Saravanan666/pypi-org huggingface dataset:
Package: gcmt3d
[![Build Status](https://travis-ci.com/lsawade/GCMT3D.svg?branch=master)](https://travis-ci.com/lsawade/GCMT3D)# GCMT3DThis is the initial commit for the revisited global cmt solution to allow for 3D
velocity structures.## InstallationIn order to install GCMT3D we first need to create a new conda environment.
Then we install the dependencies, and finally GCMT3D itself. The required steps
are the following.##### First, make sure all necessary environment vairables are solved:Check whether an mpi compiler is installed:`bash which mpicc # Shoud return the location of your mpi compiler `if nothing is returned or the output says find then install a compiler.#### 1. Create and activate a new conda environment with python 3.7`bash conda create-n<your_environment> python=3.7 conda activate <your_environment> `#### 2. Install separate dependencies:`bash # Install basemap using conda conda config--addchannelsconda-forgeconda install basemap conda install mpi4py `#### 3. Download GCMT3D`bash # Download GCMT3D git clonehttps://github.com/lsawade/GCMT3D.gitcd GCMT3D/ `#### 4. Install other requirements using pip`bash pip install-rrequirements.txt `#### 5. Install GCMT3D`bash # Install GCMT3D in the current conda environment pip install . `Test that GCMT3D was successfully installed by running the following command`bash python-c"import gcmt3d" `## Travis automatic testingThe Travis automatic system is setup to load the latest anaconda release for
Linux. Then, in a Python 3.7 environment, all required software is downloaded
and installed. For the installation steps, please refer to the.travis.ymlin
the main directory. It mainly follows the steps in the quick install.
Package: gcm-toolkit
gcm_toolkitgcm_toolkitis an open-source python package to read, post-process, and plot 3D GCM data. The goal is to have an
easy to use invironment for new GCM users, while allowing for direct access to the data for more experienced users.gcm_toolkitoriginated from the need for a consistent and easy-to-share methodology for reading and analyzing the 3D
circulation models of exoplanet atmospheres. Currently, the focus is on data produced by
theMITgcmand its implementations for exoplanets (
seeCarone et al., 2020andSchneider et al., 2022). But we envision this
package as a general tool for the analysis of data from different 3D GCMs.gcm_toolkitis currently under development. Feel free to contribute!Features (Current/Planned)Multiple read-in methods (currently onlyMITgcm)'Tag' system for easy referencing of multiple models in memoryMaking use ofxarray's intuitive system of multi-D arraysQuick plotting routinesisobaric sliceszonal meansevolution over timeDirect data access for custom plotting and post-processingMain AuthorsAaron SchneiderSven KieferRobin BaeyensGet StartedRead thedocsInstallationpip install gcm-toolkit(Note the dash)Packages neededPlease install the following packages beforehand:general:xarray, netcdf4exPERT/MITgcm - raw files:xmitgcm, xgcm, f90nml,cubedsphereRunning the first exampleCheck the get started in thedocsMiscellaneous DocumentationAll quantities are expressed inSI units.Latitudes run from -90° to 90° ; Longitudes run from -180° to 180°.The substellar point for tidally locked planets is located at (0°, 0°).The radius of the planet is defined at the bottom boundary of the vertical grid.ContactFeel free to contact one of the main authors:Aaron Schneider,Sven Kiefer, orRobin Baeyens.Project url:https://github.com/exorad/gcm_toolkit
Package: gcndesign
GCNdesignA neural network model for prediction of amino-acid probability from a protein backbone structure.Built withpytorchnumpypandastqdmGetting StartedInstallTo install gcndesgn throughpippipinstallgcndesignUsageQuick usage as a python modulefromgcndesign.predictorimportPredictorgcndes=Predictor(device='cpu')# 'cuda' can also be appliedgcndes.predict(pdb='pdb-file-path')# returns list of amino-acid probabilitiesUsage of scriptsgcndesign_predict.pyTo predict amino-acid probabilities for each residue-sitegcndesign_predict.pyYOUR_BACKBONE_STR.pdbgcndesign_autodesign.pyTo design 20 sequences in a completely automatic fashiongcndesign_autodesign.pyYOUR_BACKBONE_STR.pdb-n20For more detailed usage, please run the following commandgcndesign_autodesign.py-hNoteThe gcndesign_autodesign script requirespyrosettasoftware.
Installation & use ofpyrosettamust be in accordance with their license.External Packagesgcndesign_autodesign.py:PyRosettaDocumentsMethod summaryNoteA critical issue has fixed and the parameters were re-trained on a new dataset (CATH v4.3 S40 dataset).
This change has stabilized the prediction, but has not been reflected in the document above. So there are inaccuracies in the description and figures.DatasetThe dataset used for training GCNdesign is availableheredataset.tar.gz: Training/T500/TS50 datasetdataset_cath40.tar.bz2: CATH-v4.3 S40 dataset (used for the latest parameter training)LisenceDistributed underMITlicense.AcknowledgmentsThe author was supported by Grant-in-Aid for JSPS Research Fellows (PD, 17J02339).
Koga Laboratory of Institutes for Molecular Science (NINS, Japan) has provided a part of the computational resources.
Koya Sakuma (yakomaxa) gave a critical idea for neural net architecture design in a lot of deep discussions.
Naoya Kobayashi (naokob) created excellent applications to help broader needs,ColabGCNdesignandFolditStandalone_Sequence_Design.
Package: gcnParser
A python package and command-line tools toParse GCN Notices and Circulars into a MySQL Database.InstallationThe easiest way to install gcnParser is to usepip:bash pip install gcnParserOr you can clone this repo and install from a local version of the code:bash git clone git@github.com:thespacedoctor/gcnParser.git cd gcnParser python setup.py installDevelopmentIf you want to tinker with the code, then install in development mode.
This means you can modify the code from your cloned repo:bash git clone git@github.com:thespacedoctor/gcnParser.git cd gcnParser python setup.py developPull
requestsare welcomed!IssuesPlease report any issueshere.LicenseCopyright (c) 2018 David YoungPermission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
“Software”), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Package: gco
gcoA Python interface to thegcolibrary (modified for repackaging fromthe original source)The exposedGCO<XXX>Graphclasses are available under thegcoroot namespace.See theresearch homepagefor license and usage information.NeighborhoodWithout the ability to easily create C++ arrays-of-arrays in Python, aGCONeighborhoodclass is exposed which builds pointers into flat arrays:neighborhood=gco.GCONeighborhood(count,site,cost)wherecount[i]is the number of neighbours for sitei,site[j]is the site of the jth cumulative neighbour, andcostthe corresponding cost for such a neighbour.
Package: gcode2dplotterart
IntroductionG-Codewrapper to generate G-Code for 2D plotter art. Add paths, points, lines, circles, and more and get G-Code instructions to send to your 2D Plotter orconverted 3D Printer.Here are a few examples of what's been made with this library.Quick StartBelow is a quick start example to get you up and running. For a quick start, gallery, and documentation, .check out the website.fromgcode2dplotterartimportPlotter2D# Change to `Plotter3D` if using a converted 3D printer.plotter=Plotter2D(# Specify the dimensions of your plotterx_min=0,x_max=200,y_min=0,y_max=200,feed_rate=10000,# G-Code files are located in `output_directory/title/layer.gcode`title="Plotter2D Quickstart",output_directory="./output",# Give a warning if a plotted point is outside the plotting device's dimensions.handle_out_of_bounds="Warning",)# Setup a layer per plotting instrument usedblack_pen_layer="black_pen_layer"blue_marker_layer="blue_marker_layer"green_marker_layer="green_marker_layer"# Create the layersplotter.add_layer(black_pen_layer,color="black",line_width=1.0)plotter.add_layer(blue_marker_layer,color="blue",line_width=4.0)plotter.add_layer(green_marker_layer,color="#027F00",line_width=4.0)# Add some dots, lines, shapes, and paths.plotter.layers[black_pen_layer].add_rectangle(x_start=10,y_start=15,x_end=40,y_end=50)plotter.layers[black_pen_layer].add_point(x=30,y=40)plotter.layers[blue_marker_layer].add_circle(x_center=10,y_center=30,radius=10)plotter.layers[blue_marker_layer].add_rectangle(x_start=50,y_start=50,x_end=75,y_end=75)plotter.layers[green_marker_layer].add_path([(10,10),(20,25),(30,15),(1,100)])plotter.layers[green_marker_layer].add_line(x_start=70,y_start=80,x_end=70,y_end=15)# Generate a graphical preview to get a rough idea of what will be plotted.plotter.preview()# Output creation to G-Code files to be used in plotting.plotter.save()ChangelogView the changelog
Package: gcode2zaxe
gcode2zaxeA CLI application that converts gcode files to Zaxe print-ready files. You can use it from the command line after installing it. The executable name isg2z.Don't forget to star the project onGitHub.InstallationRun:python -m pip install --upgrade gcode2zaxeUsageShow help:g2z -hConvert gcode file to zaxe file:g2z -g <gcode_file_path>Optional Parameters-n, --name:Output file base name. Defaults to the gcode file name -> (-g <gcode_file_path>).-f, --filament:Filament type. Defaults tozaxe_pla. Materials mostly start withzaxe_.-d, --nozzle_diameter:Nozzle diameter. Defaults to0.4.-m, --model:Zaxe printer model. Defaults toX1. See available models in themodels list.ContributingIf you have any suggestions or found any bugs, please open an issue or create a pull request.Don't hesitate to open an issue if you have any questions about the code.FootnotesThis application does not guarantee that the output file will be valid or compatible with the printer.Use at your own risk. I take no responsibility for any damage to your printer.This application has no affiliation with Zaxe or its affiliates.This project is licensed under theAGPLv3 license.
Package: gcodeBuddy
gcodeBuddygcodeBuddy is a python library intended to ease the processof writing to, reading from, and interpreting g-code files, particularly geared towards3D printer g-code flavors like Marlin.InstallationUse the package managerpipto install gcodeBuddy.pipinstallgcodeBuddyView the Documentation with Example Usageshttps://gcodebuddy.readthedocs.io/Supported G-code FlavorsMarlinContributionsPull requests are more than welcome. For most cases, openan issue first to discuss what you would like to change.LicenseMIT
Package: gcode-documentation-parser
gcode-documentation-parserSee ademousage of the outputA utility that parses the documentation pages from Marlin, RepRap, and Klipper,
to generate an index of commands usage.OutputYou can access the output from theoutput branchof this repo. Here are the
raw links that you can reference or copy:all_codes.json: A JSON file containing the documentationall_codes_window.js: A JS file that definesAllGcodeson the globalwindowobjectall_codes_const.js: A JS file that defines aconst AllGcodesall_codes_export.js: A JS file that exports anAllGcodesvalueThe documentation is updated semi-regularly, at the start of every month, and
published on this repo.You can also generate it locally by running the following, and checking theoutputfolderpoetryrun./update_documentation.pyUsageNormally, the output would be used by something likegcode-documentation, to
allow users to search and understand how a GCode command should be used.This was originally created inOctoprintpluginMarlinGcodeDocumentation,
and needs the parsed documentation data to function.
Package: gcodepy
gcodepygcodepyis a g-code generator for 3D printers that useMarlin Firmware.
This project was heavily inspired byFull Control GCODE.
It is essentially my own take on the concept of writing g-code through an abstraction layer, using Python instead of Excel/VBA.Why would I want to write g-code with Python?To be honest, there aren't usually many occasions where using an interface layer likegcodepyor Full Control GCODE are better than the CAD/slicer workflow.
However, there are occasions where being able to programmatically define your printer's movements can be useful.
One possible use of interface layers is in defining motions using mathematical functions.
For example,gcodepysupports essentially any other Python code, so you can create any function with the correct output as input for movement even using other libraries such asnumpy.Thomas Sanladerer created ablog post and associated videoabout the potential uses of Full Control GCODE, which also applies togcodepy. Notably, he created some very interesting geometric lampshade-esque objects.Installationgcodepyisavailable on PyPIand so can be installed withpip.$ pip3 install gcodepyNote thatgcodepyhas only been tested with Python 3.X and no guarantees are made about compatibility with the deprecated Python 2.X.ExamplesOne of the most interesting things to do withgcodepyis to do toolhead movements using mathematical functions.
For example, you can make your printer go in a spiral:This example is defined inexamples/zspiral.py.
For more examples, check theexamplesfolder.Planned featurescleaner gcode output (particularly feedrates)better interfacing for absolute movementsbetter detection + handling of invalid inputs/movements
Package: gcodereader
gcodeReaderRead gcode and translate into peridigm inputTodos to setup projectin gitlab activate CI/CD (settings→general→visibility→CI/CD)create token for pypi (todo: more text)adapt coverage percentageFeaturesFree software: BSD licenseDocumentationTODO: describe featuresInstallationInstallation from sourceGet gcodereader source fromhttps://gitlab.dlr.de/fa_sw/peridynamik/gcodereader.gitand add the /src folder to pythonpath in the environment variablesInstallation as python packageInstall it fromthe gitlab packacke registryYou can download the latest artifact (*.whl) and install it usingcd gcodereader
python setup.py install gcodereader.whlTest the installationIn python execute:import gcodereaderDevelopersDevelopers may also install the pre-commit hook.Precommitinstall the pre-commitpip install pre-commit
or
conda isntall pre-commitIn the gcodereader folderpre-commit installThis enables the pre-commit hooks defined in.pre-commit-config.yamland eases your commits and successful pipline runs.UsageContributing togcodereaderWe welcome your contribution!If you want to provide a code change, please:Create a fork of the GitLab project.Develop the feature/patchProvide a merge request.If it is the first time that you contribute, please add yourself to the list
of contributors below.CitingNo citing requiredLicenseFree software: BSD licenseDocumentation:https://gcodereader.readthedocs.io.Change LogseechangelogCI Pipeline and Jobs for DevelopersIf you encounter any failed job on the pipeline you can run them locally for more information.
(prerequisite: havemakeandpoetryinstalled [e.g. conda install make poetry])See all availabe make targets used for the ci-jobsmake listFind the target with matching names and execute them locally e.g.:make testIfcheck-formattingfails, run the following to fix issues.make formattingIfcheck-license-metadatafails, runmake check-license-metadataidentify the corresponding filename and run the following (include the filename in $filename)poetry run reuse addheader --copyright="German Aerospace Center (DLR)" --license="MIT" $filenameAuthorsJan-Timo Hesse
Package: gcodeutils
GCodeUtils is a set of utilities to manipulate GCode programs.
It is targetting RepRap oriented GCode but isn’t limited to RepRap.Currently, it is composed of one calibration generation program, a basic gcode modifier (which translates code along
X/Y or convert extrusion distance to relative), a stretcher to increase hole size of printed parts and a GCode converter which generate arc opcodes from arc interpolation as segments.InstallationGCodeUtils is installable from PyPI with a single pip command:pip install gcodeutilsAlternatively, GCodeUtils can be run directly from sources after a git pull:git clone https://github.com/zeograd/gcodeutils.git
cd gcodeutils && python setup.py installor directly from its git repository:pip install git+https://github.com/zeograd/gcodeutils.gitOnce GCodeUtils is installed, the .py files located in the cura_plugins
subdirectory can be copied into thepluginsdirectory of Cura to be callable
from within Cura itself.DocumentationLatest documentation can be found online at this address:http://gcodeutils.readthedocs.org/en/latest/AcknowledgementGCode parsing is borrowed from GCoder as found in Printrun (https://github.com/kliment/Printrun)
Package: gcody
gcodyGcody is a python wrapper for GCODE. It gives common programming language functionality to GCODE as well as several visualization tools.
This is an early draft of gcody and it is intended for general writing of GCODE, not printer specific code.
Gcody was inspired bymecode.Basics:# gcody example creating a serpentine pattern and an elephant# these are both normally imported from gcodyfromgcodyimport*# creating parametersdistance=10cycles=10# creating gcode objectg=gcode()# writes the GCODE command to use relative coordinates# this changes how position is recorded internally (in gcode object)# abs_coords is the default setting for gcode and is the default for gcody as wellg.rel_move()# moves the print head back and forth in xg.move(distance,speed=10,com='Moves head 10 in x')# moves the print head back and forth in xforiinrange(1,cycles):# simple move allows for modality (not repeating commands)# it makes the GCODE prettier :)# unfortunately, not all printers support it :(g.simple_move(y=10)# movement in yg.simple_move((-1)**i*distance)# movement in x# creates a matplotlib figure matching the path of the printer headg.view('b')# This is an animated figure showsing the progression of the printer pathg.animated('b',save_file='snake.gif')# saves the GCODE to a fileg.save('snake')# outputs file 'snake.gcode'g.save('snake','txt')# outputs file 'snake.txt'The output GCODE is:G91; use relative coordinatesF600; 10 mmps motionG1X10.000000; Moves head 10 in xY10.000000X-10.000000Y10.000000X10.000000Y10.000000X-10.000000Y10.000000X10.000000Y10.000000X-10.000000Y10.000000X10.000000Y10.000000X-10.000000Y10.000000X10.000000Y10.000000X-10.000000The other features of gcody are readying existing GCODE and displaying it:# file from https://www.thingiverse.com/thing:998999/#files# gcode generated with latest Cura (https://ultimaker.com/en/products/ultimaker-cura-software)file='elefante_small.gcode'# This reads the GCODE file line by line and converts it into a gcode object# GCODE file can be hundreds of thousands of lines, if not more. This means reading them# can be slow. The math comes out to is roughly 13,000 move lines per second.elefante=read(file)# This figure colors the lines draw with a color that corresponds to a print timeelefante.cbar_view()# This method takes ~60 seconds to work.# this view has a slider bar that allows one to select the print timeelefante.slide_view('r')See images ongithub!Dependencies:NumpyMatplotlibOptional Dependenciespillow, ImageMagic, of FFmpeg as optional dependancies for matplotlib to save videosMayavifor viewing backendsTo Do:Add clockwise motion commandsAdd in other GCODE commandsAdd more complex combinations of moveTake requests for features
Package: gcommon
Common Python LibraryAbout"gcommon" is a python utility library for server and client application development.Installinggitclonehttps://github.com/liguopeng80/gcommon.git
pipinstall-egcommonUsageUsage for server applicationimportasynciofromgcommon.webimportmonkey_patchmonkey_patch.monkey_patch_flask()fromgcommon.aio.gserverimportSimpleServerclassDemoServer(SimpleServer):SERVICE_NAME='demo'asyncdefinit_server(self):# parse configuration and init any dependencies to start service.# "init_server" can be async or not async."""do whatever you want"""importdemo_serviceself.logger.debug("init database...")demo_service.init_database(self.config)self.logger.debug("init demo service...")demo_service.init_service()defstart_server(self):# "start_server" can be async or not async."""do whatever you want"""fromweb.webappimportapphost=self.config.get('service.web.host')port=self.config.get('service.web.port')auto_reload=self.config.get_bool('service.auto_reload')asyncio.create_task(app.run_task(host=host,port=port,use_reloader=auto_reload))self.logger.info("starting web service on%d...",port)if__name__=='__main__':DemoServer.start()Usage for client applicationfromgcommon.utils.gglobalimportGlobalfromgcommon.utils.gmainimportinit_main# load configuration and init loggerGlobal.config=init_main()Usage for just utilsfromdatetimeimportdatetimefromgcommon.utils.gtimeimportDateUtillast_monday=DateUtil.last_monday(datetime).now()ConfigurationFor server and client applications, gcommon will load configuration from "deploy/default.yaml" by default.# deploy/default.yamlservice:web:base_url:/v3host:0.0.0.0port:12580Secret ConfigurationYou can also have a secret config file which will not be committed to git repository.# deploy/secret.default.yamldemo_postgre:server_address:"127.0.0.1"server_port:5432username:"admin"password:"password"How to load secret config:fromgcommon.utils.gglobalimportGlobaldb_config=Global.config.get("secret.demo_postgre")password=db_config.passwordpassword=Global.config.get("secret.demo_postgre.password")HistoryThe library was named "common" in 2008 and then renamed to "gcommon" in 2010 to avoid name conflict. Its initial "g" comes from the author's name (Guo Peng Li).It was implemented on Pytohn 2.6 and then upgraded to Python 2.7, while its all asynchronous functionalities were based on twisted.On 2018, it was firstly migrated to Python 3 (3.6) but kept using twsited as its aysnc infrastructure until 2021.At the middle of 2021, most async functionalities in gcommon were re-implemented with asycio and the library was published as MIT license.