FAIRmat-NFDI / pynxtools / 7992599510

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Add files as argument in CLI (#246)

* Adds file arguments to click

* Updates docs

* Add deprecation warning

* Remove remaining `--input-file` arguments

* Remove `--input-file` from jupyter notebooks

* Fix line duplication from formatting

* Reformat deprecated text for input-file

* Don't require `--nxdl` in click

* Updates help text

* Add test for params file

* Switch back to current workdir in params file test

29 of 37 new or added lines in 3 files covered. (78.38%)

4738 of 10840 relevant lines covered (43.71%)

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