Saravanan666/pypi-org huggingface dataset:
Package: cl-repos
clone-reposa basic git repo clone script, with special support for pip and/or editable installs, usingreorder_editableThis supports running a preinstall (after cloning) or postinstall step (a shell command) as wellFor examples of aclone-repos.yamlfile this expects at~/.config/clone-repos.yaml, see:clone-reposcomputer-clone-reposhpi-clone-reposI also use this to install plugins/addons for things likerangerortodotxt:ranger-pluginstodotxt-actionsInstallationRequirespython3.9+To install with pip, run:pip install cl-reposUsageUsage: clone-repos [OPTIONS] CONFIG_FILE

  Clones and sets up your repos.

  Can provide a CONFIG_FILE instead of using the default

Options:
  -b, --base-repos DIRECTORY   base repository directory to clone repos into
                               [env var: REPOS; required]
  -P, --parse-config           test parsing the config file instead of running
                               clone
  -B, --break-system-packages  pass the --break-system-packages flag to pip
  --help                       Show this message and exit.The full format for a repo is:"urltorepository":base:path# overwrite base-path for this repodirname:directory_name# directory name to clone intosymlink_to:directory_name# the parent directory to symlink the cloned repo topip:how# 'install', 'editable' or 'editable_system'preinstall:-"shellcommand1"-"shellcommand2"postinstall:"shellcommandhere"pipefail:false# if true, stops multiple preinstall/postinstall if any command failsThepreinstallandpostinstallscripts can either be one command (a string), or multiple (a list)Forpip,editableby default uses the--userflag, if you know what you're doing and want to install in your system lib directory, useeditable_system(Note that this only works in particular python installations. In a lot of cases, pip will still default to installing into your--userdirectory instead). Seereorder_editablefor context.This expects a$REPOSenvironment variable to be set, which is the base directory to clone into, e.g. in your shell config set:exportREPOS="${HOME}/Repos"... or you can provide the--base-reposflag when runningTo clone, runclone-reposorpython3 -m clone_reposTo run this quickly on new machines, I setup an alias in my dotfiles like:alias cr="python3 -m pip install --break-system-packages 'git+https://github.com/seanbreckenridge/clone-repos' && clone-repos -B"Testsgitclone'https://github.com/seanbreckenridge/clone-repos'cd./clone-repos
pipinstall'.[testing]'flake8./clone-repos
mypy./clone-repos
Package: clrfterm
clrftermModule that decorates your consoleSource codeDescriptionclrfterm makes it easy to work with ANSI escape sequences that decorate your console.
ANSI escape sequences are a standard for in-band signaling to control cursor location, color, font styling, and other options on video text terminals and terminal emulators. Certain sequences of bytes, most starting with an ASCII escape character and a bracket character, are embedded into text. The terminal interprets these sequences as commands, rather than text to display verbatim.InstallationTested on CPython 3.7, 3.8, 3.9, 3.10 and PyPy 3.7.10No requirements other than the standard library.pip install clrftermUsageColored Outputfromclrftermimport(Style,Foreground,Background,rprint,reset,)print(Foreground.RED+"Red foreground text")print(Background.WHITE+"White backgrounds text")print(Style.UNDERLINE+"Underlined text")reset()print("Back to normal text")rprint("Auto reset",foreground=Foreground.GREEN)print("Normal text")Available formatting constants are:Foreground: BLACK, RED, GREEN, YELLOW, BLUE, MAGENTA, CYAN, WHITE, RESET
Background: BLACK, RED, GREEN, YELLOW, BLUE, MAGENTA, CYAN, WHITE, RESET
Style: BOLD, UNDERLINE, RESET_ALLreset the function resets the foreground, background. It must be called upon exiting the program.Fluent interfaceIn software engineering, a fluent interface is an object-oriented API whose design relies extensively on method chaining.clrfterm has a Message, Phrase, PhraseStyle classes that implements the Fluent interfacefromclrftermimportForeground,Background,Stylefromclrfterm.messagesimportMessage,Phrase,PhraseStylestyle=(PhraseStyle().set_foreground(Foreground.RED).set_background(Background.CYAN).set_style(Style.BOLD))print(Message().add(Phrase().set_text('hello').set_style(style)).add(Phrase().set_text('world').set_style(style)))WindowsTheWindows Consoledid not support ANSI escape sequences, nor did Microsoft provide any method to enable them.
But In 2016, Microsoft released the Windows 10 version 1511 update which unexpectedly implemented support for ANSI escape sequences, over two decades after the debut of Windows NT.clrfterm can enable ANSI escape sequences in CMD.fromclrftermimport(enable_ansi,Foreground,reset)enable_ansi()print(Foreground.RED+"Hello")reset()ProgressBarA progress bar is a graphical control element used to visualize the progression of an extended computer operation, such as a download, file transfer, or installation.fromtimeimportsleepfromclrfterm.progressimportBarbar=Bar(50)foriinrange(50):bar.next()sleep(0.01)LicenseThis module  is licensed under the terms of the MIT license.
Name by @xterdd
Package: clrmagic
IPython cell magic to use .NET languages (C#, VB.NET, F#) from jupyter notebooks:https://pypi.python.org/pypi/clrmagic/Based on a blog post from Xavier Dupré @sdpython:http://www.xavierdupre.fr/blog/2014-09-20_nojs.htmlSimple wheel installation:pip install clrmagicLaunch Jupyter notebook with IPython kernel:jupyter notebookIn open notebook load clrmagic extension:%reload_ext clrmagicMagic cell with C# code:%%CS mypower System.dll
public static double mypower(double x, double y)
{
  if (y == 0) return 1.0 ;
  return System.Math.Pow(x,y) ;
}
<function clrmagic.create_cs_function.<locals>.<lambda>>Next evaluate in normal IPython cell:mypower(3.0,3.0)
27.0
Package: clrprint
clrprint v2.0Colorful outputWork's on IDLE, command prompt, windows powerShell, and terminalSimply input() with clrinput() and print() with clrprint()Basic colors only. Red, green, yellow, blue, purple, and black/white (default)Flexible to print or take input only on demand (on DEBUG)User input timeout feature (This is supported only on interactive shell)ABOUTThisclrprintis developed to print a colorful output on idle, windows power shell and terminal. It has red, blue, green, yellow, purple and black/white (default) colors.clrinput() includes a timeout feature that returns None if no user input is received within a certain amount of time.It prints with default color if given color is not available.InstallationYou can install clrprint by running the following commandpip install clrprintUsageIt's as simple as using Python's print() and input() functions.Argumentclrto represent color,debugto print only when debug=True are added.clrinput() takestimeoutargument that returns None if no user input is received within a certain amount of time.Note:timeoutfeature is not supported in IDLE. It is neglected by IDLE if it is passedYou can use clrhelp() to print out and see how to use it.Example Code:fromclrprintimport*clrprint('text1','text2',clr='r')# single letter is enough to represent color.clrprint('text1_clr1','text2_clr2','text3_clr3','text4_clr4',clr='r,y,g')# prints 3 colors in same lineclrprint('ERROR:','error information','suggestions 1','suggestion2','suggestion3',clr='r,y,g')# print#Supported on terminal, command prompt and powershellcolord_text=clrit('text1','text2',clr='r,g')# returns ASCII coloured textprint(colord_text)user_input=clrinput('Choose yes/no?',clr='r',timeout=10)or"DEFAULT"# Take user input in 10 sec else Choose any Default valueprint(user_input)The input timeout functionality was inspired byWereCatffrom the projectwerecatfScreenshotsTerminal:IDLE:Powershell:Example Code'''Developed by Abhijith Boppe - linkedin.com/in/abhijith-boppe/'''fromclrprintimport*userclr=clrinput('Enter color: ',clr='green').strip()# prompt color textclrprint('You enterd',userclr,clr=userclr)# print it in that color# If color not available it print's with default color (white/black)# Input timeout and clrit (Works on terminal, cmd and powershell. Not supported on IDLE)continue_=clrinput('Continue FUZZING? :',clr='p',timeout=15)orFalse# if no user input in 15, take Falseifcontinue_:FUZZ()colored_text=clrit('Text1','Text2',clr='r,g')# Returns ASCII colored textclrhelp()# to list out usage and available colors.License & copyrightÂ© Abhijith Boppe, Security analystLinkedInÂ© Dheeraj Kakkar, Software DeveloperLinkedInLicensed under theMIT License
Package: clru
clruCython LRU StructuresFree software: GNU LESSER GENERAL PUBLIC LICENSE v3Documentation:https://clru.readthedocs.io.FeaturesTODOReleaseUpdate the changelog release date onCHANGELOGCommit the changes to master (there is no need to do an PR in this case)$gitcommitCHANGELOG-m'New release'CreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.Change LogAll notable changes to this project will be documented here.Sort subsections like so: Added, Bugfixes, Improvements, Technical tasks.
Group anything an end user shouldn’t care deeply about into technical
tasks, even if they’re technically bugs. Only include as “bugfixes”
bugs with user-visible outcomes.When major components get significant changes worthy of mention, they
can be described in a Major section.More information can be foundHERE:v0.1.2 - 2021-12-27BugfixesAdd missingsixrequirementExclude generated c files from source distributions to make sure they’re
generated correctly upon install.v0.1.1 - 2020-11-18BugfixesFixed release manifest to include necessary include files for buildv0.1.0 - 2020-11-18MajorMoved cLRU code to it’s own repoTechnical TasksAdded Github Action hook to run the tests for every PRAdded the imports on the__init__.pyto import the cython version when
possible
Package: cl-runtime
CompatibL Runtime Community EditionOverviewCompatibL Runtime Community Edition provides an open source Python API
for CompatibL Platform.It includes:Polymorphic, type-safe data model and REST APIAdapters for SQL and NoSQL databases, distributed cache, and cloud storageCommand line interface (CLI)Public and private cloud supportCopyrightEach individual contributor holds copyright over their contributions to the
project. The project versioning is the sole means of recording all such
contributions and copyright details. Specifying corporate affiliation or
work email along with the commit shall have no bearing on copyright ownership
and does not constitute copyright assignment to the employer. Submitting a
contribution to this project constitutes your acceptance of these terms.Because individual contributions are often changes to the existing code,
copyright notices in project files must specify The Project Contributors and
never an individual copyright holder.
Package: clsar
CL-SARContrastive learning of structure-activity relationship stduies (SAR)Online triplet contrastive learning enables efficient cliff awareness in molecular activity predictionAbout$$\mathcal{L}_{aca}=\mathcal{L}_{mae}+{a\ast\mathcal{L}}_{tsm}$$This study proposes the activity-cliff-awareness (ACA) loss for improving molecular activity prediction by deep learning models. The ACA loss enhances both metric learning in the latent space and task learning in the target space during training, making the network aware of the activity-cliff issue. For more details, please refer to the paper titled "Online triplet contrastive learning enables efficient cliff awareness in molecular activity prediction."Comparison of models for molecular activity prediction, one without (left) and one with (right) activity cliff awareness (ACA).The left panel depicts a model without ACA, where the presence of an activity cliff triplet (A, P, N) creates a challenge for the model to learn in the latent space. Due to the similarity between A and N in their chemical structures, the model learns graph representations that result in the distance between A-P being far greater than A-N, leading to poor training and prediction results. However, the right panel shows a model with ACA that optimizes the latent vectors in the latent space, making A closer to P and further away from N. The model with ACA combines metric learning in the latent space with minimizing the error for regression learning, while the model without ACA only focuses on the regression loss and may not effectively handle activity cliffs.PerformanceACA loss vs. MAE loss on external test set and on No. of mined triplets during the training:More details on usage and performance can be foundhere.ACA loss implementationPytorchTensorflow 2.xACA loss usage#Pytorchfromclsar.model.lossimportACALossaca_loss=ACALoss(alpha=0.1,cliff_lower=0.2,cliff_upper=1.0,p=1.,squared=False)loss=aca_loss(labels,predictions,embeddings)loss.backward()#Tensorflowfromclsar.model.loss_tfimportACALossInstallationpipinstallclsarRun ACANetfromclsarimportACANet#Xs_train: list of SMILES string of training set#y_train_pIC50: the pChEMBL labels of training set## init ACANetclf=ACANet(gpuid=0,work_dir='./')## get loss hyperparameters by training setdfp=clf.opt_cliff_by_cv(Xs_train,y_train_pIC50,total_epochs=50,n_repeats=3)dfa=clf.opt_alpha_by_cv(Xs_train,y_train_pIC50,total_epochs=100,n_repeats=3)## cross-validation fitclf.cv_fit(Xs_train,y_train_pIC50,verbose=1)## 5FCV predict and convert pIC50 to ytest_pred_pIC50=clf.cv_predict(Xs_test)CitationWan Xiang Shen*, Chao Cui*, Xiang Cheng Shi, et al.Online triplet contrastive learning enables efficient cliff awareness in molecular activity prediction[J]. ChemRxiv Pub Date : 2023-05-29 , DOI: 10.26434/chemrxiv-2023-5cz7s.
Package: clscidapi
CAIC Classic ID to New ID Converter (clscidapi)In the 2021-2022 season, the CAIC website was redesigned. Along with this change, a number of old references to the "classic" CAIC website's Field Reports were broken. This tool attempts to fix that by implementing a lookup service that provides several helpful ways to pivot from a classic Field Report'sobs_idto a new CAIC Field Report or a working classic Field Report.The lookup service is backed by a simpleJSON filethat was created with the help ofcaicpy. See thescriptthat helped generate this file in myco-avy-researchrepo.Currently the lookup service only supports classic IDs back to 2010. This is a limitation with the data available via the CAIC's new APIs. Further research needs to be done to enumerate older classic IDs. Manually browse to older "classic" Field Reports by adding the classic ID to the end of the URLhttp://classic.avalanche.state.co.us/caic/obs/obs_report.php?obs_id=.Eventually this service will be running as a hosted app somewhere - the location is currently TBD.API UsageThe API has a single endpoint,clscid-lookup.This endpoint only accepts GET requests and accepts arguments in the form of URL parameters. All URL parameters have a descriptive long name and a single letter short name alias.Theq/queryparameter is the only required parameter. The value can either be a single classic ID, or an entire CAIC classic URL that has the ID stored in theobs_idURL parameter.By default, the endpoint takes the given query parameter, tries to find a corresponding new ID, and returns a JSON object containing the Field Report's new CAIC URL in thedatakey.There are several modifications to default behavior that can be controlled via boolean URL parameters:r/redirect: Tells the endpoint to initiate an HTTP redirect to the newly generated URL instead of returning a JSON object.u/url: Tells the endpoint to return a full URL instead of just the new Field Report ID. This is true by defualt and can only be set to false.c/classic: Redirect to or return the CAIC classic Field Report URL instead of the new Field Report URL. This is helpful as older Field Reports do not display fully on the new webpage.
Package: clscurves
classification-curvesA library for computing and plotting bootstrapped metrics (ROC curves,
Precision-Recall curves, etc.) to evaluate the performance of a classification
model.Examplemg=MetricsGenerator(predictions_df,label_column="label",score_column="score",weight_column="weight",score_is_probability=False,reverse_thresh=False,num_bootstrap_samples=20)mg.plot_pr(bootstrapped=True)mg.plot_roc()
Package: clsearch
Descriptionclsearch indexes files of the specified types(and the default types: mp3,aac,ogg,avi,mkv,mp4) and makes it easy to search for these files by name or metadata(currently id3 and xmp).The results are ranked using TF-IDF scores with results split into filetype results(ex. search “.mp3”),
direct results(query terms in name of the file) and tag results(query terms in any of the metadata tags)Tested with python 2.6.5 and python 2.7.5 on linux.InstallationFrom source:

Package is located in dist/clsearch*.tar.gz on github
(NOTE: Hit view raw and download)

#python setup.py install

or

From PyPI:

#pip install clsearchXMP metadata:#pip install python-xmp-toolkit

This in turn needs exempi. On Ubuntu:

#apt-get install libexempi3Usage:$clsearch -i|--index [-d|--dir <directory>] [-t|--types <types>] [-q|--quiet]
$clsearch -s|--search <query>
$clsearch -h|--help

Examples:
    $clsearch -i
    $clsearch -i -d /home/example/Music/Awesome/
    $clsearch -i -t flv,txt
    $clsearch -i -t "flv txt jpg"

    $clsearch -s lazarus
    $clsearch -s "rock and roll"

Note:
    1. For xmp tags to be indexed, python-xmp-toolkit and it's dependency Exempy 2.1.1 have to be installed.
    2. The indexing operation can be performed any number of times. Only new files are indexed each time.

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -i, --index           Index filename and id3 and xmp tags if present.
                        Searches for new files and indexes them.
  -d DIRECTORY, --dir=DIRECTORY
                        The directory to be searched for files. Defaults to
                        '~' if not specified.
  -t TYPES, --types=TYPES
                        Additional file types to index. By default
                        mp3,aac,ogg,avi,mkv,mp4 files are indexed.
  -s QUERY, --search=QUERY
                        Search and return file paths ranked by TF-IDF.
  -q, --quiet           Don't print indexed files to stdout.TestsUnit tests are located in src/clsearch/test.Though each test can be run separately, running$python test_search.pywill run all tests because it inherits from IndexTest
which in turn inherits from BaseTest.TODOBetter exception handlingMultiprocessingFuzzy search…search for “DSC” gives results for “DSC_001.jpg” but not “DSC001.jpg”
Package: clsify
CLSifyClassification ofCandidatus Liberibacter solanacearumfollowing IPPC (International Plant Protection Convention) standardDP 21: Candidatus Liberibacter solanacearum.Quick FactsLicense: MITProgramming Language PythonInput / Output - What it Does!This program takes as the input Sanger sequences from the 16S, 16S-23S, and 50S primers from the IPPC standard DP21.
It then aligns them to the GenBank reference sequencesEU812559andEU834131(as specified in DP21).
Based on the alignments and the document DP21, sequence identity is computed and haplotyping is performed, yielding:sequence identity toEU822559for identifying the speciesC. Liberibacter solanacearum, andhaplotyping of the read based on variation from the reference sequence.Sample names can be inferred from the read names or from a separate mapping TSV file.Quick StartThis is gonna be really quick!InstallationWe recommend usingBioconda.Firstinstall Bioconda.
Then:# conda install -y clsifyAnd – tadaa – you’re ready to go!RunningYou can have one FASTA (or FASTQ) file with all of your reads or one file for each.
If you have a single sequence per FASTA (or FASTQ) file then you can use the file name instead of the sequence name.# clsify -o result.tsv INPUT.fasta
## OR
# clsify [--use-file-name] -o result.tsv INPUT1.fasta INPUT2.fasta [...]
## e.g.,
# clsify [--use-file-name] -o result.tsv INPUT*.fastaHistoryv0.1.1Zapping gremlins in haplotype table.Change formatting of README.v0.1.0Initial release.Everything is new!
Package: clslq
CHANGES2022011.3.3 Bug fixed.2021111.2.9 Add some personal-use command tools.clslq gitandclslq upgradesupported.2021101.2.6 Bugs fixed.1.2.5 Images transfered to base64 format rather than url refered when Email render.1.2.4 Bug fixed.1.2.2 Notion based work report generator supported.2021091.2.1 Bug fix on v1.2.01.2.0 Notion export based on notion-py which is not officially supported by Notion.1.1.7 Tested local pypi server upload202108Initial commit1.1.6 Sphinx doc system intergated, command lauch by setup.py1.1.5 Bug fixed1.1.4 Add wrapper for SQLAlchemyhttps://www.osgeo.cn/sqlalchemy/1.1.3 Add ClslqMd5, only install pip.conf once1.1.2 Fixed a common use logger via pure python library1.1.1 Started with config paser support[json/xml/ini/yaml support]
Package: clsp
CLSPCLSP short forCommandLineSelectionPrompt, is a by fzf inspired, minimalistic, and fast to navigate single choice prompt.fromclspimportselectuser_choice=select([1,2,3],info="Please pick a number:")print("You selected:")print(user_choice)CLSP is designed to be user-friendly, minimal, and very easy to understand.Due to it's search function, it supports large lists and spares the end-user unnecessary frustration.It's especially useful if you'd like the user to choose between files, numbers, country codes, and much more.Documentation# CLSP can be easily imported using:fromclspimportselect# You can then show the actual prompt by calling the select function while passing a list type as the positional argument.user_choice=select(["Choose me!","Dare to choose me!"])# You can navigate using the arrow key up and the arrow key down while pressing enter to confirm your selection.You can provide additional key arguments for further configuration:NameTypeDescriptiontitleSTRInformation shown above the prompt.promptSTRText in front of user input.searchSTRPre-insert text into the input prompt.currentINTIndex as the default selection.rowsINTAmount of choices at a time.cutoffFLOATPrecision of search. (0 < x < 1).amount_resultsINTThe maximum amount of search results to return.highlight_colorSTRHighlight color for search (black, red, green, yellow, blue, magenta, cyan, white).full_exitBOOLExit completely or pass None on KeyBoardInterrupt or ESC.ignore_warningsBOOLIgnore warnings.# The function 'select' will return a Selection object which holds following attributes:print(f"Selected value:{user_choice.value}")# > "Choose me!" or "Dare to choose me!"print(f"Index:{user_choice.index}")# > 0 or 1ifuser_choice.search:print(f"Search-Query:{user_choice.search}")# > For example 'Dare'print(f"Search Result:{user_choice.search_result}")# > For example ["Dare to chose me!"]
Package: clsprop
Works just like @property for classes, except deleters don't work (and are
perhaps impossible).Inspired byhttps://stackoverflow.com/a/39542816/43839Exampleimport clsprop

class Full:
    _name = 'fool'

    @clsprop
    def name(cls):
        return cls._name

    @name.setter
    def name(cls, name):
        cls._name = name

    # Unfortunately, the deleter never gets called
    @name.deleter
    def name(cls, name):
        raise ValueError('Cannot delete name')

assert Full.name == 'fool'

Full.name = 'foll'
assert Full.name == 'foll'

del Full.name  # oh, wellAPI Documentation
Package: cls-python
CLS-PythonTL:DRImplements the cls-framework in python, as presented and verified in the dissertationA type-theoretic framework for software component synthesis.Free software: Apache Software License 2.0Documentation:https://cls-python.github.io/cls-python/readme.html.FeaturesLanguage AgnosticFormally VerifiedHandles Infinite ResultsFlexible JSON Import/ExportCreditsJan Bessai <jan.bessai@tu-dortmund.de>Constantin Chaumet <constantin.chaumet@tu-dortmund.de>Anne Meyer <anne2.meyer@tu-dortmund.de>Daniel Scholtyssek <daniel.scholtyssek@tu-dortmund.de>History0.1.4 (2023-02-17)Add project_urls to setup.py.bump wheel version to mitigate security issue.0.1.3 (2023-02-17)Fix readme link to new gh-page.0.1.2 (2023-02-17)Update CI to include build and deploy of gh-page.New badges for README.0.1.1 (2023-02-17)Update CI.Exclude setup.cfg from trailing whitespace checking to work with bump2version.0.1.0 (2023-02-16)First release on PyPI.