config file provided before command

[pahatz]

Related issue(s) and PR(s)
This PR closes #442 .

Description
The user should be able to provide the config file location argument ONLY before the subcommand of the cli.

How to test
For test coverage, some of the existing tests have been altered to follow the new allowed order of providing the config, i.e. before the subcommand.
To manually test, one should test individually the cli commands that are affected. Those are the ones that are using the config as an argument(upload, list htsget, download).

[codecov-commenter]

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Codecov Report

Attention: Patch coverage is 30.76923% with 18 lines in your changes missing coverage. Please review.

Project coverage is 39.39%. Comparing base (e4ef2a3) to head (9f0ef6d).

Files with missing lines	Patch %	Lines
main.go	0.00%	17 Missing ⚠️
download/download.go	66.66%	0 Missing and 1 partial ⚠️

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #458      +/-   ##
==========================================
- Coverage   39.60%   39.39%   -0.22%     
==========================================
  Files          11       11              
  Lines        2030     2036       +6     
==========================================
- Hits          804      802       -2     
- Misses       1109     1117       +8     
  Partials      117      117              

Flag	Coverage Δ
unittests	39.39% <30.76%> (-0.22%)	⬇️

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[jbygdell]

There shuld be no IFs here, the config must be set before any action i.e. sda-cli -config cli.conf ACTION -FLAGS should be the only functioning command.

Config can be as a file or as ENV flags.

Usage for all commands needs to be updated to match the new setup.

[MalinAhlberg]

Good work, @pahatz! Works well as far as I can tell!
I agree that it is a bit confusing that you can provide two configs, though... unless there's a use case I'm missing, it's probably cleaner to only allow one.

The README also needs some updates (apart from the Usage sections in the go files, that Jocke mentioned).

[pahatz]

I changed the behavior to work only for the config to be provided before the command.
Updated the tests, readme and Usage references.

[nanjiangshu]

I have just added a comment regarding path concatenation, otherwise, it looks great!

[nanjiangshu]

Looks good to me. It's weird that the integration test failed even after I reran it. Maybe a rebase to the main will fix the problem.

[pahatz]

Looks good to me. It's weird that the integration test failed even after I reran it. Maybe a rebase to the main will fix the problem.

v0.3.159 appears as the latest tag but the related sda images are missing.

[jbygdell]

Looks good to me. It's weird that the integration test failed even after I reran it. Maybe a rebase to the main will fix the problem.

v0.3.159 appears as the latest tag but the related sda images are missing.

v0.3.158 is the latest released version