Saravanan666/pypi-org huggingface dataset:
Package: compath-resources
This repository contains the different resources derived or generated usingComPath.
Among these resources, there areJupyter notebooksoutlining possible analyses that can be made using ComPath plugins as well as the results of the curation effort
(see themappingsfolder) where pathway mappings between
three of the major pathway databases (see below) are stored. As of March 2020,PathBankmappings are now available in ComPath.CitationIf you use ComPath in your work, please consider citing:[1]Domingo-Fernández, D.,et al.(2018).ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases.npj Syst Biol Appl., 4(1):43.💾 DataA total of 6 mapping files are stored in this package, one for each pairwise comparison[*].
These data are available under the CC0 1.0 Universal License.KEGG - WikiPathwaysKEGG - ReactomeWikiPathways - ReactomePathBank - KEGGPathBank - ReactomePathBank - WikiPathways[*]Pairwise mappings between KEGG, Reactome and WikiPathways were last updated in March of 2019. PathBank mappings
were last updated in March of 2020.Update: March 2020Mappings betweenPathBankand the above-mentioned databases are now available in ComPath.📊 SummaryA summary is automatically generated nightly with GitHub Actions and deployed tohttps://compath.github.io/compath-resources/.🙏 ContributingWhile it’s possible to improve the files in this repository, they have been integrated into a more
general effort for identifying mappings between biological entities,Biomappings. Please direct contributions to that repository
following itscuration guidelines.Curation GuidelinesWe have distinguished between two types of relationships between pathways (mappings): “equivalentTo” and “isPartOf”.equivalentTo. An undirected relationship denoting both pathways refer to the same biological process. The
requirements for this relationship are:Scope: both pathways represent the same biological pathway information.Similarity: both pathways must share at minimum of one overlapping gene.Context: both pathways should take place in the same context (e.g., cell line, physiology)isPartOf. A directed relationship denoting the hierarchical relationship between the pathway 1 (child) and 2
(parent). The requirements are:Subset: The subject (pathway 1) is a subset of pathway 2 (e.g., Reactome pathway hierarchy).Similarity: same as aboveContext: same as above⬇️ InstallationDownload the latest stable code fromPyPIwith:pipinstallcompath_resourcesDownload the most recent code fromGitHubwith:pipinstallgit+https://github.com/ComPath/compath-resources.git💪 Usageimportcompath_resources# get all mappings as a pandas dataframedf=compath_resources.get_df()# get all mappings as a PyBEL BEL graphbel_graph=compath_resources.get_bel()# get all mappings as an RDFLib graph.rdf_graph=compath_resources.get_rdf()⚖️ LicenseCode is licensed under the MIT License. Curated mappings are licensed under the CC-0 License.AcknowledgementsCuration TeamThe curation exercise was conducted under inter-curator agreement in a team formed by:Carlos Bobis-ÁlvarezJosep Marín-LlaóDaniel Domingo-FernándezYojana Gadiya
Package: compath-utils
A repository containing abstract classes that allBio2BELpackages should extend
in order to be adapted to the ComPath environment.Installationcompath_utilscan be installed easily fromPyPIwith the
following code in your favorite terminal:$python3-mpipinstallcompath_utilsor from the latest code onGitHubwith:$python3-mpipinstallgit+https://github.com/ComPath/compath_utils.git@master
Package: compatibilityer
Python3.11などの新しいバージョンのコードを、古いバージョンで動作するように変換するツールです。あくまでも動作するように小手先の変換を施すだけであって、複雑なパターンの変換や厳密な等価性が必要な場合には使用できません。
また、当然ですが可読性はある程度失われます。具体的には、以下のような変換を行います。代入や関数定義の型アノテーションを文字列リテラルに置き換える旧バージョンに存在しない要素のfrom typing importを削除するalias: TypeAlias = SomeTypeという形のTypeAliasの定義をする代入文の右辺を文字列リテラルに置き換えるmatch文をif文に変換する(複雑なものには未対応)
Package: compatibility-lib
A library that calls the compatibility server to get compatibility
information about Python packages, and provides utilities to store the
results into BigQuery.Running the server locallyInstallDockerDownload the code:git clone git@github.com:GoogleCloudPlatform/cloud-opensource-python.gitBuild and run the Docker imagecd cloud-opensource-python/compatbility_server
./run-in-docker.shTesting the server outcurl 'http://0.0.0.0:8888/?package=six&package=Django&python-version=3' | python3 -m json.tool
{
  "result": "SUCCESS",
  "packages": [
    "six",
    "Django"
  ],
  "description": null,
  "requirements": "absl-py==0.2.2\napparmor==2.11.1\nasn1crypto==0.24.0\nastor==0.6.2\natomicwrites==1.1.5\nattrs==18.1.0\nbleach==1.5.0\nblinker==1.3\nBrlapi==0.6.6\ncachetools==2.1.0\ncertifi==2018.4.16\nchardet==3.0.4\ncheckbox-ng==0.23\ncheckbox-support==0.22\ncolorlog==2.10.0\ncryptography==2.1.4\ncupshelpers==1.0\ndecorator==4.3.0\ndefer==1.0.6\nDjango==2.0.6\nfeedparser==5.2.1\ngast==0.2.0\nglinux-rebootd==0.1\ngoobuntu-config-tools==0.1\ngoogle-api-core==1.2.0\ngoogle-auth==1.5.0\ngoogleapis-common-protos==1.5.3\ngpg==1.10.0\ngrpcio==1.12.1\nguacamole==0.9.2\nhtml5lib==0.9999999\nhttplib2==0.9.2\nidna==2.6\nimportlab==0.1.1\nIPy==0.83\nJinja2==2.9.6\nkeyring==10.5.1\nkeyrings.alt==2.2\nLibAppArmor==2.11.1\nlouis==3.3.0\nlxml==4.0.0\nMako==1.0.7\nMarkdown==2.6.11\nMarkupSafe==1.0\nmore-itertools==4.2.0\nnetworkx==2.1\nnox-automation==0.19.0\nnumpy==1.14.5\noauthlib==2.0.4\nobno==29\nolefile==0.44\nonboard==1.4.1\nopencensus==0.1.5\npadme==1.1.1\npexpect==4.2.1\nPillow==4.3.0\nplainbox==0.25\npluggy==0.6.0\nprotobuf==3.5.2.post1\npsutil==5.4.2\npy==1.5.3\npyasn1==0.4.3\npyasn1-modules==0.2.1\npycairo==1.15.4\npycrypto==2.6.1\npycups==1.9.73\npycurl==7.43.0\npygobject==3.26.1\npyinotify==0.9.6\nPyJWT==1.5.3\npyOpenSSL==17.5.0\npyparsing==2.1.10\npysmbc==1.0.15.6\npytest==3.6.1\npython-apt==1.4.0b3\npython-debian==0.1.31\npython-xapp==1.0.0\npython-xlib==0.20\npytype==2018.5.22.1\npytz==2018.4\npyxdg==0.25\nPyYAML==3.12\nreportlab==3.3.0\nrequests==2.18.4\nretrying==1.3.3\nrsa==3.4.2\nSecretStorage==2.3.1\nsetproctitle==1.1.10\nsix==1.11.0\ntensorboard==1.8.0\ntensorflow==1.8.0\ntermcolor==1.1.0\nufw==0.35\nunattended-upgrades==0.1\nurllib3==1.22\nvirtualenv==16.0.0\nWerkzeug==0.14.1\nXlsxWriter==0.9.6\nyoutube-dl==2017.11.6\n"
  }Get Compatibility Data using the libraryThe library is sending requests to the compatibility server running GKE.from compatibility_lib import compatibility_checker

checker = compatibility_checker.CompatibilityChecker()

# Get self compatibility data
checker.get_self_compatibility(python_version='2')

# Get pairwise compatibility data
checker.get_pairwise_compatibility(python_version='2')

# Get the data and store to BigQuery
from compatibility_lib import get_compatibility_data

get_compatibility_data.write_to_status_table()DisclaimerThis is not an official Google product.
Package: compatibleversion
compatibleversioncompatibleversiontakes two parameters, a version and a specifier (i.e., version constraints), and returns a Boolean value indicating compatibility.NOTE:compatibleversionwrapspackagingin order to simplify and test its use. Versions and specifiers provided tocompatibleversionmust conform toPEP 440as required bypackaging.install$pipinstallcompatibleversionusageUsecompatibleversionin Python code:fromcompatibleversionimportcheck_versioncheck_version('1.3.0','> 1.2, < 3.3')# Truecheck_version('2.1','~= 2.2')# Falsecheck_version('1.1.dev0','>=1.0')# Truecheck_version('1.1.dev0','>=1.0',False)# False, not allowing pre/dev-final comparisoncheck_version('1.1.dev0','>=1.0.dev0')# True, dev-dev comparecheck_version('1.1.dev0','>=1.0.dev0',False)# True, doesn't affect since dev-devversion parameterThe version parameter must conform toPEP 440. These are examples of valid version parameters:1.2.0
0.0.0
0.9
0.9.1
0.9.2
0.9.10
0.9.11
1.0
1.0.1
1.1
2.0
2.0.1
1.0a1
1.0a2
1.0b1
1.0rc1
1.0.dev1
1.0.dev2
1.0.dev3
1.0.dev4
1.0b2.post345.dev456
1.0b2.post345
1.0rc1.dev456specifier parameterThe version specifier parameter must conform toPEP 440. The specifier consists of one or more version clauses separated by commas.For example, these are valid version specifiers (the last two are approximately equivalent):==1.0.1
< 1.2, > 1.3
~= 0.9, >= 1.0, != 1.3.4.*, < 2.0
~= 1.4.5.0
== 1.1.post1
~= 2.2
>= 2.2, == 2.*Here are more helpful specifier examples fromPEP 440and an explanation of their meaning:~=3.1: version 3.1 or later, but not version 4.0 or later.~=3.1.2: version 3.1.2 or later, but not version 3.2.0 or later.~=3.1a1: version 3.1a1 or later, but not version 4.0 or later.== 3.1: specifically version 3.1 (or 3.1.0), excludes all pre-releases, post releases, developmental releases and any 3.1.x maintenance releases.== 3.1.*: any version that starts with 3.1. Equivalent to the ~=3.1.0 compatible release clause.~=3.1.0, != 3.1.3: version 3.1.0 or later, but not version 3.1.3 and not version 3.2.0 or later.Changelog0.2.0Commit Delta:Change from 0.1.3 releaseReleased: 2020.03.04Summary:Allow comparison between prerelease and dev releases (e.g.,1.0.dev0) and final releases (e.g.,1.0)0.1.3Commit Delta:Change from 0.1.2 releaseReleased: 2020.01.28Summary:Update dependenciesUpdate Python compatibility versions in PyPI/wheel package0.1.2Commit Delta:Change from 0.1.1 releaseReleased: 2019.10.24Summary:Improve compatibility with Py2.60.1.1Commit Delta:Change from 0.1.0 releaseReleased: 2019.10.24Summary:Minor CI changesAdd documentation0.1.0Commit Delta:Change from 0.0.0 releaseReleased: 2019.10.22Summary:Initial release
Package: compat-patcher-core
Long term API compatibility for fast-moving projectsWelcome toCompat Patcher Core, a mini-framework to buildCompatibility Patchers. These companion applications
allow your favorite software (a framework, a library…) to keep long term API stability towards its ecosystem
(plugins, bridges to other applications…), while still keeping the main codebase clean, and getting new features at
a good pace.Compatibility Patchers inject backward/forward compatibility shims (like class/function/attribute aliases), restore
features which were dropped/externalized because “not used enough” or “outside the scope of the library”, and tweak
the signatures and behaviour of callables (eg. for arguments which disappeared, or which became mandatory). It can
even setup lazy “import aliases”, so that code can import a moved module both from its old and new location.These shims allows you to upgrade your dependencies one at a time, when their maintainer finally had some time for a
code update, or when missing features and bugfixes justify a fork. Most importantly, they allow you to not get stuck,
when deadlines are tight, and crucial dependencies have conflicting expectations regarding the software version.Note that compatibility Patchers are not supposed to undo changes related to security (default access permissions,
markup escaping, cookie parameters…), because of the risks involved. Also, changes that only impact project-level
code (eg. new mandatorysettings) should not get patched, since it’s easier and cleaner for to simply update project
code.Technically, Compatibility Patchers are packages which manage a set offixers, tiny utilities (often less than 10
lines of code) which advertise the change that they make, the software versions that they support, and which patch the
target code on demand. By applying these fixers in a proper order (sometimes before, sometimes after the
initialization of the patched software itself), Compatibility Patchers can easily “time travel”, and work around multiple
breaking changes which target the same part of the code (e.g. a content handler being added and then removed).Compat Patcher Core holds the core logice of that system, via easily extendable classes: a registry system,
monkey-patching utilities, and a generic runner to be called at the very start of your application. It also contains
acookiecutter recipeto setup your own Compatibility Patcher in a few minutes, with test scaffolding and packaging
metadata ready for launch.Documentation is available onRead The DocsSources are available onGithubWhich applications currently benefit from this system?The Django Web Framework viaDjango-Compat-Patcher
Package: compay-syntax
Help building our code and community!All contributions are welcome! Please raise an issue for a bug, feature or pull request!Tweetabout this repo!Give this repo a star! :star:Quick StartTissue mask and tiling pipelinefromsyntax.slideimportSlidefromsyntax.transformers.tissue_maskimportOtsuTissueMaskfromsyntax.transformers.tilingimportSimpleTilingfromsyntax.transformersimportPipeline,visualize_pipeline_resultsslide=Slide(slide_path=slide_path)pipeline=Pipeline([OtsuTissueMask(),SimpleTiling(magnification=40,tile_size=224,max_per_class=10)])slide=pipeline.fit_transform(slide)visualize_pipeline_results(slide=slide,transformer_list=pipeline.transformers,title_list=['Tissue Mask','Random Tile Sampling'])Installpip install compay-syntax==0.4.0You will need to install openslide. This is included in the dependencies so may be automatically installed. If not I found this to help:#!/bin/bashsudoapt-getinstallopenslide-tools
pipinstallopenslide-python
Package: compcate
This package allows you to identify competitors based on co-mentions (this could be co-mentions in news articles, social media etc.)Examples of How to Calculate Co-Mention-Based Similarity and Categorise Firmsimportcompcate.comentionascomocomention_df=como.random_comention_df()comention_simi_df=como.comention_similarity(comention_df)comention_group_df=como.community_detection(comention_simi_df)
Package: compchemparser
DescriptionThecompchemparserpackage provides parsers to convert quantum chemistry log files into a more condensed JSON format. At the moment, only one parser for Gaussian log files is implemented.InstallationThese instructions will get you a copy of the project up and running on your local machine for development and testing purposes.Virtual environment setupIt is highly recommended to use avirtual environmentfor thecompchemparserinstallation. The virtual environment can be created as follows:(Windows)$ python -m venv <your_venv>
$ your_venv\Scripts\activate.bat
(your_venv) $(Linux)$python3-mvenv<your_venv>
$sourceyour_venv/bin/activate(your_venv)$The above commands will create and activate the virtual environmentyour_venvin the current directory.Installation via pipTo install thecompchemparsersimply run the following command:(your_venv)$python-mpipinstallcompchemparserInstallation from the version-controlled source (for developers)This type of installation is only for the developers. To installcompchemparserdirectly from its repository you need to first clone theTheWorldAvatarproject. Then simply navigate to theTheWorldAvatar\thermo\CoMoCompChemParserdirectory and execute the following commands:# build and install(your_venv)$python-mpipinstall.# or build for in-place development(your_venv)$python-mpipinstall-e.Alternatively, use the providedinstall_script_pip.shorinstall_script_conda.shconvenience scripts, that can create virtual environment and install thecompchemparserin one go:# create the environment and install the project$install_script_pip.sh-v-i# create the environment and install the project for in-place development$install_script_pip.sh-v-i-eNote that installing the project for in-place development (setting the-eflag) also installs the required python packages for development and testing. To test the code, simply run the following commands:(your_venv)$pytesttestsHow to useUsage:ccparse<logFileOrDir>[-n--logExt=<LOG_EXT>]Options:-nSuppressparsercommandoutputfiles(jsonandcsv)--logExt=<LOG_EXT>Logfilesfileextensionforlogfiledirectoryinput[default:.log]AuthorsDaniel Nurkowski (danieln@cmclinnovations.com)
Angiras Menon
Package: comp-chem-py
|Documentation Status||MIT license|.. |Documentation Status| image:: https://readthedocs.org/projects/comp_chem_py/badge/?version=latest:target: http://comp_chem_py.readthedocs.io/?badge=latest.. |MIT license| image:: https://img.shields.io/badge/License-MIT-blue.svg:target: LICENSESet up and installation=======================In order to use the library, first clone it::git clone --recursive https://gitlab.com/pablobaudin/comp_chem_py.gitThen export the PATH in your ``~/.bashrc``::COMP_CHEM_PATH=/path/to/comp_chem_py/root/direxport PATH=${COMP_CHEM_PATH}/bin:$PATHexport PYTHONPATH=${COMP_CHEM_PATH}/external:$PYTHONPATHexport PYTHONPATH=${COMP_CHEM_PATH}/src:$PYTHONPATHDocumentation=============* Please take a look at the code `documentation <http://comp_chem_py.readthedocs.io/en/latest/>`_ for more details... todo::#. Keep improving documentation.#. Remove old_comp_chem_py repository/group and all subrepositories or archive it.#. Add tests. Maybe with doctest. They should also be included in the setup.py. See,https://python-packaging.readthedocs.io/en/latest/testing.html#. Consider making comp_chem_utils an external submodule.#. Add section about requirements and dependencies on documentation.#. Add the ebsel package into setup.py using the git repo as,dependency_links=['http://github.com/user/repo/tarball/master#egg=package-1.0']
Package: comp-chem-utils
CompChemUtils is a set of tools for computational catalysis workflows.RequirementsPython3.10 or laterClick(package for command line interfaces)NumPy(N-dimensional array package)SciPy(library for scientific computing)ASE(tools for atomistic simulations)Installation$ pip install comp-chem-utilsor, if you use poetry:$ poetry add comp-chem-utilsYou can also install the in-development version with:$ pip install https://gitlab.com/ugognw/python-comp-chem-utils/-/archive/development/ccu-main.zipor, similarly:$ poetry add git+https://gitlab.com/ugognw/python-comp-chem-utils/-/archive/development/ccu-main.gitDocumentationhttps://python-comp-chem-utils.readthedocs.io/en/latestTestingTo run all the tests run:$ toxNote, to combine the coverage data from all the tox environments run:Windowsset PYTEST_ADDOPTS=--cov-append
toxOtherPYTEST_ADDOPTS=--cov-append toxExamplesDetermine whether a water molecule is symmetric with respect to a 180 degree rotation about its secondary orientation axis.>>> from ase.build import molecule
>>> from ccu.structure.axisfinder import find_secondary_axis
>>> from ccu.structure.symmetry import Rotation, RotationSymmetry
>>> h2o = molecule('H2O')
>>> axis = find_secondary_axis(h2o)
>>> r = Rotation(180, axis)
>>> sym = RotationSymmetry(r)
>>> sym.check_symmetry(h2o)
TrueRetrieve reaction intermediates for the two-electron CO2 reduction reaction.>>> from ccu.adsorption.adsorbates import get_adsorbate
>>> cooh = get_adsorbate('COOH_CIS')
>>> cooh.positions
array([[ 0.        ,  0.        ,  0.        ],
       [ 0.98582255, -0.68771934,  0.        ],
       [ 0.        ,  1.343     ,  0.        ],
       [ 0.93293074,  1.61580804,  0.        ]])
>>> ocho =  get_adsorbate('OCHO')
>>> ocho.positions
array([[ 0.        ,  0.        ,  0.        ],
       [ 1.16307212, -0.6715    ,  0.        ],
       [ 0.        ,  1.343     ,  0.        ],
       [-0.95002987, -0.5485    ,  0.        ]])Place adsorbates on a surface (namely, “Cu-THQ.traj”) while considering the symmetry of the adsorbate and the adsorption sites.:$ ccu adsorption place-adsorbate CO Cu-THQ.traj orientations/Enable Shell CompletionAdd this to your ~/.bashrc::eval "$(_CCU_COMPLETE=bash_source ccu)"Add this to ~/.zshrc::eval "$(_CCU_COMPLETE=zsh_source ccu)"Add this to ~/.config/fish/completions/ccu.fish::eval (env _CCU_COMPLETE=fish_source ccu)
Package: compdb
IntroductionMotivationGetting startedInstallationGenerate a compilation database with header filesRunning the testsContributeLicenseAcknowledgmentsIntroductioncompdbis a command line tool to manipulates compilation databases.
A compilation database is a database for compile options,
it has records of which compile options are used to build the files in a project.
An example of compilation database is theJSON Compilation Databasecompdbaims to make it easier for you to run tools on your codebase
by spoon-feeding you the right compile options.compdbis not so much about generating the initial compilation database,
this, is left to other tools, such ascmakeandninja.
It is only a glue between the initial compilation database and your tool(s).MotivationWith the proliferation of Clang-based tools,
it has become apparent that the compile options
are no longer useful uniquely to the compiler.Standalone tools such asclang-tidyor text editors withlibclangintegration have to deal with compile options.Examples of such tools, dealing with compilation databases are:irony-mode,rtagsandycmd.Based on this evidence,compdbcame to life.
A tool that has knowledge of the compile options and can share it
both to inform the text editor and to run clang based tool from the shell.Getting startedInstallationInstall withpip:pip install compdbFrom Github, as user:pip install --user git+https://github.com/Sarcasm/compdb.git#egg=compdbGenerate a compilation database with header filesAssuming a build directorybuild/, containing acompile_commands.json,
a new compilation database, containing the header files,
can be generated with:compdb -p build/ list > compile_commands.jsonRunning the testsTo run the tests, type:python -m testsOr:tox --skip-missing-interpretersFor regression tests on a few open source projects:cd tests/regression/headerdb
make [all|help]ContributeContributions are always welcome!Try to be consistent with the actual code, it will ease the review.LicenseThis project is licensed under the MIT License.
See LICENSE.txt for details.Acknowledgmentsrepo: for its ubiquitous command line interface,
which served as an inspirationscan-build: for the clear Python package designgit: for thegit-configAPIjulio.meroh.net: for the interesting article serie onCLI design
Package: compdevkit
Comp-Developer-Toolkitcompdevkittests your model's functions against theCOMP criteria. If your functions pass thecompdevkittests, then you can be reasonably sure that the functions will work on COMPmodels.org.COMP Developer toolkit also provides a helper command for retrieving yourCOMP APItoken.InstallcompdevkitpipinstallcompdevkitSet up thecompdirectory$cdk-initTest your functionsfromcompdevkitimportFunctionsTestimportmatchupsdeftest_get_parameters():ta=FunctionsTest(get_inputs=matchups.get_inputs,validate_inputs=matchups.validate_inputs,run_model=matchups.get_matchup,ok_adjustment={"matchup":{"pitcher":[{"value":"Max Scherzer"}]}},bad_adjustment={"matchup":{"pitcher":[{"value":"Not a pitcher"}]}})ta.test()Get yourCOMP APItoken$cdk-token--usernamemyuser--passwordmypass
Token:your-token-hereRun the testspy.testcompconfig-v