Saravanan666/pypi-org huggingface dataset:
Package: gemseo-mma
A gemseo wrapper of Python version of Method of Moving Asymptothes in the implementation
of Arjen Deetman.DocumentationSeehttps://gemseo.readthedocs.io/en/stable/plugins.html.Bugs/QuestionsPlease use the gitlab issue tracker athttps://gitlab.com/gemseo/dev/gemseo-mma/-/issuesto submit bugs or questions.LicenseThegemseo-mmasource code is distributed under the GNU LGPL v3.0 license.
A copy of it can be found in the LICENSE.txt file.
The GNU LGPL v3.0 license is an exception to the GNU GPL v3.0 license.
A copy of the GNU GPL v3.0 license can be found in the LICENSES folder.Thegemseo-mmaexamples are distributed under the BSD 0-Clause, a permissive
license that allows to copy paste the code of examples without preserving the
copyright mentions.Thegemseo-mmadocumentation is distributed under the CC BY-SA 4.0 license.Thegemseo-mmaproduct depends on other software which have various licenses.
The list of dependencies with their licenses is given in the CREDITS.md file.Installationpip install gemseo-mmaUsageLike any other gemseo wrapped solver, MMA solver can be called setting
the algo option to"MMA". This algorithm can be used for single
objective continuous optimization problem with non-linear inequality
constraints.Advanced options:tol: The KKT residual norm tolerance. This is not the one
implemented in GEMSEO as it uses the local functions to be computed.max_optimization_step: Also known asmoveparameter control the
maximum distance of the next iteration design point from the current
one. Reducing this parameter avoid divergence for highly non-linear
problems.min_asymptote_distance: The minimum distance of the asymptotes from
the current design variable value.max_asymptote_distance: The maximum distance of the asymptotes from
the current design variable value.initial_asymptotes_distance: The initial asymptote distance from the
current design variable value.asymptotes_distance_amplification_coefficient The incremental factor
of asymptote distance from the current design variable value for
successful iterations.asymptotes_distance_reduction_coefficient: The decremental factor of
asymptote distance from the current design variable value for
successful iterations.conv_tol: If provided control all other convergence tolerances.The shortest is the distance of the asymptotes, the highest is the
convexity of the local approximation. It's another mechanism to control
the optimization step. You can find an example in
examples/analytic_example.ipynb.Contributors and acknowledgmentSimone ConiglioAntoine DechaumeOriginal implementation of Arjen Deetman, seehttps://github.com/arjendeetman/GCMMA-MMA-Python.ReferencesSvanberg, K. (1987). The Method of Moving Asymptotes -- A new method for
structural optimization. International Journal for Numerical Methods in
Engineering 24, 359-373.doi:10.1002/nme.1620240207, seehttps://onlinelibrary.wiley.com/doi/abs/10.1002/nme.1620240207.Svanberg, K. (n.d.). MMA and GCMMA -- two methods for nonlinear
optimization. Retrieved August 3, 2017 fromhttps://people.kth.se/~krille/mmagcmma.pdf
Package: gemseo-pdfo
PDFO wrapper for GEMSEODocumentationSeehttps://gemseo.readthedocs.io/en/stable/plugins.html.Bugs/QuestionsPlease use the gitlab issue tracker athttps://gitlab.com/gemseo/dev/gemseo-pdfo/-/issuesto submit bugs or questions.LicenseThegemseo-pdfosource code is distributed under the GNU LGPL v3.0 license.
A copy of it can be found in the LICENSE.txt file.
The GNU LGPL v3.0 license is an exception to the GNU GPL v3.0 license.
A copy of the GNU GPL v3.0 license can be found in the LICENSES folder.Thegemseo-pdfoexamples are distributed under the BSD 0-Clause, a permissive
license that allows to copy paste the code of examples without preserving the
copyright mentions.Thegemseo-pdfodocumentation is distributed under the CC BY-SA 4.0 license.Thegemseo-pdfoproduct depends on other software which have various licenses.
The list of dependencies with their licenses is given in the CREDITS.md file.ContributorsGEMSEO developers
Package: gemseo-petsc
PETSc GEMSEO interface.This plugin provides an interface to the PETSc linear solvers. They can
be used for direct and adjoint linear system resolution in GEMSEO.Installationgemseo-petscrelies onpetsc4py, the Python bindings forPETSc.PETScandpetsc4pyare available on pypi, but no
wheel are available. Hence, depending on the initial situation, here are
our recommendations:Linux environmentUsing CondaPETScandpetsc4pyare available on the conda-forge repository.
If you start from scratch of if you want to install the plugin in a
pre-existing conda environment, you can use the following command in
your current conda environment before installing gemseo-petsc:condainstall-cconda-forgepetsc4pyUsing pipPETScandpetsc4pycan be build from their sources by using pip.
To do so, use the following commands in your Python environment.pipinstallpetscpetsc4pyBy building PETSc and petsc4py from sourcesIt is also possible to buildPETScandpetsc4pyfrom the PETSc
sources. To do so, please follow the information provided in thePETSc
installation manual, and do not
forget to enable the compilation ofpetsc4py.Windows environmentAlthough it has not be tested, it is possible to buildPETScandpetsc4pyunder a Windows environment, and hence to have thegemseo-petscplugin working. A description of the procedure to build
these dependencies can be foundhereBugs/QuestionsPlease use the gitlab issue tracker athttps://gitlab.com/gemseo/dev/gemseo-petsc/-/issuesto submit bugs or questions.LicenseThegemseo-petscsource code is distributed under the GNU LGPL v3.0 license.
A copy of it can be found in the LICENSE.txt file.
The GNU LGPL v3.0 license is an exception to the GNU GPL v3.0 license.
A copy of the GNU GPL v3.0 license can be found in the LICENSES folder.Thegemseo-petscexamples are distributed under the BSD 0-Clause, a permissive
license that allows to copy paste the code of examples without preserving the
copyright mentions.Thegemseo-petscdocumentation is distributed under the CC BY-SA 4.0 license.Thegemseo-petscproduct depends on other software which have various licenses.
The list of dependencies with their licenses is given in the CREDITS.md file.ContributorsFrançois GallardJean-Christophe GiretAntoine Dechaume
Package: gemseo-pseven
pSeven wrapper for GEMSEOWARNING: This plugin is no longer tested nor updated, contact us in case of trouble.DocumentationSeehttps://gemseo.readthedocs.io/en/stable/plugins.html.InstallationUsing pSeven requires that is installed as well as its Python API.
The pSeven Python API is not defined as a dependency of this package,
because there is no package available in PyPI.
It shall be installed in the same environment as the one in which this plugin is installed.DevelopmentFor testing withtox,
set the environment variablePSEVEN_PIP_REQ_SPECto point to the URL or path of apipinstallable version of the pSeven Python API,
set the environment variableDATADVD_LICENSE_FILEfor the pSeven license.Bugs/QuestionsPlease use the gitlab issue tracker athttps://gitlab.com/gemseo/dev/gemseo-pseven/-/issuesto submit bugs or questions.LicenseThe GEMSEO-PSEVEN source code is distributed under the GNU LGPL v3.0 license.
A copy of it can be found in the LICENSE.txt file.
The GNU LGPL v3.0 license is an exception to the GNU GPL v3.0 license.
A copy of the GNU GPL v3.0 license can be found in the LICENSES folder.The GEMSEO-PSEVEN examples are distributed under the BSD 0-Clause, a permissive
license that allows to copy paste the code of examples without preserving the
copyright mentions.The GEMSEO-PSEVEN documentation is distributed under the CC BY-SA 4.0 license.The GEMSEO-PSEVEN product depends on other software which have various licenses.
The list of dependencies with their licenses is given in the CREDITS.rst file.ContributorsGEMSEO developers
Package: gemseo-pymoo
A GEMSEO wrapper for pymoo optimization algorithms.DocumentationHow to get the docs?Bugs/QuestionsPlease use the gitlab issue tracker athttps://gitlab.com/gemseo/dev/gemseo-pymoo/-/issuesto submit bugs or questions.LicenseThegemseo-pymoosource code is distributed under the GNU LGPL v3.0 license.
A copy of it can be found in the LICENSE.txt file.
The GNU LGPL v3.0 license is an exception to the GNU GPL v3.0 license.
A copy of the GNU GPL v3.0 license can be found in the LICENSES folder.Thegemseo-pymooexamples are distributed under the BSD 0-Clause, a permissive
license that allows to copy paste the code of examples without preserving the
copyright mentions.Thegemseo-pymoodocumentation is distributed under the CC BY-SA 4.0 license.Thegemseo-pymooproduct depends on other software which have various licenses.
The list of dependencies with their licenses is given in the CREDITS.md file.ContributorsGabriel Max DE MENDONCA ABRANTESFrancois GALLARDAntoine DechaumeLluis ARMENGOL GARCIALuca SARTORIGilberto RUIZ JIMENEZ
Package: gemseo-scilab
GEMSEO-Scilab is a GEMSEO plugin for interfacing scilab functions to
GEMSEO. It creates GEMSEO MDODisciplines from any scilab source code.Bugs/QuestionsPlease use the gitlab issue tracker athttps://gitlab.com/gemseo/dev/gemseo-scilab/-/issuesto submit bugs or
questions.LicenseThe GEMSEO-SCILAB source code is distributed under the GNU LGPL v3.0
license. A copy of it can be found in the LICENSE.txt file. The GNU LGPL
v3.0 license is an exception to the GNU GPL v3.0 license. A copy of the
GNU GPL v3.0 license can be found in the LICENSES folder.The GEMSEO-SCILAB examples are distributed under the BSD 0-Clause, a
permissive license that allows to copy paste the code of examples
without preserving the copyright mentions.The GEMSEO-SCILAB documentation is distributed under the CC BY-SA 4.0
license.The GEMSEO-SCILAB product depends on other software which have various
licenses. The list of dependencies with their licenses is given in the
CREDITS.rst file.ContributorsFrançois GallardAntoine DechaumeGilberto Ruiz Jiménez
Package: gemseo-umdo
MDO under uncertaintyDocumentationSeehttps://gemseo.readthedocs.io/en/stable/plugins.html.Bugs/QuestionsPlease use the gitlab issue tracker athttps://gitlab.com/gemseo/dev/gemseo-umdo/-/issuesto submit bugs or
questions.LicenseThe GEMSEO-UMDO source code is distributed under the GNU LGPL v3.0
license. A copy of it can be found in the LICENSE.txt file. The GNU LGPL
v3.0 license is an exception to the GNU GPL v3.0 license. A copy of the
GNU GPL v3.0 license can be found in the LICENSES folder.The GEMSEO-UMDO examples are distributed under the BSD 0-Clause, a
permissive license that allows to copy paste the code of examples
without preserving the copyright mentions.The GEMSEO-UMDO documentation is distributed under the CC BY-SA 4.0
license.The GEMSEO-UMDO product depends on other software which have various
licenses. The list of dependencies with their licenses is given in the
CREDITS.rst file.ContributorsMatthias De LozzoAntoine DECHAUME
Package: gemurl
gemurlA library for normalizing gemini:// URLsUsageThe package can be installed from PyPI using pip:$ pip install gemurlUse it like this:from gemurl import normalize_url

print(normalize_url("GEMINI://EXAMPLE.COM:1965"))
# Should print: gemini://example.com/The package also includes a command like tool:$ gemurl normalize GEMINI://EXAMPLE.COM:1965
gemini://example.com/API ofgemurlModuleTheGemurlErroris the base class for all exceptions raised by
functions in this module.normalize_url(url: str) -> strNormalize a URL according to RFC 3986 and the Gemini
specification. RaisesNormalizarionErrorif the input is not a valid
(gemini) URL. RaisesNonGeminiUrlError(which is a subclass
ofNormalizarionError) if the scheme is non-gemini.host_port_pair_from_url(normalized_url: str) -> tuple[str, int]Get a (host, port) tuple suitable for connecting a socket. The input
URL must be normalized for this function to work correctly.capsule_prefix(normalized_url: str) -> strFind the prefix of the URL that uniquely identifies its capsule. Two
URLs belong to the same capsule if the hostnames and ports match, but
if the path begins with "/~USER/" or "/users/USER/", then the USER
part needs to match too.This definition is borrowed from khuxkm's Molniya. Thanks!FeaturesThe normamlization function ensures that:Scheme and host case are always lowercase.The host is IDNA-encoded, if it has non-ASCII characters.The port is removed if it has the default 1965 value.Percent encoding hex digit are always uppercase.Non-reserved characters are never percent encoded.Non-printable (and non-ASCII) characters are always percent encoded.Percent encoding of reserved characters are not changed (since that would change the meaning).URLs with no paths get a single slash path.. and .. path segments are collapsed.Empty queries and fragments are distinct from missing ones.See test cases intest_url.pyin te source code for the full list.Ideas for Future ImprovementsFunction to resolve relative URLsFunction to convert URLs to display form (decode percent and IDNA encoding)
Package: gemviz
gemvizPython Qt5 application to visualize Bluesky data from tiled server.GH tagGH releasePyPIconda-forgePython version(s)Unit TestsCode CoverageLicenseGoalsminimum: PyQt app that can select runs, show line chartsideal: add database filters, config file, autodetect data types, and representationsstretch: data visualization integrate withhttps://github.com/BCDA-APS/qs-web2023Web Linkshttps://github.com/bluesky/tiledhttps://github.com/bluesky/bluesky-widgetsTiled Python Client Demonstration- shows the JSON API between tiled server and clientTiled Python Client Python API- terse example usingtiled.clientlibaryHow to run this code?First said, this software application is pre-release and may contain significant unhandled
bugs.  Pleasereport any you encounteror
feature requests, too.Suggested installation for developers is to usepipwith itseditablemode:This project is still in development.
We haveplans for production
release.
Until the production release, you should rungemvizas would a developer by following these instructions:Navigate to a directory where you have similar software projectsgit clone https://github.com/BCDA-APS/gemvizonly need to do this once, assumes you havegitcommandcd gemvizconda env create --force -n gemviz -f ./env.ymlonly need to do this once, assumes you havecondacommandconda activate gemvizpip install -e .gemviz &Thegemviz package is now available on PyPIwhich means
a development version can be installed viapip:pipinstallgemvizAcknowledgementsWe'd like to thank theGEM fellow programfor sponsoring
an intern fellowship for the development of this software at the Advanced Photon Source."This product includes software produced by UChicago Argonne, LLC
under Contract No. DE-AC02-06CH11357 with the Department of Energy."
Package: gen1
Gen1My Implementation of " Structure and Content-Guided Video Synthesis with Diffusion Models" by RunwayML. "Input videos x are encoded to z0 with a fixed encoder E and diffused to zt. We extract a
structure representation s by encoding depth maps obtained with MiDaS, and a content representation c by encoding one of the frames
with CLIP. The model then learns to reverse the diffusion process in the latent space, with the help of s, which gets concatenated to zt, as
well as c, which is provided via cross-attention blocks. During inference (right), the structure s of an input video is provided in the same
manner. To specify content via text, we convert CLIP text embeddings to image embeddings via a prior."Installpip3 install gen1Usageimporttorchfromgen1.modelimportGen1model=Gen1()images=torch.randn(1,3,128,128)video=torch.randn(1,3,16,128,128)run_out=model.forward(images,video)DatasetsHere is a summary table of the datasets used in the Structure and Content-Guided Video Synthesis with Diffusion Models paper:DatasetTypeSizeDomainDescriptionSourceInternal datasetImages240MGeneralUncaptioned imagesPrivateCustom video datasetVideos6.4M clipsGeneralUncaptioned short video clipsPrivateDAVISVideos-GeneralVideo object segmentationLinkStock footageVideos-GeneralDiverse video clips-Citation@misc{2302.03011,
Author = {Patrick Esser and Johnathan Chiu and Parmida Atighehchian and Jonathan Granskog and Anastasis Germanidis},
Title = {Structure and Content-Guided Video Synthesis with Diffusion Models},
Year = {2023},
Eprint = {arXiv:2302.03011},TodoAdd training scriptAdd in conditional text paramater to pass in text, not just images and or other videos
Package: gen2-connector
Gen2-connector enables Ray cluster to be deployed over IBM Gen2 infrastructureUse of python virtual environment, e.g.virtualenvis greatly encouraged, to avoid installing Python packages globally which could break system tools or other projectsInstall gen2-connector on your machinepip install gen2-connectorConfigure ibm vpcGenerate API KEYCreate/Update security groupto have SSH, Redis and Ray Dashboard ports open: 22, 8265 and 6379Create cluster config fileUse interactiveibm-ray-configconfig tool to generate cluster.yaml configuration filepip install ibm-ray-config
ibm-ray-config -o cluster.yamlUse generated file to bring ray cluster up, e.gray up cluster.yamlAfter finished, find cluster head node and worker nodes ips:ray get-head-ip cluster.yaml
ray get-worker-ips cluster.yamlTo get status of the clusterray status --address PUBLIC_HEAD_IP:6379Use browser to open ray dashboard on PUBLIC_HEAD_IP:8265. Alternatively useray dashboardto forward ray cluster dashboard to your localhost.Submit example taskray submit cluster.yaml templates/example.py
Package: gen3-tracker
Gen3 TrackerUtilities to manage Gen3 schemas, projects and submissions.Quick StartInstallation$ pip install gen3_tracker

$ g3t version
version: 0.0.1Use$ g3t --help
Usage: g3t [OPTIONS] COMMAND [ARGS]...

  Gen3 Tracker: manage FHIR metadata and files.

Options:
  --format [yaml|json|text]  Result format. G3T_FORMAT  [default: yaml]
  --profile TEXT             Connection name. G3T_PROFILE See
                             https://bit.ly/3NbKGi4

  --version
  --help                     Show this message and exit.

Commands:
  ping          Verify gen3-client and test connectivity.
  init          Create project, both locally and on remote.
  add           Add file to the index.
  commit        Record changes to the project.
  diff          Show new/changed metadata since last commit.
  push          Submit committed changes to commons.
  status        Show the working tree status.
  clone         Clone meta and files from remote.
  pull          Download latest meta and data files.
  update-index  Update the index from the META directory.
  rm            Remove project.
  utilities     Useful utilities.User GuideSeeuse cases and documentationContributingSeeCONTRIBUTING.md
Package: gen3users
gen3usersUtils for Gen3 commons user management.user.yaml validationValidate auser.yamlfile using the CLI:pip install gen3users
gen3users validate first_user.yaml second_user.yamlValidate auser.yamlfile in a Python script:from gen3users.validation import validate_user_yaml

file_name = "my-gen3-commons/user.yaml"
with open(file_name, "r") as f:
    user_yaml = f.read()
    validate_user_yaml(user_yaml, file_name)user.yaml conversionConverts auser.yamlfile from the old format to the new ABAC-based centralized auth format, required by the latest Fence and Arborist.Convert auser.yamlfile using the CLI:pip install gen3users
gen3users convert old_user.yaml [new_user.yaml]Convert auser.yamlin a Python script:from gen3users.conversion import convert_old_user_yaml_to_new_user_yaml

src_file_name = "my-gen3-commons/old_user.yaml"
dst_file_name = "my-gen3-commons/new_user.yaml"
with open (src_file_name, "r") as f:
        user_yaml = f.read()
        convert_old_user_yaml_to_new_user_yaml(user_yaml, dst_file_name)
Package: gen3-util-plugin-nvidia
nvidia-collaborationOHSU CEDAR Cyclic IF and H&E imagesGetting startedSetup python environmentsource venv/bin/activate
python3 -m pip install -r requirements.txt
python3 -m pip install -r requirements-dev.txt  
python3 -m pip install -e .Run meta import with --plugin_pathThe input directory:tests/fixtures-new/
├── HandE
├── RegisteredImages
│   ├── 17633-6-Scene-001
│   ├── 18538-6-Scene-001
│   ├── 19142-6-Scene-001
│   ├── 24952-6-Scene-001
│   ├── 30411-6-Scene-001
│   ├── 31022-6-Scene-001
│   ├── 31480-6-Scene-001
│   ├── 33548-6-Scene-001
│   ├── 38592-6-Scene-001
│   ├── 48411-6-Scene-001
│   ├── 54774-4-Scene-001
│   ├── 57494-6-Scene-001
│   └── 57658-6-Scene-001
└── annotationswill produce:gen3_util meta  import dir tests/fixtures/ tmp/output --project_id aced-nvidia --plugin_path gen3_util_plugin_nvidia --remove_path_prefix tests/fixtures/
summary:
  ResearchStudy:
    count: 1
  ResearchSubject:
    count: 13
  Patient:
    count: 13
  Specimen:
    count: 13
  DocumentReference:
    count: 738
    size: 74437
msg: OKexpected resultsOutput files:tmp/output
├── DocumentReference.ndjson
├── Patient.ndjson
├── ResearchStudy.ndjson
├── ResearchSubject.ndjson
└── Specimen.ndjsonIdentifiers:$ cat tmp/output/*.ndjson | jq -rc '. as $r | .identifier[]? | [$r.resourceType, .value]'
["Patient","P1"]
["Specimen","T1"]Run the testspytest  tests/DistributionPyPi# update pypi

# pypi credentials - see https://twine.readthedocs.io/en/stable/#environment-variables

export TWINE_USERNAME=  #  the username to use for authentication to the repository.
export TWINE_PASSWORD=  # the password to use for authentication to the repository.

# this could be maintained as so: export $(cat .env | xargs)

rm -r dist/
python3  setup.py sdist bdist_wheel
twine upload dist/*
Package: gen3utils
gen3utilsUtils for Gen3 commons managementInstall with pippip install gen3utilsmanifest.json validationValidate one or moremanifest.jsonfiles:gen3utils validate_manifest cdis-manifest/*/manifest.jsonThe validation settings can be updated by modifyingthis file.etlMapping.yaml validationValidate anetlMapping.yamlfile against the dictionary URL specified in amanifest.jsonfile:gen3utils validate_etl_mapping etlMapping.yaml manifest.jsonPortal Configuration (gitops.json) validationValidate agitops.jsonfile against the dictionary URL specified in amanifest.jsonfile and an etlMapping.yaml file. Adds a comment to a pull request listing all the errors encountered when validating against etlMapping.yamlgen3utils validate_portal_config etlMapping.yaml manifest.json gitops.json <username>/<repository> <pull request number>To run without making a pull request commentgen3utils validate_portal_config etlMapping.yaml manifest.json gitops.jsonComment on a PR with any deployment changes when updating manifest servicesThe command requires the name of the repository, the pull request number andaGITHUB_TOKENenvironment variablecontaining a token with read and write access to the repository. It also comments a warning if a service is pinned on a branch.pip install gen3utils
gen3utils post-deployment-changes <username>/<repository> <pull request number>Log parser for CTDS log pipelinepip install gen3utils
gen3utils s3log --help
gen3utils s3log [OPTIONS] BUCKET PREFIX SCRIPTRunSCRIPTin Gen3 logs under S3BUCKET:PREFIX. TheSCRIPTshould be importable defining a method like this:def handle_row(obj, line):
    if 1 + 1 == 2:
        return lineFor example, to process logs in bucketmy-commons-logsat prefixmy-logswith agen3utils/script.pyfile:pip install gen3utils
gen3utils s3log my-commons-logs my-logs gen3utils.scriptRunning tests locallypoetry install -vv
poetry run pytest -vv ./tests
Package: gen4id
InstallationUsagepip install gen4idNormalfrom gen4id import IncreaseGen
ic = IncreaseGen(key_len=8)
uid = ic.encode(increase_id=10)
print(uid)Use Random Stringby default, it user thegen4id.increase_gen.MIXEDas the random string for choose,  you can use a generate random string for you applicationfrom gen4id import random_str,IncreaseGen
from gen4id.increase_gen import MIXED

rstr = random_str(MIXED)
ic = IncreaseGen(choose=rstr,key_len=10)
uid = ic.encode(increase_id=10)
print(uid)Add Digit Check Bitfrom gen4id import random_str,IncreaseGen
from gen4id.increase_gen import MIXED

rstr = random_str(MIXED)
ic = IncreaseGen(choose=rstr,key_len=10,digit=True,digit_bit=2)
uid = ic.encode(increase_id=10)
print(uid)MoreTo Be Continue ….