Code Overview

IN CONSTRUCTION

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"CachedMetadata" -> "File" [arrowsize=0.5,style="setlinewidth(0.5)"]; "DataContainer" -> "File" [arrowsize=0.5,style="setlinewidth(0.5)"]; "FileSequence" [URL="../../../auto_source/solidipes/solidipes.loaders.file_sequence.html#solidipes.loaders.file_sequence.FileSequence",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Sequence of files"]; "Sequence" -> "FileSequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "CachedMetadata" -> "FileSequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Group" -> "FileSequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "GeofMesh" [URL="../../../auto_source/solidipes/solidipes.loaders.geof_mesh.html#solidipes.loaders.geof_mesh.GeofMesh",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Mesh file loaded with pyvista"]; "PyvistaMesh" -> "GeofMesh" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Group" [URL="../../../auto_source/solidipes/solidipes.loaders.group.html#solidipes.loaders.group.Group",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Group of files and directories."]; "ABC" -> "Group" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Image" [URL="../../../auto_source/solidipes/solidipes.loaders.image.html#solidipes.loaders.image.Image",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Image loaded with PIL"]; "File" -> "Image" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ImageSequence" [URL="../../../auto_source/solidipes/solidipes.loaders.image_sequence.html#solidipes.loaders.image_sequence.ImageSequence",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Sequence of images loaded with PIL"]; "Sequence" -> "ImageSequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "File" -> "ImageSequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "LoaderList" [URL="../../../auto_source/solidipes/solidipes.loaders.file.html#solidipes.loaders.file.LoaderList",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Lazily evaluated list of loaders"]; "Markdown" [URL="../../../auto_source/solidipes/solidipes.loaders.text.html#solidipes.loaders.text.Markdown",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Markdown file"]; "Text" -> "Markdown" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Meshio" [URL="../../../auto_source/solidipes/solidipes.loaders.meshio.html#solidipes.loaders.meshio.Meshio",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="File loaded with meshio"]; "File" -> "Meshio" [arrowsize=0.5,style="setlinewidth(0.5)"]; "PDF" [URL="../../../auto_source/solidipes/solidipes.loaders.pdf.html#solidipes.loaders.pdf.PDF",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Image loaded as base64"]; "File" -> "PDF" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ParseGEOF" [URL="../../../auto_source/solidipes/solidipes.loaders.parse_inp.html#solidipes.loaders.parse_inp.ParseGEOF",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "ParseINP" -> "ParseGEOF" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ParseINP" [URL="../../../auto_source/solidipes/solidipes.loaders.parse_inp.html#solidipes.loaders.parse_inp.ParseINP",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "PyvistaMesh" [URL="../../../auto_source/solidipes/solidipes.loaders.pyvista_mesh.html#solidipes.loaders.pyvista_mesh.PyvistaMesh",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Mesh file loaded with pyvista"]; "File" -> "PyvistaMesh" [arrowsize=0.5,style="setlinewidth(0.5)"]; "SVGWrapper" [URL="../../../auto_source/solidipes/solidipes.loaders.image.html#solidipes.loaders.image.SVGWrapper",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "Sequence" [URL="../../../auto_source/solidipes/solidipes.loaders.sequence.html#solidipes.loaders.sequence.Sequence",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Sequence of any subclass of DataContainer"]; "DataContainer" -> "Sequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Table" [URL="../../../auto_source/solidipes/solidipes.loaders.table.html#solidipes.loaders.table.Table",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Table file loaded with Pandas"]; "File" -> "Table" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Text" [URL="../../../auto_source/solidipes/solidipes.loaders.text.html#solidipes.loaders.text.Text",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Text file, potentially formatted with markdown"]; "File" -> "Text" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Video" [URL="../../../auto_source/solidipes/solidipes.loaders.video.html#solidipes.loaders.video.Video",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Video file"]; "File" -> "Video" [arrowsize=0.5,style="setlinewidth(0.5)"]; "loadable" [URL="../../../auto_source/solidipes/solidipes.loaders.data_container.html#solidipes.loaders.data_container.loadable",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; } digraph inheritancefe10ae193b { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "ABC" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="Helper class that provides a standard way to create an ABC using"]; "Binary" [URL="../../../auto_source/solidipes/solidipes.viewers.binary.html#solidipes.viewers.binary.Binary",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Viewer for (unknown) binary"]; "Viewer" -> "Binary" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Code" [URL="../../../auto_source/solidipes/solidipes.viewers.code_snippet.html#solidipes.viewers.code_snippet.Code",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; "Text" -> "Code" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Image" [URL="../../../auto_source/solidipes/solidipes.viewers.image.html#solidipes.viewers.image.Image",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Viewer for images"]; "Viewer" -> "Image" [arrowsize=0.5,style="setlinewidth(0.5)"]; "MarkdownViewer" [URL="../../../auto_source/solidipes/solidipes.viewers.text.html#solidipes.viewers.text.MarkdownViewer",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top"]; 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"ABC" -> "Viewer" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Command line options for solidipes

The following scripts are available:

command line options for solidipes

argument command

Attributes

init :

Initialize a study directory
positional arguments:

  • directory: Path to the directory to initialize. Defaults to the current directory. Cannot be your home directory.

optional arguments:

  • -h: help message

  • --force: Force the creation of solidipes configuration files in the current directory. WARNING: This could erase an existing .solidipes directory!

usage: solidipes init [-h] [--force] [directory]

view:

Generate view for the given file
positional arguments:

  • path: Path to file to be viewed

optional arguments:

  • -h: show this help message and exit

usage: solidipes view [-h] path

upload:

Upload dataset to an online repository
positional arguments:
  • {zenodo}: Target hosting platform

    • zenodo: upload study to Zenodo

optional arguments:

  • -h: show this help message and exit

usage: solidipes upload [-h] {zenodo} ...

upload zenodo:

Upload study to Zenodo
positional arguments:

  • directory: Path to the directory containing the study to upload. Default directory: root of the current Solidipes study.

optional arguments:

  • -h: show this help message and exit

  • --sandbox: use Zenodo sandbox test platform

  • --access_token ACCESS_TOKEN: Provide the Zenodo token

  • --new-deposition: create a new deposition instead of updating a previously created one

  • --existing-deposition [EXISTING_IDENTIFIER]: URL or DOI of the unpublished study to update

usage: solidipes upload zenodo [-h] [--sandbox] [--access_token ACCESS_TOKEN] [--new-deposition] [--existing-deposition [EXISTING_IDENTIFIER]] [directory]

report:

Generate a .py report
positional arguments:
  • {curation,jtcam,web_report}: The report to generate

    • curation: controls sanity of the data

    • jtcam: opens a web report for the JTCAM Journal

    • web_report: generates web_report (it also runs curation)

  • dir_path: Path to directory containing data files

  • additional_arguments: Arguments to forward to the report

optional arguments:

  • -h: show this help message and exit

usage: solidipes report [-h] {curation,jtcam,web_report} dir_path ...

download:

Download content from Zenodo
positional arguments:

  • identifier: URL or DOI of the study to download

  • destination: Path to the destination folder

optional arguments:

  • -h: show this help message and exit

  • --only-metadata: Only download metadata (overrides destination directory’s metadata!)

usage: solidipes download [-h] [--only-metadata] identifier [destination]

Note

The code for the commands can be found in the scripts directory.