Saravanan666/pypi-org huggingface dataset:
Package: che_guevara_otp
che_guevara_otpThis module generates one-time passcodes that are based either on a
counter or time using a secret key that is assumed known by server and
client.The counter-based passcodes are hash-based one-time passcodes (HOTP) and
are defined inRFC 4226. The
time-based passcodes are time-based one-time passcodes (TOTP) and are
defined inRFC 6238. For HOTP,
the pseudorandom function used is HMAC-SHA-1 and the associated counter
should be incremented after each passcode generation. TOTP is HOTP with
a specified time interval for validity. A common time interval is 30
seconds.setuppipinstallche_guevara_otpTo set up a launcher for theche_guevara_otpcommand, copyChe.svgto/usr/share/icons/hicolor/scalable/apps/and copyche_guevara_otp.desktopto/usr/share/applications/, for
example:sudocp/usr/local/lib/python3.5/dist-packages/che_guevara_otp-2018.5.11.1653-py3.5.egg/che_guevara_otp/data/Che.svg/usr/share/icons/hicolor/scalable/apps/sudocp/usr/local/lib/python3.5/dist-packages/che_guevara_otp-2018.5.11.1653-py3.5.egg/che_guevara_otp/data/che_guevara_otp.desktop/usr/share/applications/moduleHOTP passcodes can be generated in a way like the following:>>>importche_guevara_otp>>>secret="XXXXXXXXXXXXXXXX">>>fornonceinrange(0,3):...print(che_guevara_otp.HOTP(secret=secret,nonce=nonce))...561452686073840123TOTP passcodes can be generated in a way like the following, where the
default time interval is 30 seconds:>>>importche_guevara_otp>>>secret="XXXXXXXXXXXXXXXX">>>print(che_guevara_otp.TOTP(secret=secret))826402che_guevara_otp terminal loop displayThe commandche_guevara_otpdisplays time-based one-time passcodes
at 30 second intervals based on secrets stored in a specified file~/.secrets. The file is unencrypted plaintext so userspace
encryption combined with other security is assumed. The contents of the
secrets file should be of the following form:OmegaBay:         XXXXXXXXXXXXXXXXXXXXXXXX
Missile Emporium: YYYYYYYYYYYYYYYYYYYYYYYYfutureUnder consideration are functions to install the launcher and icon
infrastructure based on Python version information.
Package: chehro
ChehroChehro is a face detection library for python with amediapipebackend. It is faster and more accurate comparing to the oldHAARCASCADE Classifierway of face detection in python/OpenCV.Installation guideFrom sourceFirst of all, you have to clone this repository to your local machine:git clone https://github.com/prp-e/chehroThen, you move to the source directory and run:pip3 install -e .NOTE: In some systems(specially Linux based ones)pip3might be justpip, since most of moderl Linux distributions just left Python2 behind.From PyPiIn case you want this package to be installed usingpipthen just run this command:pip3 install chehroNOTE: In some systems(specially Linux based ones)pip3might be justpip, since most of moderl Linux distributions just left Python2 behind.How to useFirst, create a new python environment or project. Then you easily can do this:importcv2fromchehroimportChehroimage=cv2.imread('faces.jpg')detector=Chehro(image)result,bboxes=detector.detect()# In case you might need no bounding box drawn around faces, just run it like thisresult,bboxes=detector.detect(draw=False)NOTE:detect()method returns a tuple made of an image (or the result) and a list of bounding boxed. All bounding boxes are normalized and you don't need to normalize it manually.
Package: cheinsteinpy
cheinstein.pyA Python library to get information from Chegg.Note: We are not affiliated with chegg.com in any way.Chegg is a great resource for many students around the world. Though since it is a paid resource, it is not accessible to everyone. With cheinstein.py, it parses the information from chegg.com, and makes it much easier to work with.Currently SupportedSolutionsQuestionsInstallationInstall cheinstein.py using pip:$pipinstallcheinsteinpy
Package: chela
ChelaChela is a Python library to handle chemical formula.InstallationUse the package managerpipto install ChelapipinstallchelaUsageFrom bash:# Check correctness of chemical formulapython3-mchela-cCHEMICAL_FORMULA# Transform a csv file with a column containing the formulas#into a dataframe with atomic symbols as columns and save it as a csv filepython3-mchela-dFILE.csvNEW_FILE.csvFrom python script:importchelaascl# check chemical formula with a functioncl.check_formula(CHEMICAL_FORMULA)importpandasaspd# check chemical formula with a pandas extensionspd.DataFrame().chela.check_formula(CHEMICAL_FORMULA)# Transform a pandas Dataframe with a column containing the formulas#into a dataframe with atomic symbols as columnsdataset=pd.read_csv(FILE.csv)dataframe=cl.build_dataframe(dataset)dataframe=pd.DataFrame().chela.build_dataframe(dataset)# Drop formulas contaning elements with atomic number greater than Zdataframe=dataframe.chela.drop_heavy_elements(Z)LicenseMIT
Package: c-helpers
C-HelpersOverviewJust like the old saying"girls just wanna have fun", so do software
researchers.Many of us sometimes need to just get the values of some basic C native types. We can look for them in the headers or
just compile a simple C program to print them - which can be quite exhausting each time.That's wherec-helperscomes into place - Simply use thec-constandc-structdirectly from your terminal!For example:$c-struct'struct dirent'sizeof(structdirent):1048(0x418)$c-struct'struct dirent'd_ino
sizeof(structdirent):1048(0x418)offsetof(structdirent,d_ino):0(0x00)sizeof(structdirent::d_ino):8(0x08)$c-constEAGAIN35(0x23)Installationpython3-mpipinstallc-helpers
Package: chemax
ExplaintionsMol.Wt and Exact MassMol.WtThe average mass taking into account the abundance of isotopes in nature.Exact MassThe mass of the most stable isotope.Data SourceInternational Atomic Energy Agency (IAEA)International Union of Pure and Applied Chemistry (IUPAC)UsageInstallpipinstallchemaxImportfromchemaximportMoleculeCreate Molecule ObjectfromchemaximportMoleculemolecule=Molecule.simple_generate('H2O')print(molecule.mol_wt)print(molecule.exact_mass)print(molecule.electric_charge)Accepted FormulaSimple Formula:H2OStructural Formula:CH3CH2OH,CH3(CH2)2OHHydrogen Isotopes:D2O,T2O,CDCl3(Chloroform-d)Ionic Formula:{COO}-,{CH2(COO)2}2-Some group abbreviations:{PhCOO}-,EtOH
Package: chembee
serial-sphinxWhy?Rapid prototyping requires boilerplate codeWhat?serial-sphinxdistills field knowledge about using sphinx for uploading your documentation toreadthedocs.org.
Follow theblogfor more useful info.Command snippetsrm -r docs 
cd docs
sphinx-quickstartCopy the config file from the repository. Then, in thedocsfoldersphinx-apidoc -o source/ ../<package_name>
make htmlMake sure you follow the appropriate file structure outlined in the repository.Push it to you repo with the configured webhook, and you are done.Proper testingPlease make sure to setup some CI/CD pipeline. If you are avoiding commercial setups, then this is a problem.For code quality, make sure you have great coverage by usingpytest-cov. Check out the providedsetup.cfgfile.Woodpecker CIOpen-source CI. But not like Github-actions. Check the.woodpecker.ymlfor a tested standard workflow.Code-CoverageThe passing goal for the code-coverage should be edited in thesetup.cfgunder the keyaddopts
Package: chembl_business_model
chembl_business_model======.. image:: https://img.shields.io/pypi/v/chembl_business_model.svg:target: https://pypi.python.org/pypi/chembl_business_model/:alt: Latest Version.. image:: https://img.shields.io/pypi/dm/chembl_business_model.svg:target: https://pypi.python.org/pypi/chembl_business_model/:alt: Downloads.. image:: https://img.shields.io/pypi/pyversions/chembl_business_model.svg:target: https://pypi.python.org/pypi/chembl_business_model/:alt: Supported Python versions.. image:: https://img.shields.io/pypi/status/chembl_business_model.svg:target: https://pypi.python.org/pypi/chembl_business_model/:alt: Development Status.. image:: https://img.shields.io/pypi/l/chembl_business_model.svg:target: https://pypi.python.org/pypi/chembl_business_model/:alt: License.. image:: https://badge.waffle.io/chembl/chembl_business_model.png?label=ready&title=Ready:target: https://waffle.io/chembl/chembl_business_model:alt: 'Stories in Ready'This is chembl_business_model package developed at Chembl group, EMBL-EBI, Cambridge, UK.This package provides a django ORM model decorated with additional information about various aspects like searching and api exposing.It also adds some application specific logic like what to do when the compound is saved.The package uses 'chembl_core_model' as its base and declares new model by proxy inheritance.This model is required when you want to create/update (write/modify) objects to database through ORM.Core model intended only for read, with methods from this module you can also write.This module defines also some application specific models (in meta.py file) which can be kept in separate db schema.
Package: chembl-client
Documentation and repository:https://github.com/chembl/chembl_client.This is the only official Python client library developed and supported by ChEMBL (https://www.ebi.ac.uk/chembl/) group.The library helps accessing ChEMBL data and cheminformatics tools from Python.
You don’t need to know how to write SQL.
You don’t need to know how to interact with REST APIs.
You don’t need to compile or install any cheminformatics framework.
Results are cached.
Package: chembl_clippy
### What is Clippy?
Clippy is a simple desktop application that renders chemical structures using different formats as input.
The key thing is that the app reads the input directly from your clipboard (hence the name clippy) rather than a file.
Once you have a rendered structure, you can export it in different formats (via the clipboard again).### Why should one prefer it to other free viewers?
Apart from being Open Source and fully configurable, Clippy has some features currently missing from other viewer, such as the ChEMBL ID, name and InChIKey look-ups, as well as image and name conversions.
Furthermore, the clipboard interface makes Clippy really convenient when one just wants to quickly check a structure.Here’s a list of input formats that are read from clipboard and rendered in Clippy:
* ChEMBL IDs (via ChEMBL look-up)
* SMILES (via RDKit)
* InChI Strings (via RDKit)
* InChI Keys (via ChEMBL look-up)
* Nomenclature (via OPSIN)
* Images (via OSRA)### Technical notes and dependencies
The application was written in Python using wxPython and is natively cross-platform. It has been tested on Mac Mountain Lion, Windows XP and Ubuntu 12.04 machines.
Clippy uses web services calls mainly to mnowotka’s [Beaker server](https://github.com/mnowotka/chembl_beaker).
Therefore, you’ll need a running instance of Beaker in your network.
Clipper comes also packaged for MacOS. As a result, the packaged version doesn’t have any other dependencies whatsoever (apart from a network connection and an Apple machine).
Package: chembl_compatibility
chembl_compatibility======This is chembl_compatibility package developed at Chembl group, EMBL-EBI, Cambridge, UK.This package provides a compatibility layer between migration and core models and database created by migration.In simple words if you want to run your own webservices on a database created from sql dumps provided by ChEMBL orwith structure the same as the one in dumps you need to include this application is your settings file if you don'twant to manually modify webservices code.
Package: chembl_core_db
chembl_core_db======.. image:: https://img.shields.io/pypi/v/chembl_core_db.svg:target: https://pypi.python.org/pypi/chembl_core_db/:alt: Latest Version.. image:: https://img.shields.io/pypi/dm/chembl_core_db.svg:target: https://pypi.python.org/pypi/chembl_core_db/:alt: Downloads.. image:: https://img.shields.io/pypi/pyversions/chembl_core_db.svg:target: https://pypi.python.org/pypi/chembl_core_db/:alt: Supported Python versions.. image:: https://img.shields.io/pypi/status/chembl_core_db.svg:target: https://pypi.python.org/pypi/chembl_core_db/:alt: Development Status.. image:: https://img.shields.io/pypi/l/chembl_core_db.svg:target: https://pypi.python.org/pypi/chembl_core_db/:alt: License.. image:: https://badge.waffle.io/chembl/chembl_core_db.png?label=ready&title=Ready:target: https://waffle.io/chembl/chembl_core_db:alt: 'Stories in Ready'This is chembl_core_db package developed at Chembl group, EMBL-EBI, Cambridge, UK.It's a core library providing custom fields intended to use with ChEMBL database, such as BlobField (for storing binary data - not supported by django until 1.6), or ChemblIntegerField, which create database constraint for default value (not supported by standard django IntegerField).Using these fields will create a database that is maximally similar to the original oracle CheMBL database, makes interacting with existing database easier and provides database agnostic abstraction layer for creating and using ChEMBL db and it's data on all popular database engines.It also provides custom query managers to perform strictly chemical operations, such as similarity and substructure search in database independent manner.(No miracles here - it still requires certain db cartridge being installed in target database).For Oracle, the package provides custom backend, which solves some bugs and arbitrary design decisions made in standard django Oracle backend.It still requires cx_oracle as db driver and original Oracle backend as it's base.Most of the custom fields defined by the package can be well used with standard Oracle backend but it's still recommended to use the new one.Additionally the package contains some utilities, such as validators for some popular chemical formats (smiles, uniprot, refeq etc.), used by dependent packages.
Package: chembl_core_model
chembl_core_model======.. image:: https://img.shields.io/pypi/v/chembl_core_model.svg:target: https://pypi.python.org/pypi/chembl_core_model/:alt: Latest Version.. image:: https://img.shields.io/pypi/dm/chembl_core_model.svg:target: https://pypi.python.org/pypi/chembl_core_model/:alt: Downloads.. image:: https://img.shields.io/pypi/pyversions/chembl_core_model.svg:target: https://pypi.python.org/pypi/chembl_core_model/:alt: Supported Python versions.. image:: https://img.shields.io/pypi/status/chembl_core_model.svg:target: https://pypi.python.org/pypi/chembl_core_model/:alt: Development Status.. image:: https://img.shields.io/pypi/l/chembl_core_model.svg:target: https://pypi.python.org/pypi/chembl_core_model/:alt: License.. image:: https://badge.waffle.io/chembl/chembl_core_model.png?label=ready&title=Ready:target: https://waffle.io/chembl/chembl_core_model:alt: 'Stories in Ready'This is chembl_core_model package developed at Chembl group, EMBL-EBI, Cambridge, UK.This package contains Django ORM model for accessing ChEMBL db instance.Is uses fields defined in django_db_core package.This model describes all tables in ChEMBL, including COMPOUND_MOLS and COMPOUND_IMAGES and therefore is not suitable for migrations (use chembl_migration_model instead).Using the model you can create database structure that is extremely similar to the original ChEMBL for all major db backends.
Package: chembl_extras
chembl_extras======.. image:: https://img.shields.io/pypi/v/chembl_extras.svg:target: https://pypi.python.org/pypi/chembl_extras/:alt: Latest Version.. image:: https://img.shields.io/pypi/dm/chembl_extras.svg:target: https://pypi.python.org/pypi/chembl_extras/:alt: Downloads.. image:: https://img.shields.io/pypi/pyversions/chembl_extras.svg:target: https://pypi.python.org/pypi/chembl_extras/:alt: Supported Python versions.. image:: https://img.shields.io/pypi/status/chembl_extras.svg:target: https://pypi.python.org/pypi/chembl_extras/:alt: Development Status.. image:: https://img.shields.io/pypi/l/chembl_extras.svg:target: https://pypi.python.org/pypi/chembl_extras/:alt: License.. image:: https://badge.waffle.io/chembl/chembl_extras.png?label=ready&title=Ready:target: https://waffle.io/chembl/chembl_extras:alt: 'Stories in Ready'This is chembl_extras package developed at Chembl group, EMBL-EBI, Cambridge, UK.This package provides two django custom migration commands:* generate_ora2pg_conf - generates configuration file for ora2pg (http://ora2pg.darold.net/) script based on given model.* generate_backbone_models - not implemented yetAdditionally, the package defines MoleculeFinder class which uses biopython suffix trie to index Inchies and search them by fragments.It also provides Ontology (and derivatives) class to model different ontologies for future use.
Package: chembl_migrate
chembl_migrate======.. image:: https://img.shields.io/pypi/v/chembl_migrate.svg:target: https://pypi.python.org/pypi/chembl_migrate/:alt: Latest Version.. image:: https://img.shields.io/pypi/dm/chembl_migrate.svg:target: https://pypi.python.org/pypi/chembl_migrate/:alt: Downloads.. image:: https://img.shields.io/pypi/pyversions/chembl_migrate.svg:target: https://pypi.python.org/pypi/chembl_migrate/:alt: Supported Python versions.. image:: https://img.shields.io/pypi/status/chembl_migrate.svg:target: https://pypi.python.org/pypi/chembl_migrate/:alt: Development Status.. image:: https://img.shields.io/pypi/l/chembl_migrate.svg:target: https://pypi.python.org/pypi/chembl_migrate/:alt: License.. image:: https://badge.waffle.io/chembl/chembl_migrate.png?label=ready&title=Ready:target: https://waffle.io/chembl/chembl_migrate:alt: 'Stories in Ready'This is chembl_migrate package developed at Chembl group, EMBL-EBI, Cambridge, UK.This package provides custom Django management command 'migrate'.For usage type `python manage.py migrate help`.'migrate' copies data from one database to another.Both databases must be described by the same Django model.By default django model being migrated is 'chembl_migration_model' but this can be changed in settings to any other django model.If target database doesn't have tables required by the model they will be created, despite status of 'managed' meta flag.All data is copied in order that should avoid any integration errors.Migration process is done in chunks of 1000 records but this number can be configured.Each chunk is copied within a transaction.When interrupted, the migration process can be rerun and it will detect which data has already been migrated and start migration from the point where it finished.
Package: chembl_migration_model
chembl_migration_model======.. image:: https://img.shields.io/pypi/v/chembl_migration_model.svg:target: https://pypi.python.org/pypi/chembl_migration_model/:alt: Latest Version.. image:: https://img.shields.io/pypi/dm/chembl_migration_model.svg:target: https://pypi.python.org/pypi/chembl_migration_model/:alt: Downloads.. image:: https://img.shields.io/pypi/pyversions/chembl_migration_model.svg:target: https://pypi.python.org/pypi/chembl_migration_model/:alt: Supported Python versions.. image:: https://img.shields.io/pypi/status/chembl_migration_model.svg:target: https://pypi.python.org/pypi/chembl_migration_model/:alt: Development Status.. image:: https://img.shields.io/pypi/l/chembl_migration_model.svg:target: https://pypi.python.org/pypi/chembl_migration_model/:alt: License.. image:: https://badge.waffle.io/chembl/chembl_migration_model.png?label=ready&title=Ready:target: https://waffle.io/chembl/chembl_migration_model:alt: 'Stories in Ready'This is chembl_migration_model package developed at Chembl group, EMBL-EBI, Cambridge, UK.This package contains Django ORM model suitable for data exports and migrations.It excludes some tables present in chembl_core_model (such as COMPOUND_MOLS and COMPOUND_IMAGES) as well as some columns in remaining tables.The model is generated dynamically from chembl_core_model and this is why models.py file is empty.Whole logic sits in __init__.py.All classes are unmanaged by default so you can't use them to syncdb.To create tables from the model you have to run migrate command from chembl_migrate.
Package: chembl-structure-pipeline
ChEMBL Structure PipelineChEMBL protocols used to standardise and salt strip molecules. First used in ChEMBL 26.Check thewikiand paper[1]for a detailed description of the different processes.InstallationFrom source:git clone https://github.com/chembl/ChEMBL_Structure_Pipeline.git
pip install ./ChEMBL_Structure_Pipelinewith pip:pipinstallchembl_structure_pipelinewith conda:condainstall-cconda-forgechembl_structure_pipelineUsageStandardise a compound(info)fromchembl_structure_pipelineimportstandardizero_molblock="""Mrv1810 07121910172D4  3  0  0  0  0            999 V2000-2.5038    0.4060    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0-2.5038    1.2310    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0-3.2182   -0.0065    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0-1.7893   -0.0065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  01  2  1  0  0  0  01  3  1  0  0  0  01  4  1  4  0  0  0M  CHG  2   2  -1   3   1M  END"""std_molblock=standardizer.standardize_molblock(o_molblock)Get the parent compound(info)fromchembl_structure_pipelineimportstandardizero_molblock="""Mrv1810 07121910262D3  1  0  0  0  0            999 V2000-5.2331    1.1053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0-4.5186    1.5178    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0-2.8647    1.5789    0.0000 Cl  0  5  0  0  0  0  0  0  0  0  0  01  2  1  0  0  0  0M  CHG  2   2   1   3  -1M  END"""parent_molblock,_=standardizer.get_parent_molblock(o_molblock)Check a compound(info)The checker assesses the quality of a structure. It highlights specific features or issues in the structure that may need to be revised. Together with the description of the issue, the checker process returns a penalty score (between 0-9) which reflects the seriousness of the issue (the higher the score, the more critical is the issue)fromchembl_structure_pipelineimportcheckero_molblock="""Mrv1810 02151908462D4  3  0  0  0  0            999 V20002.2321    4.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  03.0023    4.7153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  01.4117    4.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  01.9568    3.6420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  01  2  1  1  0  0  01  3  1  0  0  0  01  4  1  0  0  0  0M  END"""issues=checker.check_molblock(o_molblock)References[1]Bento, A.P., Hersey, A., Félix, E. et al. An open source chemical structure curation pipeline using RDKit. J Cheminform 12, 51 (2020).https://doi.org/10.1186/s13321-020-00456-1
Package: chembl-webresource-client
Documentation and repository:https://github.com/chembl/chembl_webresource_client.
This is the only official Python client library developed and supported by ChEMBL (https://www.ebi.ac.uk/chembl/) group.The library helps accessing ChEMBL data and cheminformatics tools from Python.
You don’t need to know how to write SQL.
You don’t need to know how to interact with REST APIs.
You don’t need to compile or install any cheminformatics framework.
Results are cached.
Package: chembl_webservices
chembl_webservices version 2.x======[live documentation](https://www.ebi.ac.uk/chembl/api/data/docs)[API specification](https://www.ebi.ac.uk/chembl/ws)[Introductory blog post](http://chembl.blogspot.co.uk/2015/02/using-new-chembl-web-services.html)[![Latest Version](https://img.shields.io/pypi/v/chembl_webservices.svg)](https://pypi.python.org/pypi/chembl_webservices/)[![Downloads](https://img.shields.io/pypi/dm/chembl_webservices.svg)](https://pypi.python.org/pypi/chembl_webservices/)[![Supported Python versions](https://img.shields.io/pypi/pyversions/chembl_webservices.svg)](https://pypi.python.org/pypi/chembl_webservices/)[![Development Status](https://img.shields.io/pypi/status/chembl_webservices.svg)](https://pypi.python.org/pypi/chembl_webservices/)[![License](https://img.shields.io/pypi/l/chembl_webservices.svg)](https://pypi.python.org/pypi/chembl_webservices/)[![Stories in Ready](https://badge.waffle.io/chembl/chembl_webservices_2.png?label=ready&title=Ready)](https://waffle.io/chembl/chembl_webservices_2)