Saravanan666/pypi-org huggingface dataset:
Package: clinphen
#ClinPhen is freely available for academic, nonprofit, and personal use.
#Licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.#ClinPhen is a tool that automatically extracts phenotypes from clinical notes.
#PIP VERSION INSTRUCTIONS
##To extract phenotypes:
clinphen <path_to_clinincal_note_file>##To see how to use other features:
clinphen -h##We also have a version that parses phenotypes from a large table of notes. You can run it with:
clinphen_bulk <path_to_table_file> <path_to_output_file>##The input file for clinphen_bulk, by default, is a 2-column table delimited by a "|" character. The first column is the patient identifier, the second is the note. It should have the following header:
"MRN"|"NOTE"##To learn more, run:
clinphen_bulk -h#STANDARD (NON-PIP) VERSION INSTRUCTIONS
#Running the ClinPhen GUI on a mac:#Running the ClinPhen GUI on a non-mac:#Running the ClinPhen GUI on the command line:
##Open the terminal
##cd to the ClinPhen directory
##Run the following command:
./ClinPhenApp#Running ClinPhen directly on the command line:
##Open the terminal
##cd to the ClinPhen directory
##Run the following command:
./clinphen input.txt
##Replace "input.txt" with the path to the free-text clinical note file that you want to parse.
##You can also run the command line with a custom thesaurus:
./clinphen input.txt thesaurus.txt
##Replace "thesaurus.txt" with the path to your custom thesaurus, which should be in the format: HPO_IDSynonym
Package: clinput
ClinputClinput is an importable python package that contains tools to create command line user inputs with data type conversion, syntax checking and customizable error messages. Syntactically, the functions in this package are similar to Python default input function, with a variety of optional arguments to provide customizable performance.ContentsInstallationUsageDocumentationContributingTestingLicenseInstallationInstall usingpip:pipinstallclinputUsageIt is recommended to import each ofsingleandmultiseparately (to avoid confusion) as follows:importclinput.singleasclis# example use:input_var=clis.positive("Enter a positive number: ")or:importclinput.singleasclim# example use:input_vars=clim.positive("Enter a list of positive number inputs: ")DocumentationDocumentation can be found atRead the Docs.ContributingPull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.Please make sure to update tests as appropriate.TestingTests are run usingpytest.LicenseMIT
Package: clint-cli
English -EspañolCLint: Conventional commits linterCLintis a command line tool that allows you to validate messages related to git commits in different ways, ensuring
that the message isConventional Commits compliant.Technologiespython, for its awesomeness. Supported versions: 3.7.2+poetry, for packaging and dependency managementchange, to help generate the changelogInstallationFor now, the only way to installCLintis throughpip(or tools likepoetryandpipenv, which usepipbehind
the scenes), but we are working on makingCLintavailable through package managers, likehomebrew,chocolateyand
others.# Install with pip$pipinstallclint-cli# Install with poetry$poetryaddclint-cli# Install with pipenv$pipenvinstallclint-cliKey featuresValidate a commit message in the command line.Allow to handle gitcommit-msghook.Validate a commit message in the command line through pipes.Planned featuresMakepre-commitcompatible.Allow to build a commit message through command line prompts.Usage examples# Validate a sample message$clint"feat(scope): validate this message"YourcommitmessageisCCcompliant!# Validate from file$echo"feat(scope): validate this message">commit_message.txt
$clint--filecommit_message.txt
YourcommitmessageisCCcompliant!# Validate through pipes$catcommit_message.txt|clint
YourcommitmessageisCCcompliant!# Validation error for invalid type (typo)$echo"feta(scope): validate this message"|clint
type_valid:Type'feta'isnotvalid.# Enable git hook on /path/to/repo$clint--enable-hook
Enablehook:Hookenabledat/path/to/repo/.git/hooks/commit-msg# Disable git hook on /path/to/repo$clint--disable-hook
Disablehook:Hookdisabledat/path/to/repo/.git/hooks/commit-msgChangelogYou can view the history of changes in the projectchangelog.Project statusCLintis currently inbetastatus, and is under active development. The goal is to achieve at least
theplanned features, and then continue maintaining the code, making it compatible with future
versions of Python and the libraries used in the project.SourceCLinttries to be what other tools already are, like the
greatcommitlint. The difference
withsimilar toolsis that those are
built overNode.js, so they are focused onJavascriptdevelopers. If you are not, you will be forced to
installNode.jsanyway in order to use those tools.LicenseCLintis distributed under theGPL v3 license.
Package: clinterface
clinterfaceclinterfaceis a simple command line interface library to
display tab-completion prompts and interactive menus.Quick startImport the modulefrom clinterface import promptsCreate a default Selector instanceselector = prompts.Selector()or create a customized Selector instanceselector = prompts.Selector(
    shift = 1,
    indent = 3,
    align = 2,
    margin = 1,
    pad_left = 1,
    pad_right = 1,
    radiobullet = '*',
    checkbullet = '+',
)Set the options and defaults from a listselector.set_options([
    'Monday',
    'Tuesday',
    'Wednesday',
    'Thursday',
    'Friday',
    'Saturday',
    'Sunday',
])
selector.set_single_default('Friday')
selector.set_multiple_defaults(['Friday', 'Saturday', 'Sunday'])or alternativey set the options and defaults from a dictionaryselector.set_options({
    'Mon':'Monday',
    'Tues':'Tuesday',
    'Wed':'Wednesday',
    'Thurs':'Thursday',
    'Fri':'Friday',
    'Sat':'Saturday',
    'Sun':'Sunday',
})
selector.set_single_default('Fri')
selector.set_multiple_defaults(['Fri', 'Sat', 'Sun'])Prompt for a single choiceselector.set_message('Choose the best day of the week:')
selector.single_choice()Prompt for multiple choicesselector.set_message('Choose the good days of the week:')
selector.multiple_choices()
Package: clintest
clintestclintestis a Python framework that enables you to write efficient unit tests forclingoprograms quickly.
Devising and running multiple tests is a simple as:fromclintest.testimportAssert,Andfromclintest.quantifierimportAll,Anyfromclintest.assertionimportContainsfromclintest.solverimportClingosolver=Clingo("0","a.{b}.")test=And(Assert(Any(),Contains("a")),Assert(All(),Contains("b")),Assert(Any(),Contains("c")),)solver.solve(test)test.assert_()For details, please readthe documentation.
Package: clinv
WARNING: the program is still in development and not stable even though it's
on version 1.x.y. Use at your own risk.*ClinvDevSecOps command line asset inventoryHelpSeedocumentationfor more details.InstallingpipinstallclinvContributingFor guidance on setting up a development environment, and how to make
a contribution toclinv, seeContributing to
clinv.Donations<a href="https://liberapay.com/Lyz/donate"><img alt="Donate using
Liberapay" src="https://liberapay.com/assets/widgets/donate.svg"></a>
orIf you are using some of my open-source tools, have enjoyed them, and want to
say "thanks", this is a very strong way to do it.If your product/company depends on these tools, you can sponsor me to ensure I
keep happily maintaining them.If these tools are helping you save money, time, effort, or frustrations; or
they are helping you make money, be more productive, efficient, secure, enjoy a
bit more your work, or get your product ready faster, this is a great way to
show your appreciation. Thanks for that!And by sponsoring me, you are helping make these tools, that already help you,
sustainable and healthy.LicenseGPLv3
Package: clinvar-tsv
Clinvar-TSVThe code in this repository allows to first download,t hen convert ClinVar XML files into TSV files (one for b37 and b38).
The TSV files will contain one entry for each ClinVar<ReferenceClinVarAssertion>entry with important information extracted from ClinVar.
The code is used bybihealth/varfish-db-downloader.clinvar-tsv on PyPiclinvar-tsv on biocondaOverviewUsers usually run the tool by callingclinvar_tsv main.$ clinvar_tsv main \
    --cores 2 \
    --b37-path hs37d5.fa \
    --b38-path hs38.faThis will call a Snakemake workflow that will in turn do the followingDownload the latest ClinVar XML file to thedownloads/directory usingwget.Parse the XML file and convert it into a "raw" TSV file inparsedfor each the 37 and 38 release withclinvar_tsv parse_xml.
This file contains one record for each ClinVar VCV record.Sort this file by coordinate and VCV ID using Unixsort, and finally...Merge the lines in the resulting TSV file (for each genome build) by VCV ID and produce aggregate summaries for each VCV.There are two summaries:summary_clinvar_*-- which merges record which attempts to imitate theapproach taken by ClinVarsummary_paranoid_*-- which considers all assessment as equally important, whether the reporter provided assessment criteria or notReferencesDocumentation in ClinVar:https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/https://www.ncbi.nlm.nih.gov/clinvar/docs/help/https://www.ncbi.nlm.nih.gov/clinvar/docs/variation_report/Changelog0.6.3(2023-06-22)Bug Fixesimproved debugging for normalize (#29) (4124a34)memory usage in normalize command (#31) (33f8ac7)0.6.2(2023-06-21)Bug Fixesfailure to determine location only goes to debug level (#22) (76bc510)higher verbosity in Snakemake rules (#26) (a3fc327)interpret --cores argument (#24) (3b09803)map "low penetrance" to "uncertain significance" (#25) (b2708d7)no verbose output by default (#27) (0ad10cb)reduce tqdm progress display unless on TTY (#21) (770b0c8)0.6.1(2023-06-21)Bug Fixesmissing/problematic clinvar version (#19) (b11a8a4)0.6.0(2023-06-21)Featuresallow providing clinvar version (#17) (dd80f2d)Documentationadding badges to README (#15) (6e7ac01)0.5.0(2023-05-03)Featuresexport structural variants (#13) (db44d87)0.4.1Also writing outset_typecolumn (#10).0.4.0Greatly refining record merging strategy (#6).
Also, providing both a ClinVar-like and a paranoid merging scheme.Improving CI (#7)0.3.0Various refinements of the code.Adding tests and CI.0.2.2Fixing bug with quotes.0.2.1Fixing bug in setting clinical significance flags.0.2.0Complete refurbishing of XML parsing, using models based on python-attrs.Removing old tests.0.1.1Fixing installation of Snakefile.0.1.0First actual release, versioning done using versioneer.Everything is new!
Package: clio
ClioClio is a library based on SQLAlchemy that can be used to add a
publication workflow and archiving system to a database.The documentation is available athttp://packages.python.org/clio/Note that currently MySQL is a requirement (for running the tests, and
for the sequence support). This requirement is not a core requirement
of Clio however, and the main Clio codebase does not depend on it, so
it is expected to go away.CHANGES0.7 (2010-05-14)Changed the database schema: two new fields were added
(changed_timestampandcreated_userid).  Throw away theclio_testsdatabase and recreate it again to run the tests. You
will have to upgrade your existing databases as well.When a new version is created of an existing object, thechanged_useridwill be copied over from the last version. If a
new object is created from scratch, it will be thecreated_userid.changed_timestampis treated the same. This
makes it possible to detect changes between versions by comparing
the timestamps.Update documentation to include integer status codes as they appear
in the database.Updated documentation to include changed information about the
timestamps were recorded (as of 0.6), as well as the new timestamp.0.6.4 (2010-02-17)Provide an ‘update’ method for Sequence, so we can set the sequence
value. This can be useful in code that converts old databases that
already define the equivalent of ‘code’.0.6.3 (2010-02-12)Another bugfix with revert logic. Allow reverting already published
objects, as they may have relations that need to be reverted. Don’t
raise an error when trying to revert an archived object, instead
just don’t do anything.0.6.2 (2010-02-12)Fixed a bug in revert logic. Reversion of edited records should now
work better when there are relations.0.6.1 (2010-02-10)Added_actualproperty which is like _editable, except that deleted
items are not part of it.Also added is_actual method.0.6 (2010-02-10)userid tracking for workflow events.change the way timestamps are recorded so that queries for older
published items can more easily be constructed. This breaks existing
databases. We assume nobody but the author is using Clio yet.stop using pysqlite in the tests; the tests now depend on MySQL.Introduce ACTUAL_STATUSES. This is what is present in the edit UI,
except those things that were deleted. This can be handy in queries.0.5 (2009-11-16)Initial public release.Download
Package: cli-oauth2
CLI OAuth2This Python library help command-line tool authors to use
OAuth2 services. Built usingrequests-oauthlibwith parts ofgoogle_auth_oauthlib.Installationpip install cli-oauth2UsageDo something like this:fromoauthcliimportOpenStreetMapAuthauth=OpenStreetMapAuth(client_id,secret_id,['read_prefs']).auth_server(token_test=lambdar:r.get('user/details'))data=auth.get('user/details.json')ifdata.status_code!=200:print(f'Error{data.status_code}:{data.text})')else:print(f'Hello,{data.json()["user"]["display_name"]}')Tokens are saved to disk, so subsequent runs won't require authorization.Auth objects have these methods and properties:auth_server()opens a web browser and catches the response by
starting a local server.auth_code()opens a web browser and expected a user to copy the code
presented by the provider. It usesurn:ietf:wg:oauth:2.0:oobredirect uri.authorizedreturns whether there is an active access token.get,postetc call the relevantrequestsmethods, but often shadow
the server name. See the example above.sessionis the underlyingOAuth2Sessionobject.There are some predefined providers:OpenStreetMapAuthOpenStreetMapDevAuthGoogleAuthGitHubAuthMastodonAuth(requires aserverparameter)RedditAuthFacebookAuthLinkedInAuthNote that only OSM and GitHub providers were tested. I welcome
pull requests with fixes.If you need to use another provider, just subclassAuthFlowand
pass itprovider_id(the key for the stored token map),OAuth2Session(client_id, scope=scopes),auth_url,token_url, andclient_secret.CleanupThe tool stores tokens in a json in the configuration directory.
To clean some or all tokens, use theoauthcleancommand-line tool.Author and LicenseWritten by Ilya Zverev, published under Apache License 2.0.Contains portions ofgoogle_auth_oauthlibas of commit 1a9dca889357b93bdad17d75a28ac81e3ba6067f, published under
Apache License 2.0.
Package: clioecsv
This is the second python project after clioetxt.
This module is created to handle csv file data by importing data for removing duplicate data, removing unwanted header and footer, append data, merging multiple files and export list data to csv or txt file by specifying the delimiter.I will work on adding more useful function later in future.Cheny Lioe -Read the documentation after you install the package:
$ python -m pydoc -p 8000
Server ready athttp://localhost:8000/Server commands: [b]rowser, [q]uit
server> b
Then browse to clioecsv(package) to read documentationPackage contents:  clioecsv
import_csv_as_list, distinct_by_column, distinct_by_columns, distinct_list_bycolumns, sort_list, sorted_list, remove_blank_top, remove_blank_bottom, export_to_csv, append_file, merge_files, transpose, append_column, append_columns
Package: clioedb
This package using MySQLdb interface to connect to database.
This module will give convenience to fetch data as list (fetch_dbdata_list) and export it to text file (write_dbdata_file), or do all in 1 go using fetch_dbdata_file.CONTENTS:
1st Module - mydb.pydef fetch_dbdata_file(sql, db_credential, output_filename, mode=”w”, delimiter=”t”) # all in one
def fetch_dbdata_list(sql, db_credential, header=True)
def write_dbdata_file(data_as_list, output_filename, mode=”w”, header_as_list=[], delimiter=”t”)
def write_list_file(list_data, output_filename, mode=”w”)2st Module - mydbconn.pydef set_logger(log_name)
class Connect_DB: MySQLdb connection with additional feature to create log file
Package: clioetxt
This is the first python project that I created and shared with pypi.
I like working with excel file - importing and exporting data and data transformation using VBA, DAX and M-Code.
This module is created to handle text file data by importing data for searching, adding data, inverting data and formatting data.
Once the data is finalised, you can use “export_txt” function to convert it to text file.
I will work on adding more useful function later in future.Cheny Lioe -Read the documentation after you install the package:
$ python -m pydoc -p 8000
Server ready athttp://localhost:8000/Server commands: [b]rowser, [q]uit
server> b
Then browse to clioetxt(package) to read documentationPackage contents:load_txttransformmerge
Package: clioexlsx
This module is to compare excel worksheet or workbook, then highlight either the different rows or cells on the second book and then generate the output file.Cheny Lioe -Read the documentation after you install the package:
$ python -m pydoc -p 8000
Server ready athttp://localhost:8000/Server commands: [b]rowser, [q]uit
server> b
Then browse to clioecsv(package) to read documentationPackage contents: clioexlsx
compare_ws >highlight_diff_cells_comments, highlight_diff_rows
compare_wb > highlight_diff_cells_comments, highlight_diff_rows
Package: clion-live-templates-generator
clion-live-templates-generatorWhat is this?This is a tool to generate CLion's Live templates from a library of competitive programming.Only C++ is supported.How to useInstall$ pip install clion-live-templates-generatorGenerate Live templates$ lt-generate -d <YOUR_LIBRARY_DIR>Where to placeExampleIf you have already set up a live templates, please make a backup before you overwrite it.macOS$ cp -i C_C__.xml ~/Library/Application\ Support/JetBrains/CLion2020.1/templates/C_C__.xmlFor Linux and Windows, please refer to the following linkshttps://pleiades.io/help/clion/tuning-the-ide.html#config-directoryTry Live templatesrestart CLionpushcmd + j
Package: cliopts
Cliopts LibraryThe Cliopts Library is a Python library designed to simplify the process of parsing command line arguments. It provides a straightforward and intuitive API, reducing the amount of code required for cli argument parsing.InstallationTo install the Cliopts Library, run the following command in your terminal (cmd, bash, powershell, etc.):pipinstallclioptsUsageTo use the library in your code, follow these steps:Import theCliArgumentsclass from theclioptsmodule:fromclioptsimportCliArgumentsCreate an instance ofCliArgumentsand pass a list of argument names as a parameter:args=CliArguments(["options"])Access the parsed command line arguments as a dictionary using thetodict()method:print(args.todict())Thetodict()method returns a dictionary containing the parsed arguments.Run your Python script and pass command line arguments using the specified options:pytest.py--filename="filename"pytest.py-ffilename

pytest.py--f="filename"Replacetest.pywith the name of your script file andfilenamewith the desired value for the argument.ExampleLet's consider an example to illustrate how to use the cliopts Library. Suppose we are creating a Python script that takes a filename as input from the command line.Inscript.pyfile:fromclioptsimportCliArguments# Define the desired arguments: filepath, count, booleanargs=CliArguments(["filepath","count","boolean"])print(args.todict())In the command line:pyscript.py-f'/files/filename.txt'-c5-bTrueThe output ofargs.todict()will be:{"filepath":"/files/filename.txt","count":5,"boolean":True}Attach VersionIf you want your script to return a version number when prompted with--version, you can easily achieve that by passing a version string as the second parameter when creating an instance ofCliArguments.Example inscript.pyfile:fromclioptsimportCliArgumentsargs=CliArguments(["options"],"v1.0.0")You can now check the script version using the following command:pyscript.py--versionThe output will bev1.0.0, matching the second parameter.Attach Help FunctionIf you want your script to run a help program  when prompted with--help, you can easily achieve that by passing a help_function , callable as the third parameter when creating an instance ofCliArguments.Example inscript.pyfile:fromclioptsimportCliArgumentsdefhelp_function():print("HELP STRING")args=CliArguments(["options"],"v1.0.0",help_function)You can now run a help function using the following command:pyscript.py--helpThe output will beHELP STRING, matching the output of function passed as third parameter.Contact the DeveloperFor any inquiries or assistance, you can contact the developer atssanmeet123@gmail.com. Feel free to reach out with any questions or feedback you may have.
Package: clip
Clip is a command-line interface (CLI) tool that allows you to store and quickly access text snippets and manage your clipboard.InstallationInstalling Clip is simple with pip:$ pip install clipYou can also use a mirror by typing:$ pip install-ihttp://simple.crate.io/clipGetting the CodeYou can either clone the public repository:git clone git@github.com:silent1mezzo/clip.gitDownload the tarball:$ curl-OLhttps://github.com/silent1mezzo/clip/tarball/masterOr, download the zipball:$ curl-OLhttps://github.com/silent1mezzo/clip/zipball/masterOnce you have a copy of the source, you can embed it in your Python package, or install it into your site-packages easily:$ python setup.py installQuick StartYou can get started with clip quickly by typing clip in your terminal to pull up the help text.Here are a few commands you can try outCreating a List:$ clip <list_name>$ clip websitesViewing a List:$ clip <list_name>$ clip websites...Adding a snippet:$ clip <list_name> <key> <value>$ clip websites django1.5https://docs.djangoproject.com/en/dev/releases/1.5/Getting a snippet:$ clip <list_name> <key>$ clip websites django1.5'https://docs.djangoproject.com/en/dev/releases/1.5/'has been copied to your clipboardYou can also omit the list_name and it’ll try to find the key$ clip django1.5'https://docs.djangoproject.com/en/dev/releases/1.5/'has been copied to your clipboardDeleting a List/Key$ clip delete <list_name>$ clip delete websites$ clip delete <list_name> <key>$ clip delete websites django1.5Opening a snippet in your browser:$ clip open <list_name> <key>$ clip open websites django1.5$ clip open <key>$ clip open django1.5DocsDocs are coming soon!CHANGELOG0.2.0 (2012-01-19)Added Linux Support (polyphemus)Fixed bug where initial the initial value wasn’t being copied correctly (durden)0.1.0 (2012-12-20)Added ability to delete keysAdded ability to delete listsAdded READMEFixed bug where each character of a newly added snippet would be printed on new lines0.0.1 (2012-12-19)Initial Release