Remove ANTSPATH

[ghisvail]

Closes #1573

[ghisvail]

Looks like I am missing a few files (32 vs 34 in the search).

Got all of them.

To be noted, Scripts/multi_template_script.sh requires ANTSPATH as its first positional argument. I left the CLI as is to not break existing workflows, it just does not do anything with it anymore.

[cookpa]

Most of the scripts still need some work - removing ANTSPATH references is not sufficient because many of the checks for programs will fail.

Eg

-s "${ANTSPATH}ANTS"

can't be replaced with

-s "ANTS"

but rather needs to be -s $(which ANTS).

Is it OK if I push to your branch?

[ghisvail]

Sure, go for it 👍 Le mar. 25 juil. 2023, 13:43, Philip Cook ***@***.***> a écrit :

…

Most of the scripts still need some work - removing ANTSPATH references is not sufficient because many of the checks for programs will fail. Eg -s "${ANTSPATH}ANTS" can't be replaced with -s "ANTS" but rather needs to be -s $(which ANTS). Is it OK if I push to your branch? — Reply to this email directly, view it on GitHub <#1574 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO7U37PMUF5D5LIMN3JZM3XSAAVDANCNFSM6AAAAAA2XGVCF4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[gdevenyi]

POSIX check for a command is command -v as which may not always be available

[ghisvail]

POSIX check for a command is command -v as which may not always be available

PR updated with if ! command -v $CMD &> /dev/null guards as per this SO thread.

[cookpa]

I think you need the square brackets still

[ghisvail]

It works without brackets on my machine. I used the pattern in the accepted answer of the SO thread linked above.

[ghisvail]

# Make ANTS disappear from PATH.
$ mv $HOME/.local/ants/bin/ANTS{,.bak}

# Run wrapper script.
$ ./Scripts/ants.sh
Cannot find the ANTS program. Please \(re\)define $PATH in your environment.

# Put it back.
$ mv $HOME/.local/ants/bin/ANTS{.bak,}

# Run wrapper script again.
$ ./Scripts/ants.sh
 USAGE ::  
  sh   ants.sh  ImageDimension  fixed.ext  moving.ext  OPTIONAL-OUTPREFIX   OPTIONAL-max-iterations  OPTIONAL-Labels-In-Fixed-Image-Space-To-Deform-To-Moving-

[cookpa]

Looking good now @ghisvail

[cookpa]

Thanks for doing this @ghisvail