The `--format` option relied on `click.Context.get_parameter_source` to
determine if the default value for the `--format` parameter was passed.
A bug in click caused this to behave "correctly", click 8.4.0 fixed the
bug. Change the logic by using `None` as the default value so that it
can be checked without using the parameter source.
Overhaul the pipeline configuration logic by collapsing all dynamic
configuration options, both for analyses and pipes into a single
dictionary. Change all the interfaces so that there is no longer
distinction between the configuration of an analysis and of pipes.
Expose these options to the command line via `--{name}-configuration`
options for each pipe/analysis that is applicable to the command-line
invocation.
Add categories in the pipeline, allow an artifact to have a category
specified which allows it to be shown or hidden by default. Adapt the
CLI tools to hide artifacts of the category that don't
`show_by_default=True`.
Fix the code that handles setting the `--format`, `--tar` and `--yaml`
command line options, which incorrectly wrote to the `format` kwargs
instead of the `container_format` one.
Add the functionality the the pipeline infrastructure and CLI to run
individual pipe and analyses as subcommands instead of in-process. This
allow better debuggability of individual pipes.
Giacomo Vercesi