Saravanan666/pypi-org huggingface dataset:
Package: galaxychop
Welcome toGalaxyChopGalaxyChopis a Python package that tackles the dynamical decomposition problem by using clustering techniques in phase space for stellar galactic components.It runs in numerical N-body simulations populated with semi-analytical models and full hydrodynamical simulations, such asIllustris TNGandEAGLE.MotivationGalaxies are self-gravitating complex stellar systems formed mainly by stars, dark matter, gas and dust. Star are assembled in different stellar components, such as the disk (thin and thick), the nucleus, the stellar halo and the bar. The components interact with each other and each of them follows its own temporal evolution. For this reason, the description of the formation and evolution  of  galaxies  is  strongly  linked  to  the  formation and evolution of each of these individual components and their assemble in the final galaxy.Dynamical decomposition it is a fundamental tool to separate each galaxy component for further study. Numerous methods exist in the literature to perform this task, but there is no tool that allows us to use several of them, providing the possibility of an easy comparison.Dynamic decomposition models implementedJHistogram:Implementation of the dynamic decomposition model of galaxies described byAbadi et al.(2003).JThreshold:Implementation of the dynamic decomposition model of galaxies used inTissera et al.(2012),Vogelsberger et al.(2014),Marinacci et al.(2014),Park et al.(2019), etc.KMeans:Implementation ofScikit-LearnK-means as a model for dynamical decomposing of galaxies.GaussianMixture:Implementation of the dynamic decomposition model of galaxies described byObreja et al.(2018).AutoGaussianMixture:Implementation of the  dynamic decomposition model of galaxies described byDu et al.(2019)And many moreRequirementsYou need Python3.7,3.8,3.9to run GalaxyChop.Standard InstallationYou could findGalaxyChopat PyPI. The standar instalation via pip:$pipinstallgalaxychopDevelopment InstallClone this repo and then inside the local directory execute$gitclonehttps://github.com/vcristiani/galaxy-chop.git
$cdgalaxy-chop
$pipinstall-e.AuthorsValeria Cristiani <valeria.cristiani@unc.edu.ar> (IATE-OAC-CONICET,FaMAF-UNC).Antonela Taverna (IATE-OAC-CONICET).Juan Cabral (IATE-OAC-CONICET,CONAE).Rafael Pignata (OAC-CONICET,FaMAF-UNC).Bruno Sanchez (Duke University).Martin Chalela (IATE-OAC-CONICET).Federico Benelli (IPQA-CONICET,FCEFyN-UNC).Ornela Marioni (IATE-OAC-CONICET,FaMAF-UNC).Nelson Villagra (UNPSJB).
Package: galaxycloudrunner
GalaxyCloudRunner enables bursting of user jobs to remote compute resources for
theGalaxy application. It provides a dynamic job
runner that can be plugged into Galaxy.OverviewGalaxyCloudRunner enables bursting of user jobs to remote compute
resources for theGalaxy application.
It provides several dynamic job rules that can be plugged into Galaxy,
enabling Galaxy to submit jobs to remote cloud nodes.How it worksThe GalaxyCloudRunner provides a library of rules that can be plugged
into Galaxy throughjob_conf.xml. Once configured, you can get your
jobs to be automatically routed to remote Pulsar nodes running on the
cloud. The GalaxyCloudRunner will discover what Pulsar nodes are
available by querying theCloudLaunchAPI.
Adding a new node is a simple matter of visiting theCloudLaunchsite and launching a new
Pulsar node on your desired cloud.Getting StartedGetting started with the GalaxyCloudRunner is a simple process.First, install galaxycloudrunner into your Galaxy's virtual
environment viapip install galaxycloudrunner.Add a job rule to Galaxy which will determine the Pulsar node to
route to.Configure yourjob_conf.xmlto use this rule.Launch as many Pulsar nodes as you need throughCloudLaunch.Submit jobs as usual.For detailed instructions, see:https://galaxycloudrunner.readthedocs.io/Developer installationClone the source code repository and install the library with the dev
dependencies.git clone https://github.com/CloudVE/galaxycloudrunner.git
cd galaxycloudrunner
pip install --upgrade .[dev]To build the HTML docs locally, run the following commands. The built site will
be available indocs/_build/html.cd docs
make htmlContributingCommunity contributions for any part of the project are welcome. If you have
a completely new idea or would like to bounce your idea before moving forward
with the implementation, feel free to create an issue to start a discussion.Contributions should come in the form of a pull request. The code needs to be
well documented and all methods have docstrings. We are largely adhering to thePEP8 style guidewith 80 character
lines, 4-space indentation (spaces instead of tabs), explicit, one-per-line
imports among others. Please keep the style consistent with the rest of the
project.Release processUpdate any dependencies insetup.pyand commit the changes.Increment the library version number ingalaxycloudrunner/__init__.pyas
persemver rules.Add release notes toCHANGELOG.rst, adding the most recent commit hash to
the changelog. List of commits can be obtained usinggit shortlog <last release hash>..HEAD
Package: galaxy-containers
OverviewTheGalaxycontainers module - interfaces for modeling and interacting with container backends (docker and docker swarm currently).Free software: Academic Free License version 3.0Code:https://github.com/galaxyproject/galaxyHistory21.1.1.dev021.1.0 (2021-03-19)First release from the 21.01 branch of Galaxy.20.5.0 (2020-07-04)First release from the 20.05 branch of Galaxy.19.9.0 (2019-12-16)Initial import from dev branch of Galaxy during 19.09 development cycle.
Package: galaxy-environment
Building an environmental catalog for galaxiesAuthor: Kayleigh Meneghini |Email:kayleighmeneghini@gmail.comHow to useThis package is available onPyPi.For more details, please check thistutorial, usingS-PLUSdata.# Installing 
pip install galaxy-environment# import 
from galaxy_environment import environmentAny doubts about this package, please write tokayleighmeneghini@gmail.comIntroductionHow much the environment affects galaxies is still part of the unknown, as some results are discrepant depending on the sample selection, according to Lai
et al. (2016), such as the chosen magnitude or velocity dispersion limit for sample.Furthermore, the very definition of environment makes this type of study not trivial, after allhow to define the environment?
We can consider the local environment, such as the associated with a central galaxy and its satellites, or on larger scales such as those associated
to groups and clusters.According to Muldrew et al. (2012), there are two wide methods used to define the galactic environment, these are:Nearest Neighbors and Fixed Apertures.In this package I have implemented the calculation of environmental estimators by these two methods, using the Python routines developed by Wright (2006) for calculating distances in cosmology.Method 1: Nearest NeighborsThe principle of Nearest Neighbors is that galaxies with closest neighbors are in denser environments and, therefore, have higher density fields.
This method defines the galactic environment using a variable scale, depending on the number of neighbors of each galaxy.
For each galaxy in the sample, values for k are chosen, this being the number of neighbors and calculate the distance to each of them around an interval of z.Method 2: Fixed AperturesThis method, unlike the previous one, defines a scale for the environment around a fixed area or volume for each galaxy.
So, the more galaxies within that area or volume, the denser the environment.ReferencesEtherington J., Thomas D., Measuring galaxy environments in large-scale photometric
surveys, Monthly Notices of the Royal Astronomical Society, 2015, vol. 451, p. 660Lai et al. (2016), CAN WE DETECT THE COLORâ€“DENSITY RELATION WITH
PHOTOMETRIC REDSHIFTS?, The Astrophysical Journal, 2016, vol. 825, p. 40Mendes de Oliveira et al. (2019), The Southern Photometric Local Universe Survey
(S-PLUS): improved SEDs, morphologies and redshifts with 12 optical filters,
Monthly Notices of the Royal Astronomical Society, 2019, vol. 489, p.
241â€“267Muldrew et al. (2012), Measures of galaxy environment â€“ I. What is â€˜environmentâ€™?,
Monthly Notices of the Royal Astronomical Society, 2012, vol. 419, p. 2670Wright E., A Cosmology Calculator for the World Wide Web, Publications of the Astro-
nomical Society of the Pacific, 2006, vol. 118, p. 1711â€“1715
Package: galaxy-files
OverviewTheGalaxyfile sources framework and default plugins.Code:https://github.com/galaxyproject/galaxyHistory23.2.1 (2024-02-21)Bug fixespin fs.dropboxfs to >=1 by@bernt-matthiasin#16451Write to a temp filename in posix file source plugin by@natefooin#17350Set webdav file source to use temp files by default by@davelopezin#17388More defensive access of extra props in filesources by@nuwangin#17445EnhancementsAdd Invenio RDM repository integration by@davelopezin#16381Refactor FilesDialog + Remote Files API schema improvements by@davelopezin#16420Use fs.onedatarestfs for Onedata files source plugin implementation by@lopiolain#16690Remove record access handling for Invenio RDM plugin by@davelopezin#16900Enhance Invenio RDM integration by@davelopezin#1696423.1.4 (2024-01-04)Bug fixesSeparate collection and non-collection data element by@mvdbeekin#1723623.1.3 (2023-12-01)No recorded changes since last release23.1.2 (2023-11-29)Bug fixesImplement missing upload for S3 file sources by@davelopezin#1710023.1.1 (2023-10-23)Bug fixesFix some drs handling issues by@nuwangin#15777Fix filesource file url support by@nuwangin#15794Fix unittest mocks to support us checking geturl()  by@dannonin#16726Fix allowlist deserialization in file sources by@mvdbeekin#16729EnhancementsUnify url handling with filesources by@nuwangin#1549723.0.6 (2023-10-23)No recorded changes since last release23.0.5 (2023-07-29)No recorded changes since last release23.0.4 (2023-06-30)No recorded changes since last release23.0.3 (2023-06-26)No recorded changes since last release23.0.2 (2023-06-13)Bug fixesFix dropbox import to support newer versions by@nuwangin#1623923.0.1 (2023-06-08)No recorded changes since last release22.1.1 (2022-08-22)Initial standalone release of this package.
Package: galaxygetopt
You write stuff that looks like this, containing all of the information
you would ever need about a tool; options, test cases, metadatafromgalaxygetopt.ggoimportGalaxyGetOptasGGOc=GGO(options=[['int','An integer parameter',{'required':True,'validate':'Int','default':10}],['float','A float',{'required':True,'validate':'Float','default':1e-4}],['string','A string value',{'required':True,'multiple':True,'default':['Hello','World'],'validate':'String'}],And you get data back in a nice dict{'int':40,'float':'1e-4','string':['Hello','World']}Known BugsCurrently there is a known bug in the galaxy XML, under highly specific
circumstances. If you define a parameter that isrequiredhiddenvalidate String(probably not a hard req)_galaxy_specificand expect it to properly generate the value, it will not. See lines
206/207 ofgalaxygetopt/ggo.pyfor the current hack I use to get
around this.OtherThis library features a number of subclasses ofgalaxygetopt.parameter.parameter, all of which have myriad numbers
of options. In order to brutally test these, I have added a classgalaxygetopt/tests/parameter_generator.pywhich can generate every
single possible combination of functional calls, given rules you
specify. You can then generate hundreds of objects with different sets
of options, which you can filter a subset out and test at will. See that
classes’s documentation for more information.
Package: galaxy-importer
InstallFrom pypipip install galaxy-importerFrom sourceClone repo and go into project directoryInstall into environment the local setup.py including its development dependencies:pip install -e .[dev]Run importerRun parsing/validation standalone to view log output and importer result for a build collection artifact file:python -m galaxy_importer.main [collection_artifact_file]Supports legacy roles (note: must be in the parent directory of the legacy role):python -m galaxy_importer.main --legacy-role [legacy_role_directory] --namespace [namespace]Supports converting markdown to html:python -m galaxy_importer.main --markdown [readme_md_directory]View log output in terminal, and view the importer result in the written fileimporter_result.jsonStructure of Outputmetadata(all data from MANIFEST.json, set by CollectionLoader._load_collection_manifest())docs_blob(set by CollectionLoader._build_docs_blob())collection_readmedocumentation_filescontentscontentsrequires_ansibleConfigurationAn optional ini configuration file is supported, the following locations are checked in this order:/etc/galaxy-importer/galaxy-importer.cfg
<code_source>/galaxy_importer/galaxy-importer.cfgYou can override the above paths by settingGALAXY_IMPORTER_CONFIGin the environment. For example:$ export GALAXY_IMPORTER_CONFIG=~/galaxy-importer.cfgConfiguration options and their defaults are defined inDEFAULTSatgalaxy_importer/config.pyExample configuration file with subset of config options:[galaxy-importer]
LOG_LEVEL_MAIN = INFO
RUN_ANSIBLE_TEST = False
ANSIBLE_LOCAL_TMP = '~/.ansible/tmp'ANSIBLE_LOCAL_TMP- Set to any desired local Ansible temp directory. Defaults to~/.ansible/tmp.ANSIBLE_TEST_LOCAL_IMAGE- Set toTrueto runansible-testsandboxed within a container image. Requires installation of either Podman or Docker to run the container. Defaults toFalse.CHECK_CHANGELOG- Set toFalseto not check for aCHANGELOG.rst orCHANGELOG.mdfile under the collection root ordocs/dir, or achangelogs/changelog.ymlfile. Defaults toTrue.CHECK_REQUIRED_TAGS- Set toTrueto check for a set of tags required for Ansible collection certification. Defaults toFalse.LOCAL_IMAGE_DOCKER- Set toTrueto run theansible-testcontainer image via Docker; otherwise, Podman will be used. Defaults toFalse.LOG_LEVEL_MAIN- Set to the desired log level. Defaults toINFO.OFFLINE_ANSIBLE_LINT- Set toFalseif you wantansible-lintto check for a new version. Defaults toTrue.REQUIRE_V1_OR_LATER- Set toTrueto require a version number1.0.0or greater. Defaults toFalse.RUN_ANSIBLE_DOC- Set toFalseto skipansible-doc. Defaults toTrue.RUN_ANSIBLE_LINT- Set toFalseto skip runningansible-lint --profile productionover the whole collection. Defaults toTrue.RUN_ANSIBLE_TEST- Set toTrueto runansible-testduring collection import. Defaults toFalse.RUN_FLAKE8- Set toTrueto run flake8. Defaults toFalse.Issues and ProcessTo file an issue, visit theAutomation Hub Jira projectProcess details forgalaxy-importer:PROCESS.mdAdditional NotesPlace.mdfiles in thedocs/dir to have them show up in an imported collection's "Documentation" tab on Galaxy or Automation Hub.
Package: galaxy-job-execution
OverviewTheGalaxyjob execution runtime module.Code:https://github.com/galaxyproject/galaxyHistory23.2.1 (2024-02-21)EnhancementsReplace file_name property with get_file_name function by@SergeyYakubovin#16783Enable some flake8-logging-format rules in ruff by@nsoranzoin#16915Move and re-use persist_extra_files by@mvdbeekin#16955optimize object store cache operations by@SergeyYakubovin#1702523.1.4 (2024-01-04)No recorded changes since last release23.1.3 (2023-12-01)No recorded changes since last release23.1.2 (2023-11-29)Bug fixesFix library import from path linking files by@davelopezin#16919Don’t store job in JobIO instance attributes by@mvdbeekin#16965Fix extra files collection if usingstore_by="id"andoutputs_to_working_directoryby@mvdbeekin#1706723.1.1 (2023-10-23)Bug fixesFix tags ownership by@davelopezin#16339Push to object store even ifset_metafails by@mvdbeekin#16667Fix metadata setting in extended metadata + outputs_to_working_directory mode by@mvdbeekin#16678Fix ItemOwnerShipException in tag removal by@mvdbeekin#16773Fix and prevent persisting null file_size by@mvdbeekin#16855EnhancementsEmpower Users to Select Storage Destination by@jmchiltonin#14073Towards SQLAlchemy 2.0: drop session autocommit setting by@jdavcsin#15421Unify url handling with filesources by@nuwangin#15497Handle “email_from” config option consistently, as per schema description by@jdavcsin#15557Record input datasets and collections at full parameter path by@mvdbeekin#15978Code cleanups from ruff and pyupgrade by@nsoranzoin#16035Improved Cache Monitoring for Object Stores by@jmchiltonin#16110Remove various fallback behaviors by@mvdbeekin#1619923.0.6 (2023-10-23)Bug fixesFix extra files path handling by@mvdbeekin#16541Make sure job_wrapper uses a consistent metadata strategy by@mvdbeekin#16569Fixes for extra files handling and cached object stores  by@mvdbeekin#1659523.0.5 (2023-07-29)No recorded changes since last release23.0.4 (2023-06-30)No recorded changes since last release23.0.3 (2023-06-26)No recorded changes since last release23.0.2 (2023-06-13)No recorded changes since last release23.0.1 (2023-06-08)No recorded changes since last release20.9.0 (2020-10-15)First release from the 20.09 branch of Galaxy.20.5.0 (2020-07-04)First release from the 20.05 branch of Galaxy.
Package: galaxy-job-metrics
OverviewTheGalaxyjob metrics framework and default plugins.Code:https://github.com/galaxyproject/galaxyHistory23.2.1 (2024-02-21)Bug fixesAdd support for Cgroupsv2 by@natefooin#17169EnhancementsSupport configuring job metrics inline, update documentation by@natefooin#1717823.1.4 (2024-01-04)No recorded changes since last release23.1.3 (2023-12-01)No recorded changes since last release23.1.2 (2023-11-29)No recorded changes since last release23.1.1 (2023-10-23)No recorded changes since last release23.0.6 (2023-10-23)No recorded changes since last release23.0.5 (2023-07-29)No recorded changes since last release23.0.4 (2023-06-30)No recorded changes since last release23.0.3 (2023-06-26)No recorded changes since last release23.0.2 (2023-06-13)No recorded changes since last release23.0.1 (2023-06-08)No recorded changes since last release20.9.0 (2020-10-15)First release from the 20.09 branch of Galaxy.20.5.0 (2020-07-04)First release from the 20.05 branch of Galaxy.19.9.0 (2019-12-16)Initial import from dev branch of Galaxy during 19.09 development cycle.
Package: galaxy-jukebox-gui
Galaxy Jukebox GUIGraphical user interface for Galaxy Jukebox, which is a schematic exporter for Minecraft Note Block Studio.The actual conversion happens byGalaxy Jukebox.InstallationThe project is available onPyPI, so you can install it via pip, if you have Python3 installed:pip3installgalaxy-jukebox-guiAlternatively, (hopefully) you will be able to download an executable fromGitHub Releases, if you don't have Python.UsageIf you downloaded the pip version, you can launch it by entering the commandpython3 -m galaxy_jukebox_guiorgalaxy-jukebox-gui. If you downloaded the executable, then e.g. double click the executable to execute it (you may need to give it permission).You should see something similar to this (theming may be different):(It's qt, isn't it :D?)You can choose a single, or multiple input files, and an output file (if you chose a single input file) or an output path (if you chose multiple input files). The chosen files/path will be printed on the right. The 2 options available are the same as for the command line program (and choosing different options should change the image):Use redstone lamp: whether or not to place redstone lamp next to the note block (it looks cooler with lamp, but playback performance may be compromised).Sides mode is how many sides the noteblocks should have (-1, or between 1 and 3):-1 (automatic): using one of the following 3 based on noteblock count1: 2n wide, n high rectangle in front2: 2n×n rectangle to the right, and another in front3: 2n×n rectangles on all 3 sidesFeedbackBe sure to tell me if something ain't right, e.g. by opening anissue!Used librariesThe project uses PyQt5 for the GUI.
Package: galaxykit
GalaxykitGalaxykit is a client library forgalaxy_ng, designed for use in internal testing.It's intended to be a low-dependency and low-abstraction client for performing actions on a remote Automation Hub or galaxy_ng instance.Installing:To install the latest development version, runpip install -e .in the root of your checked-out copy of this repository.To set up the pre-commit hooks we are using (currently just autoformatting withblack), run the following snippet:pre-commitinstall
pre-commitinstall-hooksAfter that's been done, the first commit you make will have to install any of those dependencies, and may take a few minutes.
Package: galaxy-library-maker
galaxy-library-makerThis set of scripts facilitate the create of Galaxy libraries from files filesystem that the Galaxy
process has access to (currently this is the only mechanism supported, more could be added).InstallationCurrently, a git clone + local pip install is required. We will add this to pypi soon.Clone this repo and cd inside.Create a python3 virtual environment:python3 -m venv myVenvName
source myVenvName/bin/activate
pip install --upgrade pip
pip install wheelInstall this packagepip install .Requirements for runningGalaxy API keyYou need to obtain a Galaxy API Key on the instance where you want the files loaded as Galaxy Libraries.
To obtain an API key, in the main Galaxy screen, go to User -> Preferences, and there click on
Manage API key. Copy the key text (or pressCreate a new keyif there is none).YAML authentication file for GalaxyYou will need a YAML auth file for Galaxy, following the formatting from parsec:__default: instance_a

instance_a:
    key: "94c9894706fd97b36dbd1acdaa88b749"
    url: "http://localhost:8080/"

instance_b:
    key: "kajshdkajsdhaksjh3ek3jeh327ycei"
    url: "http://my.galaxy.ins/"Paste the Galaxy key and the appropiate URL (where you access Galaxy). You can have more than one instance
in the same YAML if desired (although will be only connection to one at once).Library definition YAML fileLibraries to be added to Galaxy are defined for this package in a YAML that follows this schema:---
- library: 'My data project 1'
  desc: 'Descriptio about my data project'
  synopsis: 'A lot of expression data'
  base_dir: /path/to/files/on/a/filesystem/that/galaxy/can/see/and/read
  recursive: true
  extensions:
    - txt: txt
    - gtf: gtf
- library: 'Another project'
  desc: 'Desc about another project'
  synopsis: 'More cool data'
  base_dir: /other/path
  recursive: true
  extensions:
    - _sce.rds: rdata.sce
    - _tab.txt: tabularYou can have as many libraries on the same YAML, each one will become a separate library in Galaxy,
where all files that respond to the extensions listed inextensionswill be made available, in the same
directory structure starting from thebase_dir.How do I know which datatypes are available in my Galaxy instance to use in the extensions part?Galaxy datatypes are instance dependant and as such you need to know which datatypes are available in your instance.
To do this, you can execute theget-datatypes.pyscript:get-datatypes.py -C creds.yaml -G instance_aRunningAssuming the above examples are available in creds.yaml and libs_def.yaml, and that the Galaxy instance where
those directories are available isinstance_a(and that the virtualenv is activated):load-into-galaxy-library.py -C creds.yaml -G instance_a -l libs_def.yamlTesting the packageMake sure that you have docker installed and that you can execute it without sudo, then run:bash run_tests_with_containers.sh
Package: galaxy-navigation
OverviewTheGalaxyclient DOM navigation framework.Navigation data that feeds tours generation, Jest testing, and Selenium testing.Code:https://github.com/galaxyproject/galaxyHistory23.2.1 (2024-02-21)No recorded changes since last release23.1.4 (2024-01-04)No recorded changes since last release23.1.3 (2023-12-01)No recorded changes since last release23.1.2 (2023-11-29)No recorded changes since last release23.1.1 (2023-10-23)EnhancementsInitial end-to-end tests for separate quota sources per object store by@jmchiltonin#1580023.0.6 (2023-10-23)No recorded changes since last release23.0.5 (2023-07-29)No recorded changes since last release23.0.4 (2023-06-30)No recorded changes since last release23.0.3 (2023-06-26)No recorded changes since last release23.0.2 (2023-06-13)No recorded changes since last release23.0.1 (2023-06-08)No recorded changes since last release22.9.0.dev0 (2022-06-24)First release from the 22.09 branch of Galaxy.