Saravanan666/pypi-org huggingface dataset:
Package: isedit
Interactive Score EditorA python library that combines score editing tools with audio output.OverviewInteractive Score Editor is a python library that helps bridge a music notation library (such as Lilypond via Abjad(https://abjad.github.io/index.html) to an audio player (such as pydub). The goal is to resolve the following: "Abjad provides no audio output beyond LilyPond’s built-in MIDI functionality" (https://abjad.github.io/first_steps/audience.html).A successful implementation will be helpful both for individuals creating music-composition tools / applications, as well as individuals looking to play around with music composition and sound in a notebook, and will cut the time from starting a music project to hearing actual sound (an element which has been a personal annoyance).InstallationPrerequisites:Python >=3.7,lilypond, portaudionumpy, pyaudio, midiutil, ipython, pygameTo install python packages:$pipinstallnumpy
$pipinstallpyaudio
$pipinstallmidiutil
$pipinstallipython
$pipinstallpygameLilypond (https://lilypond.org) and portaudio (http://www.portaudio.com) can be installed from their websites, with brew$ brew install lilypond
$ brew install portaudioor with apt# sudo apt install portaudio19-dev python3-pyaudio
# sudo apt install -y lilypondEnsure that lilypond runs from the command line by running$lilypond--versionQuick start exampleimportiseditPiece=isedit.Piecep1=Piece(60,"3/4")p1.addVoice("e' f' g'",4)p1.addVoice("e' f' g'",4)p1.addVoice("c'4 d'4 e'4 f'4 g'4 a'4 b'4 c''4 b'4 c''2.")p1.play()p1.getScore()The above example demonstrates the primary functionality of the piece object; the ability to play and display notes using the same object. In the newest release, the experimentalp1.getScoreObject()option makes editing notes even easier.ContributionsSee the guidelines forContributing
Package: isegeval
isegevalThis is a library to evaluate click-based interactive segmentation models. isegeval could evaluate
the number of click (NoC) performance of the given model on the given dataset.UsageYou could evaluate your model as follows. Seenotebooksfor more detail.fromisegevalimportevaluatefromisegeval.coreimportModelFactory# Each item is the tuple of an image and its correspoinding ground truth mask.dataset:Sequence[tuple[np.ndarray,np.ndarray]]=YourDataset()# A factory of your model that you want to evaluate. The factory should implement get_model method.model_factory:ModelFactory=YourModelFactory()evaluate(dataset,model_factory)Installationpipinstallisegeval
Package: iseg-nhr
iseg-nhrPython interface for an ISEG NHR high-voltage power supplyExamplefromiseg_nhrimportNHR,Polaritypsu=NHR("COM3")polarity=psu.channel0.voltage.polarityprint(polarity)psu.channel0.voltage.setpoint=1_000psu.channel0.on()print(psu.channel0.voltage.measured)print(psu.channel0.current.measured)ImplementationThe main NHR class has the following attributes and methods:NHRchannel{i}Channelclass specifying all options for a specific channelsupplySupplyclass containing the supply voltagesidentity*IDN?; model, serial number etc.status_clear()*CLSreset*RSToperation_complete*OPCinstruction_setinstruction set used by the modulelockout()Disable local control of the modulelocal()Enable local control of the modulecontrol_registermodule control registerstatus_registermodule status registerevent_registermodule event registerevent_clear()clear the module event registertemperaturemodule temperaturenumber_channelsnumber of module channelsfirmware_versionfirmware versionfirmware_releasefirmware release dateconfigconfig mode, either normal or configuration modeconfig_savesave current configurationvoltagesreturn the measured voltage of each channelcurrentsreturn the measured current of each channelsetpointsreturn the setpoint voltage of each channelon([0,1])turn on channels 0 and 1off([0,1])turn off channels 0 and 1ChannelvoltageVoltageclasscurrentCurrentclasson_stateboolean for on state of channelon()turn channel onoff()turn channel offemergency_off()turn channel off immidiately, ignoring ramp settingsemergencyboolean for channel emergencyemergency_clearclear channel emergencyevent_clear()clear channel eventscontrol_registerchannel control registerstatus_registerchannel status registerevent_registerchannel event registerpolaritychannel polaritypolarity_listlist of channel polarity optionsoutput_modechannel output modeoutput_mode_listchannel output mode optionsinhibitchannel inhibit settinginhibit_optionschannel inhibit optionsVoltagerampRampclassmeasuredmeasured output voltagesetpointvoltage setpointlimitvoltage limitmaximumnominal output voltagemaximumvoltage mode with polarity signmode_listvoltage mode optionsboundsoutput voltage boundsCurrenthas the same attributes and methods, excluding the setpointRampspeedramp speed in unit/sspeed_upupward ramp speed in unit/sspeed_downdownward ramp speed in unit/sspeed_minminimum ramp speed in unit/sspeed_maxmaximum ramp speed in unit/s
Package: isehole
ISEholeBusiness Ready Documents for Cisco Identity Services EngineCurrent API CoverageActive DirectoryActive SessionsAdmin UsersAllowed ProtocolsAuthentication DictionariesAuthorization DictionariesAuthorization ProfilesCommand SetsConditionsCSRsDACLsDeployment NodesEndpoint GroupsEndpointsEval LicensesFailure ReasonsHot PatchesIdentity GroupsIdentity Store SequencesIdentity StoresInternal UsersLast BackupLicense Connection TypeLicense Feature MapLicense RegisterLicense Smart StateLicense Tier StateNBAR AppsNetwork Access Condition AuthenticationNetwork Access Condition AuthorizationNetwork Access Condition Policy SetsNetwork Access ConditionsNetwork Access Dictionary AuthenticationNetwork Access Dictionary AuthorizationNetwork Access Dictionary Policy SetsNetwork Access DictionariesNetwork Access Identity StoresNetwork Access Policy SetsNetwork Access Security GroupsNetwork Access Service NamesNetwork Authorization ProfilesNetwork Device GroupsNetwork DevicesNode InterfacesNode ProfilesNodesPAN HAPatchesPolicy Set DictionaryPolicy SetsPortalsPosture CountProfiler CountProfilersProxiesRepositoriesSelf Registration PortalsService NamesSGT ACLsSGTsShell ProfilesSponsor GroupsSponsored Guest PortalsSponsor PortalsSystem CertificatesTransport GatewaysTrusted CertificatesVersionInstallation$python3-mvenvISE$sourceISE/bin/activate(ACI)$pipinstalliseholeUsage - Help(ISE)$isehole--helpUsage - In-line(ISE)$isehole--url<urltoISE>--username<ISEusername>--password<ISEpassword>Usage - Interactive(ISE)$iseholeISE URL: <URL to ISE>ISE Username: <ISE Username>ISE Password: <ISE Password>Usage - Environment Variables(ISE)$exportURL=<URLtoISE>(ISE)$exportUSERNAME=<ISEUsername>(ISE)$exportPASSWORD=<ISEPassword>Recommended VS Code ExtensionsExcel Viewer - CSV FilesMarkdown Preview - Markdown FilesMarkmap - Mindmap FilesOpen in Default Browser - HTML FilesContactPlease contact John Capobianco if you need any assistance
Package: iselenium
iselenium (innovata selenium)Revised Date : 2019-11-14Home-page:https://github.com/innovata/iseleniumAuthor: innovata Sambong
Author-email:iinnovata@gmail.comLicense: UNKNOWN
Description: # iselenium (innovata selenium)Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Package: is-empty
is_emptyPython package to check whether a variable is empty or not.DescriptionInstallationExamplesAuthorLicenseDescriptionThe package has two functions namedempty()andnot_empty()which can check if a variable is empty or not.The following values evaluate to empty:00.0""NoneFalse[](){}set()b""InstallationTo install, write the following command in your terminal.pipinstallis_emptyExamplesImport the functions to your code.fromis_emptyimportempty,not_emptyCheck whether a list is empty or not using empty().#The function will return True in this caseitems=[]ifempty(items):#Do somethingelse:#Do something elseCheck whether a tuple is not empty using not_empty.#The function will return True in this caseitems=(1,2,3)ifnot_empty(items):#Do somethingAuthorWahid Sadique KolyGithubPortfolioLicenseThis project is licensed under the MIT License - see theLICENSEfile for details
Package: isensing
intelligent-sensing-toolboxIntelligent Sensing Toolbox (Isensing) is a Python package that focuses on multivariate time series analysis. This toolbox includes multiple open-source machine learning algorithms and statistic calculations.In data analytics, making sense of massive numbers of data requires machine learning to work on datasets from different multiple sources in order to generate insights. For situation where a node that generates data points of multiple features in time series, massive number of nodes will make analysis more challenging.Isensing provides a list of algorithms that does features extraction, decomposition and anomaly detections.InstallationIsensing is built upon Python 3. To install Isensing, make sure Python 3 and pip is installed.pipinstallisensingDependenciespandas
numpy
scipy
sklearn
statsmodels
matplotlib
plotly
shapelyThese dependencies will be installed automatically using pip.Modulesanomaly# classAlphaHullHDR# functionsoutlier_detection()isensing_anomalies()decomposition# classRobustPCAfeatures_extraction# functionsmultiple_regression()fast_DTW()pearsonr_correlation()TutorialLinkReferenceshttps://github.com/robjhyndman/anomalous-acmhttp://blog.thehumangeo.com/2014/05/12/drawing-boundaries-in-python/https://feb.kuleuven.be/public/u0017833/Programs/pca/robpca.txtLicenseApache License 2.0
Package: isensus
isensusisensus, contraction between '(MPI-)IS' and 'census' is a tool for the IT systems admins of the Max Planck Institute for Intelligent System to track the status of their users.It is no much more than a fancy todo list reading a database of users encapsulated in a JSON formated file.RequirementsPython 3.8or higher.InstallationAfter cloning the repository:cdisensus
pipinstall.or directly:pipinstallisensusTestsTo run the tests:gitclonehttps://github.com/MPI-IS/isensus.gitcdisensus
python3-mpytest./tests/tests.pyDocumentationSee:https://mpi-is.github.io/isensus/To build the documentation:pipinstallsphinxsphinx-bootstrap-theme
gitclonehttps://github.com/MPI-IS/isensus.gitcdisensuscddoc
makehtmlThe html documentation will be built in thebuildfolder.AuthorVincent Berenz, Max Planck Institute for Intelligent SystemsLicenseBSD-3-Clause (see LICENSE.md).Copyright© 2021, Max Planck Society
Package: iseqcbioportal
ISEQcBioPortalScripts that allow you to:Create/Update database fromcBioPortalAnnotate VCF with information such as:number of samples with one or more mutationspercentage of samples with one or more mutationsInstall iseqcbioportal libraryOptional steps (create virtual environment):python3 -m venv venv
source venv/bin/activateObligatory steps:python3 -m pip install --upgrade pip
pip3 install iseqcbioportalRequirementspython >=3.6pandas >= 1.4.2requests >= 2.28.1SQLAlchemy >= 1.4.0loguru >= 0.6.0pysam >= 0.21.0Create databasescreate_cbioportal_databaseAnnotate VCFvcf_annotate_cbioportal --input-vcf "/path/to/input.vcf.gz" \
                        --studies "studyId" \
                        --output-vcf "/path/to/output.vcf.gz"
Package: iseqclinicaltrials
Iseq clinical trialsA bunch of scripts to operate on clinical trials API offlineInstallOptional steps (create virtual environment):python3 -m venv venv
source venv/bin/activateObligatory steps:python3 -m pip install --upgrade pip
pip install iseqclinicaltrialsSet up a databaseYou need to pass the conditions or diseases and other terms according to clinicaltrials.gov as the files with comma separated valuesget_content_as_sql -d conditions_or_diseases.txt -o other_terms.txtwhere conditions_or_diseases.txt content is:Acute Myeloid Leukemia,Myelodysplastic Syndromes,Chronic Myeloid Leukemiaand other_terms.txt content is:BRAF,MPL,GATA2,IKZF1,TP5,JAK1,KMT2C,PAX5,SF3B1,DNMT3A,BCOR,CHEK2,U2AF1,TGIF2LY,BIRC3,ASXL1,GNAS,RAD21,CREBBP,STAT5B,CEBPA,ZRSR2,RUNX1,CDKN2A,NFE2,STAG2,BTK,EZH2,AMELY,EP300,PPM1D,FBXW7,IDH2,NF1,NPM1,TET2,CUX1,GATA1,TP53,CTNNA1,AMELX,FLT3,PHF6,STAT3,BCORL1,CALR,JAK2,NOTCH1,ETV6,SETBP1,IDH1,SRSF2,WT1,KIT,MYD88,KRAS,TGIF2LX,JAK3,XPO1,SH2B3,CSF3R,CXCR4,PLCG2,CBL,KMT2A,ABL1,GNB1,PTPN11,PTEN,IDH2 IKZF1,NRAS,PDGFRA,HRAS,DDX41,IRF1,ETKN1Do not be surprised if the waiting time takes a while: there is sleep(5) after each query online in order to not make too many requests.Get all records in single .csv file with the limit of 20 latest studiesget_all_records -l 20 -p clinicaltrials.dbThe results will be saved into single .csv file. The structure of the header will be similar to the example below (get_specific_records). In that case filename will beTOP_20_all_records.csv.Get all records in .csv files (each disease-term combination with any records in it) with the limit of 20 latest studiesJust simply add-sflag to the previous command. It stands for--split-into-files.get_all_records -l 20 -p clinicaltrials.db -sThe results will be saved into catalog namedclinicaltrials_records. Each name and header structure will be similar to the example below (get_specific_records).Get all records in single .csv file with no limitAdd-nflag to the previous command. It means--no-limit.get_all_records -p clinicaltrials.db -nDo not use -l and -n flags together. They are mutually exclusive.Get latest 20 studies for conditon or disease and other termget_specific_records -c "lung cancer" -t "ALK" -p clinicaltrials.db -l 20There will appear a file named after combination of condition name and other term (TOP_20_lung_cancer_ALK.csv).
It's header will look like:nct_number	study_title	study_status	conditions	drugs	phases	start_date	locations	disease	term	countriesYou can use defined above flags to limit the number of the results.REMEMBERCurrently we query clinicaltrials online and just pick results from offline API.
In order to enable such quering with synonyms as available online UMLS needs to be implemented offline.
Package: iseqdockertools
Install iseqdockertools libOptional steps (create virtual environment):python3 -m venv venv
source tutorial_env/bin/activateObligatory steps:python3 -m pip install --upgrade pip
pip install iseqdockertoolsFile containing versions for tools: docker-versions.jsonIn workflows' directory it is located insrc/main/resources/docker-versions.jsonIt contains info about the tools' versions in .json format.
For example:{
    "PHARMCAT_VER": "2.3.0",
    "FASTQC_VER": "0.12.1"
}To update it you need to use iseqresources.
The details are there:https://gitlab.com/intelliseq/iseqresourcesBuild docker imagesScript automatically takes name and version of the docker image from its header.
It has to be in the following format (at the beginning of the Dockerfile):# name: name
# version: 1.0.0If you want to update the tools' versions automatically:Check if it is generated by iseqresources to the docker-versions.jsonAdd to the beginning of dockerfile (belowFROM)ARG TOOL1_VER
ARG TOOL2_VERThe version (if found) will be automatically taken from the docker-versions.jsonBuilding has default context to repository and you can use ADD with path to the files from here.
Default option is to push to the dockerhub. If the dockerfile exists it won't be pushed. To develop dockerimage locally use flag --nopush.Usage (when you are in workflows' root directory):dockerbuilder -d path/to/dockerfilefor example:dockerbuilder -d src/main/docker/reports/reports/DockerfileScript dockerbuider contains --help section with all the flags:Print 'docker build' and 'docker push' logsdockerbuilder -d path/to/dockerfile --quietDo not push docker image(s) to repositorydockerbuilder -d path/to/dockerfile --nopushDo not use cache when building the docker image(s)dockerbuilder -d path/to/dockerfile --nocacheBuild separate images for all chromosomesdockerbuilder -d path/to/dockerfile --chromosomeProvide custom path to docker-versions.jsondockerbuilder -d path/to/dockerfile --versionsIgnore docker-versions.jsondockerbuilder -d path/to/dockerfile --ignore-versionsIgnore version number from image name (for example # name tool-1.15b version won't be updated to the newest found (tool-1.18c) in docker-versions.json)dockerbuilder -d path/to/dockerfile --ignore-name-versionPush image even if exists in repositorydockerbuilder -d path/to/dockerfile --forcepushSet current directory as contextdockerbuilder -d path/to/dockerfile --contextYou can mix flags whenever you need to.Name of the docker image vs location of its dockerfileLocation:src/main/docker/[catalog-name]/[version]/DockefileName of the image:intelliseqngs/[catalog-name]:[version]More info here:https://workflows-dev-documentation.readthedocs.io/en/latest/Docker.html
Package: iseqmetatools
Iseq metaA bunch of scripts to operate on iseq metaMore info here:https://workflows-dev-documentation.readthedocs.io/en/latest/index.htmlInstallOptional steps (create virtual environment):python3 -m venv venv
source venv/bin/activateObligatory steps:python3 -m pip install --upgrade pip
pip install iseqmetatoolsParsing google spreadsheet to metaYou can parse inputs, outputs or workflows parameters for the workflow.
Example use for workflows parameters (after installing):parse_inputs \
  --workflow-name "germline" \
  --credentials "/path/to/credentials.json" \
  --meta-json "/path/to/wdl/meta.json" \
  --spreadsheet-key "key" \
  --output-meta-json "/path/to/output/meta.json"parse_outputs \
  --workflow-name "germline" \
  --credentials "/path/to/credentials.json" \
  --meta-json "/path/to/wdl/meta.json" \
  --spreadsheet-key "key" \
  --output-meta-json "/path/to/output/meta.json"parse_workflows \
  --workflow-name "germline" \
  --credentials "/path/to/credentials.json" \
  --meta-json "/path/to/wdl/meta.json" \
  --spreadsheet-key "key" \
  --output-meta-json "/path/to/output/meta.json"More info here:https://workflows-dev-documentation.readthedocs.io/en/latest/Developer%20tools.html#parsing-google-spreadsheet-to-metaGenerating meta.json from .wdl file codeThere are two ways to generate meta.json from .wdl file.First way, when deprecated meta is present:parse_meta \
  --path /path/to/wdlSecond way, when deprecated meta is not present or is not complete:create_meta \
  --path /path/to/wdl > /new/meta/directoryYou can also change templates configuration path (if the fields.json change before iseqmetatools update):create_meta \
  --path /path/to/wdl
  --templates-path /path/to/templates > /new/meta/directoryMore info here:https://workflows-dev-documentation.readthedocs.io/en/latest/Developer%20tools.html#creating-meta-json-from-scratchConverting meta.json after an update of meta rulesYou can convert meta.json just by providing a json file containing translated new keys and removed old keys in meta.json conversion.
An example of this file:{
    "rename": {
        "workflows": {},
        "inputs": {"extension": "constraints.extensions", "paired": "constraints.paired", "groupname": "groupId"},
        "outputs": {"groupname": "groupId"},
        "groups": {"hReadableName": "name", "minInputs": "constraints.minInputs", "maxInputs": "constraints.maxInputs"}
    },
    "remove": {
        "workflows": ["keywords"],
        "inputs": ["multiselect", "constraints.multiselect"],
        "outputs": [],
        "groups": []
    }
}"Rename" section stands for changing keys names or even embedding keys into subdict structure.
"Remove" section takes list of parameters to remove.After preparing such a file you can start conversion:convert_meta \
  --input-meta-json /path/to/meta.json
  --input-dict-json /path/to/translated-keys.json
  --output-meta-json /path/to/meta.json
Package: iseqpharmgkb
ISEQPHARMGKBScripts that allow you to:Create databases (clinical and variant) fromPharmGKBGet clinical or variant annotations from PharmGKB for own queriesInstall iseqpharmgkb libraryOptional steps (create virtual environment):python3 -m venv venv
source venv/bin/activateObligatory steps:python3 -m pip install --upgrade pip
pip install iseqpharmgkbRequirementspython >=3.6pandas >= 1.2.4requests >= 2.22.0SQLAlchemy >= 1.3.17Create databasescreate_databaseGet clinical annotationsget_clinical_annotation --queries /path/to/query.json --output-filename /output/filename.jsonAn examplequery.jsonfile should look like this:{
    "rs1050828": "CC",
    "rs5030868": "CC",
    "CYP2D6*2": "*2",
    "CYP2D6*1": "*1/*1"
}Get variant annotationsget_variant_annotation --queries /path/to/query.json --output-filename /output/filename.jsonAn examplequery.jsonfile should look like this:{
    "rs1050828": "CC",
    "rs5030868": "CC",
    "CYP2D6*2": "*2",
    "CYP2D6*1": "*1/*1"
}
Package: iseqresources
Iseq resourcesScripts that allow you to:Adding a new tool to the JSON fileIterating over the tools in the JSON file and checking the latest version, and in the case of a new version, adding a tooltip to JIRAUpdate existing tool/database record in JSON after updating tool/databaseUpdate docker-versions.json in workflows repositoryInstallpip install iseqresourcesRequirementspython >=3.6jira >= 3.3.0requests >= 2.22.0python-gitlab >= 3.7.0Adding a new toolFirst specify if you want to add tool or database. Input JSON file (--input-json) is from gitlab repo at pathjson/tools.jsonorjson/databases.json. Default isjson/tools.json.add_tool --toolsoradd_tool --databasesYou can also run on a local file:add_tool \
    --input-json "/path/to/json/tools_or_databases.json"It is better to add new tool directly to json file.Checking versions and add task to JIRAInput JSON file (--input-jsonand--info-json) are from gitlab repo at pathjson/tools.jsonorjson/databases.jsonandjson/info.json. Default isjson/tools.json.check_versions --toolsorcheck_versions --databasesYou can also run on a local files:check_versions \
    --input-json "/path/to/json/tools_or_databases.json" \
    --info-json "/path/to/json/info.json"Update existing tool/database record in JSONInput JSON file (--input-json) is from gitlab repo at pathjson/tools.jsonorjson/databases.json. Default isjson/tools.json.update_record --toolsorupdate_record --databasesYou can also run on a local file:update_record \
    --input-json "/path/to/json/tools_or_databases.json"Update docker-versions.json in workflows repository (based on tools.json)After updating tools.json atjson/tools.jsonyou need to get into root directory of workflows repository and type in bash:update_docker_versionsFor possible customization options and help use flag-hupdate_docker_versions -h
Package: iservice
iserviceHelper class to make FastAPI dependencies with ease.Simple use# iservice_a.pyimporttypingimportiserviceclassServiceA(iservice.Service,typing.Protocol):@staticmethoddefsend(name:str)->None:...# service_a1.pydefsend(name:str)->None:print(f"Hello{name}")# service_a2.pydefsend(name:str)->None:print(f"Greetings{name}")# service_a.pyimportiservice_aimportservice_a1importservice_a2def_welcome_user(service:iservice_a.ServiceA,name:str)->None:service.send(name)# inject will provide an inferred type that are matching the expected signature# (str) -> Nonehello=iservice.inject(_welcome_user,service_a1)greeting=iservice.inject(_welcome_user,service_a2)In this case, in case of incorrect calls, mypy will raise errors like:hello(1)# Argument 1 has incompatible type "int"; expected "str"greeting(1)# Argument 1 has incompatible type "int"; expected "str"
Package: iservices.rssdocument
Introductioniservices.rssdocument: A dynamic RSS content-type for ploneThis is a dynamic RSS content-type for plone. This idea comes from the
necessity to insert or embedd RSS content within Plone. This products
will provide a simple content-type which will display RSS feeds by using jQuery,
which is already available from Plone.You will only need to add the RSS feed URL and configure how many items to
display. The jquery app will download the RSS fedd and show it inside plone.ChangelogPlease, see README.txt instead.0.5 (unreleased)New automatic id generation for div container [erikriver]0.4.1 (unreleased)Added MANIFEST.in so all files included when creating an egg from this package [kcleong]0.4 (unreleased)Plone 4.1 compatibility0.3 (unreleased)Working product. Changes:Full Test CoverageFully working0.2 (unreleased)Don’t remember0.1dev (unreleased)Initial releaseChangelogPlease, see README.txt instead.0.1dev (unreleased)Initial release