Saravanan666/pypi-org huggingface dataset:
Package: gocamgen
gocamgenBase repo for constructing GO-CAM model RDFInstallationpip install gocamgenTestspython3 test_gocamgen.pyUsagefrom gocamgen.gocamgen import GoCamModel

model = GoCamModel("model title")
model.declare_class("PomBase:SPBC12C2.02c")
uri_a = model.declare_individual("GO:0016757")
uri_b = model.declare_individual("PomBase:SPBC12C2.02c")
axiom = model.add_axiom(uri_a, URIRef(expand_uri("RO:0002333")), uri_b)
model.add_evidence(axiom, "EXP", "PMID:1234567")

model.write("output_file.ttl")Quick generation of models from GPADSpecify source GPAD file. All possible models will be generated and exported to.ttl.python3 gen_models_by_gene.py --gpad_file wb.gpadAdditionally, a gene product identifier can be specified to only translate and export that GP's model.python3 gen_models_by_gene.py --gpad_file wb.gpad --specific_gene WB:WBGene00004055In general, annotation lines will be grouped by gene product identifier (col 2) with some lines filtered out due to various evidence code/reference rules.Generating annotation extensions usage spreadsheetTo be clear, this creates a spreadsheet aggregating all extensions "patterns" (e.g.happens_during(GO:P),positively_regulates(GO:P)) that are decided to be invalid according to the rules currently encoded in this same script. These same rules are used by the model generation import.Example to generate spreadsheet from one GPAD file:python3 gpad_extensions_mapper.py --filename wb.gpad --out_file bad_extensions.tsvExample to generate spreadsheet (results compiled into one .tsv) from directory of GPADs:python3 gpad_extensions_mapper.py --dir gpad_files/ --out_file bad_extensions.tsvSnippet from created spreadsheet:AspectTotal countExtensionUniProtWBParkinsonsUK-UCLF2happens_during(GO:P),happens_during(WBls)200F2happens_during(WBls)020F4regulates_activity_of(geneID)040F1occurs_in(WBbt),part_of(GO:P)100F3occurs_in(WBbt)210F1activated_by(geneID)010Drilling down to offending GPAD lines "by extension pattern"If you'd like to get the actual GPAD containing the invalid extension pattern, just copy-paste the pattern into the--patternoption and rerun on the same GPAD(s):python3 gpad_extensions_mapper.py --filename wb.gpad --pattern "regulates_activity_of(geneID)"By default this will output the lines to a[pattern].gpadfile likeregulates_activity_of(geneID).gpadbut this can be overidden with--pattern_outfile. There's also an option for running multiple patterns at once by plugging the path to a newline-separated list of patterns into the--pattern_sourcefile, which then creates multiple GPAD files named after each pattern.
Package: gocardless
This API library is only for developers who already have an integration using the [Legacy GoCardless API](https://developer.gocardless.com/legacy). If you’re starting a new integration, you should use the new [GoCardless API](https://developer.gocardless.com) with the [gocardless-pro-python](https://github.com/gocardless/gocardless-pro-python) library. If you’re not sure whether this is the right library for you, get in touch - you can reach our developer support team at <api@gocardless.com>.
Package: gocd
The reason for this project is to provide a wrapper to easily perform operations
against Go. I’ve been writing a lot of shell scripts to interact with Go using
curl, but when going a little further than the most basic interactions I’ve
always started to feel the need for doing all of this in a proper programming
language. I.e. something that is beyond bash.I’ve chosen to use Python and version 2.6.6 and newer as my target platform,
with no external dependencies, to make it really straightforward to install/run
on RHEL6 and other similarstabledistributions.This library was created to supporta Go CLI, to handle some common
scenarios you as an admin or advanced user would do.API documentationavailable on read the docs.UsageThe main interaction point for this library is theServerclass,
it contains helpers to instantiate the different API endpoints.An example interaction:>>>fromgocdimportServer>>>server=Server('http://localhost:8153',user='ba',password='secret')>>>pipeline=server.pipeline('Example-Pipeline')>>>response=pipeline.history()>>>bool(response)True>>>response.status_code200>>>response.content_type'application/json'>>>response.is_okTrue>>>response.body{"pagination":{"offset":0,"total":1,"page_size":10},"pipelines":[...]"}StyleThis project aims to follow theGoogle Python Style Guideand particularly
the section oncommenting the code.VersioningSemantic versioningis used.LicenseMIT License.
Package: gocd-bridge
The reason for this project is to provide a wrapper to easily perform operations
against Go. I’ve been writing a lot of shell scripts to interact with Go using
curl, but when going a little further than the most basic interactions I’ve
always started to feel the need for doing all of this in a proper programming
language. I.e. something that is beyond bash.I’ve chosen to use Python and version 2.6.6 and newer as my target platform,
with no external dependencies, to make it really straightforward to install/run
on RHEL6 and other similarstabledistributions.This library was created to supporta Go CLI, to handle some common
scenarios you as an admin or advanced user would do.API documentationavailable on read the docs.UsageThe main interaction point for this library is theServerclass,
it contains helpers to instantiate the different API endpoints.An example interaction:>>>fromgocdimportServer>>>server=Server('http://localhost:8153',user='ba',password='secret')>>>pipeline=server.pipeline('Example-Pipeline')>>>response=pipeline.history()>>>bool(response)True>>>response.status_code200>>>response.content_type'application/json'>>>response.is_okTrue>>>response.body{"pagination":{"offset":0,"total":1,"page_size":10},"pipelines":[...]"}StyleThis project aims to follow theGoogle Python Style Guideand particularly
the section oncommenting the code.VersioningSemantic versioningis used.LicenseMIT License.
Package: gocd-dashboard
gocd-dashboard==============A [GoCD] dashboard for showing pipeline status at a glance. Details about eachpipeline and all of it's materials (even grandparents!) are collected to showthe authors of commits that caused each pipeline to run.![Screenshot](docs/screenshot.png)Usage-----_Requirements: Python 3.3 or above, the `gocd_dashboard` python package (andit's dependencies)._```bashgocd-dashboard run --host localhost --port 5000```You will need to create a JSON configuration file that describes your GoCDserver. The server will look `config.json` in the current directory, or use thepath of the `GOCD_DASHBOARD_CONFIG` environment variable.```json{"gocd": {"server": "https://gocd.example.com","username": "guest","password": "guest"},"groups": [{"name": "example","pipelines": ["pipeline-a","pipeline-b"]}]}```Pipelines will be colored depending on their status:- Failed: red.- Running: yellow.- Passed: white (green if the entire group has passed).Development-----------_Requirements: Python 3.3 or above, the `virtualenv` python package, NodeJSand the `npm` package manager._Install the module into a Python virtualenv in development mode:```bashpip install -e .```Install a [Sass] compiler and [materialize.css]:```bashnpm install```Compile CSS files using `node-sass`:```bash./node_modules/.bin/node-sass --watch gocd_dashboard/static --output gocd_dashboard/static```Run the development server:```bashFLASK_DEBUG=1 gocd-dashboard run```License-------Released under the MIT licence. See [LICENSE](./LICENSE).Authors-------- [Sam Clements][GoCD]: https://www.go.cd/[materialize.css]: http://materializecss.com/[Sam Clements]: https://github.com/borntyping/[Sass]: http://sass-lang.com/
Package: gocd-tools
gocd-toolsA tool for automating the configuration of aGoCDserver.
It achieves this by utilizing the publishedGoCD APIspecification.Getting StartedBefore thegocd-toolcan be used, it has to be built and installed.
The easiest way to accomplish this is to use the PyPI installer:pip install gocd-toolsHow-toFor additional information about how to use the tool and how it should be
configured and etc. Please see theDocumentation.
Package: gocept.arecibologger
Arecibo is a GAE application that is useful to gather errors from a set of
servers, specifically errors that occur while processing web requests.gocept.arecibologger is a patch for Zope 2’s site error log that will send as
much data (tracebacks, request data, user name, …) to the Arecibo server as
possible.How to useInstall the gocept.arecibologger egg into your Zope 2 runtime environment.Activate it by pulling the egg in via ZCML.Configure the Arecibo account and server address in your zope.conf:<product-config gocept.arecibologger>
    server http://myarecibo.appspot.com/v/1/
    account u8orukajlfdjklafda
</product-config>0.1.2 (2010-10-19)Another brown bag: ZCML files were missing in the source distribution.0.1.1 (2010-10-19)Fix brown-bag release.0.1 (2010-10-19)Implement initial patch to the site error log.
Package: gocept.bender
Bender is a Jabber-Bot.Its main functionality is to be always online, joined to a groupchat (MUC), and
to accept messages to say there via HTTP POST. Thus, other systems (e.g.
Nagios, Continuous Integration etc.) can perform Jabber notifications without
having to speak Jabber themselves (and without any join/part noise).You can tell Bender to say something like this:curl -d "Say something" http://user:password@host:portQuotesBender also sometimes randomly says things by itself (Bender quotes).
To avoid flooding the channel, there are three thresholds:Only say something with a given probability.Only say something if we haven’t said anything for a given time.Only say something if at least a given number of messages from other people
have been said in the chatroom.DeploymentBender is deployed and configured using buildout. Here is an example
configuration file:[buildout]
extends = profiles/prod.cfg

[config]
chatroom = my-chat@jabber.org
jabber_user = bender-user
jabber_password = secret
min_silence_duration = datetime.timedelta(minutes=5)
min_human_messages = 10
speaking_probability = 1.0 / (10 * 60)
loglevel = INFO
http_address = 0.0.0.0:8099
http_user = bender
http_password = http_secretCHANGES1.0 (2011-10-09)first release.
Package: gocept.cmmi
zc.buildout recipe to build a software package from source by the usual
configure/make/make install procedure. Uses the gocept.download recipe to
download and extract the source archive.Attention!This recipe has been deprecated in favour ofzc.recipe.cmmi. Version
1.3 ofzc.recipe.cmmihas acquired the features that it used to lack
in comparison withgocept.cmmi.
Package: gocept.cvs
gocept.cvszc.buildout recipe to checkout cvs modules, supporting tags and branchesOptionscvsrootThe cvs root the modules you want to fetch are in (ending with a /)modulesmodules you want to checkout (list of module;tag;destination)destinationdestination directory for the checkouts (ending with a /)ContributorsRoman Joost <rj at gocept dot com>Michael Howitz <mh at gocept dot com>Changelog0.1.10Verbosity of output now depends on verbosity set in
buildout. Default is beeing not verbose.0.1.9Bugfix: The check for changes on uninstall no longer sets a sticky
tag.Bugfix: Uninstall now also stopps if there are added or deleted
files which are not yet commited or conflicts.Silenced update: No longer shows processed directory names.0.1.8Bugfixing: Nested checkouts don’t ‘inherit’ sticky tags from
checkout ‘above’0.1.7Bugfixing: HEAD checkouts don’t have any sticky tags0.1.5support for specifying a path instead of a directory
as destination for a single module0.1.4support for offline/newest buildout options0.1initial version
Package: gocept.datetimewidget
Changes1.4.1 (2012-02-20)Fixed a sequence problem when loading the calendar.1.4 (2012-02-16)Fixed compatability to newer versions iffanstatic.1.3.1 (2012-02-15)Moved install requirementfanstaticto an extra requirement.Provide directfanstaticresources for the javascript, css and language
files.1.2 (2012-02-15)Provided a library to be able to use the zc.datetimewidget resources with
fanstatic.1.1 (2011-02-18)changed external to use resources of zc.datetimewidget 0.6.4, which
contains a fix for IE in calendar.js1.0 (2009-05-20)initial revisionHow to use zc.datetimewidget with Zope21. Add gocept.datetimewidget egg to your instanceThis should automatically install the following dependencies:zc.datetimewidget, zc.i18n and zc.resourcelibrary2. Make sure the correct set of zcml gets loaded.If you use a custom site.zcml, Include the following IN THIS ORDER:<!-- Enable zc.datetimewidget to load its zcml.
     Do not include zc.resourcelibrarys configure.zcml, as this
     will not work in z2. -->
<include package="zc.resourcelibrary" file="meta.zcml" />
<!-- Contains a copy of the resource directory of zc.datetimewidget
     registered as a browser:resourceDirectory.
     Also contains a viewlet manager with viewlets providing html
     snippets for including the javascripts in your templates (see below). -->
<include package="gocept.datetimewidget" />
<include package="zc.datetimewidget" />
<!-- Replace the formlib datetimewidget with the zc one. -->
<includeOverrides package="zc.datetimewidget" />
<!-- Overwrite the zc.resourcelibrary resourcedirectory
     of zc.datetimewidget with a browser:resourceDirectory. -->
<includeOverrides package="gocept.datetimewidget" />If you use the zcml parameter of plone.recipe.zope2instance you can just set:zcml = zc.resourcelibrary-meta
       gocept.datetimewidget
       zc.datetimewidget
       zc.datetimewidget-overrides
       gocept.datetimewidget-overrides3. Add javascript resources to your templates.Place a line like this in a template where your forms will be displayed:<tal:jsviewlets replace="structure provider:zc.datetimewidget.resources" />Or make sure the following resources are loaded
(i.e. using plone portal_javascript/portal_css):/++resource++zc.datetimewidget/calendar-system.css
/++resource++zc.datetimewidget/calendar.js
/++resource++zc.datetimewidget/datetimewidget.js
/++resource++zc.datetimewidget/languages/calendar-en.js
/++resource++zc.datetimewidget/calendar-setup.jsOr useFanstatic:import gocept.datetimewidget.resource
gocept.datetimewidget.resource.datetimewidget.need()
Package: gocept.download
zc.buildout recipe to download and extract an archive.Configuration optionsurl:The URL of the archive to download.strip-top-level-dir:(optional)
Whether to remove the top-level directory from the extracted archive
contents.md5sum:MD5 checksum of the archive.destination:Where to put the extracted archive contents.download-directory:(optional)
Where to put the downloaded archive.This option uses a buildout option of the same name as a default if that
is specified.CachingThe download directory, if given, acts as a cache. In addition,
gocept.download takes advantage of zc.buildout’s download cache.
Package: gocept.filestore
ContentsFilestoreInitialize a FileStoreUse a FileStoreCleanupChanges1.0 (2023-07-14)0.5 (2023-03-16)0.4 (2019-11-29)0.3 (2009-10-08)0.2 (2007-08-30)FilestoreThe filestore is an easy way to to process files with multiple processes
without needing locks.Initialize a FileStoreCreate a filestore in a temporary area:>>> import tempfile, os
>>> temp_dir = tempfile.mkdtemp()
>>> store_dir = os.path.join(temp_dir, 'store1')
>>> os.mkdir(store_dir)
>>> from gocept.filestore import FileStore
>>> filestore = FileStore(store_dir)
>>> filestore
<gocept.filestore.filestore.FileStore object at 0x...>So far nothing has happend:>>> import os
>>> os.listdir(store_dir)
[]Before using the store we need to prepare it:>>> filestore.prepare()Prepare has created the tmp/new/cur directory structure:>>> sorted(os.listdir(store_dir))
['cur', 'new', 'tmp']Calling prepare again does nothing:>>> filestore.prepare()
>>> sorted(os.listdir(store_dir))
['cur', 'new', 'tmp']If the store_dir is removed, it is created again by calling prepare.>>> import shutil
>>> shutil.rmtree(store_dir)
>>> os.listdir(temp_dir)
[]
>>> filestore.prepare()
>>> os.listdir(temp_dir)
['store1']
>>> sorted(os.listdir(store_dir))
['cur', 'new', 'tmp']Use a FileStoreAdding files to the store works with thecreatemethod:>>> f = filestore.create('a-file')Files are created in the ‘tmp’ area with the ‘w’ mode (if not specified):>>> f.name
'.../tmp/a-file'
>>> f.mode
'w'We find the file in the tmp area. Note thatfilestore.listlists files with
their full path names, so we could feed the name directly to file/open:>>> filestore.list('tmp')
['.../tmp/a-file']We got a plain file back, so write to it:>>> _ = f.write('Die Ente bleibt draussen!')
>>> f.close()We have finished writing our file, so we can move it to thenewspace for
other applications to pick it up:>>> filestore.move('a-file', 'tmp', 'new')
>>> filestore.list('tmp')
[]
>>> filestore.list('new')
['.../new/a-file']The move operation uses os.move which is supposed to be atomic. When another
processes “sees” the file it can directly work with it and move it to ‘cur’:>>> filestore.move('a-file', 'new', 'cur')
>>> filestore.list('new')
[]
>>> filestore.list('cur')
['.../cur/a-file']Files can be copied, too:>>> filestore.copy('a-file', 'cur', 'tmp')
>>> filestore.list('cur')
['.../cur/a-file']
>>> filestore.list('tmp')
['.../tmp/a-file']Finally, files can be removed:>>> filestore.remove('a-file', 'cur')
>>> filestore.list('cur')
[]CleanupRemove the temporary directory after testing:>>> import shutil
>>> shutil.rmtree(store_dir)Changes1.0 (2023-07-14)Drop support for Python 2.7, 3.5, 3.6.0.5 (2023-03-16)Add support for Python 3,9, 3.10, 3.11.Use GitHub actions as CI.0.4 (2019-11-29)Migrate repository to Bitbucket.Migrate repository to GitHub.Made Python 3 compatible (tested with Python 2.7, 3.7 and 3.8).Replace bootstrap/buildout with tox.Increase test coverage to 100%.0.3 (2009-10-08)Added copy() method.0.2 (2007-08-30)Initial public release.
Package: gocept.form
gocept.formprovides some extended functionality for zope.formlib and
z3c.form. To use the package with formlib support, require it usinggocept.form[formlib]. To use the package with z3c.form support, require it
usinggocept.form[z3cform].Destructive ActionsDestructive actions allow marking actions that can potentially cause harm.
Those actions will be rendered as buttons and - on JavaScript-capable
platforms - be disabled by default. Additionally a checkbox is rendered that
allows enabling the corresponding button.Grouped Fieldsgocept.form.grouped provides a very low-tech way of grouping schema fields
into field sets. The styling is applied only via CSS.Base Add and Edit formsgocept.form.base.Add and gocept.form.base.Edit providing some common code
to make implementing basic forms more convenient.Changes0.8.0 (2016-01-12)Got rid of dependencies on zope.app.pagetemplate (in favour of
zope.browserpage) and zope.testing (in favour of the standard lib).0.7.6 (2008-07-17)Fixed a bug in sorting of grouped widgets when a remainder group was
explicitly specified.0.7.5 (2008-07-17)Fixed a bug the grouped forms: The widgets were stored on a class variable
and thus shared in different threads.0.7.4 (2008-05-23)Added a javascript confirm action.0.7.3 (2008-03-27)Added Base Add and Edit forms0.7.2 (2008-01-24)Fixed a bug which prevented the automatic gerneration of remaining fields iffield_groupswas a tuple.0.7.1 (2007-12-19)Added a css class for the field groups (field-group).0.7 (2007-12-07)Added averysimple way of client side javascript validation.0.6Added locales for gocept.form (i18n for string in gocept_form_macros)IMPORTANT: Usage changed. Please look at the first paragraph of this
README.Added pagelet support for z3c.form forms (see pagelet.py)0.5Added small functionapplySchemaDatato apply data to an object according
to a schema. This is useful in constructors or in add forms.0.4Made grouped forms ignore missing fields.0.3Addeddestructive actionfeature.0.2Added support for grouping generic forms (subclass of zope.formlib.form.Form).0.1Initial release.
Package: gocept.httop
httop is a console tool to monitor the responsiveness of websites (or any URL)
like monitoring  your system processes withtop.URLs are re-checked 3 seconds after their last result was received.UsageCreate a configuration file in your home directory called.httoplisting
the URLs that should be monitored:http://localhost:8080
http://www.foodibar.comThen, start the script without any parameters:$ httopWhile running, you can update the configuration file. New URLs will be
picked up automatically and removed URLs will be dropped.
Package: gocept.imapapi
gocept.imapapiThis package provides an object-oriented API for accessing IMAP servers. It
was written to provide an API that is simple to use while still maintaining
good performance.Contentsgocept.imapapiAboutObject-oriented APIPerformanceStatusRunning the testsCHANGES0.5 (2011-01-31)0.4.1 (2010-11-30)0.4 (2010-09-24)0.3 (2010-08-09)0.2 (2010-08-04)0.1 (2008-07-22)Aboutgocept.imapapiis sponsored by theTechnical University of Munichas part
of a research co-operation geared towards an integrated webmail system for the
university’s student portalMyTum. Other components of this project includegocept.restmailandCMFWebmail.This project was initially developed bygocept gmbh & co. kg.Object-oriented APIOne of the first goals of the webmail project was to factor out the
lower-level utilities to allow others to build on our efforts.This library takes on to provide a better abstracted, more object-oriented,
well, morepythonicapproach than the builtinimaplibdoes.Let us give you an example of what we feel a good API looks like:>>> from gocept.imapapi import Account
>>> account = Account('localhost', 10143, 'tim', 'mightywizard')
>>> account.folders.keys()
['INBOX']
>>> account.folders['INBOX'].messages
<Messages object at 0x...>
>>> for message in account.folders['INBOX'].messages.values():
...     repr(message.headers['subject'])
u'Re: your spell from last week'
u'Enlarge your magic wand!'Some of the aspects that come to mind when looking at this example:Object model on top of protocol specificsUse of native Python data structuresDecode protocol-specific data as early as possible (see the unicode headers)With this approach we try to make programming IMAP clients simpler and more
convenient.PerformanceThe imapapi layer tries to keep the amount and size of communication as small
as possible, only retrieving data when really needed and re-using data already
retrieved.As an examples, body content isn’t downloaded until needed and even when
looking at the body structure we differentiate between metadata and content.StatusThis package is still in early development and published for experimental
purposes and to invite a wider community to join us developing an IMAP library
that is more convenient than Python’s builtinimaplib.Running the testsThe tests expect an IMAP server to be available on localhost:10143. The
default buildout environment provides adovecotinstallation for this.As we aim to be compatible with as many IMAP servers as possible, you should
be able to provide any IMAP server on this port, as long as a user ‘test’ with
the password ‘bsdf’ is configured.Warning: Do not let the tests run against a production system. Theymightwreak havoc.CHANGES0.5 (2011-01-31)Added Folder.unread_message_count.Added some debug output to help with #6830 and #7769.Made some recently introduced logging more useful, adapted tests.0.4.1 (2010-11-30)Made the test infrastructure load test messages in a more stable order.0.4 (2010-09-24)Added filter criterion “seen” (#7263).0.3 (2010-08-09)Filter messages on the IMAP server. (#4699)0.2 (2010-08-04)Lots of changes (see svn log for details).0.1 (2008-07-22)initial release.