PFHub CLI tool #1510
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PFHub CLI tool #1510
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Zip and unzip are required for zipping files in the upload form.
upload.md is now a notebook in results/ as that directory is the correct environment.
Implement the conversion of meta.yaml records to a Zenodo record.
Necessary templages for the meta -> zenodo translation
This removes the htmlproofer checks. This isn't currently available in Nixpkgs and doesn't play well with the jekyll ruby environment in the latest Nix.
Updated pykwalify so needed to change the schema slightly.
Testing distributing a command line too for pfhub. - Add versioneer to deal with version numbers
zenodo_client will be used to upload to zenodo in the CLI. Also added twine and versioneer to upload to PyPI and genearte version numbers, respectively.
Update setup.cfg to include all the dependencies to make python-pfhub work in a Pip/Conda environment. Also, update setup.cfg for CLI script and versioneer.
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Cool!!! |
Nix develop was broken in the base directory due to dotwiz after recent changes. Dotwiz now installed with Nix. - Use separate nix file for python packages - revert to dotwiz 0.2.0 as easier to install with nix
CLI tool will check valid files so needs a valid schema present
Run the CLI tool outside of the working copy to ensure that required files are installed.
CLI now has a validate command to validate YAML files against the schemas. In addition - reorder some of the code - using linkml CLI tool from Python - make file path checking better with Click arguments - make the command names more sensible - sys.exit(1) when invalid files
linkml needs to added to nixpkgs along with other libraries
Using _data/python-pfhub/.loca for local python installs.
Reverse order of flake check so that _data/python_pfhub/flake.nix is first. Checking to see if linkml will work.
Nix build is broken due to unforseen issues with linkml
Greenlet is pinned for linkml which requires it to be pinned. If not pinned then something else is installing a version to new for linkml.
Download command of the CLI gets records from PFHub only including linking back to Zenodo. The old download command is not download_zenodo, which makes more sense.
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A CLI to download, submit and convert PFHub results
Some of these commits are in #1508
Todo:
convert-to-zenodoconvert-to-metaIdeas:
pfhub upload {zenodo-record} --sandbox ???sandbox=trueto submit to Zenodo sandbox~.pfhubrcfile locally to set parameters for zenodo and pfhub submissionpfhub submit --path=./ --config_path=~/pfhubrc --sandbox=truepfhub convertpfhub checkpfhub generate_notebook?pfhub generate_yaml?Done:
pfhubCLIdownloadcommand for both meta.yaml and Zenodo links