode-remote.remote-containers) installed.
Then open this repository in vscode and run the commandRemote-Containers: Reopen in Containerfrom the vscode "Command Palette".This will give you a full-fledged, pre-configured development environment including:infrastructural dependencies of the service (databases, etc.)all relevant vscode extensions pre-installedpre-configured linting and auto-formatinga pre-configured debuggerautomatic license-header insertionMoreover, inside the devcontainer, a convenience commandsdev_installis available.
It installs the software with all development dependencies, installs pre-commit.The installation is performed automatically when you build the devcontainer. However,
if you update dependencies in the./setup.cfgor the./requirements-dev.txt, please run it again.LicenseThis repository is free to use and modify according to theApache 2.0 License.Readme GenerationThis readme is autogenerate, please seereadme_generation.mdfor details.
Package: ghga-validator
Ghga ValidatorGHGA Validator - A Python library and command line utility to validate metadataDescriptionghga-validator is a Python library and command line utility to validate metadata
w.r.t. its compliance to theGHGA Metadata
Model. It takes metadata encoded in JSON of YAML format and produces a validation report in JSON format.InstallationWe recommend installing the latest version of ghga-validator using pip:pip install -U ghga-validatorUsageUsage: ghga-validator [OPTIONS]

  GHGA Validator

  ghga-validator is a command line utility to validate metadata w.r.t. its
  compliance to the GHGA Metadata Model. It takes metadata encoded in JSON of
  YAML format and produces a validation report in JSON format.

Options:
  -s, --schema PATH               Path to metadata schema (modelled using
                                  LinkML)  [required]
  -i, --input FILE                Path to submission file in JSON format to be
                                  validated  [required]
  -r, --report FILE               Path to resulting validation report
                                  [required]
  --target-class TEXT             The root class name
  --install-completion [bash|zsh|fish|powershell|pwsh]
                                  Install completion for the specified shell.
  --show-completion [bash|zsh|fish|powershell|pwsh]
                                  Show completion for the specified shell, to
                                  copy it or customize the installation.
  --help                          Show this message and exit.DevelopmentFor setting up the development environment, we rely on thedevcontainer featureof vscode
in combination with Docker Compose.To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers"
extension (ms-vscode-remote.remote-containers) installed.
Then open this repository in vscode and run the commandRemote-Containers: Reopen in Containerfrom the vscode "Command Palette".This will give you a full-fledged, pre-configured development environment including:infrastructural dependencies of the service (databases, etc.)all relevant vscode extensions pre-installedpre-configured linting and auto-formatinga pre-configured debuggerautomatic license-header insertionMoreover, inside the devcontainer, a convenience commandsdev_installis available.
It installs the service with all development dependencies, installs pre-commit.The installation is performed automatically when you build the devcontainer. However,
if you update dependencies in the./setup.cfgor the./requirements-dev.txt, please run it again.LicenseThis repository is free to use and modify according to theApache 2.0 License.
Package: ghget
DescriptionDownload single files or directories from a GitHub repository without cloning its entire contents.FeaturesNo need to manually create a raw GitHub url for individual files, just provide the web url.Recursively download entire directories.Download from private repos by setting aGITHUB_TOKENenvironment variable.Lightweight, easy to install, and easy to use.InstallationTheghgetpackage can be installed directly usingpip.pip install ghgetUsageEasily download single files given the GitHub url:$ ghget https://github.com/naiquevin/pipdeptree/blob/master/pipdeptree.py
Downloading pipdeptree.py file...
Done!Recursively download a specific directory from a GitHub repo:$ ghget https://github.com/pandas-dev/pandas/tree/master/scripts
Downloading scripts directory...
Done!

$ tree
.
└── scripts
    ├── __init__.py
    ├── generate_pip_deps_from_conda.py
    ├── list_future_warnings.sh
    ├── no_bool_in_generic.py
    ├── pandas_errors_documented.py
    ├── sync_flake8_versions.py
    ├── tests
    │   ├── __init__.py
    │   ├── conftest.py
    │   ├── test_no_bool_in_generic.py
    │   ├── test_sync_flake8_versions.py
    │   ├── test_use_pd_array_in_core.py
    │   └── test_validate_docstrings.py
    ├── use_pd_array_in_core.py
    ├── validate_docstrings.py
    └── validate_rst_title_capitalization.pyOptionsusage: ghget [-h] url

positional arguments:
  url         The url for the file or directory you want to download.

optional arguments:
  -h, --help  show this help message and exit
Package: ghgql
ghgqlThin wrapper for interacting with theGithub GraphQL API.StatusDocumentationPlease find the documentation and usage examples here:https://ghgql.readthedocs.io/en/latest/Installation$pipinstallghgqlUsageFor a more in-depth example, take a look atthe example in the documentation. Here's a basic example.importosimportfncimportghgqlquery="""query ($searchQuery: String!) {search(query: $searchQuery, type: ISSUE, first: 1) {edges {node {... on Issue {idnumbertitleurl}}}}}"""withghgql.GithubGraphQL(token=os.getenv("GITHUB_TOKEN"))asghapi:result=ghapi.query(query=query,variables={"searchQuery":"llvm/llvm-project"})print(fnc.get("search.edges",result))Should output something like this:[{'node':{'id':'I_kwDOHicqdc5RG-tC','number':16,'title':'llvm/llvm-project','url':'https://github.com/KhushP786/open-sauced-goals/issues/16'}}]ContributingInterested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.Commit message conventions and semantic versioniong (semver)We use semantic versioning andthese commit message conventionscan be used to automatically bump the version number and generate the changelog.Licenseghgqlwas created by Konrad Kleine. It is licensed under the terms of the MIT license.CreditsThis project was created with the help ofthis python packaging documentation.ghgqlwas created withcookiecutterand thepy-pkgs-cookiecuttertemplate.
Package: ghgrenamer
GHG RenamerA Python tool to rename various names used for Greenhouse Gas emissions or
concentrations tables to a common naming scheme.Example:fromghgrenamerimportto_shortnameto_shortname("CO2_emissions")# => 'CO2'Example usage:fromghgrenamerimportto_shortnameimportpandasaspddf=pd.read_excel("Supplementary_Table_UoM_GHGConcentrations-1-1-0_annualmeans_v23March2017.xls",skiprows=21,index_col=0,sheet_name=1)print([to_shortname(i)foriindf.columns])"""['CO2', 'CH4', 'N2O', 'HFC-134a', 'HFC-23', 'HFC-32', 'HFC-125', 'HFC-143a', 'HFC-152a', 'HFC-227ea', 'HFC-236fa', 'HFC-245fa', 'HFC-365mfc', 'HFC-43-10mee', 'NF3',  # ..."""Alternative names are defined innames.yaml.
Runmaketo update them into themappings.pysubmodule.
Package: ghgrep
List all your Github repositories containing a filename matching a
search pattern.ghgrepis partiallygrep-land partiallyfind-name- you
can pretend it is a special version ofgrep(1)in which files are
actually repositories and each line of a file is actually a filename
inside the repository.ExamplesShow all repositories with a readme:ghgrep 'README.*'List all repositories that have a file named ‘COPYING’:ghgrep -f COPYINGList all repositories that don’t have a license file:ghgrep -v (COPYING|LICENSE)Installation[$]> pip install ghgrepor[$]> easy_install ghgrepHackingI highly recommend using virtualenv:[$]> virtualenv --no-site-packages --distribute env
[$]> source env/bin/activate
[$]> pip install -r requirements.txt
[$]> pip install -e . # So we can import the version from inside bin/ .
Package: ghicon
ghiconghiconis a GitHubesque identicon generator. It uses seed text and a hashing function,MD5by default, to create unique icons calledidenticons.UsageInstallghiconusing,pip install ghicon==5.2.2Then use thegeneratefunction,importghiconimage=ghicon.generate("agzg")image.save("agzg.png")Note:Followingv5.2.0, you can use custom hashing functions to generate identicons via thehasherargument. Ensure the function you use only accepts a single string argument, and returns a hexadecimal string hash which is longer than 15 characters.Tip:You can also invert the colours of the identicon to mix things up! Use theinvertargument to do so.ExamplesLicenseGoverned under theMIT license.
Package: ghidrapy
JARV1S-GhidraGhidra build for Kam1n0 & Jarv1s:rocket: Installation:Required: Python 3+. [Optional: OpenJDK 13+]pipinstallghidrapy:fire: Usage:python-mghidrapybinary_file_to_decompileDuring the first run, the required jar and JDK will be downloaded to~/.jarv1s-ghidraif needed.:star: Contributors:Christopher Bennett - Carleton UniversityMiguel Garzon - University of Ottawa, Bell CanadaSteven Ding - Queen's Computing
Package: ghidra-stubs
Ghidra.pyiGeneratorThe Ghidra.pyiGenerator generates.pyitype stubsfor the entire Ghidra API.
Those stub files can later be used in PyCharm to enhance the development experience.You can either use the stubs releasedhere, or follow the instructions below to generate them yourself.Using The StubsInstallationThe release containsPEP 561 stub package, which can simply be installed withpip install ghidra-stubs*.whlinto the environment in which the realghidramodule is available. Any conformant tool will then use the stub package
for type analysis purposes.If you want to manually add the stub files to PyCharm, follow the instructions inInstall, uninstall, and upgrade interpreter paths.UsageOnce installed, all you need to do is import the Ghidra modules as usual, and PyCharm will do the rest.importghidraTo get support for the Ghidra builtins, you need to import them as well. The type hints for those exist in
the generatedghidra_builtins.pyistub. Since it is not a real Python module, importing it at runtime will fail.
But the.pyigives PyCharm all the information it needs to help you.try:fromghidra.ghidra_builtinsimport*except:passIf you are usingghidra_bridgefrom a Python 3 environment where no realghidramodule
exists you can use a snippet like the following:importtypingiftyping.TYPE_CHECKING:importghidrafromghidra.ghidra_builtinsimport*else:b=ghidra_bridge.GhidraBridge(namespace=globals())# actual code follows heretyping.TYPE_CHECKINGis a special value that is alwaysFalseat runtime butTrueduring any kind of type checking or completion.Once done, just code & enjoy.DependenciesGhidra DocsTo properly extract all types from Ghidra, make sure to extract the API documentation.Open the Ghidra CodeBrowserGo toHelp -> Ghidra API HelpWait for Ghidra to extract the docsPython PackagesThe script depends on both theattrandtypingpackages.
They are now vendored under thevendordirectory as Python2.7 support is gradually
being dropped from the ecosystem, making it hard to install and fetch packages.# Create Jython's site-pacakges directory.jython_site_packages=~/.local/lib/jython2.7/site-packages
mkdir-p$jython_site_packages# Create a PTH file to point Jython to our vendored site-packages# Outside a virtualenv, useecho"$(realpath./vendor)">$jython_site_packages/python.pthCreating the.pyifilesGUIAdd this directory to theScript Directoriesin the Ghidra Script ManagerRefresh the script listRungenerate_ghidra_pyi.py(will be located underIDE Helpers)When a directory-selection dialog appears, choose the directory you'd like to save the.pyifiles in.CLI$GHIDRA_ROOT/support/analyzeHeadless/tmptmp-scriptPath$(pwd)-preScriptgenerate_ghidra_pyi.py./Python Packagegenerate_ghidra_pyi.pygenerates asetup.pyinside the directory that was selected.This allows usingpip installto install aPEP 561 stub packagethat is recognized by PyCharm and other tools as containing type information for the ghidra module.