Saravanan666/pypi-org huggingface dataset:
Package: dockonsurf
DockOnSurfDockOnSurf is a program to automatically find the most stable geometry for molecules
on surfaces.old webpage:https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurfcurrent repository:https://gitlab.com/lch_interfaces/dockonsurfFeaturesGenerate a handful of adsorbate-surface structures by
combining:surface sitesadsorbate's anchoring pointsconformersorientationsprobe dissociation of acidic HGuess the direction where to place the adsorbate.
Useful for nanoparticles or stepped/kinked surfaces.Sample different orientations efficiently by using internal angles.Detect and correct atomic clashes.Optimize the geometry of the generated structures using CP2K or VASP.Submit jobs to your computing center and check if they have finished normally.Track progress by logging all events on a log file.Customize the execution by changing chemically meaningful  the edition of a simple input file.Documentationhttps://dockonsurf.readthedocs.io/Installation:Download thedockonsurfdirectory and place it somewhere in your computer,
by typing in your terminal:git clone https://gitlab.com/lch_interfaces/dockonsurfIn order to be able to execute DockOnSurf by simply typingdockonsurf.pyYou need
to add the DockOnSurf directory in yourPATH. Assuming you download it in your$HOMEdirectory, add$HOME/dockonsurfto yourPATHvariable by typing:PATH="$PATH:$HOME/dockonsurf/"If you downloaded it elsewhere, replace$HOMEfor the actual path where your DockOnSurf is
(where you did thegit clonecommand).
If you want to permanently add the DockOnSurf directory in yourPATHaddPATH="$PATH:$HOME/dockonsurf/"at the end of your$HOME/.bashrcfile.DockOnSurf needs the python libraries listed underRequirementsto be installed
and available. The easiest way to do this is with thecondapackage and environment
manager (seehttps://docs.conda.io/en/latest/). You can alternatively install
them using pip except from RDKit, which is not available as its core routines are
written in C.Requirements:Python>= 3.6Matplotlib~= 3.2.1NumPy>= 1.16.6RDKit~= 2019.9.3scikit-learn~= 0.23.1HDBSCAN~= 0.8.26ASE~= 3.19.1NetworkX>= 2.4python-daemon~= 2.2.4pymatgen~= 2020.11.11pycp2k~= 0.2.2ExampleExecute DockOnSurf by typingdockonsurf.py -i dockonsurf.inpwheredockonsurf.inpis the dockonsurf input file. See a samplehere.Testing(To be done)Contact/ContributeSubmit an issue on:https://gitlab.com/lch_interfaces/dockonsurfPlease send us bug-reports, patches, code, ideas and questions.LicenseDockOnSurf is licensed under the MIT license.
Package: dockontext
dockontextcontext manager that runs and closes docker containersWhen integration or end-to-end test needs temporal docker container to fake remote systems, this package will help to create/close/remove the temporal docker container.FeaturesCreate docker container by giving image name. The container will be named as 'docontext={name}'Close and remove the container when exit.Examplepytest.fixtureimport pytest
from dockontext import container_generator_from_image, Result, Config

create_container = pytest.fixture(container_generator_from_image)

def test_fixture(create_container):
     config = Config(name, "alpine:latest")
     container = create_container(config)
     result = container.execute("echo hello", timeout: float)
     assert result == Result(returncode=0, stdout="hello\n", stderr="")TODODockerfiledocker-compose.ymlcontainer group contextFree software: MIT LicenseCreditsThis package was created withCookiecutterAlso was copied and modified from theaudreyr/cookiecutter-pypackageproject template.
Package: dockre
dockre======.. image:: http://hera.physchem.kth.se:9090/api/badges/bjodah/dockre/status.svg:target: http://hera.physchem.kth.se:9090/bjodah/dockre:alt: Build status.. image:: https://img.shields.io/pypi/v/dockre.svg:target: https://pypi.python.org/pypi/dockre:alt: PyPI version.. image:: https://img.shields.io/pypi/l/dockre.svg:target: https://github.com/bjodah/dockre/blob/master/LICENSE:alt: License`dockre <https://github.com/bjodah/dockre>`_ provides acommand line interface (through a `Python <http://www.python.org>`_ packge) for using **dock**er **re**producibly to builde.g. documents, binaries or host services. The default docker image used is the authorspersonal one for work related tasks but it is changeable by specifying ``--image``.Documentation-------------Autogenerated API documentation is found `here <http://hera.physchem.kth.se/~dockre/branches/master/html>`_.Installation------------Simplest way to install ``dockre`` is to use ``pip``:::$ pip install --user dockreExamples--------Here is a simple example:.. code:: bash$ mkdir input$ echo -e "report.txt:\n\techo 'silly example'>\$@" > input/Makefile$ mkdir output$ dockre build$ cat output/report.txtsilly exampleLicense-------The source code is Open Source and is released under the simplified 2-clause BSD license. See `LICENSE <LICENSE>`_ for further details.Contributors are welcome to suggest improvements at https://github.com/bjodah/dockreAuthor------Björn I. Dahlgren, contact:- gmail address: bjodah- kth.se address: bda
Package: dockship
# dockship### Installation
You can install dockship from PyPI:pip install dockshipdockship requires python == 3.6 and docker installed.### How to usedockshipis a command line application. It supports two commands:### runDownloads model from Dockship and runs the model in docker container.Args:modelID (string) : Model’s unique id shown at dockship.io
port (string)    : Port number for running model### stopStops the already runnng model.Args:modelID : Model’s unique id which needs to be stopped.
Package: dockswap
Tool for easier switching between projects that uses docker containers to set up working environmentInstallationpipinstalldockswapUsageUsage:dockswap[OPTIONS]COMMAND[ARGS]...DockSwap.Toolforswappingprojects.Commands:addRegisteracomposerforprojectdeleteDeleteregisteredcomposerlistListallregisteredcomposersprunePruneexistingregisteredcomposers.startStartcontainersforregisteredcomposerstopStopcontainersforregisteredcomposerstopallStop(and/orremove)allrunningcontainersversionShowversionofcurrentlyuseddockswapAdding composerUsage:dockswapadd[OPTIONS]PROJECT_NAMERegisteracomposerforprojectArguments:PROJECT_NAME[required]Options:--pathPATHPathto.ymlor.jsonfilethatmustberunusingdocker-compose[required]--env-pathPATHIfyourdocker-composefileusesenv_filethenspecifypathforthatfileShowing composersUsage:dockswaplist[OPTIONS]ListallregisteredcomposersOptions:--full/--no-fullshowmoreinfo[default:False]StartingUsage:dockswapstart[OPTIONS]PROJECT_NAMEStartcontainersforregisteredcomposerArguments:PROJECT_NAME[required]Options:--remove-other/--no-remove-otherRemovestoppedcontainers[default:False]--dry/--no-dryDonotruncommand,insteadjustprintit[default:False]Why?If your are using docker containers to set up your working environment then this tool is for you.
I used to do like this:$ cd ~/projects/foo
$ docker stop $(docker ps -aq) && docker rm $(docker ps -aq)
$ docker-compose -f _dev/docker-compose.yml up -dThen I want to switch to another project, and again:$ cd ~/projects/bar
$ docker stop $(docker ps -aq) && docker rm $(docker ps -aq)
$ docker-compose -f _directory_with_another_name/docker-compose.yml up -dThis is a bit verbose for such a simple task. Now what I do is just:$ dockswap start foo --remove-other
Package: docktgrid
DockTGridGenerate voxel representations of protein-ligand complexes for deep learning applications.📌 FeaturesGPU-accelerated voxelization of protein-ligand complexes.Easy customization of voxel grid channels and parameters.Readily usable withPyTorch.Support for multiple file formats (to be expanded).✅ PDB❌ MOL2❌ SDF🚀 Getting StartedInstallation (pip)Install DockTGrid usingpip:$ python -m pip install docktgridDevelopmentThese instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
Python 3.11 is recommended, other versions may work but are not tested.Clone the repository:$ git clone https://github.com/gmmsb-lncc/docktgrid.git
$ cd docktgridCreate a new environment usingvenvand activate it:$ python3.11 -m venv env
$ source env/bin/activateOr if you prefer usingconda:$ conda create --prefix ./venv python=3.11
$ conda activate ./venvInstall the required packages:$ python -m pip install -r requirements.txtRun the tests:$ python -m pytest tests/🖥️ UsageSee thedocumentationfor more information on how to use DockTGrid.There are also some examples in thenotebooksfolder.📄 LicenseThis project is licensed under theLGPL v3.0license.📙 DatasetWe provide a dataset of voxel representations of protein-ligand complexes generated using DockTGrid.
The dataset is available for download atZenodo.
For more information, see the associated publication.🖋️ CitingIf you use DockTGrid in your research, please cite the following paper:@article{silva2023deep,title={Deep Learning-Ready Voxel Representation of Protein-Ligand Complexes from an Enhanced PBDbind v.2020 Dataset},author={da Silva, Matheus M. P. and Guedes, Isabella A. and Lima, Fabio C. and Dardenne, Laurent E.},journal={ChemRxiv},year={2023},publisher={Cambridge: Cambridge Open Engage}}
Package: docktor
manage and run multiple tor containershow to……installcurl-sSLhttps://raw.githubusercontent.com/smthnspcl/docktor/master/install.sh|bash# orgitclonehttps://github.com/smthnspcl/docktorcddocktorsudopython3setup.pyinstall…use from cli$docktor--helpusage:docktor[-h][--hostHOST][--portPORT][-iINSTANCES][--control-passwordCONTROL_PASSWORD]optionalarguments:-h,--helpshowthishelpmessageandexit--hostHOST--portPORT-iINSTANCES,--instancesINSTANCES--control-passwordCONTROL_PASSWORDex:$docktor-i2# runs 2 tor containers$curlhttp://127.0.0.1:1337/api/instances# should ouput something like this[{"id":"64b0cd480f6a9e1653d10556cf6c99138a2607b18f52415b0b60c6b7f75cdc4e","short_id":"64b0cd480f","name":"docktor-0","status":"running","ports":[{"8118\/tcp":"33038"},{"8123\/tcp":"33037"},{"9050\/tcp":"33036"},{"9051\/tcp":"33035"}]},{"id":"5c0955a0f20c2b92e8bc2d3adcb663f8142a3878f5ba83657462c0bd4d430ff8","short_id":"5c0955a0f2","name":"docktor-1","status":"running","ports":[{"8118\/tcp":"33042"},{"8123\/tcp":"33041"},{"9050\/tcp":"33040"},{"9051\/tcp":"33039"}]}]# renew ip addresses for all containerscurlhttp://127.0.0.1:1337/api/renew# renew ip address for one containercurlhttp://127.0.0.1:1337/api/renew/docktor-0…use from codefromdocktorimportManagermanager=Manager(2)manager.start()manager.wait_until_ready()print(manager.get_containers())manager.stop()notice:if your code crashes you might need to stop the containers by hand
Package: docktree
Displays the tree structure of your Docker images.Meant as a replacement for the removed functionality ofdocker images -t.Usage: docktree [-h] [IMAGE]Positional arguments:IMAGE       show only parents and children of IMAGEOptional arguments:-h,--helpshow this help message and exit-s,--show-sizeshow the virtual size of each layerUsage example:(env2)pi@raspberrypi [work/docktree] % docktree
└─ 71a76a74c237
   ├─ 92b43b34adf9 test1:latest
   └─ 2f5ca2d69bf4
      └─ ba37442b01bb
         ├─ 643e1371a625 test2:latest
         │  └─ 7e548b8390f2 test3:latest
         └─ c89a6bc5d884
            └─ baee49e775b3 resin/rpi-raspbian:latest,resin/rpi-raspbian:jessie,resin/rpi-raspbian:jessie-2015-10-21
(env2)pi@raspberrypi [work/docktree] % docktree test2
└─ 71a76a74c237
   └─ 2f5ca2d69bf4
      └─ ba37442b01bb
         └─ 643e1371a625 test2:latest
            └─ 7e548b8390f2 test3:latest
Package: dockubeadt
Docker Compose and K8s manifests to (MiCADO) ADTTranslate a single or multi-part YAML file containing
Kubernetes manifests or a Docker compose into a MiCADO ADT.RequirementsPython >= 3.6clickruamel.yamlKompose>= 1.31.xUsageInstall compose binary:curl -L https://github.com/kubernetes/kompose/releases/download/v1.31.2/kompose-linux-amd64 -o kompose
chmod +x kompose
sudo mv ./kompose /usr/local/bin/komposeClone the repository:git clone <repository> dockubeadt
cd dockubeadtInstall and run dockubeadt with pip:pip3 install .
dockubeadt PATH/TO/FILENAME.YAMLOr skip the install and simply:python3 -m dockubeadt PATH/TO/FILENAME.YAMLGenerated output file will be saved to your current directory asadt-FILENAME.YAMLThings to note(Docker Compose)All the volume mounts in docker compose are by default converted to 'hostPath' volume mounts in MiCADO ADTUse therestartproperty in docker compose to manage the container restarts. The values can bealways,on-failureornone.Use the long port syntax in docker-compose for services that needs to be exposed externally using a domain name or public IP. A sample of long port syntax is given below.ports:
     - target: 8080
       published:8080
       protocol: tcp
       mode: hostDocker Compose VariablesThe variables in docker compose file needs to be in these form:- TEST_MESSAGE={ get_input:TEST_MESSAGE }
TEST_MESSAGE: '{ get_input:TEST_MESSAGE }'
command: 'python3 start.py {get_input:DB_MODEL_}'RoadmapSupport appending translated nodes to an existing ADT
Package: dockup
Dockup is a command line interface tool which allows to easily publish applications at a given path through docker containers and nginx.A Dockup package is a compressed file containing:the content you want to publish: python script, HTML file, ...thedockup.ymlconfiguration file which contains the following infonameof the package, must be the same name as the archive containing itpathat which the package will be accessible. For example/app1forwebsite.com/app1typeof the package. For example,website,fletapplicationoptional:Dockerfileandnginx.confin case customization is neededWhen you publish a Dockup package, the tool will do the following things automatically for you:Docker compose stopExtract the package archive in the Dockup app folderIf necessary, build the nginx configurationIf necessary, build the docker fileRebuild the docker compose fileDockup compose build and upThe nginx reverse proxy used by Dockup is also installed as Dockup package. This makes it convenient to configure and update the reverse proxy, for example to configure HTTPS on your server.InstallationFirst of all install the docker engine:https://docs.docker.com/engine/install/Then install Dockup as a pip packagepip3 install dockupUsageAs a command line toolInstall the proxy Packagegiven that your reverse proxy package is located in your current working directoryyou can prepare the reverse proxy package according to you needs:reverse_proxy_httpis an example of simple HTTP proxy (not configured for HTTPS)you can also specify the package as an archive if it is present in your working directory.python3 -m dockup installproxy reverse_proxy_httpPublish a packageyou can also specify the package as an archive if it is present in your working directory.pyhton3 -m dockup install flet_app1To remove a packagepython3 -m dockup uninstall flet_app1As a python packageimportdockupdockup.down()dockup.reset()dockup.set_proxy('./reverse_proxy_http.tar.gz')dockup.add('flet_app1.tar.gz')build_nodes()dockup.up()
Package: dockupdater
Docker + Updater = DockupdaterAutomatically keep your docker services and your docker containers up-to-date with the latest version.OverviewDockupdaterwill monitor (all or specified by a label) running docker containers and running service (in Docker swarm) and update them to the (latest or tagged) available image in the remote registry.Push your image to your registry and simply wait your defined interval for dockupdater to find the new image and redeploy your container autonomously.Notify you via many platforms courtesy ofAppriseUse with Docker swarm to update services on the latest available versionLimit your server SSH accessUseful to keep 3rd party container up-to-dateGetting StartedMore detailed usage and configuration can be found onthe docs.Docker containerDockupdateris deployed via docker image in a standalone container like so:dockerrun-d--namedockupdater\-v/var/run/docker.sock:/var/run/docker.sock\dockupdater/dockupdaterThis is image is compatible for amd64, arm32, and arm64 CPU architecturesDocker swarm (service)Dockupdatercan be deploy on a service like this:version:"3.6"services:dockupdater:image:dockupdater/dockupdaterdeploy:placement:constraints:-node.role==managerDockupdater needs to run on a manager nodeGetting helpsIssues listDocumentationReleases and changelogsFrequently Asked QuestionsReporting bugs and contributingAll contributions are welcome!Want to report a bug or request a feature? Please openan issue.Want to help us? Your contribution and your pull request are welcome. We need all the help we can get!
Package: doclick
doclickdoclick is a Python library working as a programmable pseudo-language simulating desktop actions such as clicking, sending keys etc.InstallationUse the package managerpipto install doclick.pipinstalldoclickUsageimportdoclick.doclick_coreasdcdc.execute_script("script.txt")script.txt contains:Click(100,100)ContributingPull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.LicenseMIT
Package: doclifter
doclifterThe doclifter program translates documents written in troff macros to DocBook.Lifting documents from presentation level to semantic level is hard, anda really good job requires human polishing.  This tool aims to do everythingthat can be mechanized, and to preserve any troff-level information that mighthave structural implications in XML comments.This tool does the hard parts.  TBL tables are translated into DocBooktable markup, PIC into SVG, and EQN into MathML (relying on pic2svgand GNU eqn for the last two).Install by doing "make install". To install to a prefix other thanthe default (/usr), set a PREFIX environment variablee.g. "PREFIX=/usr/local make -e install"Test loads are included in the distribution; do "make check" to runthe regression tests.  The code has been live tested in about the mostbrutal possible way; it has been run against every single man page inall sections of a desktop Ubuntu installation.  It lifts over 93% ofthese pages without requiring any hand-hacking.There is a detailed change log in the NEWS file.
Package: doclink
*******Doclink*******.. image:: https://travis-ci.org/Luoyufu/doclink.svg?branch=master:target: https://travis-ci.org/Luoyufu/doclink.. image:: https://codecov.io/gh/Luoyufu/doclink/branch/master/graph/badge.svg:target: https://codecov.io/gh/Luoyufu/doclink.. image:: https://img.shields.io/pypi/v/doclink.svg:target: https://pypi.python.org/pypi/doclink.. image:: https://img.shields.io/pypi/pyversions/doclink.svg:target: https://pypi.python.org/pypi/doclink| Build client for Web APIs from pydoc. Inspired by `Uplink <https://github.com/prkumar/uplink>`_.Overview========| Doclink turns a Python function into HTTP API by writting pydoc to declare the api meta.| It is based on Requests and uses YAML with predefined schema as api declaration.| When calling the function, response from HTTP API will be passed in as a parameter for futher handling.Features========* create python function as HTTP API with **pydoc*** **YAML** based schema for api declaration* handle api response in the **same** function* response hook as **middleware*** **all** args for Requests supported* select base_uri dynamicly from simple **router**Quick through, with httpbin=====Create a consumer instance... code-block:: pythonfrom doclink import Consumerconsumer = Consumer('http://httpbin.org/')Add response hook(middleware)... code-block:: python@consumer.resp_hookdef json_hook(resp):resp.json = resp.json()Add function for api declaration... code-block:: python@consumer.get('get')def get(resp):"""<meta>args:query:- arg1: arg1- arg2: arg2</meta>"""return resp.json['args']Use you api... code-block:: python>>> get(){"arg1": "arg1","arg2": "arg2"}
Package: doclinter
DocLinter 📝: Python Docstring Complexity AnalyzerDocLinter is a command-line tool written in Python that helps you maintain consistent and readable documentation across your projects.FeaturesLint the complexity of docstrings in Python files.Customize analysis by specifying a maximum complexity level.Easily integrate into your workflow with a simple command-line interface.InstallationYou can install DocLinter using pip:pip install doclinterUsageTo analyze the complexity of docstrings in Python files, use the following command:doclinter <file_or_directory_glob>Optional arguments:--max-ari-level <int>: Specify the maximum automated readability index to report as an error.-v, --verbose: Display verbose output.Example:doclinter my_module.py --max-ari-level 10 -vHow It Works 🛠️DocLinter utilizes the abstract syntax tree (AST) module in Python to parse Python files and extract docstrings. It rates the complexity of each docstring using the Automated Readability Index (ARI), a formula that takes into account factors such as word count, letter count, and sentence count. Docstrings with complexity levels above the specified threshold are reported as errors.Why Use DocLinter? 🚀Enhance Documentation Quality: Ensure that your docstrings meet readability standards, making your codebase more accessible and maintainable.Catch Complex Docstrings: Identify and address overly complex docstrings that may hinder understanding and collaboration among team members.Improve Code Review Process: Streamline code reviews by flagging complex docstrings early in the development cycle, saving time and effort.Foster Best Practices: Encourage the adoption of clear and concise documentation practices across your projects, promoting consistency and professionalism.Roadmap 🗺️Better reporting so you can find the function easilyArguments for ARI complexity thresholdsSupport linting multiple files at oncePackage on PyPIMake GitHub Actions taskImprove documentationSupport different measures of complexity (adverbs/passive voice...)Parse different kinds of Python docstrings to lint relevant partsNot just Python files, lint markdown tooSupport different formulas of complexitySupport pyproject.toml configurationContributingContributions are welcome! If you encounter any issues or have suggestions for improvement, pleasesubmit an issueorcreate a pull requeston GitHub.LicenseThis project is licensed under the MIT License - see theLICENSEfile for details.AcknowledgementsDocLinter is developed and maintained byEugene Prout.