Saravanan666/pypi-org huggingface dataset:
Package: omen2
Simple library that makes working with classes and databases more convenient in python.omen2will take a set of classes, and a database, and link them together.omen2 allows the user to:serialize created objects to the dbquery the db and return objects, not rowsquery for related objectsaccess/lock/update singleton objects across multiple threadsroll back changes on exceptionscreate objects not-bound to the db, and later, bind themcache objects in use, flexible cache-controlomen2 is not fully flexible with regards to database structure:related tables must have primary keysautodoc documentationfromnotanormimportSqliteDbfromomen2importOmenclassMyOmen(Omen):version=2@staticmethoddefschema(version):# use an omen2-compatible schema, which is a semicolon-delimited sqlite-compatible create statementreturn"""create table cars(id integer primary key, color text not null, gas_level double default 1.0);create table doors(carid integer, type text, primary key (carid, type));"""# or, just return a list of type-annotated classes derived from ObjBase# or, don't have one at all, it's ok# you don't have to codegen, you can also just derive from omen2.ObjBase# but you have to match your database system to the model one way or another# either manual, codegen, or dbgenMyOmen.codegen()# assuming this is example.pyimportexample_genasgen_objs# every table has a row_type, you can derive from itclassCar(gen_objs.cars_row):def__init__(self,color="black",**kws):self.not_saved_to_db="some thing"self.doors=gen_objs.doors_relation(self,kws.pop("doors",None),carid=lambda:self.id)super().__init__(color=color,**kws)@propertydefgas_pct(self):# read only props are finereturnself.gas_level*100# if you're using code generation, every db table has a type, you can derive from itclassCars(gen_objs.cars):# feel free to redefine the row_type usedrow_type=Cardb=SqliteDb(":memory:")mgr=MyOmen(db,cars=Cars)# there's always a mapping from table class to instance# so Omen knows what classes are in charge of what tablesmgr.cars=mgr[Cars]# fine too (or stick in init)mgr.cars=Cars(self)# by default, you can always iterate on tablesassertmgr.cars.count()==0car=Car()# creates a default car (black, full tank)car.color="red"car.gas_level=0.5# you don't need to create a class, if you use the code-generated onecar.doors.add(gen_objs.doors_row(type="a"))car.doors.add(gen_objs.doors_row(type="b"))car.doors.add(gen_objs.doors_row(type="c"))car.doors.add(gen_objs.doors_row(type="d"))mgr.cars.add(car)# cars have ids, generated by the dbassertcar.idmgr.cars.add(Car(color="red",gas_level=0.3,doors=[gen_objs.doors_row(type=str(i))foriinrange(4)]))assertsum(1for_inmgr.cars.select(color="red"))==2# 2print("cars:",list(mgr.cars.select(color="red")))car=mgr.cars.select_one(color="red",gas_level=0.3)withcar:car.gas_level=0.9assertlen(car.doors)==4To run codegen manually, rather than "inline", you can run:omen2-codegen my.package.MyClassName.Commiting this file, and running this as a git-hook on any change is a useful pattern.
Package: omero-arc
OMERO-ARCA plugin foromero-cli-transferto export imaging projects from the OMERO database to ARC repositories.UsageOnce installed, your can "pack" omero projects to ARC repositories.If the ARC repository already exists, the OMERO project is added as a new study and connected assays. If the ARC repo does not exist, a new ARC repository is created.Examples:omero transfer pack --plugin arc Dataset:111 path/to/my/new/arc_repo
omero transfer pack --plugin arc Dataset:111 path/to/my/already/existing/arc_repoInstallationInstall DependenciesInstallARCCommander(and Git and Git LFS) as describedhereInstallomero-cli-transferas describedhereInstall omero-arc plugingit clone git@github.com:cmohl2013/omero-arc.git
cd omero-arc
pip install omero-arcDevelopment Environment Setupconda create -n myenv -c conda-forge python=3.8 zeroc-ice=3.6.5
conda activate myvenvInstallationgit clone git@github.com:cmohl2013/omero-arc.git
cd omero-arc
pip install -e .[dev] # installs optional dependencies including omero-cli-transfer
conda install pytestStart OMERO test databaseLaunch OMERO test environment with docker-compose.sudo chmod a+x .omero/compose # enure that compose is executable
sudo .omero/compose upRun testsOMERODIR="." ICE_CONFIG="test/ice.config" pytest
Package: omero-bifrost
OMERO-BifrostBifrost bridge for large-scale transfer of bioimage data using anOMERO server. A simplified Python CLI tool and package to transfer image data/metadata from and to an OMERO server.RequirementsPython3.8typer0.9.0rich13.5.2zeroc-ice3.6.5omero-py5.13.1(downgraded from5.15.0given ezomero2.1.0requirements)omero-upload0.4.0ezomero2.1.0Install with PyPIpip install omero-bifrostUsageTypeomero-bifrost --helpto see the full range of commands and subcommands.Development notesTo install packages inrequirements.txtin the current conda env.:pip install -r requirements.txtTo test package, install using pip:pip install -e .
Package: omero-certificates
OMERO server certificate management pluginGenerate self-signed certificates and configure OMERO.server.If you prefer to configure OMERO manually see the examples in these documents:https://github.com/ome/docker-example-omero-websocketshttps://docs.openmicroscopy.org/omero/latest/sysadmins/client-server-ssl.htmlInstallationInstallopensslif it's not already on your system.
Then activate your OMERO.server virtualenv and run:pip install omero-certificatesUsageSet theOMERODIRenvironment variable to the location of OMERO.server.Run:omero certificatesOpenSSL 1.1.1d  10 Sep 2019
Generating RSA private key, 2048 bit long modulus (2 primes)
.+++++
.............................+++++
e is 65537 (0x010001)
certificates created: /OMERO/certs/server.key /OMERO/certs/server.pem /OMERO/certs/server.p12to update your OMERO.server configuration and to generate or update your self-signed certificates.
If you already have the necessary configuration settings this plugin will not modify them, so it is safe to always runomero certificatesevery time you start OMERO.server.
You can now start your omero server as normal.This plugin automatically overrides the defaults for the following properties if they're not explicitly set:omero.glacier2.IceSSL.Ciphers=HIGH: the default weaker ciphers may not be supported on some systemsomero.glacier2.IceSSL.ProtocolVersionMax=TLS1_3: Support TLS 1.2 and 1.3omero.glacier2.IceSSL.Protocols=TLS1_2,TLS1_3: Support TLS 1.2 and 1.3omero.glacier2.IceSSL.DH.2048=ffdhe2048.pem: use a pre-defined 2048-bit Diffie-Hellman groupThe pre-defined Diffie-Hellman group is fromRFC 7919.  Newer versions of OpenSSL will prefer ECDHE and have their own 2048-bit or greater primes but it's safe to use this one.
When RHEL 7 (OpenSSL 1.0.2) support is dropped this will be removed.NOTE:If RHEL 7 is detected, only TLS 1.2 support will be enabled.The original values can be found onhttps://docs.openmicroscopy.org/omero/5.6.0/sysadmins/config.html#glacier2Certificates will be stored under{omero.data.dir}/certsby default.
Setomero.glacier2.IceSSL.DefaultDirto change this.If you see a warning message such asCan't load ./.rnd into RNGit should be safe to ignore.For full information see the output of:omero certificates --helpDeveloper notesThis project usessetuptools-scm.
To release a new version just create a tag.
Package: omero-cli-duplicate
omero-cli-duplicatePlugin for use in the OMERO CLI.RequirementsOMERO 5.6.0 or newerPython 3.6 or newerInstalling from PyPIThis section assumes that an OMERO.py is already installed.Install the command-line tool usingpip:$ pip install -U omero-cli-duplicateRelease processThis repository usesbump2versionto manage version numbers.
To tag a release run:$ bumpversion releaseThis will remove the.dev0suffix from the current version, commit, and tag the release.To switch back to a development version run:$ bumpversion --no-tag [major|minor|patch]specifyingmajor,minororpatchdepending on whether the development branch will be amajor, minor or patch release. This will also add the.dev0suffix.Remember togit pushall commits and tags.LicenseThis project, similar to many Open Microscopy Environment (OME) projects, is
licensed under the terms of the GNU General Public License (GPL) v2 or later.Copyright2017-2020, The Open Microscopy Environment
Package: omero-cli-render
omero-cli-renderOMERO CLI plugin for bulk application of rendering settings.
Settings can be applied from yaml files or copied from other Images in OMERO.RequirementsOMERO 5.6.0 or newerPython 3.6 or newerInstalling from PyPIThis section assumes that an OMERO.py is already installed.Install the command-line tool usingpip:$ pip install -U omero-cli-renderUsageCall via the OMERO command line. Use-hto show available sub-commands:$ omero render -hRelease processThis repository usesbump2versionto manage version numbers.
To tag a release run:$ bumpversion releaseThis will remove the.dev0suffix from the current version, commit, and tag the release.To switch back to a development version run:$ bumpversion --no-tag [major|minor|patch]specifyingmajor,minororpatchdepending on whether the development branch will be amajor, minor or patch release. This will also add the.dev0suffix.Remember togit pushall commits and tags.LicenseThis project, similar to many Open Microscopy Environment (OME) projects, is
licensed under the terms of the GNU General Public License (GPL) v2 or later.Copyright2017-2020, The Open Microscopy Environment
Package: omero-cred
<H2>OMERO.web integrated with OME Oauth2</h2>
<hr>This is a combination of two packages the OMERO.web available from The Open Microscopy Environment, Glencoe Software, Inc.
copyright 2009-2022 and the OMERO.oauth which is a fork off of the openmicroscopy github repos developed by a separate team.This package is built to be used by the CReD Portal project exclusively.<hr>
Package: omero-demo-cleanup
OMERO demo cleanupThis OMERO command-line plugin allows you to compute the space per user, find
the users with the biggest amount of data and free disk space on a serverTo generate the list of users which data must be deleted to free 300GB on the
system without running the deletion:$ omero demo-cleanup --gigabytes 300To ignore users who’s data whose data must not be deleted, you can Tag those users
and specify theTagor parentTag GroupbyNameorID.
This is enabled by default using a Tag named “NO DELETE”.
So it is preferable to Tag users on the server with aTagnamed “NO DELETE” or create
aTag Groupnamed “NO DELETE” containing Tags linked to users.# Add a Tag to a User via CLI (not possible to see this in the clients)
$ omero obj new ExperimenterAnnotationLink child=TagAnnotation:123 parent=Experimenter:52# Choose a non-default Tag or Tag Group (by ID or Name) to ignore the tagged users
$ omero demo-cleanup –gigabytes 300 –ignore-tag “Tag Name”You can also specify individual users by ID or user name, e.g:–ignore-users 123,user-1,ben,234To generate the list of users which data must be deleted to free 300GB on the
system and running the deletion (WARNING: data belonging to these users will
be removed permanently):$ omero demo-cleanup --gigabytes 300 --force
Package: omero-dropbox
IntroductionOMERO.dropbox provides a server for watching directories
for new files which are then imported into OMERO.DependenciesDirect dependencies of OMERO.dropbox are:ZeroC IcePyOMERO.pyInstallationSee:OMEROdocumentationUsageSee:OMEROdocumentationContributingSee:OMEROdocumentationRunning testsUnit tests are located under thetestdirectory and can be run with pytest.Integration testsIntegration tests are stored in the main repository (ome/openmicroscopy) and depend on the
OMERO integration testing framework. Reading aboutRunning and writing testsin theOMEROdocumentation
is essential.Release processThis repository usesbump2versionto manage version numbers.
To tag a release run:$ bumpversion releaseThis will remove the.dev0suffix from the current version, commit, and tag the release.To switch back to a development version run:$ bumpversion --no-tag [major|minor|patch]specifyingmajor,minororpatchdepending on whether the development branch will be amajor, minor or patch release. This will also add the.dev0suffix.Remember togit pushall commits and tags.LicenseOMERO.dropbox is released under the GPL v2.Copyright2009-2020, The Open Microscopy Environment, Glencoe Software, Inc.
Package: omero-fpbioimage
OMERO.FPBioimageFPBioimageis a volumetric visualization tool.
FPBioimage as an OMERO.web app.RequirementsOMERO.web 5.6 or newer.Installing from PyPIThis section assumes that an OMERO.web is already installed.Install the app usingpip:$ pip install -U omero-fpbioimageAdd fpbioimage custom app to your installed web apps:$ bin/omero config append omero.web.apps '"omero_fpbioimage"'Optionally add fpbioimage to the ‘Open with’ config, to enable
open-with menu for Images in OMERO.webclient:$ bin/omero config append omero.web.open_with '["omero_fpbioimage", "fpbioimage_index",
  {"script_url": "fpbioimage/openwith.js", "supported_objects": ["image"], "label": "FPBioimage"}]'Now restart OMERO.web as normal.LicenseOMERO.FPBioimage is released under the AGPL.
FPBioimage was originally published inNature
PhotonicsCopyright2017-2020, The Open Microscopy Environment
Package: omero-iviewer
OMERO.iviewerAn OMERO.web app for visualizing images in OMERO.RequirementsOMERO 5.6.0 or newer.Installing from PyPIThis section assumes that an OMERO.web is already installed.Install the app usingpip:NB: You need to ensure that you are runningpipfrom the python environment
whereomero-webis installed. Depending on your install, you may need to
callpipwith, for example:/path/to/venv/bin/pip install ...$ pip install -U omero-iviewerAdd iviewer custom app to your installed web apps:$ omero config append omero.web.apps '"omero_iviewer"'To replace the default omero.web viewer:$ omero config set omero.web.viewer.view omero_iviewer.views.indexTo enable the “open with” feature:$ omero config append omero.web.open_with '["omero_iviewer", "omero_iviewer_index",
  {"supported_objects":["images", "dataset", "well"],
   "script_url": "omero_iviewer/openwith.js", "label": "OMERO.iviewer"}]'Now restart OMERO.web as normal.UsageA guide to using OMERO.iviewer can be found onhttps://omero-guides.readthedocs.io/en/latest/iviewer/docs/iviewer.htmlLicenseOMERO.iviewer is released under the AGPL.Copyright2017-2022, The Open Microscopy Environment
Package: omero-marshal
OMERO MarshalExtensible marshaling code to transform various OMERO objects into
dictionaries which can then be marshalled using JSON or alternative
encodings.RequirementsOMERO.py 5.6 or newerPython 3.6 or newerDevelopment InstallationClone the repository:git clone git@github.com:ome/omero-marshal.gitSet up a virtualenv (http://www.pip-installer.org/) and activate it:curl -O -k https://raw.github.com/pypa/virtualenv/master/virtualenv.py
python virtualenv.py omero-marshal
source omero-marshal/bin/activate
pip install -r requirements.txt
pip install -r requirements-dev.txtRunning TestsUsing py.test to run the unit tests:py.test tests/unit/LicenseThis project, similar to many Open Microscopy Environment (OME) projects, is
licensed under the terms of the GNU General Public License (GPL) v2 or later.Referencehttps://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome.htmlhttps://docs.openmicroscopy.org/latest/omero/developers/Model/Units.htmlhttps://docs.openmicroscopy.org/latest/omero/developers/Model/KeyValuePairs.html
Package: omero-prometheus-tools
Tools for monitoring OMERO with PrometheusThis repository is under development.
Breaking changes may be made without warning.Installationpython3 -mvenv /opt/prometheus-omero-tools
/opt/prometheus-omero-tools/bin/python setup.py installRunning/opt/prometheus-omero-tools/bin/omero-prometheus-tools.py
  -s omero.example.org -u public -w public
  [-c /opt/prometheus-omero-tools/etc/prometheus-omero-counts.yml ...]Metrics will be published onhttp://localhost:9449
Package: omero-rdf
omero-rdfA plugin for exporting rdf from OMERORequirementsOMERO 5.6.0 or newerPython 3.6 or newerInstalling from PyPIThis section assumes that an OMERO.py is already installed.Install the command-line tool usingpip:$ pip install -U omero-rdfRelease processThis repository usesversioneerto manage version numbers. A tag prefixed withvwill be detected by
the library and used as the current version at runtime.Remember togit pushall commits and tags.FundingFunded by theDelta TissueProgram ofWellcome Leap.LicenseThis project, similar to many Open Microscopy Environment (OME) projects, is
licensed under the terms of the GNU General Public License (GPL) v2 or later.Copyright2022, German BioImaging
Package: omero-rois
OMERO ROI utilitiesOMERO Python utilities for handling regions of interest (ROIs).RequirementsOMERO 5.6.0 or newerInstalling from PyPIThis section assumes that an OMERO.py is already installed.Install the command-line tool usingpip:$ pip install -U omero-roisRelease processThis repository usesbump2versionto manage version numbers.
To tag a release run:$ bumpversion releaseThis will remove the.dev0suffix from the current version, commit, and tag the release.To switch back to a development version run:$ bumpversion --no-tag [major|minor|patch]specifyingmajor,minororpatchdepending on whether the development branch will be amajor, minor or patch release. This will also add the.dev0suffix.Remember togit pushall commits and tags.LicenseThis project, similar to many Open Microscopy Environment (OME) projects, is
licensed under the terms of the GNU General Public License (GPL) v2 or later.Copyright2019-2020, The Open Microscopy Environment
Package: omero-scripts
OMERO Core ScriptsThis directory contains OMERO scripts which use the
OMERO.scripts API. All scripts (e.g.*.py) present in the
directory will be automatically distributed with all binary
builds. Which file-endings will be detected and how they
will be launched are both configured centrally in the server..py,.jy, and.m(MATLAB) files should all be detected
by default starting with OMERO 5.CategoriesScripts are separated into several categories, one per directory.DirectoryDescriptionanalysis_scriptscrunch images to produce numerical results and similar tasksexport_scriptstake one or more images as an input, and produce a representation for exchangefigure_scriptstake one or more images as an input, and produce a summary representationimport_scriptsare run on images after import for extra processingutil_scriptsperform other miscellaneous tasks like cleaning up or optimizing OMERO itselfScripts which would like to rely on other scripts can
use:import omero.<sub_dir>.<script_name>For this to work, the official script in question must
be properly importable, i.e.:def run():
    client = omero.scripts.client(...)

if __name__ == "__main__":
    run()OMERO User ScriptsIf you would like to provide your own scripts for others to install
into their OMERO installations, please seehttps://openmicroscopy.org/info/scriptsTestingIntegration tests undertest/require an OMERO server with scripts installed.
The tests are run by Travis for open PRs using omero-test-infra to deploy OMERO
via Docker containers.To run tests locally:# All tests
$ python setup.py test

# Single test in a single file
$ python setup.py test -t test/integration/test_util_scripts.py -k test_dataset_to_plateUsageSeehttps://omero-scripts.readthedocs.io/en/stable/Release processThis repository usesbump2versionto manage version numbers.
To tag a release run:$ bumpversion releaseThis will remove the.dev0suffix from the current version, commit, and tag the release.To switch back to a development version run:$ bumpversion --no-tag [major|minor|patch]specifyingmajor,minororpatchdepending on whether the development branch will be amajor, minor or patch release. This will also add the.dev0suffix.Remember togit pushall commits and tags.s essential.The CI pipeline will automatically deploy the tag onto PyPI.Copyright2010-2021, The Open Microscopy Environment
Package: omero-server
OMERO.server CLI PluginIntroductionOMERO.py provides a plugin infrastructure for CLI tools.
Most tools are intended for the general user wanting to
login to a running OMERO.server. Other plugins like this
one are intended for the management of the installation
itself.DependenciesDirect dependencies of this plugin are:OMERO.pyZeroC IcePyInstallationSee:OMEROdocumentationUsageSee:OMEROdocumentationContributingSee:OMEROdocumentationDeveloper installationomero-server `depends on OMERO.py. If you want a developer installation of OMERO.py, replace ``pip install omero-py`with instructions athttps://github.com/ome/omero-py.For a development installation we recommend creating a virtualenv with the following setup (example assumespython3.6but you can create and activate the virtualenv using any compatible Python):python3.6 -mvenv venv
. venv/bin/activate
pip install zeroc-ice==3.6.5
pip install omero-py          # OR dev install (see above)
git clone https://github.com/ome/omero-cli-server
cd omero-server
pip install -e .This will install the server plugins into your virtualenv as an editable
package, so any edits to source files should be reflected in your installation.Note some tests may not run when this module and/or omero-py are installed in editable mode.Running testsUnit tests are located under thetestdirectory and can be run with pytest.Integration testsIntegration tests are stored in the main repository (ome/openmicroscopy) and depend on the
OMERO integration testing framework. Reading aboutRunning and writing testsin theOMEROdocumentation
is essential.Release processThis repository usesbump2versionto manage version numbers.
To tag a release run:$ bumpversion releaseThis will remove the.dev0suffix from the current version, commit, and tag the release.To switch back to a development version run:$ bumpversion --no-tag [major|minor|patch]specifyingmajor,minororpatchdepending on whether the development branch will be amajor, minor or patch release. This will also add the.dev0suffix.Remember togit pushall commits and tags.Licenseomero-cli-server is released under the GPL.Copyright2020-2022, The Open Microscopy Environment
Package: omero-signup
OMERO.signupOMERO.web app to allow anyone to signup for an OMERO account.Generated usernames are formed from the alphanumeric unicode characters in a user’s first and last names, with a numeric suffix if the username already exists.
If OMERO.web is configured to connect to multiple OMERO servers the user account will be created on the default one.RequirementsOMERO.web 5.6 or newer.Python 3.6 or newer.InstallationThis section assumes that an OMERO.web is already installed.$ pip install omero-signup
$ omero config append omero.web.apps '"omero_signup"'Required configuration settings:omero.web.signup.admin.user: OMERO admin username, must have permission to create groups and usersomero.web.signup.admin.password: Password for OMERO admin usernameomero.web.signup.group.name: Default group for new users, will be created if it doesn’t existOptional configuration settings:omero.web.signup.group.templatetime: IfTrueexpandomero.web.signup.group.nameusingstrftimeto enable time-based groups, default disabledomero.web.signup.group.perms: Permissions on default group for new users if it doesn’t existThese configuration settings are untested due to the difficulty of configuring email on a test server:omero.web.signup.email.enabled: IfTruesend emails to new users with their username and password instead of displaying the password, default disabledomero.web.signup.email.subject: Email subject for new-user emailsomero.web.signup.email.body: Email body for new-user emails.
It should include template strings{username}and{password}that will be substituted with the created user’s username and password.Example:$ omero config get
omero.web.apps=["omero_signup"]
omero.web.signup.admin.password=root-password
omero.web.signup.admin.user=root
omero.web.signup.group.name=testgroup-%Y-%m
omero.web.signup.group.templatetime=trueRestart OMERO.web in the usual way.$ omero web restartNew users will be able to sign-up for an account athttp://omero.web.host/signup.Release processUsebumpversionto increment the version, commit and tag the repo.$ bumpversion patch
$ git push origin master
$ git push --tagsLicenseOMERO.signup is released under the AGPL.Copyright2019, The Open Microscopy Environment