Saravanan666/pypi-org huggingface dataset:
Package: marbl-python
Marbl-Python is a Python implementation of theMarbl specificationfor normalized representations of Markov blankets in Bayesian networks.It provides objects and methods for serializing and hashingMarbls(Markov
blankets normalized per the Marbl spec), and unordered collections of them.InstallationTo install the latest release:pipinstallmarbl-pythonTo install the latest development version:pipinstall"git+https://github.com/wmayner/marbl-python@develop#egg=marbl-python"UsageSee theAPI documentation.
Package: marburg-biobank
marburg_biobankIntroductionThe marburg_biobank python module offers a high level interface to the data sets
stored in the [Ovarian Cancer Effusion Biobank and Database])(https://www.ovara.net/biobank).The basic usage is as follows:importmarburg_biobankdb=marburg_biobank.OvcaBiobank("marburg_ovca_revision_15.zip")#  you need to download that file from your biobank.print(db.list_datasets())df_wide=db.get_wide('transcriptomics/rnaseq')# to retrieve the data in a one sample per column / one row per measured variable formatdf_tall=db.get_dataset('transcriptomics/rnaseq')# to retrieve the data in one row per data point formatData formats availablewideUsingdb.get_wide(dataset):A pandas DataFrame that looks like thisIndexPatient12, TAMPatient12, TUPatientX, CompartmentVariableA, unitA23.23112.2nanVariableB, unitB3.2312.212.7Caveats: If a dataset has only one compartment, the compartment information is ommited by get_wide(), unless .get_wide(standardized=True) is used.
The same applies for the unit in the index.
If there is a 'name' column in dataset, it get's added to the index, regardless of the value of standardized.tallUsing:db.get_dataset(dataset)):A pandas DataFrame that looks like thisvariableunitpatientcompartmentvalueoptional columns...variableAunitAPatient12TAM23.23variableAunitAPatient12TU112.2variableBunitBPatient13TAM3.23variableBunitBPatient13TU12.2This is the internal storage format.compartmentsCompartments are an abstraction on top of 'cells' and 'bio-liquid'. Examples are Tumor associated macrophages (TAMs), Tumor cells (TU), ascites, blood...db.get_compartments()provides a listDatasetsDatasets are organized three levels deep. The first one defines the whether
you're looking t ex-vivo (=primary) data or in-vitro experiments (=secondary)
or literature data (=tertiary).
The second level defines *omics being measured (transcriptomics, proteomics, ... or 'clinical'), while
the third levels defines the actual method (RNaseq, FACS,...)Survival data is in primary/clinical/survival.Please remember: if usinghttps://pypi.python.org/pypi/lifelines, censored and event are negations of each other.Excluded patients:Exclusion can either be on a patient, or a patient+compartment level.
In addition, there is per dataset exclusion and global exclusion.Exclusion is by default applied to db.get_wide(), but not to db.get_dataset(),
you can change the default by passing apply_exclusion=True|False.Exclusion information can be retrieved by db.get_excluded_patients(dataset),
which return a set of patients (or patient+compartment tuples),
or db.get_exclusion_reasons(), which lists why the exclusion happend.
Package: marc2excel
Convert MARC files to Excel spreadsheets and vice-versa.InstallationFrom PyPI:pip install marc2excelFrom GitHub:git clone https://github.com/alexandermendes/marc2excel
cd marc2excel
python setup.py installUsageRunning scripts:The following scripts can be run from anywhere, once the package is
installed.Converting MARC to Excel:Usage: marc2excel_cli.py [OPTIONS] MARC_PATH

  Convert MARC_PATH to an Excel spreadsheet.

  The path to the saved spreadsheet will be the same as MARC_PATH but with a
  .xlsx extension.

  If a directory is specified for MARC_PATH all files found in that
  directory with .mrc, .marc or .lex extensions will be converted and the
  .xlsx versions saved in the same directory.

  The option to force utf-8 encoding is included to help deal with any
  poorly formed MARC records that you might encounter. For example, those
  that are utf-8 encoded but without the leader set appropriately, or those
  that contain mostly utf-8 data but with a few non-utf-8 characters (any
  non-utf-8 characters will be replaced with the official U+FFFD REPLACEMENT
  CHARACTER).

Options:
  -d        Specify a directory for MARC_PATH.
  --silent  Don't display progress.
  --utf8    Force utf-8 encoding.
  --help    Show this message and exit.Converting Excel to MARC:Usage: excel2marc_cli.py [OPTIONS] EXCEL_PATH

  Convert EXCEL_PATH to an MARC file.

  The path to the saved MARC file will be the same as EXCEL_PATH but with a
  .mrc extension.

  If a directory is specified for EXCEL_PATH all files found in that
  directory with .xlsx extensions will be converted and the .mrc versions
  saved in the same directory.

  The option to force utf-8 encoding is included to help deal with any
  poorly formed data found in the spreadsheet. For example, where rows
  contain data that is utf-8 encoded but without the leader set
  appropriately, or rows that contain mostly utf-8 data but with a few non-
  utf-8 characters (any non-utf-8 characters will be replaced with the
  official U+FFFD REPLACEMENT CHARACTER).

Options:
  -d        Specify a directory for EXCEL_PATH.
  --silent  Don't display progress.
  --utf8    Force utf-8 encoding.
  --help    Show this message and exit.Running from Python:Converting MARC to Excel:importmarc2excelmarc2excel.marc2excel('path/to/file.mrc','path/to/save/file.xls')Converting Excel to MARC:importmarc2excelmarc2excel.excel2marc('path/to/file.xls','path/to/save/file.mrc')Spreadsheet guidelinesSpreadsheets require a header row that must adhere to the following
guidelines:The field tag is required for all fields.For non-control fields, the indicator and subfield tags are also
required.Backslashes should be used to indicate blank spaces in indicators.Subfields should be prepended with a dollar symbol.Leaders can be added from a column with the heading LDR (optional).Repeated fields can be created by appending headers with [number].Example:001245 \\ $a852 \1 $j852 \1 $j [2]123some_valueanother_valueanother_valueTestingTests can be run using:python setup.py test
Package: marcelle
Marcelle - Python PackageA python package for interacting with a Marcelle backend from python.See:http://marcelle.devStatus ⚠️Marcelle is still experimental and is currently under active development. Breaking changes are expected.Installingpipinstall.Basic UsageKeras CallbackfrommarcelleimportMarcelleCallbackmrc_callback=KerasCallback(backend_root="http://localhost:3030",disk_save_formats=["h5","tfjs"],remote_save_format="tfjs",model_checkpoint_freq=None,base_log_dir="marcelle-logs",run_params={},)model.fit(# ...callbacks=[mrc_callback,# other callbacks])Writer (for custom training loops)frommarcelleimportWriterwriter=Writer(backend_root="http://localhost:3030",disk_save_formats=["h5","tfjs"],remote_save_format="tfjs",base_log_dir="marcelle-logs",source="keras",)writer.create_run(model,params,loss.name)writer.train_begin(epochs)forepochinrange(epochs):# ...logs={"loss":1.3,"accuracy":0.7,"val_loss":2.3,"val_accuracy":0.52,}assets=["path/to/asset1.wav","path/to/asset2.wav"]self.writer.save_epoch(epoch,logs=logs,save_checkpoint=True,assets=assets)writer.train_end(save_checkpoint=True)Batch uploadUseful when training was done offline or connection to server failed during the training.fromglobimportglobimportosfrommarcelleimportMarcelleRemote,MarcelleUploaderif__name__=="__main__":LOG_DIR="marcelle-logs"uploader=MarcelleUploader(MarcelleRemote(backend_root="http://localhost:3030",save_format="tfjs",source="keras",))runs=[dfordinglob(os.path.join(LOG_DIR,"*"))ifos.path.isdir(d)]forruninruns:uploader.upload(run)✍️ Authors@JulesFrancoise@bcaramiaux
Package: marcelotsvaz-python-project-template
🐍 Python Project TemplateTemplate to quickly bootstrap Python projects.UsesPDMto manage dependencies, build distributions and publish to package repositories.✨ FeaturesCentralized configuration inpyproject.tomlDependency management withPDMTesting withunittestLinting withPylintIntegration withVisual Studio CodeBuilding and publishing toPyPIDocumentation hosted onGitLab PagesCI/CD withGitLabSeveral useful examplesType hintsLoggingCLIFor a detailed description of all features check thedocumentation.ContributingTODO: Contributing.
Package: marcflow
MarcflowMarcflow is a Python library for MARC (MAchine-Readable Cataloging) data
preprocessing. It can be used to extract data from records that meet specified
criteria and convert the data to JSON.Generalmarcflow.select(statement)Specifies a scheme for parsing MARC records.statement(str): field-expr [condition-expr]field-expr indicates the (sub)fields whose values will be
extracted.condition-expr, if given, indicates the condition(s) that
(sub)fields must satisfy to be selected.Returns True if the parameter is a valid statement and False otherwise.marcpick.marc(source)Parses MARC records and extracts data based on specific criteria.source(str|TextIO): one or more MARC recordsReturns a generator that can be iterated over to obtain the extracted data.Installation$ pip install marcflowUsage>>> from marcflow import MarcFlow
>>> marcflow = MarcFlow()
>>> # The wildcard _ (Low Line) represents any single character in tags,
>>> # indicators and subfield codes.
>>> statement = 'LDR 001 010a 5__a (200__a\(?i\)java & !200__a\(?i\)script) \
... | 606__a^JAVA'
>>> marcflow.select(statement)
True
>>> with open('test.mrc', encoding='UTF-8') as fr:
...     data = marcflow.marc(fr)
...     next(data)
Package: march
MARCH - Multi Arch Wrapper ScriptUtility program for the execution of machine-optimised alternatives.
The general system setting is done via kernel command line: march={v2,v3,v4}
If the parent directory of some program exists with a -march suffix and contains
an executable with the same name, run that instead of program.ExampleExisting layout/usr/bin/prog       # standard program
/usr/bin-v3/prog    # optimised version of program

# executing prog via march

march -mv3 prog

# result in execution of /usr/bin-v3/progNotesThe same holds true, if you insert/usr/bin-v3before/usr/binin$PATHof course, butmarchdoes not require any$PATHmodification and will work
with executables in non-standard paths as well.
Package: marchanddesable
Turn off your server when you sleep.What it doesGive it some IPs, and it will call halt five minutes after the given computers have stopped pinging. Except if we are
in the middle of the day or if we are disconnected from the internet (because we don’t want the computer to stop just
because the network went off).InstallThe easiest way is to just grab the filemarchanddesable.py.If you want to install it,Marchanddesableis onpypi, so this should do the trick :pip install marchanddesableArch users, you can installmarchanddesablefrom AUR.UsageTo halt the current machines 5 minutes after both 192.168.0.1 and 192.168.0.2 stop pinging,
put this in your crontab. It will also log to the given file and rotate every night:* * * * *       /usr/bin/marchand 192.168.0.1 192.168.0.2 -f /var/log/marchanddesable.logIf you don’t like cron, and think running daemon or programs in screen are better, you can usemarchand -l 192.168.0.1 192.168.0.2TODOThese features may or may not be implemented at some point :Play a sound to warn when the machines stopped pingingA way to tell it not to halt the computer tonight without having to disable itA way to change the rules without having to modify the scriptIf you want any of those, or anything else, give me a shout.
Package: marcosgeo-bumbo
Bumbo: Python Web Framework built for learning purposesBumbo is a Python web framework built for learnig purposes. You can learn this ontestdriven.io.It's a WSGI framework and can be used with any WSGI application server such as Gunicorn.Installationpipinstallmarcosgeo-bumboHow to use itBasic usagefrombumbo.apiimportAPIapp=API()@app.route("/home")defhome(request,response):response.text="Hello from HOME page"@app.route("/hello/{name}")defgreeting(request,response,name):restponse.text=f"Hello,{name}"@app.route("/book")classBookResouce:defget(self,req,resp):resp.text="Book Page"defpost(self,req,resp):resp.text="Endpoint to create a book"@app.route("/template")deftemplate_handler(req,resp):resp.body=app.template("index.html",context={"name":"Bumbo","title":"Best Framework"}).encode()Unit TestsThe recommended way of writing unit test is withpytest.  There are two built in fixtures that you may want to use when writing unit tests with Bumbo. The first one isappwhich is an instance of the mainAPIclass:deftest_route_overlap_throws_exception(app):@app.route("/")defhome(req,resp):resp.text="Welcome Home."withpytest.raises(AssertionError):@app.route("/")defhome2(req,resp):resp.text="Welcome Home 2."The other ons isclientthat you can use to send HTTP requests to your handlers. It is based on the famousrequestsand should fell very familiar:deftest_parameterized_route(app,client):@app.route("/{name}")defhello(req,resp,name):rest.text=f"hey{name}"assertclient.get("http://testserver/marcos").text=="hey marcos"TemplatesThe default folder for templates isapp/templates. You can change it when initializing the mainAPI()class:app=API(templates_dir="templates_dir_name")Then you can use THML files in that folder like so in a handler:@app.route("/show/template")defhandler_with_template(req,resp):resp.html=app.template("example.html",context={"title":"Awesome Framewokr","body":"welcome to the future!"})Static FilesJust like templates, the default folderfor static files isstaticand you can overwrite it:app=API(static_dir="static_dir_name")Then you can use the files inside this folder as HTML templates:<!DOCTYPE html><htmllang="en"><head><metacharset="UTF-8"><title>{{title}}</title><linkhref="/static/main.css"rel="stylesheet"type="text/css"></head><body><h1>{{body}}</h1><p>This is a praragrapha</p></body></html>MiddlewareYou can create custom middleware classes by inheriting from thebumbo.middleware.Middlewareclass and overriding ist two methods:frombumbo.apiimportAPIfrombumbo.middlewareimportMiddlewareapp=API()classSimpleCustomMiddleware(Middleware):defprocess_request(self,req):print("Before dispatch",req.url)defprocess_response(self,req,resp):print("After dispache, req.url)add.add_middleware(SimpleCustomMiddleware)
Package: marcus
Index and search browser bookmarks from the command line.Works with Chrome and Firefox.Installpip install marcus(hint: use--userto install into~/.local/bin/)Then runmarcus(or~/.local/bin/marcus) with no arguments to
get help.Index your bookmarksThe first time you run this it will take a while, depending on how many
bookmarks you have.$ marcus --index ~/.config/chromium/Default/Bookmarks
Start 2017-01-12 21:20
Indexing 10 / 1081 bookmarks
Indexing https://www.mozilla.org/en-US/firefox/central/ (0 / 1081) 0% done
Indexing http://www.ubuntu.com/ (1 / 1081) 0% done
...To find a list of bookmark files belonging to the current user:$ marcus --find-bookmark-filesFirefox on Linux example:$ marcus --index ~/.mozilla/firefox/*.default/places.sqliteFull-text bookmark search$ marcus privacy
found 84

1.  Privacy and control need to be put back into the hands of the individual – Decentralize Today
    https://decentralize.today/privacy-and-control-need-to-be-put-back-into-the-hands-of-the-individual-301c4c318ef8#.9uk0e4ysu
    Added: 2016-09-05
    > ...a worldwide problem. **Privacy** and control need...which will bring...
    > ...**privacy**, money and communication...be blended into one **privacy**...
    > ...ecosystem. The pinnacle...

2.  How ‘strong anonymity’ will finally fix the privacy problem
    http://venturebeat.com/2016/10/08/how-strong-anonymity-will-finally-fix-the-privacy-problem/
    Added: 2016-10-09
    > ...You have zero **privacy** anyway. Get over...to protect their **privacy** in...
    > ...an online world...

3.  Germany planning to ′massively′ limit privacy rights | Germany | DW.COM | 25.11.2016
    http://m.dw.com/en/germany-planning-to-massively-limit-privacy-rights/a-36529692
    Added: 2016-12-02
    > ...major limitation of **privacy** rights in Germany...massive" erosion of...
    > ...**privacy** in Germany. De Maiziere...authorities, say **privacy** groups "The...
    > ...limitation...

...You can also usemore complex
querieslikeprivacy AND github.comfor example.Automated indexingEdit your user’s crontab withcrontab-eand then add a line at the
bottom like this:17 * * * * $PATH-TO-BINARY/marcus --index ~/.config/chromium/Default/Bookmarks >> $HOME/.marcus.log 2>&1Which will run the indexer every hour at 17 minutes past the hour. Pages
which have already been indexed will not be indexed again.Patches welcome. Enjoy!
Package: marcusdb
# mdbA client to [my database](https://db.marcusweinberger.repl.co)## Installationpip install marcusdbSorry,mdbwas taken## Usageimport mdbkeys = mdb.generate()
# {“priv”:”XXXXXXXX”, “pub”:”XXXXXXXXX”}
# tip: the public key is just a hashed version of the private key [sha256(sha256(key) + salt)]
# protip: you can choose your own key using mdb.register(“YOUR_TOKEN_HERE”), but remember - if your token isn’t secure, someone could crack the hashprivclient = mdb.Client(keys[‘priv’])
pubclient = mdb.Client(keys[‘pub’])
# yep, both use the same class. attempting priv methods with pub keys just dont workprivclient.store(“hello”, “world”)
# can store all types of data by using the jsonpickle librarypubclient.retrieve(“hello”)
# > “world”pubclient.store(“test”, “wa”)
# will return Falseprivclient.delete(“hello”)
# returns Trueprivclient.unregister(conf=True)
# conf defaults to false, when false will do nothing
# deletes your account from the DB, making both keys invalid and out of the system## Github: [https://github.com/AgeOfMarcus/mdb](https://github.com/AgeOfMarcus/mdb)
## View post on repl.it: [post & demo](https://repl.it/talk/share/MDB-A-database-with-seperate-readwrite-keys-perfect-for-small-projects-to-store-JSON/35762)
Package: marcuslion
ml-lib-pythonMarcus Lion Python Libraryhttps://www.google.com/search?q=youtube+pypi&rlz=1C1JSBI_enUS1066US1066&oq=youtube+pypi&gs_lcrp=EgZjaHJvbWUyBggAEEUYOTIICAEQABgWGB4yCAgCEAAYFhgeMgoIAxAAGA8YFhgeMggIBBAAGBYYHjIICAUQABgWGB4yCAgGEAAYFhgeMgoIBxAAGIYDGIoFMgoICBAAGIYDGIoFMgoICRAAGIYDGIoF0gEINTE1OWowajeoAgCwAgA&sourceid=chrome&ie=UTF-8#fpstate=ive&vld=cid:882dd603,vid:v4bkJef4W94,st:0https://packaging.python.org/en/latest/tutorials/packaging-projects/py -m pip install --upgrade pip
py -m pip install --upgrade build
py -m pip install --upgrade twine
py -m buildTestpy -m twine upload --repository testpypi -u __token__ --skip-existing dist/*
password:provide tokenReleasepy -m twine upload -u __token__ --skip-existing dist/*
password:provide tokenLocal Installpip install -i https://test.pypi.org/simple/ marcuslion --upgrade
pip install -i https://pypi.org/simple/ marcuslion --upgrade
Package: marcus-main
Marcus mainAn assignment that refactors the main function from Max's code into its own libraryInstallationpip install marcus-mainGet startedHow to run Max's code using the MarcusMain libraryfrommarcus_mainimportMarcusMain# Instantiate a MarcusMain object and save it to a variablerun=MarcusMain()# Call the main function. We have to pass the main function a number of arguments that are defined elsewhere in Max's code.run.main(currency_pairs,initialize_raw_data_tables,initialize_aggregated_tables,aggregate_raw_data_tables,reset_raw_data_tables,ts_to_datetime,)
Package: marcxml2csv
marcxml2csvA simple converter of (possibly gzipped) MARCXML/PICAXML to (possibly gzipped) CSV/TSV.The resulting CSV/TSV has been designed to be easy to use as a data table, but also to retain all ordering informaation in the original when such is needed. The format is as follows:record_number,field_number,subfield_number,field_code,subfield_code,valueHere,record_numberidentifies the MARC/PICA+ record, whilefield_numberandsubfield_numbercan be used for more exact filtering / reconstructing the original field flow if needed.For the MARC leader and control fields,subfield_numberwill be empty.For MARC data fields,ind1andind2values are reported as separate rows with thesubfield_codebeingind1orind2, but only when non-empty. The also have an emptysubfield_number.InstallationInstall from pypi with e.g.pipx install marcxml2csv.UsageUsage: marcxml2csv [OPTIONS] [INPUT]...

  Convert from MARCXML (gz) input files into (gzipped) CSV/TSV

Options:
  -o, --output TEXT  Output CSV/TSV (gz) file  [required]
  --help             Show this message and exit.Usage: picaxml2csv [OPTIONS] [INPUT]...

  Convert from PICAXML (gz) input files into (gzipped) CSV/TSV

Options:
  -o, --output TEXT  Output CSV/TSV (gz) file  [required]
  --help             Show this message and exit.Files will be read/written using gzip if the filename ends with.gz. TSV format will be used if the output filename contains.tsv, otherwise CSV will be used.
Package: marcxml2mods
IntroductionThis package provides conversion functions to convert data fromMARC XML/OAIformat toMODSXML format used inNational Library of the Czech Republic(NK CZ).DocumentationFull module documentation and description can be found at Read the Docs:http://marcxml2mods.readthedocs.org/ContributorsBystroushaak <bystrousak@kitakitsune.org>, DeveloperChangelog0.2.5Postprocessing API redefined slightly.Added MARC XML record parameter for all postprocessing functions.Added fix_missing_lang_tags().Added test coverage of fix_missing_lang_tags().0.2.4Code rewritten to use first() getter.Addedfix_missing_electronic_locator_tag().API changed, addedurlparameter.0.2.3Fixed MANIFEST.in0.2.2Added type_decisioner.Added skipping of duplicite parsing to _add_namespace().0.2.1Fixed run_tests.sh.License changed to MIT.setup.py improved. Added more classifiers.0.2.0Added code, documentation and test coverage.Package is now capable of transforming MARC XML / OAI to MODS in case of monographic publications.Multimonograph and periodical publications should work, but are untested and postprocessing is not defined.0.1.0Project created.
Package: marcxml_parser
IntroductionThis module contains parser forMARC XML/OAIformat, with some highlevel
getters, which can retreive names of authors, or titles of books from MARC XML
/ OAI records.DocumentationFull module documentation and description can be found at Read the Docs:http://marcxml-parser.readthedocs.org/ContributorsBystroushaak <bystrousak@kitakitsune.org>, DeveloperChangelog1.2.3Fixed ability to query tags codes using indexing operator.1.2.2Updated set of possibleicharacters.1.2.1Fixed bug in the publication type parser.1.2.0Implemented.get()method.1.1.0 - 1.1.7Fixed typos in documentation.Addedrecord_itrator().Added support for file-like objects.ISBN is now discriminated to valid and invalid. Added new method.get_invalid_ISBNs(),.get_ISBNs()now returns just valid ISBNs.Fixed bugs in.get_binding().Added fieldURLuto output from.get_internal_urls().Added one more test.Fixed few typos in documentation.Added support for ISSN querying.Fixed bug inrun_test.sh.Fixed parsing of the place to reflect changes in RDA.Added more RDA fixes.Fixed bug in parsing of the dates.1.0.1Fixed small bugs in code and documentation.Added more tests.1.0.0First working version.Fully documented and tested.0.1.0Project created.