Saravanan666/pypi-org huggingface dataset:
Package: pathing
Usageimportpathingroot=({0:{'some':['data','right'],'here':True},'is':{False:'too','deep':{'for':{'this':{'depth':'level'}},'but':{'here':'it is just right'}}}})forkeys,valueinpathing.derive(root,max=4):print(keys,'->',value)Installingpython3 -m pip install pathing
Package: pathins
Path InspectorPath Inspector is a quadratic font curve path inspection application.  The Python package installs thepathinscommand line executable and requires a Python v3.6+ interpreter.The following sub-commands are available:contours: path contour number reportcoordinates: path coordinates reportdirection: outermost contour path direction reportpath: curve path reportsegments: curve segment report, with line distances and quadratic curve arc lengthsInstallationpathins requires a Python 3.6+ interpreter.Installation in a Python3 virtual environment is recommended.Use any of the following installation approaches:pip install from PyPI$ pip3 install pathinspip install from source$ git clone https://github.com/source-foundry/path-inspector.git
$ cd path-inspector
$ pip3 install -r requirements.txt .Developer install from sourceThe following approach installs the project and associated optional developer dependencies, so that source changes are available without the need for re-installation.$ git clone https://github.com/source-foundry/path-inspector.git
$ cd path-inspector
$ pip3 install --ignore-installed -r requirements.txt -e ".[dev]"Usage$ pathins [SUB-COMMAND] [OPTIONS] [FILEPATH] [OPTIONAL GLYPH NAME]Seepathins --helpfor additional details.IssuesPlease report issues on theproject issue tracker.ContributingContributions are warmly welcomed.  A development dependency environment can be installed in editable mode with the developer installation documentation above.Please use the standard Github pull request approach to propose source changes.Source file lintingPython source files are linted withflake8.  See the Makefiletest-linttarget for details.TestingThe project runs continuous integration testing on the GitHub Actions service with thepytesttoolchain.  Test modules are located in thetestsdirectory of the repository.Local testing by Python interpreter version can be performed with the following command executed from the root of the repository:$ tox -e [PYTHON INTERPRETER VERSION]Please see thetoxdocumentation for additional details.Test coverageUnit test coverage is executed with thecoveragetool.  See the Makefiletest-coveragetarget for details.AcknowledgmentsThe Path Inspector project is built with the fantasticfontToolsandskia-pathopsfree software libraries.LicenseCopyright 2020 Source Foundry Authors and ContributorsLicensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Package: pathlab
Pathlab provides an object-oriented path interface to archives, images, remote
filesystems, etc. It is built uponpathliband includes built-in support for:tararchivesziparchivesisodisc images (inc Rock Ridge; exc Joliet and UDF)JFrog Artifactory (viarequests)You can also define your ownPathsubclass with its own accessor.InstallationRequires Python 3.6+. Use pip:pip install --user pathlabUsageThese usage examples are adapted from thepathlibdocumentation.Getting a path type:>>> from pathlab import TarAccessor
>>> TarPath = TarAccessor('project.tgz').TarPathListing subdirectories:>>> root = TarPath('/')
>>> [x for x in root.iterdir() if x.is_dir()]
[TarAccessor('project.tgz').TarPath('/docs')
 TarAccessor('project.tgz').TarPath('/etc'),
 TarAccessor('project.tgz').TarPath('/project')]Listing Python source files in this directory tree:>>> list(root.glob('**/*.py'))
[TarAccessor('project.tgz').TarPath('/setup.py'),
 TarAccessor('project.tgz').TarPath('/docs/conf.py'),
 TarAccessor('project.tgz').TarPath('/project/__init__.py')]Navigating inside a directory tree:>>> p = TarPath('/etc')
>>> q = p / 'init.d' / 'reboot'
>>> q
TarAccessor('project.tgz').TarPath('/etc/init.d/reboot')
>>> q.resolve()
TarAccessor('project.tgz').TarPath('/etc/rc.d/init.d/halt')Querying path properties:>>> q.exists()
True
>>> q.is_dir()
FalseOpening a file:>>> with q.open() as f: f.readline()
...
'#!/bin/bash\n'
Package: pathlib2
Theold pathlibmodule on bitbucket is no longer maintained.
The goal of pathlib2 is to provide a backport ofstandard pathlibmodule which tracks the standard library module,
so all the newest features of the standard pathlib can be
used also on older Python versions.DownloadStandalone releases are available on PyPI:http://pypi.python.org/pypi/pathlib2/DevelopmentThe main development takes place in the Python standard library: see
thePython developer’s guide.
In particular, new features should be submitted to thePython bug tracker.Issues that occur in this backport, but that do not occur not in the
standard Python pathlib module can be submitted on
thepathlib2 bug tracker.DocumentationRefer to thestandard pathlibdocumentation.Known IssuesFor historic reasons, pathlib2 still uses bytes to represent file paths internally.
Unfortunately, on Windows with Python 2.7, the file system encoder (mcbs)
has only poor support for non-ascii characters,
and can silently replace non-ascii characters without warning.
For example,u'тест'.encode(sys.getfilesystemencoding())results in????which is obviously completely useless.Therefore, on Windows with Python 2.7, until this problem is fixed upstream,
unfortunately you cannot rely on pathlib2 to support the full unicode range for filenames.
Seeissue #56for more details.
Package: pathlib-abc
Base classes forpathlib.Path-ish objects. Requires Python 3.8+.This package is a preview ofpathlibfunctionality planned for a future
release of Python; specifically, it provides two ABCs that can be used to
implement path classes for non-local filesystems, such as archive files and
storage servers:PurePathBaseAbstract base class for paths that do not perform I/O.PathBaseAbstract base class for paths that perform I/O.These base classes are under active development. Once the base classes reach
maturity, they will be made part of the Python standard library, and this
package will continue to provide a backport for older Python releases.ContributingChanges topathlib_abc.pyandtest_pathlib_abc.pymust be made in the
upstream CPython project, and undergo their usual CLA + code review process.
Once a change lands in CPython, it can be back-ported here.Other changes (such as CI improvements) can be made as pull requests to this
project.
Package: pathliberty
pathlibertyExtended object-oriented filesystem paths library.pathlibertyis the Python package that allows you to subclass a pathlib.PosixPath in a proper way.
To define your own custom path subclass, declare subclasses AbstractPathAccessor and AbstractPath.FeaturesSupport SSH remote path viaParamiko:frompathlibertyimportSSHPathfrompathliberty.sshimportSSHSessionfromgetpassimportgetuserhost='localhost'ssh_session=SSHSession(host,password=******,)ssh_path=SSHPath(f'/home/{getuser()}',ssh=ssh_session)assertssh_path.parent==SSHPath('/home',host=host)Installationpipinstallpathliberty
Package: pathlib-extensions
Pathlib Extensions – Backported and Experimental Filesystem Path Features for PythonThepathlibmodule was added to the standard library in Python 3.4, but
many new features have been added to the module since then.This means users of older Python versions who are unable to upgrade will not be
able to take advantage of new features added to thepathlibmodule, such aspathlib.PurePath.with_stem().Thepathlib_extensionsmodule contains backports of these changes.
Experimental filesystem path features that are not found in thepathlibmodule are also included inpathlib_extensions.
Package: pathlib-mate
Welcome topathlib_mateDocumentationpathlibis an awesome library handling path in different OS. And it’s been added into standard library since Python3.4.pathlib_mategives extensive methods and attributes, makespathlibmore powerful and user-friendly.Features:Convenient Attribute Accessor:>>>p=Path("/Users/username/test.py").>>>p.abspath/Users/username/test.py>>>p.basenametest.py>>>p.fnametest>>>p.ext.py>>>p.dirnameusername>>>p.dirpath/Users/username>>>p.size1500>>>p.size_in_text1.46KB>>>p.create_datetimedatetime(2018,1,15,8,30,15)>>>p.md5415f12f07a7e01486cc82856621e05bf>>>p.sha256d51512cb0ac71484c01c475409a73225d0149165024d7aac6d8e655eedf2c025>>>p.sha5127882fc375840cafa364eaf29dc424645b72fcdbe61fc3326c5afd98e70f696e4f390e0e3f159eac2cb60cedc0992ef7b5f8744a4481911e914a7c5b979e6de68Powerful Path Search:>>>p=Path("/Users/username/Documents")>>>forpathinp.select_file(recursive=True)...>>>forpathinp.select_file(recursive=False)...>>>forpathinp.select_dir(recursive=True)...>>>forimage_fileinp.select_by_ext([".jpg",".png"])...>>>forbig_fileinp.select_by_size(min_size=1000000)...>>>forvideo_fileinp.select_video():...# You can customize the filter anyway you want>>>defpy_filter(p):return".py"==p.ext.lower()>>>forpy_fileinp.select_file(py_filter):...Eazy to use File / Dir Operation:>>>p=Path("/Users/username/Documents/Readme.txt")# mutate>>>p.change(new_ext=".md")/Users/username/Documents/Readme.md>>>p.change(new_fname="Tutorial")/Users/username/Documents/Tutorial.txt>>>p.change(new_basename="README.rst")/Users/username/Documents/README.rst>>>p.change(new_dirname="Downloads")/Users/username/Downloads/Readme.txt>>>p.change(new_dirpath="/User/username/Downloads)/Users/username/Downloads/Readme.txt>>>p.change(new_abspath="/Users/username/Downloads/Readme.txt")/Users/username/Downloads/Readme.txt# copy>>>p.moveto(new_ext=".md",makedirs=True)# cut>>>p.copyto(new_ext=".md",makedirs=True)# delete>>>p.remove()# delete file or directory recursively, ignore if not exists>>>p.remove_if_exists()# make dir and required parents recursively, if not exists>>>p.mkdir_if_not_exists()Atomic Write Support:If anything wrong happens during writing big chunk of data into a file. It may leave you an incomplete file. Atomic write can guarantee either 100% done or nothing happens.Thanks forboltonsproject. Nowpathlib_matesupports atomic write API:>>>p=Path("test.dat")>>>s="Hello World">>>b=s.encode("utf-8)>>>p.atomic_write_bytes(b,overwrite=True)>>>p.atomic_write_text(s,overwrite=True)>>>withp.atomic_open("wb")asf:...f.write(b)# write large binary dataPowerful Production Tools:>>>p=Path("/Users/username/Documents/Github/pathlib_mate-project")>>>p.print_big_dir_and_big_file()...>>>p.file_stat(){"file":122,"dir":41,"size":619682}# file statistics, include sub folder>>>p.file_stat_for_all()# make an zip archive for the directory, auto naming>>>p.make_zip_archive()# make an zip archive for the directory, auto naming>>>p.backup()Installpathlib_mateis released on PyPI, so all you need is:$pipinstallpathlib_mateTo upgrade to latest version:$pipinstall--upgradepathlib_mate
Package: pathlit
PathLit Python SDKPathLit provides developers and quants with APIs that take the complexity out of writing code for financial portfolio calculations.We provide a scalable and secure API-first engine with a library of investment methodologies that can calculate weights, run simulations, auto-backtest and more.You bring product identifiers, we do the rest.This python package acts as a simple interface with the PathLit APIreferenceUsing the packagepre-requisite:A PathLit account is required to interact with the API with a unique key to the account. It can be done at theaccount creation page.installationpip3 install pathlit
Package: pathmatch
Python implementation ofgit’swildmatchandPOSIX.1-2008fnmatch.The aim of this package is to provide a file matching module complying with the POSIX standard and
allow compatibility withgit.Examplefrompathmatchimportwildmatch# Pattern matching auto-generated test files (extension .pyc, .pyo or .pyd inside tests/)pattern=u'tests/**/*.py[cod]'# Match single files:wildmatch.match(pattern,u'tests/auto.pyc')# Truewildmatch.match(pattern,u'auto.pyc')# False# Filter a collection:files=[u'tests/deep/auto.pyd',u'tests/module.py',u'package/auto.pyc',u'tests/auto.pyo']list(wildmatch.filter(pattern,files))# [u'tests/deep/auto.pyd', u'tests/auto.pyo']# Compile a patterncompiled=wildmatch.WildmatchPattern(pattern)compiled.match(u'tests/')# FalseFeatureswildmatch supportCurrently, the followingwildmatchfeatures are supported:Wildstar**operator and associated semantics (/requires a literal match)Literal matchingQuestion mark?(any character) and asterisk*(any string) operatorsBracket expressions[abc](character alternatives)Bracket expression features:Negation (supports both^and!meta-characters)Range expressionsa-zCollation Symbol[.ch.]Equivalence classes syntax[=e=], but fallback to collation symbol semanticsSupports thepath_nameflag to exclude/(which requires a literal match)Seetest_wildmatch.pyfor more details.Limitations:case_fold(case insensitive) option is not supportedperiod(require literal match for leading period) option is not supportedNegated bracket expression with multi-character collating elements are not supportedCharacter classes[:alpha:]for bracket expressions are not supportedContributions are welcomedfnmatch supportThe dedicatedfnmatchmodule is not yet configured (this should just be a subset of wildmatch).ContributingTestsYou can execute the tests with the following command:python-munittestdiscover-s.-ptest*.pyReferences:fnmatch, see  alsopattern matchingwildmatch C implementation for gitwildmatch C implementation (alternative)wildmatch Javascript implementationLicenseMIT License, Copyright (c) 2016 Charles Samborski
Package: pathmod
pathmodIntroductionpathmodis a CLI program which allows you to easily modify the PATH using the terminal on Windows.pathmodcan persistently modify the PATH, and provides an easy way to refresh the path in the current session.RequirementsYou need to have Python 3.6 or higher installed. This will allow you to installpathmodwith Python's package manager,pip.How to installTo installpathmodwithpip:pipinstallpathmodAfter this command completes, thepathmodexecutable should be available on the PATH.Quick startUser vs system PATHsBy default,pathmodmodifies the user PATH, which does not require elevated permissions. You can use the-s/--systemflag to modify the system PATH instead.Addaddis used to add an item to the PATH.You can use relative paths, and paths using tilde (~):# Add the current working directory to the PATH.>>pathmodadd.# Add 'C:\Users\%USERNAME%\scripts' to the PATH.>>pathmodadd~/scriptsAbsolute file paths are also valid:>>pathmodadd"C:\Program Files\my program"Prependprependis used to prepend an item to the PATH. THis may be useful if you require items in your newly added location to be prioritised over items of the same name in other locations.>>pathmodprepend.Removepathmod removeis used to remove an item from the PATH.>>pathmodremove.As withaddandprepend, this defaults to modifying the user PATH. To remove an item from the system PATH, ensure you use the-s/--systemflag:>>pathmodremove.-sShowshowis used to show the items currently on the user and system PATHS. This prints the persistent values - the values which will be present in a new session - rather than the values in the current session.>>pathmodshow----------------------------------------------------------------------PathLocation----------------------------------------------------------------------[user]'C:\Users\username\AppData\Local\Programs\Python\Python39\Scripts\'[user]'C:\Users\username\AppData\Local\Programs\Python\Python39\'...[system]'C:\Windows\system32'[system]'C:\Windows'...Refreshrefreshallows you to update the PATH in the current session. This is especially useful in terminals such as the Windows Terminal, where you would need to open a new terminal instance and be unable to migrate your tabs.Updating the PATH directly frompathmodis not possible becausepathmodcannot modify the environment of its parent process; however, a relatively easy workaround is to run the command:Invoke-Expression$(pathmodrefresh-gq)This will update the PATH in your current session so that it is equivalent to the PATH which would be used in a new session.HelpYou can use the--helpflag to show help info. This also works for subcommands.LicenseYou may freely use, modify and redistribute this program under the terms of the MIT License. SeeLICENSE.
Package: pathnav
pathnavNavigate paths with ease for pythonDocsInstall pathnavpip install pathnavCreate new path objectimportpathnavpath=pathnav.path("C:\\Users\\titushm\\Repos\\Github")# create a directory path object# Propertiesprint(path.path)# get the path as a stringprint(path.dir_name)# get the name of the directoryprint(path.child_dirs)# get a list of directorys in the directoryprint(path.child_files)# get a list of files in the directoryprint(path.dir_size)# get the size in bytes of the directoryprint(path.resolved_path)# get the full path without relative parts such as .. and %enviroment_varible%# Methodsprint(path.up())# go up one directoryprint(path.into("example-repo"))# go down one specified directoryprint(path.get_file("text-file.txt"))# get a file by name in the directory, returns None if no file is presentparent_path=pathnav.path("C:\\Users\\titushm\\Repos")print(path.is_subdir(parent_path))# check if a path is a subdirectory of another pathpath=pathnav.path("C:\\Users\\titushm\\Repos\\Github\\test-file.txt")# create a file path object# Propertiesprint(path.path)# get the path as a stringprint(path.file_name)# get the file name as stringprint(path.file_type)# get the file type as a stringprint(path.parent_dir)# returns a directory path object for the directory that the file is in# Methodsprint(path.is_subdir(parent_path))
Package: pathogen
another path managing packagenote that this package isstill in developmentat this stage, I’m only building thing as they come to mind
version 1.0 will be the first major release
until then, consider this code heavily volatileyet, install simply by callingpip install pathogenorpip install –pre pathogenfor the latest
development
release.we endeavor to followhttps://scikit-learn.org/stable/developers/performance.html
Package: pathogen-decision-engine
Pathogen Decision Engine PackageThe Decision Engine Package is a Python package for building and using decision engines based on rule sets defined in CSV files.
Its main purpose is to implement the decision mechanism described in the SOVAD1paper to classify the pathogenicity of a mutation given a well-known set of predictors.InstallationYou can install the package via pip:pip install pathogen-decision-engineUsageCommand-Line Interface (CLI)The package provides a command-line interface (CLI) for performing inference using the decision engine.To use the CLI, you can provide either the path of a rule table path made as a CSV file. The engine expect a rule table file made of a table of shape N x M+1 where N is the number of rules, M is the number of predictors and +1 is referring to the classification label for each rule.
Each cell can be empty or filled with a symbol (>, >=, ==, <, <=) and a value, indicating a numeric constraint for a certain predictor regarding a certain rule.
Example:decision_engine_cli --rule_table_path table.csv --input_dict '{"PA":1, "PVS":0, "PS":1, "PM":2, "PP":1, "BA":1, "BS":0, "BP":0}'You can pass a rule table in the form of dict expressed as a string
Example:decision_engine_cli --rule_table_dict "{'PA':{'0':1,'1':0},'PVS':{'0':0,'1':1},'PS':{'0':0,'1':'>=1'},'PM':{'0':0,'1':0},'PP':{'0':0,'1':0},'BA':{'0':0,'1':0},'BS':{'0':0,'1':0},'BP':{'0':0,'1':0},'Output':{'0':'Pathogenic','1':'Pathogenic','2':'Pathogenic'}}" --input_dict '{"PA":1, "PVS":0, "PS":1, "PM":2, "PP":1, "BA":1, "BS":0, "BP":0}'Python APIYou can also use the package programmatically in your Python code. Here's an example of how to use the DecisionEngine class:frompathogen_decision_engineimportPathogenDecisionEnginedf=None### ... create a df dataframe as you wish# Create a DecisionEngine objectdecision_engine=PathogenDecisionEngine(df)# Define input dictionaryinput_sample={"PA":1,"PVS":0,"PS":1,"PM":2,"PP":1,"BA":1,"BS":0,"BP":0}# Or you can define your input as list of sovad predictors, then the engine will take care of the counting:input_sample=["PA2","PS1","PP4","PM3"]# in this case you can omit the predictors with 0 count# Perform inferenceresult=decision_engine.infer(input_sample)print(result)References[1] [Koeppel, Florence et al.] “Standardisation of pathogenicity classification for somatic alterations in solid tumours and haematologic malignancies.” [European journal of cancer (Oxford, England : 1990) vol. 159 (2021): 1-15].
Package: pathogen-embed
pathogen-embedCreate reduced dimension embeddings for pathogen sequencespathogen-embed is an open-source software for scientists, epidemiologists, etc. to run reduced dimension embeddings (PCA, MDS, t-SNE, and UMAP) on viral populations. This is the source code from the paper Cartography written by Sravani Nanduri and John Huddleston.Change logDocumentationSource CodeBug reportsInstallationSimply install the package using pip.pip install pathogen-embedBuild documentationBuild theDocumentation:make -C /docs htmlClean the docs.make -C /docs cleanReleasing a new versionInformation about each fileREADME.mdcontains the description of the package pathogen-embed.setup.pyGives PyPi the instructions about where to find dependent packages, the authors and relevant links, etc. Also gives the entry points for the console script, which tells Pypi to call the main function ofmain.py.init.pyInitializes the package, creates the parser to parse the command line arguments and pass them into the embed.py function.main.pyCalls the "run" function ininit.py, which calls embed.py.embed.pyThe main code for the package.To create new versionRunpython3 -m buildThis creates the dist folder that gets uploaded to pypi.python3 -m twine upload dist/*Input the username and password, upload new dist files to pypi. Make sure the version of the dist folders does not already exist within pypi.Run testsRun tests with cram.cramtests
Package: pathology
# pathologyProvide a a subclass of pathlib's Path that adds a static script_dir() method to Path, which returns the Path to thedirectory of the calling script. It could have been just a standalone function, but for discoverability reasons itseems better to stick it on top of pathlib's Path.# UsageIt's a drop-in replacement to pathlib's Path:```from pathology import Pathprint('The script dir is:', Path.script_dir())```# TutsPlusThis package was developed as sample code for a TutsPlus article. Check it out:[How to Write, Package and Distribute a Library in Python](http://code.tutsplus.com/tutorials/how-to-write-package-and-distribute-a-library-in-python--cms-28693)
Package: path-parent
path_parentAppend ‘..’ to path setting.This package append string ‘..’ to the path setting when being imported.Installpip install path_parentUsageimportpath_parent.p# append '..' to path setting;importpath_parent.pp# append '../..' to path setting;importpath_parent.ppp# append '../../..' to path setting;importpath_parent# nothing happen;path_parent.clear("../..")# remove only '../..';path_parent.clear("..\..\..")# nothing removed, not backslash;path_parent.clear()# remove all '..', '../..' and '../../..';