Saravanan666/pypi-org huggingface dataset:
Package: treesapp
TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic ProfilerOverviewTreeSAPP is a python package for functional and taxonomic annotation of proteins
from genomes and metagenomes using phylogenetic placement.Quick startWe recommend installing TreeSAPP into its own conda environment with the following command:condacreate-ntreesapp_cenv-cbioconda-cconda-forgetreesapp
condaactivatetreesapp_cenvTo list all the sub-commands runtreesapp.To test theassignworkflow, run:treesappassign-iTreeSAPP/tests/test_data/marker_test_suite.faa-mprot--trim_align-oassign_test-tMcrA,DsrABTo classify sequences in your genome of interest:treesappassign-imy.fasta-o~/path/to/output/directory/TreeSAPP comes installed with 33 reference packages involved in a variety of biogeochemical and cellular processes.
We also have many more reference packages available on ourRefPkgs repositoryand you can view the complete listhere.TutorialsAll of our tutorials are available on theGitHub wikipage.
Here are some specific tutorial examples:If we do not yet have a reference package for a gene you are interested in,
please trybuilding a new reference package.
Of course, if you run into any problems or would like to collaborate on building many reference packages
don't hesitate to email us or create a new issue with an 'enhancement' label.To determine whether the sequences used to build your new reference package are what you think they are,
and whether it might unexpectedly annotate homologous sequences,
see thepurity tutorial.If you are working with a particularly complex reference package, from an orthologous group for example, or have extra
phylogenetic information you'd like to include in your classifications,
tryannotating extra featureswithtreesapp layer.CitationIf you found TreeSAPP useful in your work, please cite the following paper:Morgan-Lang, C., McLaughlin, R., Armstrong, Z., Zhang, G., Chan, K., & Hallam, S. J. (2020).TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler.
Bioinformatics, 1–8.This was brought to you by the team:Connor Morgan-Lang (cmorganl, maintainer)Ryan McLaughlin (McGlock)Grace Zhang (grace72)Kevin Chan (kevinxchan)Zachary ArmstrongSteven J. HallamReferencesIf you're feeling extra citation-happy, please consider citing the following works as well:Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics (Oxford, England), 14(9), 755–763.Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10(1).Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455.Barbera, P., Kozlov, A. M., Czech, L., Morel, B., & Stamatakis, A. (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Systematic Biology, 0(0), 291658.
Package: treeschema
Version:1.0.8Documentation:https://developer.treeschema.com/python-clientDownload:https://pypi.org/project/treeschemaSource:https://github.com/tree-schema/tree-schema-pythonKeywords:data lineage, metadataYour ETL/ELT processes are diverse, your pipelines are serverless - the Tree Schema Python client aims to provide you the flexibility to integrate into any ecosystem!What You Can DoTheTree Schemalibrary is a simple interface that enables data creators and data users to manage their Tree SchemaData Catalogas code. The Tree Schema library enables you to:Managedata lineageas codeCapture the values of your fields and their definitionsExplore your catalog in the same notebook as your data analysisHere are a few quick snippets:Manage Your Data Lineage as Code# Import Tree SchemafromtreeschemaimportTreeSchemats=TreeSchema('<your email>','<your secret key>')# Define the source and target fieldssrc_field=ts.data_store('Kafka Cluster').schema('dvc.user:v1').field('user_id')tgt_field=ts.data_store('Kafka Cluster ').schema('usr.clickstream:v1').field('user_id')link=(src_field,tgt_field)# Select your transformationt=ts.transformation('Kafka Pub-Sub')# Create the data lineaget.create_links(link)The complexity of your transformation is only limited by your own imagination. Data lineage can be explored within the Tree Schema GUI
once created, a slightly more complex example may look like:Create Definitions for Field Values# Import Tree SchemafromtreeschemaimportTreeSchemats=TreeSchema('<your email>','<your secret key>')# Select the field to add sample values tosrc_field=ts.data_store('Kafka Cluster').schema('dvc.user:v1').field('user_status')# Define the value and it's definitionsample_value={'field_value':'02','description':'User has converted from lead to customer'}field.field_value(sample_value)How to Get StartedMake sure you sign up for Tree Schema - it’s completely free to sign up with no card required - and follow the instructions forhow to get your secret key.Check out all of theExamplesin the documentation to see all of the library features and to explore more in-depth and complex use-cases.Have Questions or Need Help?Shoot an email todeveloper@treeschema.comto get help integrating Tree Schema.
Package: treesearchsolverpy
Tree Search Solver (Python)A solver based on heuristic tree search.This is the Python3 version of the C++ packagefontanf/treesearchsolver.image sourceDescriptionThe goal of this repository is to provide a simple framework to quickly implement algorithms based on heuristic tree search.Solving a problem only requires a couple hundred lines of code (see examples).Algorithms:GreedygreedyBest First Searchbest_first_searchIterative Beam Searchiterative_beam_searchExamplesTravelling Salesman ProblemUsage, running examples from command lineInstallpip3installtreesearchsolverpyRunning an example:mkdir-pdata/travellingsalesman/instance
python3-mexamples.travellingsalesman-agenerator-idata/travellingsalesman/instance
python3-mexamples.travellingsalesman-aiterative_beam_search-idata/travellingsalesman/instance_50.jsonUpdate:pip3install--upgradetreesearchsolverpyUsage, Python librarySee examples.
Package: treeshake
TreeshakeEver used a CSS framework and cried about all the overhead it caused? Ever wrote so much CSS that you were no longer aware what parts of it were actually used? Fear no more. Just usetreeshakebefore deployment and all of your troubles will melt away.Dead code eliminationTree shaking is a concept mostly used in ECMAScript languages like Dart, JavaScript and Typescript that helps to eliminate unused code. Optimizing your code in a single bundle.This project aims to bring the power of tree shaking for css to your Python projects. This small library is written inCythonand allows you to get the best performance out of your (potentially) bloated web applications.InstallationIt is recommended to install treeshake via pip:pip install treeshakeCommand Line SupportTo quickly use treeshake, call it via command line:shake <css dir> <html dir>
python3 -m treeshake <css dir> <html directory>If you wish to see an interactive prompt, just useshakeorpython3 -m treeshake. The current support is only for a single directory.
To see help, please run:shake -h.Quick exampleThe following piece of codes recursively adds all css files from/styles/and all html files from/htmland compares the contents. Where possible, it will eliminate styling.The new file is written to the/out/output directory.fromtreeshakeimportShakertreeshaker=Shaker()treeshaker.discover_add_stylesheets('./styles/',True)treeshaker.discover_add_html('./html/',True)treeshaker.optimize('./out')ContributingAny contribution to this project is very welcome. Please open an issue when you are dealing with a problem or want to discuss a feature. All contributions are handled by pull requests.Please refer toCONTRIBUTING.mdfor more information.
Package: treeshape
treeshape allows you to quickly make file and directory structures on disk.For example:from treeshape import (
    CONTENT,
    make_tree,
    PERMISSIONS,
    )

make_tree('.', {
    'logs/': None,
    'README': {CONTENT: "A simple directory layout\n"},
    'data/input': {CONTENT: "All of our input data\n"},
    'bin/script': {CONTENT: "#!/bin/sh\necho 'Hello'\n", PERMISSIONS: 0755},
    })Will create a directory structure that looks like this:$ find .
.
./logs
./data
./data/input
./README
$ cat README
A simple directory layout
$ cat data/input
All of our input dataThis is particularly useful for tests that touch the disk.If being explicit isn’t really your thing, you can also create the same
directory structure from a rough specification:from treeshape import (
    from_rough_spec,
    make_tree,
    )

make_tree('.', from_rough_spec([
    'logs/',
    ('README', "A simple directory layout\n"),
    ('data/input', "All of our input data\n"),
    ('bin/script', "#!/bin/sh\necho 'Hello'\n", 0755),
    ]))This is also provided as aFixture(seepython-fixtures). Thus, if you
are usingtesttools, then you can also do this during your tests:def test_a_thing(self):
    self.useFixture(FileTree(from_rough_spec([
        'logs/',
        ('README', "A simple directory layout\n"),
        ('data/input', "All of our input data\n"),
        ])))
    # your test here
Package: tree-sitter-builder
python-tree-sitter-builderInstallpoetryinstall
ln-s$(poetryrunwhichtree-sitter-builder)~/.local/bin/UsagebuildClone specified repository and build tree-sitter language parser.If it contains://, it assumes that the entire git URL has been specified. Otherwise, assume it is GitHub and clone the repository.tree-sitter-builderbuildconao3/tree-sitter-sqlClone into$XDG_DATA_HOME/tree-sitter-builder/repos/*.If you omit the repository name, tree-sitter-builder will build all repositories.distReturns the path to builded parser shared object.$python-tree-sitter-builder%tree-sitter-builderdistconao3/tree-sitter-sql
/Users/conao/Library/ApplicationSupport/tree-sitter-builder/build/conao3__tree-sitter-sql.soupdateUpdate all repositories.tree-sitter-builderupdatelistList all repositories.tree-sitter-builderlistremoveRemove specified repository.tree-sitter-builderremoveconao3/tree-sitter-sqlcleanRemove all build files.tree-sitter-builderclean
Package: tree-sitter-builds
py-tree-sitter-buildsThepy-tree-sitterproject
(not to be confused with tree-sitter-python)
provides Python bindings for the awesometree-sitterparsing library.
The documentation of py-tree-sitter says that you need to have a C compiler installed to use it,
but installing a C compiler can be highly non-trivial depending on which operating system you have.
It's also a huge dependency for what is otherwise a small and simple parsing library.This project lets you use py-tree-sitter without a C compiler
by providing binary wheels that were built using a C compiler,
but don't require a C compiler to be installed.
The wheels contain:thetree_sittermodule frompy-tree-sitterv0.20.1thetree_sitter_languagesmodule frompy-tree-sitter-languagesv1.5.0Installation$ pip install tree-sitter-buildsAfter installing,import tree_sitterandimport tree_sitter_languagesshould work.
For documentation, see the documentation of:py-tree-sitter-languagespy-tree-sitter(usetree_sitter_languagesinstead of the "Setup" part)How does it work?Read.github/workflows/build.ymlto see how GitHub actions builds the wheels.
Here are the steps, at a high level:Download py-tree-sitter v0.20.1 and py-tree-sitter-languages v1.5.0 from GitHub
(these are the latest released versions at the time of writing this)Move downloaded files to the correct places,
so that the resulting wheels will contain bothtree_sitterandtree_sitter_languagesApply patches to the tests oftree_sitterandtree_sitter_languagesso that they work hereInvokecibuildwheelwith the same configuration as py-tree-sitter-languages usesOnce the above steps have ran on Windows, MacOS and Linux, upload the wheels to PyPILicenseThe wheels consist of various parts licensed under MIT and Apache 2.0 licenses:This project is licensed underthe Apache 2.0 license.py-tree-sitter is licensed underthe MIT license.py-tree-sitter-languages is licensed underthe Apache 2.0 license.py-tree-sitter-languages includes various other projects licensed under MIT and Apache 2.0 licenses.
There isa full listin its README.
Package: tree-sitter-cairo
tree-sitter-cairoThis is an automatically generated python package usingpython-tree-sitter-types.It provides nice typed bindings for the tree-sitter raw parser.Installationpipinstalltree-sitter-cairoExamplefromtree_sitter_cairoimportload_language,parse_nodefromtree_sitterimportParserlanguage=load_language('tree-sitter-cairo','cairo')parser=Parser()parser.set_language(language)tree=parser.parse(bytes("<some cairo code>","utf-8"))typed_tree=parse_node(tree.root_node)# Your cool clean code:
Package: tree-sitter-hlsplaylist
tree-sitter-hlsplaylisthlsplaylist(m3u, m3u8) grammar fortree-sitter.It can be used by:Syntax highlighteditorsnvim-treesitter: forneovimtree-sitter-langs:
foremacskak-tree-sitter: forkakounehelixzedatomsyntax-highlighter:
forVS Codepagerssyncattree-sitter highlight:
Make sure/the/parent/directory/of/this/repoinparser-directoriesof
your~/.config/tree-sitter/config.jsonLanguage serversvscode-anycodeNavigating code on GitHub:
supported bysemanticLibrariestree-sitter-hlsplaylist:
for nodetree-sitter-hlsplaylist:
for rusttree-sitter-hlsplaylist:
for pythontree-sitter-languages:
for python
Package: tree-sitter-jinja2
Bindings for PythonTo use the bindings in your project:# requirements.txt
tree-sitter==0.19.0
tree-sitter-jinja2fromtree_sitter_jinja2importJINJA2_LANGUAGEfromtree_sitterimportParsersource=bytes("{{ True }}","utf8")parser=Parser()parser.set_language(JINJA2_LANGUAGE)tree=parser.parse(source)To build the wheel locallymake bindings
Package: tree-sitter-muttrc
tree-sitter-muttrc(neo)muttrc grammarfortree-sitter.It can be used by:Syntax highlighteditorsnvim-treesitter: forneovimtree-sitter-langs:
foremacskak-tree-sitter: forkakounehelixzedatomsyntax-highlighter:
forVS Codepagerssyncattree-sitter highlight:
Make sure/the/parent/directory/of/this/repoinparser-directoriesof
your~/.config/tree-sitter/config.jsonLanguage serversmuttrc-language-servervscode-anycodeNavigating code on GitHub:
supported bysemanticLibrariestree-sitter-muttrc:
for nodetree-sitter-muttrc:
for rusttree-sitter-muttrc:
for pythontree-sitter-languages:
for pythonRelated Projectsneomutt.vim: vim syntax
Package: tree-sitter-pymanifest
A tree-sitter parser for PyPA manifest files.Python packageInstallationpipinstalltree-sitter-pymanifestUsageimporttree_sitter_pymanifestaspymanifestwithopen('MANIFEST.in','r')asmf:# parse a MANIFEST.in filetree=pymanifest.parse(mf.read())# get the highlight groupshl_groups=pymanifest.highlights(tree)# run an arbitrary querydir_patterns=pymanifest.query("""
   (command dir_pattern: (pattern) @dir_pattern)
   """,tree.root_node)ReferencesControlling files in the distributionUnix filename pattern matchingEditors☑ Neovim☐ Helix☐ Emacs☐ ZedChangelogv0.4.0Change bindings layoutv0.3.0Move totree-sitter-grammarsorgv0.2.1Drop Python 3.7 supportRemove injections queriesUse tree-sitter core highlight capturesv0.2.0Add Python package testsv0.1.1Bundle queries in the package
Package: tree-sitter-requirements
A tree-sitter parser for pip requirements files.Python packageInstallationpipinstalltree-sitter-requirementsUsageimporttree_sitter_requirementsasrequirementswithopen('requirements.txt','r')asrf:# parse a requirements.txt filetree=requirements.parse(rf.read())# get the highlight groupshl_groups=requirements.highlights(tree)# run an arbitrary querypackages=requirements.query("""
   (requirement (package) @package)
   """,tree.root_node)ReferencesRequirements File FormatDependency SpecifiersVersion SpecifiersVCS SupportEditors☑ Neovim☐ Helix☐ Emacs☐ ZedChangelogv0.3.1Replace deprecated resource APIv0.3.0Change bindings layoutv0.2.0Move totree-sitter-grammarsorgv0.1.5Resolve_version_listconflictFix inline commentsv0.1.4Make URL scheme case-insensitivev0.1.3Support per-requirement optionsParse paths and URLs in optionsv0.1.2Support environment variables in URLsv0.1.1Fix environment markers
Package: tree-sitter-solidity
tree-sitter-solidityThis is an automatically generated python package usingpython-tree-sitter-types.It provides nice typed bindings for the tree-sitter raw parser.Installationpipinstalltree-sitter-solidityExamplefromtree_sitter_solidityimportload_language,parse_nodefromtree_sitterimportParserlanguage=load_language('tree-sitter-solidity','solidity')parser=Parser()parser.set_language(language)tree=parser.parse(bytes("<some solidity code>","utf-8"))typed_tree=parse_node(tree.root_node)# Your cool clean code:
Package: tree-sitter-tmux
tree-sitter-tmuxtmux grammarfortree-sitter.It can be used by:Syntax highlighteditorsnvim-treesitter: forneovimtree-sitter-langs:
foremacskak-tree-sitter: forkakounehelixzedatomsyntax-highlighter:
forVS Codepagerssyncattree-sitter highlight:
Make sure/the/parent/directory/of/this/repoinparser-directoriesof
your~/.config/tree-sitter/config.jsonLanguage serverstmux-language-servervscode-anycodeNavigating code on GitHub:
supported bysemanticLibrariestree-sitter-tmux:
for nodetree-sitter-tmux:
for rusttree-sitter-tmux:
for pythontree-sitter-languages:
for pythonRelated Projectsvim-tmux: vim syntax
Package: tree-sitter-type-provider
Type Providers for Tree SitterCreate a type AST from anynode-types.jsonfile, as well as a generic visitor class and a transformer class, and a function to convert to the AST from thetree_sitter.Nodetype.For example, the following code defines a module namedtree_sitter_javascriptfromtree-sitter-javascript/src/nodes.json:importpathlibimporttree_sitter_type_provideraststpnode_types_json=pathlib.Path("tree-sitter-javascript/src/node-types.json")node_types=tstp.NodeType.schema().loads(node_types_json.read_text(),many=True)defas_class_name(node_type_name:str)->str:class_name_parts:typing.List[str]=["Js"]forpartinnode_type_name.split("_"):class_name_parts.append(part.capitalize())return"".join(class_name_parts)sys.modules[__name__]=tstp.TreeSitterTypeProvider("tree_sitter_javascript",node_types,error_as_node=True,# Include ERROR as a node in the ASTas_class_name=as_class_name,# How to convert node types to Python class namesextra=["comment"],# Nodes which are marked as 'extra' in the grammar)The module contains a number of dataclasses which represent the AST nodes:importtree_sitterastsimporttree_sitter_type_provideraststpimporttyping@dataclassclassJsArray(tstp.Node):text:strtype_name:strstart_position:tstp.Pointend_position:tstp.Pointchildren:typing.List[typing.Union[JsExpression,JsSpreadElement]]@dataclassclassJsDeclaration(tstp.Node):text:strtype_name:strstart_position:tstp.Pointend_position:tstp.Point@dataclassclassJsWhileStatement(tstp.Node):text:strtype_name:strstart_position:tstp.Pointend_position:tstp.Pointbody:JsStatementcondition:JsParenthesizedExpression...As well as a function to convert to the AST:deffrom_tree_sitter(self,tsvalue:typing.Union[ts.Tree,ts.Node,ts.TreeCursor],*,encoding:str='utf-8')->tstp.Node
Package: tree-sitter-types
🔧 python-tree-sitter-typesThis repository contains a python typed interface generation tool for tree-sitter grammars.InstallationInstallation is simple with pip:pipinstalltree-sitter-typesUsageThis library provides two functions.As a CLI you can use it to generate the types for your tree-sitter grammar:python-tree-sitter-typesnode-types.jsonyour_language_types.pyYou can then package these and distribute them on pypi, following tree-sitters naming standardtree-sitter-yourlang.As a library it provides the functions to install tree-sitter parsers and to load them into python.Why is this useful?Tree-sitter is a great library for parsing source code. It is fast, easy to use and has a lot of great features.
However, it is written in C and does not provide a typed interface for python. This makes writing tools on top of it a bit cumbersome.With this library you'll be able to use pythons types for your advantage, leveraging autocompletion for fast coding,
types for correctness, and nice features like matching.
Package: tree-sitter-zathurarc
tree-sitter-zathurarczathurarcgrammar fortree-sitter.It can be used by:Syntax highlighteditorsnvim-treesitter: forneovimtree-sitter-langs:
foremacskak-tree-sitter: forkakounehelixzedatomsyntax-highlighter:
forVS Codepagerssyncattree-sitter highlight:
Make sure/the/parent/directory/of/this/repoinparser-directoriesof
your~/.config/tree-sitter/config.jsonLanguage serverszathura-language-servervscode-anycodeNavigating code on GitHub:
supported bysemanticLibrariestree-sitter-zathurarc:
for nodetree-sitter-zathurarc:
for rusttree-sitter-zathurarc:
for pythontree-sitter-languages:
for pythonRelated Projectszathurarc.vim: vim syntax
Package: treesp
TreespThis module helps you to perform operations on trees. The functions this module holds areInsertmaxDepthIndorderPreorderPostorderLevelorderLowest common ancestorInstallationpip install treespHow to use itwe need to import modulefrom treesp import treesp as tpTo create a bst:-
You need to define a class which holds tree data structure
then you can simply use insert function to insert the nodestp.insert(j, 2)To run other functionsk = tp.inorder(j)Note:- the functions resturns a ListGithub repositoryhttps://github.com/sidharth0611LicenseÂ© 2021 Sidharth ParekhThis repository is licensed under the MIT license. See LICENSE for details.
Package: treespace
treespacetreespace - Copyright (C) 2023-2024 Hengchi Chen
Contact:heche@psb.vib-ugent.beExamples runcd example_data
treespace treerun config_iqtree -o config_iqtree_output
treespace treerun config_mrbayes -o config_mrbayes_output
treespace treerun config_iqtree_seqfam -o config_iqtree_seqfam_output
Package: treestamps
TreestampsA library to set and retrieve timestamps to speed up operations run recursively
on directory trees.Documentation is pretty poor. Read the code for now.UsageUsed inpicoptandnudebomb. You can see how it's used in
those projects.frompathlibimportPathfromtreestampsimportGrovestamps,GrovestampsConfigconfig=GrovestampsConfig("MyProgramName",paths=("/foo","/bar"),program_config={"option_a":True,"option_b":False})gs=Grovestamps(config)timestamp=gs[Path("/foo")].get()assertNone==timestamp.get("file_relative_to_foo.txt")mtime=timestamp.set("file_relative_to_foo.txt")# mtime ~= now()# Also writes to `/foo/.MyProgramName_treestamps.wal.yaml`gs.dump()Dumping removes/foo/.MyProgramName_treestamps.wal.yamland writes to/foo/.MyProgramName_treestamps.yamland/bar/.MyProgramName_treestamps.yaml# With similar config to abovegs=Grovestamps(config)# Auto loads timestamps relevant to paths in config.timestamp_foo=gs[Path("/foo")].get()mtime_b=timestamp_foo.get("file_relative_to_foo.txt")mtime_a=timestamp_foo.get("another_file_relative_to_foo.txt")# mtime will be the time gs.dump() you called above.assertmtime_a==mtime_btimestamp_bar=gs[Path("/bar")].get()mtime_c=timestamp_foo.get("file_relative_to_bar.txt")assertmtime_c==mtime_a
Package: tree-storage
OverviewTree the library for saving many files by they hash.
For preservation it is enough to you to transfer a binary code of the file and the Tree will keep him.ExampleSuperficial uses in the tree hash storagefrom tree_storage import TreeStorage

tree = TreeStorage(path="/path/to/storage")

# If you want add file to the Tree Storage
with open("/path/to/file", "rb") as file:
    tree.breed(file_byte=file.read(), mode='wb')
# after add file, method return status of writing.
# If add file status is success, tree save last
# hash of the file in the attribute file_hash_name

# For remove file from the Tree Storage
# you can call cut method and past
# to him hash name of file which you have delete
tree.cut(file_hash_name=tree.file_hash_name, greedy=True)InstallingDownload and install the latest released version from PyPI:pip install tree-storageDownload and install the development version from GitHub:pip install git+https://github.com/valeriiduz/TreeInstalling from source (installs the version in the current working directory):python setup.py install(In all cases, add –user to the install command to install in the current user’s home directory.)
Install and Update Tree library using pip:DocumentationRead full documentation onhttps://tree.readthedocs.io/.LicenseThis repository is distributed under The MIT license