Saravanan666/pypi-org huggingface dataset:
Package: pordego-complexity
SummaryPordegoplugin that analyzes code using theRadonlibrary.If the code does not meet a specified threshold, it will print the complex blocks and cause the pordego tool to return an error code.Configurationsource_pathsThere is one required parameter “source_paths”. This parameter should be a list of paths to directories containing Python source code (other types of code are ignored). The paths are searched recursively, so only the top level folder need be specified.
The paths can be absolute or relative to the directory where pordego is run.ignore_pathsOptional. A list of file patterns to ignore, such as “test” which will ignore all files containing “test”complexity_thresholdOptional (default “B”). The maximum allowable complexity. Seehttps://radon.readthedocs.io/en/latest/api.html#radon.complexity.cc_rankfor a description of the ranks.ignore_block_listOptional. For lsiting all that legacy code that hasn’t been refactored yet.Each entry in the list should be a string formatted like so:
<path to file> <class name.method name or function name> <Max complexity grade><Path to file> should start with one of the paths specified in source_paths, so if the source path is relative, this should be as well
Functions are specified with just the function name, methods that are part of a class (including class/staticmethods) are joined to the class name with a ‘.’
<Max complexity grade> specifies the worst grade that is allowed for the block of code. If the calculated grade is at or above the threshold grade, it will pass.The easiest way to generate the ignore_block_list is to run the complexity plugin without ignore_block_list. The plugin prints the list of complex blocks in the same format as the ignore_block_list.Example:
path/to/my/src/mymodule.py MyClass.some_method D
path/to/my/src/mymodule.py some_free_function E
Package: pordego-dependency3
SummaryPordegoplugin that analyzes package dependencies using theSnakefoodlibrary.Forked for Python3 support.Configurationsource_pathsThere is one required parameter “source_paths”. This parameter should be a list of paths to directories containing Python source code (other types of code are ignored). The paths are searched recursively, so only the top level folder need be specified.
The paths can be absolute or relative to the directory where pordego is run.ignore (optional)The ignore parameter is used to specify a list of file patterns to exclude from the analysis. Glob style patterns are accepted.Example:ignore:
    - "*test*"This will ignore all files and directories containing “test”analysis_packages (optional)The analysis_packages parameter can be use to limit the dependency analysis to a list of packages.
The package names must match the one specified in the setup.py “name” field.dependency_map (optional)This parameter is used to specify a list of acceptable dependencies for a package.
An error will be thrown if the package imports any package other than the ones in the list.
Only local packages (in source dirs) are considered, not dependencies downloaded from pypi.
An empty list means that the package cannot depend on any other package.
If a package is not in dependency_map, it may depend on any package.Example:dependency_map:
  my-package-name:
     - some-package
  my-no-depend-package: []In this case, my-package-name can only import from some-package, while my-no-depend-package may not import from any other package (other than ones found on pypi)check_requirements (optional)If check_requirements is true, the requirements from the package setup will be compared against the actual dependencies.
Any missing or extraneous requirements will cause a failure.“Local” packages (those that can be found in the source_paths) are detected fairly reliably, assuming that all possible local requirements can be found in those paths.Packages downloaded from pypi are included in the analysis with some caveats.
The required package must be either installed in the environment the plugin is executing in or downloadable from pypi.
You might have to use the package_server_url and pip_options configuration parameters to specify additional options if you are behind a corporate firewall or have a local package server.
Package: porE
porEPORosity Evaluation toolMain developer:Kai Trepte (KT,kai.trepte1987@gmail.com)Sebastian Schwalbe (SS,theonov13@gmail.com)Installation (global pip installation)$pip3installporEInstallation (local pip installation)$gitclonehttps://gitlab.com/kaitrepte/porE.git
$cdporE
$pip3install-e.Running the codeThere are several calculations types one can choose from:HEA : He approach.Calculates the He void fraction using a cell list approach.OSA : Overlapping sphere approach.Calculates the porosity via two-body overlaps of spheres.GPA : Grid point approach.Void and accessible porosity are calculated using a grid in the unit cell.PSD : Pore size distribution.Using a Monte-Carlo scheme, the pore size distribution is calculated.To run the code, go to theexamplesfolder.The file run_porE.py contains examples for theexecution on the non-GUI level.The file run_GUI.py will execute the graphicaluser interface, including the OSA, GPA and PSD functionalities.The HEA will be implemented soon.Special thanks goes to Sebastian Schwalbe for writing the GUI and for many other useful discussions.Additional informationThe basic outline of the porE code and its applications are summarized inK. Trepte and S. Schwalbe, Systematic Analysis of Porosities in Metal-Organic FrameworksChemRxiv, DOI: 10.26434/chemrxiv.10060331.v1, 2019ChemRxiv, DOI: 10.26434/chemrxiv.10060331.v2, 2020ChemRxiv, DOI: 10.26434/chemrxiv.10060331.v3, 2020Please also see the published version in the Journal of Computational Chemistry (JCC)Trepte, K, Schwalbe, S. porE: A code for deterministic and systematic analyses of porosities. J Comput Chem. 2021; 42: 630-643.https://doi.org/10.1002/jcc.26484We create some YouTube videos to introduce and explain the porE codeIntroductionTutorialReference resultsSeveral results from porE are summarized in theporE/resultsfolder (Status: Early 2021).
Package: poreana
PoreAna: An Analysis Tool for Pore SimulationsDocumentationOnline documentation is available atajax23.github.io/PoreAna.The docs include an example for analyzingdensityanddiffusion, and anAPI reference.DependenciesPoreAna supports Python 3.5+.Installation requiresnumpy,pandas,chemfiles 0.10.0,seabornandporems.InstallationYou may instead want to use the development version from GitHub:pip install git+https://github.com/ajax23/PoreAna.git#egg=poreana

pip install git+https://github.com/ajax23/PoreAna.git@develop#egg=poreanaOr download the repository and install in the top directory via:pip install .TestingTo test PoreAna, run the test in the test directory.DevelopmentPoreAna development takes place on Github:www.github.com/Ajax23/PoreAnaPlease submit any reproducible bugs you encounter to theissue tracker.How to Cite PoreAnaWhen citing PoreAna please use the currentZenodo DOIcorresponding to the used PoreAna version. (Current DOI is listed in the badges.)
Package: pore-c-py
Pore_c_pyThis package provides Python scripts for working with Pore-C data. It
is not intended to be used directly by end uses, but rather as part of
our Nextflow workflowwf-pore-c.
Hence the terse nature of this documentation.InstallationA package is available to install through eitherpip:pip install pore-c-pyor through conda:conda install -c nanoporetech pore-c-pyUsage$ pore-c-py --help
usage: pore_c_py [OPTIONS] COMMAND [ARGS].

Available subcommands are:
    digest       Digest concatemer sequences into monomers using a restriction enzyme.      
    annotate     Annotate alignments with a "walk", which simply
                 enumerates the alignment coordinates of the monomers comprising the
                 concatemer.ExampleThe following is indicative use, similar to that performed bywf-pore-c.INPUT="myreads.bam"
ENZYME="NlaIII"
REF="myref.fasta"
OUTPUT="all"

pore-c-py digest "${INPUT}" "${ENZYME}" \
    | samtools fastq -T '*' \
    | minimap2 -ay -t 8 -x map-ont "${REF}" - \
    | pore-c-py annotate - "${OUTPUT}" --monomers --stdout --summary --chromunity \
    | tee "${OUTPUT}.ns.bam" \
    | samtools sort --write-index -o "${OUTPUT}.cs.bam" -
samtools index "${OUTPUT}.ns.bam"Thedigestprogram can read its input from standard input, so it can be used withbamindexin
order to process a subset of a file. This is particularly useful for
distributing the workload on a cluster.
Package: poremks
Table of contentsGeneral infoDependenciesSetupUsageStatusReferencesIssuesGeneral infoporeMKS is a tool for the analytics of porous molecular structures.The Molecular Structure of DDR:The pore region of DDR embedded within the molecular structure.The pore region of DDR accessible by a 1.5A radius probe is visualized as below:The skeleton of the pore structure overlayed on the pore volume is visualized as below:The shortest paths for the probe through the pore structure are visualized as below:DependenciesProject is created with:ase: 3.16.2scikit-image version: 0.14.0scipy version: 1.1.0numpy version: 1.16.0numba version: 0.39.0pytorch version: 0.4.1pytoolz version: 0.9.0SetupTo run this project, install it locally using conda:$ cd ../<project_directory>
$ conda create -n poremks python=3.6
$ conda activate poremks
$ pip install -r requirements.txt
$ conda install pytorch-cpu torchvision-cpu -c pytorch
$ pip install poremksConda is a package and environment manager bundled with anaconda python distribution.
See,https://www.continuum.io/downloadsfor more details on installing and using Conda.Windows Usersneed to install visual studio build tools, in order to the compile c/c++ files assosciated with some of the dependencies.UsageRefer to thejupyter notebookin the doc folder.StatusporeMKS is currently under active development.ReferencesEDTscikit-imageReadMeIssuesPlease send questions and issues about installation and usage of PyMKS toapaar92@gmail.com
Package: porems
PoreMS: A Pore Generator for Molecular SimulationsDocumentationOnline documentation is available atajax23.github.io/PoreMS.The docs include an example for generatingmoleculesandpores, and anAPI reference. Visitprocessfor an overview of the programs operating principle.An examplaryworkflowhas been provided for using the PoreMS package to create a pore system and run molecular dynamics simulation usingGromacs.DependenciesPoreMS supports Python 3.5+.Installation requiresnumpy,pandasandmatplotlib.InstallationThe latest stable release (and older versions) can be installed from PyPI:pip install poremsYou may instead want to use the development version from Github:pip install git+https://github.com/ajax23/porems.git#egg=porems

pip install git+https://github.com/ajax23/porems.git@develop#egg=poremsOr download the repository and install in the top directory via:pip install .TestingTo test porems, run the test in the test directory.DevelopmentPoreMS development takes place on Github:www.github.com/Ajax23/PoreMSPlease submit any reproducible bugs you encounter to theissue tracker.How to Cite PoreMSWhen citing PoreMS please use the following:Kraus et al., Molecular Simulation, 2021, DOI:10.1080/08927022.2020.1871478Additionaly, to assure reproducability of the generated pore systems, please cite theZenodo DOIcorresponding to the used PoreMS version. (Current DOI is listed in the badges.)Published WorkKraus et al., 2021. PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions. Molecular Simulation, 47(4), pp.306-316, doi:10.1080/08927022.2020.1871478.Data-Repository: doi:10.18419/darus-1170Ziegler et al., 2021. Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N-Heterocyclic Carbene Complexes. ACS Catalysis, 11(18), pp. 11570-11578, doi:10.1021/acscatal.1c03057Data-Repository: doi:10.18419/darus-1752Kobayashi et al., 2021. Confined Ru-catalysts in a Two-phase Heptane/Ionic Liquid Solution: Modeling Aspects. ChemCatChem, 13(2), pp.739-746, doi:10.1002/cctc.202001596.Data-Repository: doi:10.18419/darus-1138Ziegler et al., 2019. Olefin Metathesis in Confined Geometries: A Biomimetic Approach toward Selective Macrocyclization. Journal of the American Chemical Society, 141(48), pp.19014-19022, doi:10.1021/jacs.9b08776.Data-Repository: doi:10.18419/darus-477
Package: poresim
PoreSim: Pore System Simulation GeneratorDocumentationOnline documentation is available atajax23.github.io/PoreSim.The docs include an example for creatingsimulation boxes, and anAPI reference.DependenciesPoreSim supports Python 3.5+.Installation requirespyyamlandjinja2.InstallationYou may instead want to use the development version from GitHub:pip install git+https://github.com/ajax23/PoreSim.git#egg=poresim

pip install git+https://github.com/ajax23/PoreSim.git@develop#egg=poresimOr download the repository and install in the top directory via:pip install .TestingTo test PoreSim, run the test in the test directory.DevelopmentPoreSim development takes place on Github:www.github.com/Ajax23/PoreSimPlease submit any reproducible bugs you encounter to theissue tracker.How to Cite PoreSimWhen citing PoreSim please use the currentZenodo DOIcorresponding to the used PoreSim version. (Current DOI is listed in the badges.)
Package: porfavor
Por favorPublishing static documentation the easiest way possible!Install$pipinstallporfavorUseOn the server side, you should run the matching server-side implementation.
It listens to any client and puts the given documentation in its right place.On the server, run:$pipinstallporfavor...$porfavorserve.# replace '.' with the desired working directory...Now, to deploy documentation on the server, all you have to do is runningporfavor publishwith the right arguments:$# porfavor publish <server's URL> \><projectname>\><documentationroot>$porfavorpublishlocalhost:5000my_amazing_projectdocs/_build/html/Zipping content of folder 'docs/_build/html'... DONE!Publishing content for project 'my_amazing_project'... DONE!Alternatively, you can write the following script, to make deployment more
automatic:fromporfavorimportpublishif__name__=='__main__':publish(host="localhost:5000",project="project_name",file_or_directory="root_dir")
Package: por.gdata
for more details visit:http://getpenelope.github.com/1.7.2 (2013-07-31)increase max projects to 107 [amleczko]1.7.1 (2013-07-15)make iteration activation function much simplier [amleczko]1.7 (2013-04-30)gracefully ignore request errors1.6 (2013-04-10)Increase number of active projects in spreadsheet to 80 [amleczko]1.5 (2013-04-03)fix configuration for spreadsheet [amleczko]use online iteration template [amleczko]1.4 (2013-04-02)fix problem with user role in iteration generation [amleczko]1.3 (2013-01-30)move to github [amleczko]
Package: pori-cbioportal
PORI cBioportalThis repository is part of thePlatform for Oncogenomic Reporting and Interpretation (PORI).This python package uses the IPR and GraphKB PORI adaptors to create PORI reports from dumps
of cbioportal data.Getting StartedInstall via pippipinstallpori_cbioportalDownload Study DataStudy data should be downloaded from cbioportal, for examplewgethttps://cbioportal-datahub.s3.amazonaws.com/laml_tcga_pan_can_atlas_2018.tar.gz
tar-xvzflaml_tcga_pan_can_atlas_2018.tar.gzThe folder should have the variant and metadata files, for examplelaml_tcga_pan_can_atlas_2018
|-- data_clinical_patient.txt
|-- data_clinical_sample.txt
|-- data_CNA.txt
|-- data_fusions.txt
|-- data_log2CNA.txt
|-- data_mutations_extended.txt
`-- data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txtGenerate ReportsThis is then used to generate individual reports for all patients included in the study.
Note to do this you will need access to both a GraphKB server for matching and an IPR
server for upload.pori_cbioportallaml_tcga_pan_can_atlas_2018\--study_id"LAML TCGA"\--password$PASSWORD\--ipr_urlhttps://YOUR_IPR_API_HOST/api\--graphkb_urlhttps://YOUR_GRAPHKB_API_HOST/apiThe loader will expect default names for the files but this can be overwritten with the other command line arguments. See the help menu for more optionspori_cbioportal--helpGetting Started (For developers)Installclone this repositorygitclonessh://git@svn.bcgsc.ca:7999/dat/pori_cbioportal.gitcdpori_cbioportalcreate a virtual environmentpython3-mvenvvenvsourcevenv/bin/activateinstall the package and its development dependenciespipinstall-e.[dev]Run the testspytesttestsDeployment (Publishing)Install the deployment dependenciespipinstall.[deploy]Build the distribution filespythonsetup.pyinstallsdistbdist_wheelUpload the distibutions to the package server (-r defined in your pypirc)twineupload-rbcgscdist/*Deployment (Scripts)A buildout config is included by default which will build all console scripts defined
in the package.create a virtual environment and install buildoutpython3-mvenvvenvsourcevenv/bin/activate
pipinstall-Upipsetuptoolszc.buildoutrun buildoutbuildoutThis will create a directorybinwith the executable scripts
Package: porkbun-api
Porkbun APIThis is an API wrapper for Porkbun written in Python with few extra features/shortcuts.Porkbun API documentationThis project is subject to breaking changes as Porkbun API may change and/or become invalid. I do not guarantee anything.InstallingYou can install this through PyPi with pip:pip install porkbun-apiOr you can grab a .whl or .tar.gz file fromCodeberg releases.UsageThis wrapper supports everything other than operations with ID's for now.Available functions and arguments:Please keep in mind every function requires anapikeyandsecretapikeyarguments, but you can setAPIKEYandSECRETAPIKEYvariables with their respective values and not have to give keys as arguments at every function call.ping()Optional:ipv4only(takes True or False and returns IPv4 only if True and IPv6 if available otherwise. Default = True).Returns IP address.nsupdate()Requiresdomain(takes a string of the domain you want to work on)andnslist(a list containing nameservers).Does not return anything, changes the authoritative nameservers for given domain.create()Requiresdomain,rtype(string of the record type such as A, AAAA, MX, etc), andcontent(string value for said request type such as the IP address).Optional:subdomain(string subdomain for said domain)andttl(integer number for time to live, default and minimum for Porkbun is 600).prio(integer priority for record types that support it)Does not return anything. Creates a new DNS record with given arguments.read()Requiresdomain,rtype.Optional:subdomain.Returns alist of records.update()Requiresdomain,rtype, andcontent.Optional:namettl, andprio.Does not return anything. Updates the matching record with givencontentdelete()Requiresdomainandrtype.Optionalsubdomain.Does not return anything. Deletes the matching record.ddns_update()Requiresdomain.Optional:ip(the string IP address to update the record with. If not given, uses the return of ping() as IP),subdomain, andipv4only.Does not return anything. Updates thedomainorsubdomain's A or AAAA record depending on the IP type given.Examplesimportporkbun_apiaspbfromtimeimportsleep# only as an example, not required.pb.APIKEY="pk1_..."pb.SECRETAPIKEY="sk1_..."pb.ping()pb.create(domain="m3r.one",rtype="A",content="23.94.123.251")pb.delete(domain="m3r.one",rtype="A",subdomain="bin",apikey="pk1_overwrite-the-variable",secretapikey="sk1_overwrite-the-variable")whileTrue:pb.ddns_update(domain="m3r.one")sleep(86400)NotesIt is recommended to usetry-exceptblocks with every function because it raises aPorkbunErrorexception if Porkbun returns an error for whatever reason. Plus,requestslibrary will raise exceptions itself if something goes wrong with the request.Feel free to open issues or contact me in case you wish to see extra features added.This project is not affiliated with Porkbun LLC.
Package: porkbundns
porkbun-dnsManage DNS records using Porkbun API.NOTICEThis package is not endorsed, related or developed by Porkbun. No relationship between the developers of this package and Porkbun exists, beyond Ivan being a Porkbun customer and writing this package to make his life easier. Don't go knock on their door if you have any questions, bugs or screw up your DNS config! (Also, please report bugs and ask questions, but don't knock on my door either. This is a very small project that I developed in my spare time.)
Package: porkyddns
PorkyDDNSSimple Porkbun DDNS Client💡 FeaturesSupport for multiple subdomains on multiple domainsEasily and quickly configurable, with cron-able error reporting💾 InstallationInstall PorkyDDNS usingpip$pipinstallporkyddns$porkyddns🔨 UsageEdit the values inporkyddns.toml.exampleas requiredCopyporkyddns.toml.exampleto/etc/porkyddns.tomlRun theporkyddnsscript on a cron job or systemd timer however often you want!📜 LicenseGPLv3-only
Package: pormalizer
PormalizerThere are different unicode for lots of persian characters and for computers do not understand this. So before any NLP
task first we need to normalize our text and come to singular form for any characters. We also remove any non-alphabet
characters and all change all white-space characters into a single space.InstallationSimply you can install it from PyPi by following command:pipinstall-Upormalizeror if you prefer the latest development version, you can install it from the source:gitclonehttps://github.com/xurvan/pormalizer.gitcdpormalizer
pythonsetup.pyinstallQuickstartA very simple usage could be like:frompormalizerimportPormalizerpormalizer=Pormalizer()pormalizer.normalize("متن امتحانی")
Package: por.models
for more details visit:http://getpenelope.github.com/1.3.22 (2013-07-31)fix #558 [amleczko]1.3.21 (2013-07-15)fix #9 [amleczko]1.3.20 (2013-06-26)Update sidebar [amleczko]1.3.19 (2013-06-26)New contract integration [amleczko]make sure only estimated CR get’s new time entries [amleczko]1.3.18 (2013-06-13)simplify svn login [amleczko]1.3.17 (2013-05-08)fix email urls for fastticketing [amleczko]1.3.16 (2013-04-23)add email notification support to ticket_store [amleczko]1.3.15.1 (2013-04-02)fix populate scripts [amleczko]1.3.15 (2013-04-02)added addTicket method to Trac [massimoazzolini]add SVN authz manage screen [amleczko]1.3.14 (2013-03-26)move karma to separate package [amleczko]1.3.13 (2013-02-25)add support for custom SVN url [amleczko]fix quality reports [amleczko]1.3.12 (2013-02-12)add last QA date [amleczko]add google upload for QA reports [amleczko]1.3.11 (2013-02-11)add quality export scripts [amleczko]1.3.10 (2013-02-04)refactor non-invoiced tickets validation [amleczko]1.3.9 (2013-01-30)move to github [amleczko]user can select only tickets within those that have an open invoice [massimoazzolini]update models for karma integration [amleczko]fixes for the subversion integration [amleczko]
Package: pornhubapi
Unofficial API for pornhub.com in PythonUsageCreate clientimportpornhubclient=pornhub.PornHub()Create client with proxyimportpornhubclient=pornhub.PornHub("5.135.164.72",3128)#With proxy, given a Proxy IP and Port. For the countries with restricted access like Turkey, etc.Grab starsforstarinclient.getStars(10):print(star)print(star["name"])Create client with search keywordskeywords=["word1","word2"]client=pornhub.PornHub(keywords)forvideoinclient.getVideos(10,page=2):print(video)print(video["url"])LicenseMIT license