Saravanan666/pypi-org huggingface dataset:
Package: clonalEvolution
IntroductionPython software for simulating celluar/microbial clonal evolution with Gillespie algorithm usageInstallation and UsageThe simpliest installation:python -m pip install clonalEvolutionUsage in python:from microbialClonalEvolution import mainView
mainView.run()Usage from console:python -m clonalEvolution 
#   for simply run graphic verion of software

python -m clonalEvolution -h
#   to see instructions for command line parametrizationUsage InstructionsGeneral Tab:\file name - used in multiple functions: saving files, plots, parameters; specify name of file (according to windows acceptable characters), data files will have cycle number (name_number.csv/.txt)file path - used in multiple functions: saving files, plots, parameters; specify absolute path to folder where simulation data should be savedfile description - 'TODO' add description in params/data file about simulation specyfied by userclone diagram - button, fire the muller plot creation. It is needed to specify path with muller plot data generated from simulaitonfile structure (file-name_muller_plot_'binned'_data.txt):clone, cells, previous clone
(0, 5000, 0)mutations histograms - button, fire the VAF plot creation for all clones in specified file. File is needed to be one of generated simulation datafile structure (file-name_cycle.csv/.txt):,Clone number,Cells number,Mean fitness,Mean mutation number,Driver mutation list,Passener mutation list,Previous clone number
0,0,5000,1,0,[],[],0Generated tab:select which files should be saved automaticaly after one cycle specified in parameters (skip). Not all types works for both algorithm versions 'TODO'Parameters tab:Plot tab:Threads tab:Main controls:LicenseGNU GENERAL PUBLIC LICENSE  Version 3, 29 June 2007Copyright (C) 2007 Free Software Foundation, Inc.https://fsf.org/Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.DisclaimerCellular/Microbial Clonal Evolution simulations basing on Gillespie algorithm.
Copyright (C) 2022 by Jarosław GilThis program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.You should have received a copy of the GNU General Public License
along with this program.  If not, seehttps://www.gnu.org/licenses/.AuthorJarosław Gil, Silesian Univeristy of Technology, Department of Computer Graphics, Vision and Digital Systems.
Package: clone-all-from-org
clone-all-from-orgHomePyPICLI tool to clone all repos from a given organization or userInstall into your Python project usingpip install clone-all-from-orgInstall as a CLI tool usingpipx:pipx install clone-all-from-org.What does this do?For any given GitHub users or orgs (or yourself) this will enumerate all the repos you can see and clone them to a prefix. This allows you to keep up to date with any repos in the uses or orgs you follow.This script requires a GitHub OAuth token, or Personal Access Token, to talk to the GitHub API. The easiest way to get one is to login with theGitHub CLI tool. This script knows how to read the token from that tool's config.To run give it a list of orgs to clone:clone-all-from-orgmeorg:codinggraceuser:micktwomey# clones all the repos into ~/src/github.com/{organization or user}/{repo name}This tool recognizes:org:someorg- a GitHub organizationuser:someuser- GitHub userme- yourselfNote that the GitHub APIs will only show you publicly available repos for users and orgs by default. If you are a member of the organization you can see all repos (if you have access).meis a special case, this will show all repos you have access to (including your own private repos). If you useduser:your-usernameit would only show your public repos.Combining with gitupThis combines well withgitupto fetch all new repos and then update all your cloned repos:# one off setuppipxinstallgitupclone-all-from-org
gitup-a~/src/github.com# run periodicallyclone-all-from-orgmeorg:my-org
gitup--pruneGitHub EnterpriseYou can override the default base URl with--base-url. This is most useful for accessing GitHub Enterprise servers.Typically you'd need something likehttps://git.example.com/api/v3/as a base URl for enterprise:clone-all-from-org--base-urlhttps://git.example.com/api/v3/me
Package: clonedetective
clonedetectiveA python package for automated cell lineage analysis.What does it do?clonedetectiveis a package for analysing fluorescent imaging data from cell lineage experiments (e.g. FLP-out, MARCM or Cre-lox clones).Outputted quantifications include:counts of each cell type per “clone”spatial metrics e.g. number of nearest neighbors of each cell per clonecell and clone properties e.g. area, mean intensity etc.If clones label genetic mutations, these metrics can be useful in addressing biological questions such as:does my gene of interest regulate clone size (i.e. cell proliferation) or clone composition (i.e. cell differentiation)?does the local cell neighbourhood (e.g. number and type of neighbours) non-autonomously impact cell proliferation or differentiation?does my gene of interest regulate the expression of other (immunostained) proteins?Under the hoodclonedetectiveis constructed using many amazing python libraries, including scikit-image, numpy, Xarray, pandas, numba, Dask, Dask-image and pyclesperanto-prototype.Many functions are lazy-loaded and parallelized usingDask, enabling clonedetective to scale to large multi-dimensional datasets that do not fit in RAM.InstallIt is recommended to installclonedetectiveinto a virtual environment e.g. usingconda. Once you have anaconda or miniconda installed, you can create a virtual environment using the following command. It is often helpful to install something into an empty environment, in this case we install scipy:conda create -n myenv scipyYou can then install clonedetective via pip:pip install clonedetectiveHow to usePlease see the tutorials:Example walkthroughDownstream Analysis using PythonDownstream Analysis using RGenerating nuclei segmentation using StarDistIn progress, more to come!
Package: clonedigger
available athttp://clonedigger.sourceforge.netClone Digger is the tool for finding software clones.
Currently only Python language is supported, Java support will be added soon.
See the site for details.UsageThe simplest way of running Clone Digger is:clonedigger source_file_1 source_file_2 ...Or:clonedigger --recursive path_to_source_treeDon’t forget to remove automatically generated sources, tests and third party libraries from the source tree.Seehttp://clonedigger.sourceforge.net/documentation.htmlfor more complex arguments.The available arguments can be obtained using ‘–help’ also.
Package: clone-env
virtualenv cloning script.A script for cloning a non-relocatable virtualenv.Virtualenv provides a way to make virtualenv's relocatable which could then be
copied as we wanted. However making a virtualenv relocatable this way breaks
the no-site-packages isolation of the virtualenv as well as other aspects that
come with relative paths and/usr/bin/envshebangs that may be undesirable.Also, the .pth and .egg-link rewriting doesn't seem to work as intended. This
attempts to overcome these issues and provide a way to easily clone an
existing virtualenv.It performs the following:copiessys.argv[1]dir tosys.argv[2]updates the hardcodedVIRTUAL_ENVvariable in the activate script to the
new repo location. (--relocatabledoesn't touch this)updates the shebangs of the various scripts in bin to the new Python if
they pointed to the old Python. (version numbering is retained.)it can also change/usr/bin/env pythonshebangs to be absolute too,
though this functionality is not exposed at present.checkssys.pathof the cloned virtualenv and if any of the paths are from
the old environment it finds any.pthor.egglink files within sys.path
located in the new environment and makes sure any absolute paths to the
old environment are updated to the new environment.finally it double checkssys.pathagain and will fail if there are still
paths from the old environment present.NOTE: This script requires Python 2.7 or 3.4+
Package: clone-gh
Github Cloner (clone_gh)clone_ghis a command-line tool that allows you to clone all of your Github repositories, or repositories belonging to any user, into a local directory. You can optionally filter repositories by programming language and specify an output directory for the cloned repositories.InstallationTo installclone_gh, you can use pip:pip install clone_ghUsageClone Starred RepositoriesTo clone all of your starred Github repositories, simply run:clone_gh <username> -t clone-likesReplace<username>with your Github username. This will clone all of your starred repositories into the current working directory.You can also specify a programming language to filter by:clone_gh <username> -t clone-likes -l pythonThis will clone only your starred repositories that are written in Python.You can specify an output directory for the cloned repositories:clone_gh <username> -t clone-likes -o /path/to/output/directoryThis will clone all of your starred repositories into the specified output directory.Clone User RepositoriesTo clone all of the repositories for a specific Github user, run:clone_gh <username> -t clone-user -u <target_username>Replace<target_username>with the Github username of the user whose repositories you want to clone. This will clone all of the repositories for the specified user into the current working directory.You can also specify a programming language to filter by:clone_gh <username> -t clone-user -u <target_username> -l pythonThis will clone only the repositories for the specified user that are written in Python.You can specify an output directory for the cloned repositories:clone_gh <username> -t clone-user -u <target_username> -o /path/to/output/directoryThis will clone all of the repositories for the specified user into the specified output directory.If you have a Github access token that you want to use for the API requests, you can provide the file path to the access token file:clone_gh <username> -t <task> -a /path/to/access/token/fileReplace<task>with eitherclone-likesorclone-userdepending on which action you want to perform.Licenseclone_ghis licensed under the MIT License. SeeLICENSEfor more information.Creditsclone_ghwas created by Güvenç USANMAZ.
Package: clone-github
# clone-github> Clone github repos in bulk# Installation- `sudo pip install clone-github --upgrade`- On Mac: Installs to `/Library/Python/2.X/site-packages`# Instructions```Usage: clone-github [options]Options:-h, --help                Show this help message and exit-o ORG, --org=ORG         Github.com organization name. Assumes Oauth user ifomitted.-u USER, --user=USER      Github.com user name. Assumes Oauth user if omitted.-t TOKEN, --token=TOKEN   OAuth Access Token.-p, --private             List only Private repos. Default is Public.-r, --run                 Execute changes. Default is Dry Run.```
Package: clone-org
Clone GitHub namespaceClone an organization's repos.Clone an organization's repos. A common situation that folks find themselves
in when starting to work with an organization is the ability to check out all
the code and essentially familiarize themselves with the code base and even
grep the code base looking for things. clone-org is designed to lessen
the pain and give you a one-stop clone the organization toolkit. This module
queries the GitHub graphql endpoint.Clone-org uses the installed version of git on your machine and executes shell
commands.Currently, clone-org only supports GitHub and other cloud providers will be
tested in the future.For https remotesYou must have 'GITHUB_TOKEN' defined in your environment for the organization
to be queried. The clone may be optionally either https or sshFor ssh remotesYou must have your ssh keys set up in current shell.Installing$pipinstallclone-orgA Simple Example$clone-org-okubernetes-client-phttps-f~/dev/kub-client-reposHelp$clone-org-husage:clone-org[-h][-oORGANIZATION][-lLANGUAGES][-p{https,ssh}][-fFOLDER][-c][-d][-v]Clone an organization's repos. A common situation that folks find themselves
in when starting to work with an organization is the ability to check out all
the code and essentially familiarize themselves with the code base and even
grep the code base looking for things. clone-org is designed to lessen
the pain and give you a one-stop clone the organization toolkit. This module
queries the GitHub graphql endpoint.Clone-org uses the installed version of git on your machine and executes shell
commands.Currently, clone-org only supports GitHub and other cloud providers will be
tested in the future.For https remotesYou must have 'GITHUB_TOKEN' defined in your environment for the organization
to be queried. The clone may be optionally either https or sshFor ssh remotesYou must have your ssh keys set up in current shell.options:-h,--helpshowthishelpmessageandexit-oORGANIZATION,--organizationORGANIZATIONTheorganizationinGithubthatyouwishtoclonealltherepositoriesfor-lLANGUAGES,--languagesLANGUAGESGithubclasseslanguageswithwellknownnamessuchasPython,Go,shelletc.Youmaypassafilter-lpythonanditwillcompareittothegivenprimarylanguageassignedtotherepo.Commaseparatedstringssuchaspython,java,javascriptarealsoaccepted.Namesaredefinedbygithubinthegithub/linguistrepo.-p{https,ssh},--protocol{https,ssh}Theprotocoltouseeitherhttps,whichwillrequireGITHUB_TOKENtobedefinedinyourenvironmentvariables.Orsshwhichwillrequirethatyouhaveyoursshkeyssetupincurrentshell.-fFOLDER,--folderFOLDERThetargetfoldershouldbeafullyqualifiednameandthedirectorystructurestestedareOSxandLinux.Anexamplewouldbe-f/home/Users/alice/dev/-c,--createTocreatethetargetfoldersetthisflagandthedirectorystructurewillbecreatedifpossibleAnexamplewouldbeclone-org-oyour_org_name-phttps-f~/temp/my_repos-c-d,--dry-runTheusermaysimplywishtoquerytheorganizationbeforecloning.Thedryrunoptionwillprintouttherepositoriesintheorganizationspecifiedandexit.-v,--versionPrintversionandexit
Package: cloner
A tiny utility to quickly clone github reposUsageSet your local repo directory via the CLONER_PATH environment variableecho"export CLONER_PATH=\"~/repos\"">>~/.bash_profileThen you can clone any github repo into that directory with the username and repo name, like this:clonerkardasisclonerwill clone this repo into~/repos/kardasis/clonerYou can also use the web URL from the repoclonerhttps://github.com/kardasis/cloneror any URL from within the repoclonerhttps://github.com/kardasis/cloner/blob/master/cloner/cli.py
Package: clone-repo
clone-repo: Easily clone reposHomePyPIWhat is this?For years I've been using a noddy script which clones many types of repos into a fixed location which is generated based on the repo itself. Similar to how go packages are cloned into go/src I typically clone my stuff into ~/src.e.g.clone-repo git@github.com:micktwomey/clone-repo.gitwill clone using git to~/src/github.com/micktwomey/clone-repo.This allows me to clone many different repos without worrying about stepping on each other. It also makes it easy to see where stuff comes from (e.g.rm -rf ~/src/old.git.example.comwill wipe out clones from git server I don't use any more).Install viapip install clone-repo.Install withpipxusingpipx install clone-repoto make it available as a CLI tool everywhere.Supports:/path/to/repogit cloneto~/src/localhost/file/{repo}file:///path/to/repogit cloneto~/src/localhost/file/{repo}git@example.com:org/repo.gitgit cloneto~/src/{host}/{org}/{repo}https://github.com/org/repo.gitgit cloneto~/src/github.com/{org}/{repo}https://github.com/org/repogit cloneto~/src/github.com/{org}/{repo}https://gitlab.example.com/org/repo.gitgit cloneto~/src/{host}/{org}/{repo}https://hg.mozilla.org/mozilla-central/hg cloneto~/src/hg.mozilla.org/{org}/{repo}https://hg.sr.ht/~org/repohg cloneto~/src/hg.sr.ht/{org}/{repo}keybase://team/org/repogit cloneto~/src/keybase/{org}/{repo}man@man.sr.ht:~org/repogit cloneto~/src/man.sr.ht/{org}/{repo}ssh://git@example.com:7999/somegroup/myrepo.gitgit cloneto~/src/{host}/{org}/{repo}ssh://hg@bitbucket.org/org/repohg cloneto~/src/{host}/{org}/{repo}Forhttps://URLs the default is git but some will behave differently based on the domain.DevelopmentIf you want to quickly develop you can usepoetryandpytest:poetry installpytest -vvIf you want to test across all supported Python versions you can install them viaasdfand then usenox:asdf installpoetry installnoxIf you want to runpre-commithooks before committing:poetry installpre-commit installFinally, there is ajustjustfile to run some commands.
Package: clonerepos
Clone Github and Bitbucket RepositoryInstallation:pip install clonereposUsing for Github:github("GITHUB USERNAME", "REPOSITORY NAME")Using for Bitbucket:bitbucket("BITBUCKET USERNAME", "REPOSITORY NAME")Sample App:#call module

from clonerepos.clone import github
from clonerepos.clone import bitbucket
import sys

if sys.argv[1] and sys.argv[2] and sys.argv[3] == "--github":
    github(sys.argv[1], sys.argv[2])
elif sys.argv[1] and sys.argv[2] and sys.argv[3] == "--bitbucket":
    bitbucket(sys.argv[1], sys.argv[2])Sample App2:from clonerepos.clone import github #for github
from clonerepos.clone import bitbucket #for bitbucket

github("agoren", "Blog") #for github http://github.com/agoren/Blog
bitbucket("aligoren", "blog") #for bitbucket https://bitbucket.org/aligoren/blog
Package: clongen
Clongen: ClonMapper Reference GeneratorInstallationpipxinstallclongenpython3<(curl-fsSLviv.dayl.in/viv.py)shimclongenFor one-time use consider usingviv runto use an ephemeral venv, see below for an example.NOTE: make sure to separatevivandclongenflags with--python3<(curl-fsSLviv.dayl.in/viv.py)run\clongen----lineages./lineages.csvUsageTo generate a clonmapper-compatible reference genome we
first need to produce afastaandgtffile of our expected lineages.
This is whereclongencomes in.
The only input is a singlecsvthat can come in one of two forms.id,lineage
lineage1,ATGATCATGGTACCATAAGG
...You may also provide a simpler version with only lineage sequences:ATGATCATGGTACCATAAGG
...The header is optional, however we will only attempt to match withid,lineageorlineage.
Any other header will likely not be removed and assumed to be a lineage and id.If the input list contains id's these will be used as thegene_name.
Otherwise we will use the full lineage sequence proceeded by the prefix designated by prefix flag, by default "lin-".Then we can generateclonmapper.gtfandclonmapper.faby default in./references:clongen--lineages./lineages.csv
Package: clonosGP
IntroductionTumours are mixtures of phylogenetically related cancer cell populations orclones, which are subject to a process of Darwinian evolution in response to selective pressures in their local micro-environment.clonosGPis a statistical methodology for tracking this latent heterogeneity continuously in time based on longitudinally collected tumour samples. In technical terms, it combines Dirichlet Process Mixture Models with Gaussian Process Priors to identify clusters of mutations and track their cellular prevalence continuously in time. If only cross-sectional data are available, then it performs standard non-parametric clustering of mutations based on their observed frequency, similarly toPyCloneand other software in the same category. The statistical models underlyingclonosGPwere implemented in the excellent probabilistic programming systemPyMC3on which we also rely for inference using variational methods.InstallationclonosGPrequires Python 3.7 or later. It can be easilly installed as follows:Create a virtual environment:python3 -m venv myenvActivate the newly created environment:source myenv/bin/activateInstallclonosGPas follows:pip install -U clonosGPAll necessary dependencies will also be installed.UsageA guide to start usingclonosGPquickly is availablehere. A more thorough tutorial can be foundhere.CitationFor citation information checkhttp://github.com/dvav/clonosGP
Package: cloogy
CloogyPython client for CloogySee Demo.ipynb for a working Jupyter Notebook0. Install cloogyIn your terminal:pip3 install cloogyor in a python shell or notebook:importpippip.main(['install','cloogy'])importyamlfromcloogyimportCloogyClient1. Get your credentialsGet your login and password.In this example we'll load it from a YAML file.withopen('credentials.yaml','r')asf:credentials=yaml.load(f)login=credentials['login']password=credentials['password']2. Create a CloogyClientIf you supply a login and password, authentication will be handled for you.client=CloogyClient(login=login,password=password)3. List your Unitsunits=client.get_units()units4. Get a specific Unit by ID# Lets grab the first ID from the list aboveunit_id=units[0]['Id']print(unit_id)unit=client.get_unit(unit_id=unit_id)unit5. Find out some stuff about your unitTheUnitclass is an extension to the regular python dict. This means it behaves like a normal dict, but adds some extra features.# Get date and time of the last communicationunit.get_last_communication_date()6. List all available Tags for your loginclient.get_tags()7. List available Tags for a Unittags=unit.get_tags()tags[tag['Id']fortagintags]8. Get a specific Tag directlytag_id=tags[0]['Id']print(tag_id)tag=client.get_tag(tag_id=tag_id)tagtag.get_last_communication_date()9. Get consumptions# pick a start and end time, as POSIX timestampimportpandasaspdstart=int(pd.Timestamp('20180414').timestamp()*1000)end=int(pd.Timestamp('20180416').timestamp()*1000)print(start,end)client.get_consumptions(granularity='hourly',# can be Instant, Hourly, Daily, Monthly, Yearlystart=start,end=end,tags=[tag_id],# List of tag Id'sinstants_type=None# How instant measurements should be aggregated. Can be Avg, Max, Min, Stdev. Default is Avg.)10. Get consumptions as a DataFrameFor some easy analysis, methods to get data as a Pandas DataFrame are includedLet's say we want to analyse the active energy consumption, which has TagTypeId 20001tags=client.get_tags(where='TagTypeId=20001')tag_ids=[tag['Id']fortagintags]start=pd.Timestamp('20180101')end=pd.Timestamp('20180417')client.get_consumptions_dataframe(granularity='monthly',start=start,end=end,tags=tag_ids)A flat table like this is nice, but it can contain multiple TagIds, and it has way to many columns we don't need.We can also get a table for only the readings:df=client.get_readings_dataframe(granularity='monthly',start=start,end=end,tags=tag_ids,metric='Read')df# make a plot!%matplotlibinlinedf.plot.bar()