Saravanan666/pypi-org huggingface dataset:
Package: xomega
[![Build Status](https://travis-ci.org/roxyboy/xomega.svg?branch=master)](https://travis-ci.org/roxyboy/xomega)
[![Documentation Status](https://readthedocs.org/projects/xomega/badge/?version=latest)](https://xomega.readthedocs.io/en/latest/?badge=latest)
[![DOI](https://zenodo.org/badge/125751493.svg)](https://zenodo.org/badge/latestdoi/125751493)# xomega: Inversion of the QG Omega equation
Functions to invert the [generalized Omega equation](https://journals.ametsoc.org/doi/full/10.1175/1520-0493%282000%29128%3C2270%3AMAAOAC%3E2.0.CO%3B2),
developed by [Takaya Uchida](https://roxyboy.github.io/), a Physical Oceanographer with interest in eddy tracer transport.
Package: xomics
Welcome to the xOmics documentationxOmics(eXplainable Omics) is a Python framework developed for streamlined and explainable omics analysis, with a
spotlight on differential proteomics expression data. It introduces the following key algorithms:cImpute: Conditional Imputation - A transparent method for hybrid missing value imputation.xOmicsIntegrate: Protein-centric integration of multiple (prote)omic datasets to find commonalities and differences.xOmicsRank: Protein-centric ranking of (prote)omic data, leveraging functional enrichment results.In addition,xOmicsprovides functional capabilities for efficiently loading benchmark proteomics datasets viaload_datasets, accompanied by corresponding enrichment data.A suite of supportive functions is also available to
facilitate a smooth and efficient (prote)omic analysis pipeline.InstallxOmicscan be installed either fromPyPiorconda-forge:pipinstall-uxomicsorcondainstall-cconda-forgexomicsContributingWe appreciate bug reports, feature requests, or updates on documentation and code. For details, please refer toContributing Guidelines. For further questions or suggestions, please emailstephanbreimann@gmail.com.CitationsIf you use xOmics in your work, please cite the respective publication as follows:xOmics:[Citation details and link if available]cImpute:[Citation details and link if available]xOmicsIntegrate:[Citation details and link if available]
Package: xomx
xomxis an open-source python library providing data processing and
machine learning tools for computational omics, with a
particular emphasis on explainability.It relies onAnnDataobjects, which makes it
fully compatible withScanpy.xomx is currently in beta version.InstallOption 1: conda (preferred option)This option is preferred because it relies mainly on conda-forge  (which among other things simplifies the installation of JAX).git clone https://github.com/perrin-isir/xomx.git
cd xomx
conda update condaInstall micromamba if you don't already have it (you can also simply use conda, by replacing belowmicromamba create,micromamba updateandmicromamba activaterespectively byconda env create,conda env updateandconda activate, but this will lead to a significantly slower installation):conda install -c conda-forge micromambaChoose a conda environment name, for instancexomxenv.The following command creates thexomxenvenvironment with the requirements listed inenvironment.yaml:micromamba create --name xomxenv --file environment.yamlIf you prefer to update an existing environment (existing_env):micromamba update --name existing_env --file environment.ymlThen, activate thexomxenvenvironment:micromamba activate xomxenvFinally, to install thexomxlibrary in the activated environment:pip install -e .Option 2: pipFor the pip install, you need to properly install JAX yourself. Otherwise, if JAX is installed automatically as a pip dependency ofxomx, it will probably not work as desired (e.g. it will not be GPU-compatible). So you should install it beforehand, following these guidelines:https://github.com/google/jax#installationThen, installxomxwith:pip install xomxJAXThe neural network-based machine learning algorithms inxomxare written in JAX (and flax), so it needs to be installed properly for them to work.To verify that the JAX installation went well, check the backend used by JAX with the following command:python -c "import jax; print(jax.lib.xla_bridge.get_backend().platform)"It will print "cpu", "gpu" or "tpu" depending on the platform JAX is using.TutorialsTutorials are the best way to learn how to usexomx.The xomx-tutorials repository contains a list of tutorials (colab notebooks) for xomx:https://github.com/perrin-isir/xomx-tutorialsAcknowledgementsMaintainer and main contributor:Nicolas Perrin-Gilbert (CNRS, ISIR)Other people who contributed toxomx:Joshua J. Waterfall (Curie Institute)Julien Vibert (Curie Institute)Mathias Vandenbogaert (Curie Institute)Paul Klein (Curie Institute)Citing the projectTo cite this repository in publications:@misc{xomx,author={Perrin-Gilbert, Nicolas and Vibert, Julien and Vandenbogaert, Mathias and Waterfall, Joshua J.},title={xomx},year={2021},publisher={GitHub},journal={GitHub repository},howpublished={\url{https://github.com/perrin-isir/xomx}},}
Package: xonia.py
xonia.py 🐍xonia.py- An easy to use, and async API wrapper forXoniawritten in Python.ContentsDocumentationInstallationBasic UsageUninstallDocumentationDocumentation forxonia.pywill be available soon.InstallationInstall or upgrade xonia.py using pippip install -U xonia.pyBasic UsagefromxoniaimportClientfromxoniaimportCredentialscreds=Credentials(email="your@email.com",password="your password")client=Client(creds)@client.eventasyncdefon_ready():print(f"Connected to Xonia!\nLogged in as{client.user}.")@client.eventasyncdefon_disconnect():print(f"Disconnected from API.")client.start()UninstallUninstall xonia.pypip uninstall xonia.py
Package: xonotic-exporter
Xonotic metrics exporter forPrometheus monitoring system.
Metrics are obtained by querying server via rcon (status 1command).Installationexecutepip install xonotic_exporteror runpip install-egit+https://github.com/bacher09/xonotic_exporter#egg=xonotic_exporterto install latest development version from githubConfigurationXonotic exporter is configured by file and CLI options. CLI options is used to
specify which port or address to listen, what configuration to use and
configuration file is used to specify servers from where metrics will be
exported. Configuration file is YAML dictionary, where keys are server names
(instancelabel in prometheus) and values are server connection options.
Here’s example configuration:public:
  server: 172.16.254.1
  port: 26000
  rcon_password: "secretpassword"
  rcon_mode: 1
private:
  server: private.example.com
  rcon_password: "secret"
ipv6-server:
  server: 2001:db8:85a3::8a2e:370:7334
  port: 26001
  rcon_mode: 2
  rcon_password: "password"Connection options have few required fields (server,rcon_password) and
also some optional fields (port,rcon_mode) which have default value.serverfield might contain IPv4 or IPv6 address or DNS name. If you are using
DNS name, it will be resolved each time before making request to server, so if
you change DNS record you don’t need to restart exporter to use new IP.
For more info about configuration file format you can checkit’s JSON schema.
Also, you can check correctness of configuration using--validateCLI option.If you edit configuration file, you can update configuration without restarting
Xonotic exporter, just sendHUPsignal to process or send POST request to/-/reloadendpoint.For example:$ kill -HUP 4429   # 4429 is exporters PID
$ curl -XPOST http://localhost:9260/-/reloadPrometheus ConfigurationThe exporter needs server name to be passed as target parameter. It similar toblackboxandsnmpexporters.Example prometheus configuration:scrape_configs:
  - job_name: 'xonotic_exporter'
    relabel_configs:
      - source_labels: [__address__]
        target_label: __param_target
      - source_labels: [__param_target]
        target_label: instance
      - target_label: __address__
        replacement: 127.0.0.1:9260
    static_configs:
      - targets: ['public', 'private', 'ipv6-server']  # server namesOther featuresInstead off using configuration file you can start xonotic exporter using
Python API. For more informationsee this code. This gives you ability for
dynamic configuration and server autodiscovery.If you going to deploy this service with systemd check examples folder, there
is examplesystemd unitfor this service.
Package: xonsh
xonshis a Python-powered, cross-platform, Unix-gazing shell language and command prompt.The language is a superset of Python 3.6+ with additional shell primitives.
xonsh (pronouncedconch) is meant for the daily use of experts and novices alike.If you like xonsh, :star: the repo,write a tweetand stay tuned by watching releases.First stepsInstall xonsh from pip:python -m pip install 'xonsh[full]'And visithttps://xon.shfor more information:Installation- using packages, docker or AppImage.Tutorial- step by step introduction in xonsh.ExtensionsXonsh has the certain term for extensions and additional materials - xontrib - the short version of “contribution” word.Xontribs on GithubAwesome xontribsCore xontribsCreate a xontrib step by step from templateProjects that use xonsh or compatiblegitsome: Supercharged Git/shell autocompleter with GitHub integration.xxh: Using xonsh wherever you go through the SSH.rever: Cross-platform software release tool.Regro autotick bot: Regro Conda-Forge autoticker.Jupyter-based interactive notebooks viaxontrib-jupyter:jupyter and jupyterlab: Interactive notebook platform.euporie: Terminal based interactive computing environment.The xonsh shell communityThe xonsh shell is developed by a community of volunteers. There are few ways to help the xonsh shell:Become a sponsor to xonsh.Write a tweet, post or an article to spread the good word about xonsh in the world.Solve apopular issue.Solve agood first issue.Get theideaandcreate new xontrib.Become xonsh core by deep diving into xonsh and improve the threading and subprocess logic.Give a star to xonsh repository and toxontribsyou like.We welcome new contributors!
Package: xonsh-apt-tabcomplete
xonsh-apt-tabcomplete - APT tab completion for the Xonsh shellInstallingInstallation is done the normal way for setuptools-based projects:python setup.py installYou can also use pip, of course:pip install xonsh-apt-tabcompleteNote that in the specific case of Xonsh, make sure you use your Python 3
executable to run setup.py, since as of this writing that’s all Xonsh
supports.Next, you’ll have to add a line to your .xonshrc file to load the
plugin:xontrib load apt_tabcompleteIf you have the bash completer installed, then you should also add the
following lines to ensure that apt_tabcomplete is loaded before the bash
completer:completer remove auto_apt
completer add auto_apt apt_completer "<bash"Reload your shell, and you’re good to go.UsageTabcomplete works the way you’d expect when using apt. Just hit tab when
you’d like to see what packages have a name starting with what you’ve
typed so far. Currently just the install/remove commands for apt-get and
the search command for apt-cache are supported (with apt-get remove only
tabcompleting to installed packages), but I am open to adding more
functionality upon request.Known issuesYou may have to hit tab twice to get the plugin to autocomplete. I’m
still not sure why this is, unfortunately.
Package: xonsh-direnv
direnvsupport for thexonsh shellhttps://direnv.nethttps://xon.shThis works with python 3.7.0, xonsh 0.8.8 and direnv 2.17.0.xpip install xonsh-direnv
xontrib load direnvchange log1.6.1
—Reverted to 1.5.0 to halt on_post_rc1.6.0
—PRhttps://github.com/74th/xonsh-direnv/pull/121.5fixhttps://github.com/74th/xonsh-direnv/issues/21.4fix xonsh has a history of breaking its built-inshttps://github.com/74th/xonsh-direnv/pull/31.3$HOME/.envrceffectingdirenv allowimmediately
Package: xonsh_kernel
A Calysto Jupyter kernel for Xonsh.To install:pip install xonsh_kernel
python -m xonsh_kernel.installTo use it, run one of:jupyternotebook# In the notebook interface, select 'Calysto Xonsh' from the 'New' menuipythonqtconsole--kernelcalysto_xonshipythonconsole--kernelcalysto_xonshThis is based onMetaKernel,
which means it features a standard set of %%magics.  Note that this is
different from the kernel that is distributed withXonsh.A sample notebook is availableonline.
Package: xonsh-tcg
# xonsh-tcgThis is a [Xonsh](https://xon.sh/) plugin for tcg. To install this plugin, do`bash xpip installxonsh-tcg`After installation, add`xonsh xontrib load tcg `to your.xonshrcto load it automatically. Thentcgwill automatically create
cgroup for your shells. The cgoup of the current shell will be displayed in$PROMPTand$TITLE.
Package: xontib-kitty
xontrib-kittyXonsh hooks for the Kitty terminal emulator.This xontrib provides extra tools for interacting with the combination of
the xonsh shell and the kitty terminal emulator in the best possible way!It provides all of the standard aliases, tab completions, and even matplotlib
integrations! This allows you to render plots right in your terminal!InstallationTo installxontrib-kitty, get the source from your favorite package manager.conda:$condainstall-cconda-forgexontrib-kittypip:$pipinstallxontrib-kittySetupTo usexontrib-kitty, just load it in your current session or in your~/.xonshrcfile with the following line:xontribloadkitty
Package: xontrib-abbrevs
Expands input words as you type in xonsh shell.If you like the idea click ⭐ on the repo andtweet.InstallationTo install use pip:xpipinstallxontrib-abbrevs# or: xpip install -U git+https://github.com/xonsh/xontrib-abbrevsUsageThis expands input words fromabbrevsdictionary as you type.
Addsabbrevsdictionary to hold user-defined "command abbreviations.
The dictionary is searched as you type the matching words are replaced
at the command line by the corresponding dictionary contents once you hit
'Space' or 'Return' key.For instance a frequently used command such asgit statuscan be abbreviated togstas follows:xontrib load abbrevs
abbrevs['gst'] = 'git status'
gst # Once you hit <space> or <return> 'gst' gets expanded to 'git status'.one can set a callback function that receives current buffer and word to customize the expanded word based on contextabbrevs['ps'] = lambda buffer, word: "procs" if buffer.text.startswith(word) else wordIt is also possible to set the cursor position after expansion with,abbrevs['gp'] = "git push <edit> --force"CreditsThis package was created withxontrib template.
Package: xontrib-add-variable
Version number: 1.1.1Author:Erick TuctoOverviewThis package allow add new variable to$PROMPT_FIELDSand
create new aliases.Installation / UsageTo install use pippipinstallxontrib-add-variableAdd on~/.xonshrcNow you can create new variables to $PROMPT on~/.xonsh/add_variable.xsh,
also create new aliases, please seeExampleor mywiki1xontribloadadd_variableContributingErick TuctoExampleOn~/.xonsh/add_variable.xshor~/.xonsh/add_variable.py1fromtimeimportstrftime2fromxontrib.add_variable.decoratorsimportvariable34@variable5deftimeNow():6returnstrftime('%H:%M:%S')On~/.xonshrc1xontribloadadd_variable23$RIGHT_PROMPT='{timeNow}'See imageCreditsThis package was created withCookiecutterand thexontribtemplate
Package: xontrib-argcomplete
Argcompletesupport for python and xonsh scripts inxonshshell.If you like the idea click ⭐ on the repo and stay tuned by watching releases.Screenshot made withxontrib-prompt-barandKonsole.Installxpipinstallxontrib-argcompleteecho'xontrib load argcomplete'>>~/.xonshrc# Reload xonshUsageBefore usage you mustadd the argcomplete support to your script. ThePYTHON_ARGCOMPLETE_OKmarker should be found in the first 10 lines of the file.The argcomplete xonsh completer will be activated with this cases:pythonscript.py
./script.py
./path/script.py

xonshscript.xsh
./script.xsh
./path/script.xsh# scripts without extension should have "env python" or "env xonsh" or path to python/xonsh in the shebang./script
script# script should be found in $PATHExamplexpipinstallxontrib-argcomplete
xontribloadargcompletecd/tmp&&gitclonehttps://github.com/anki-code/xontrib-argcompletecdxontrib-argcomplete/tests

pythonproto.py<Tab># Suggestions: --help --proto -h./proto.py--protott<Tab># Suggestions: http https./proto.xsh--protott<Tab># Suggestions: http https./proto--protott<Tab># Suggestions: http https$PATH.append($PWD)proto--protott<Tab># Suggestions: http httpsKnown issuesWindows is not supported. PRs are welcome!DevelopmentTo switch on the debug mode run$XONTRIB_ARGCOMPLETE_DEBUG = True.Argcomplete environment variablesArgcomplete documentationLinksThis package is the part ofergopack- the pack of ergonomic xontribs.This package was created withxontrib cookiecutter template.
Package: xontrib-autojump
Xonsh configuration for autojumpSets upautojumpfor use withxonshshell.UsageLoad it interactively or in your xonsh startup file like this:xontribloadautojumpand use these aliases:j		'autojump' to a directory
jc		'autojump' to a child directory
jo		'autojump' to a directory in the default file manager
jco		'autojump' to a child directory in the default file managerInstallationInstall from source with:pythonsetup.pyinstallor from pypi withpipinstallxontrib-autojump
Package: xontrib-avox-poetry
Overviewauto-activate venv as one cd into a poetry project folder.InstallationTo install use pip:xpipinstallxontrib-avox-poetry# or: xpip install -U git+https://github.com/jnoortheen/xontrib-avox-poetryUsagexontribloadavox_poetryConfiguration# If found, the env name is searched inside the $VIRTUALENV_HOME# rather than invoking `poetry env info -p` command every time `cd` happens# It is faster setting this variable. It will also be used by poetry.$VIRTUALENV_HOME="~/.virtualenvs"# name of the venv folder. If found will activate it.# if set to None then local folder activation will not work.$XSH_AVOX_VENV_NAME=".venv"# exclude activation of certain paths by setting$XSH_AVOX_EXCLUDED_PATHS={"xsh-src"}CreditsThis package was created withxontrib cookiecutter template.
Package: xontrib-back2dir
Return to the most recently used directory when starting the xonsh shell.If you like the idea click ⭐ on the repo and andtweet.InstallationTo install use pip:xpipinstallxontrib-back2dir# or: xpip install -U git+https://github.com/anki-code/xontrib-back2direcho"xontrib load back2dir">~/.xonshrcUsageNo additional actions needed. The xontrib just saves the latest directory and uses it when
xonsh starts:bash~$xonsh
xonsh~$cd/etc
xonsh/etc$exit# the latest directory is /etcbash~$xonsh
xonsh/etc$# the latest directoryIf you run xonsh not from the$HOMEdirectory the latest directory will be ignored:bash~$cd/tmp
bash/tmp$xonsh
xonsh/tmp$# latest directory ignoredLinksThis package is the part ofergopack- the pack of ergonomic xontribs.This package was created withxontrib cookiecutter template.
Package: xontrib-base16-shell
Version number: 0.1.0Author:Erick TuctoOverviewSupport tobase16 shell. Allow change base16 shell themes.Installation / UsageTo install use pippython3-mpipinstallxontrib-base16-shellAdd on~/.xonshrc1$BASE16_SHELL=$HOME+"/.config/base16-shell/"2xontribloadbase16_shellTip: Please see mywikiSee imageContributingErick TuctoCreditsThis package was created withCookiecutterand thexontribtemplate
Package: xontrib-bash-completions-dirs
Xontrib Bash Completions DirsAutocomplete loading from directories.InstallationTo install use xpip:xpipinstallxontrib-bash-completions-dirsorxpipinstall-Ugit+https://codeberg.org/taconi/xontrib-bash-completions-dirsUsagexontribloadbash_completions_dirsAdd the variableBASH_COMPLETIONS_DIRS(which must be an iterable of strings) with the paths of the directories that contain the autocomplete files.For example:$BASH_COMPLETIONS_DIRS=['/usr/share/bash-completion/completions']Note: The file name must be the same as the command to be used in autocompleteFor example, the file/usr/share/bash-completion/completions/gitwill be used to autocomplete thegitcommand
Package: xontrib-bashisms
Bash-like interactive mode extensions for the xonsh shell.If you like the idea click ⭐ on the repo andtweet.NoteWe're not recommend to use this xontrib (see issues section). Use it carefully only if you have very strong muscle memory after hundred of years using Bash or for the education reasons and demonstration how agile is xonsh shell.InstallationTo install use pip:xpipinstallxontrib-bashisms# or: xpip install -U git+https://github.com/xonsh/xontrib-bashismsUsagexontribloadbashismsEnables additional limited Bash-like syntax and commands while at the interactive command prompt:AddedMeaning!!Get the last command.!^Get the first argument from the preceding command.!$Get the last argument from the preceding command.!*Get all argument from the preceding command.aliasAdd alias.export NAME=PeterSetting an environment variable.shopt -s dotglobGlobbing files with * or ** will also match dotfiles, or those "hidden" files.completeShow list of completers.set <-e/+e>Cause a failure after a non-zero return code.set <-x/+x>Turns on tracing of source code lines during execution.unset NAMEUnsetting/deleting an environment variable.See alsoBash to Xonsh Translation Guide.Known issuesThexontrib-bashismsappeared in the beginning of xonsh history as part of the default xontribs. It has issues and we recommend to usexontrib-shinstead.Threading issuesBecause of xontrib-bashisms setsTHREAD_SUBPROCS=Falsethere are issues around the threading could appear. If you're using bashisms and faced with issues try the same inxonsh --no-rcmode before reporting the issue.Only interactive modeThe xontrib features are implemented ason_precommand eventsand
these additions do not affect the xonsh language when run as script.
That said, you might find them useful if you have strong muscle memory in interactive mode.DebugThis xontrib may modify user command line input to implement its behavior.
To see the modifications as they are applied (in unified diffformat), please set$XONSH_DEBUGto2or higher.See alsoBash to Xonsh Translation Guidexontrib-sh- Paste and run commands from bash, zsh, fish, tcsh in xonsh shell.CreditsThis package was created withxontrib template.
Package: xontrib-brace-expansion
Implements simple brace expansion:@ echo a{d,c,b}e
ade ace abeNested expansion is not supported:@ echo /usr/{ucb/{ex,edit},lib/{ex?.?*,how_ex}}
SyntaxError: Unmatched "}" at line 1, column 16See also:https://www.gnu.org/software/bash/manual/html_node/Brace-Expansion.htmlUsagexpip install xontrib-brace-expansion
xontrib load brace_expansion
Package: xontrib-broot
Overviewbrootsupport function for xonsh shellInstallationTo install use pip:xpipinstallxontrib-broot# or: xpip install -U git+https://github.com/jnoortheen/xontrib-brootUsageIt addsbralias function. So commands likecdwill work from broot.$xontribloadbroot
$brbrootcan also be launched with shortcutCtrl+N.
This can be changed by$XONSH_BROOT_KEY="c-n"or disabled with$XONSH_BROOT_KEY="".
(PSPTK's keybinding guidefor full list of key names.)CreditsThis package was created withxontrib cookiecutter template.