How can I compose a list of option flags and pass them to a command in Fish Shell?

Fish splits command substitutions on newlines only.

You are using echo -n, which explicitly doesn't add a newline. So your option printing code

for file in *.yml; echo -n -- "-f $file "; end

ends up printing something like

-f compose-service1.yml -f compose-service2.yml -f compose-service3.yml -f compose-service4.yml -f compose-service5.yml

As one line, which, to fish, is one argument. It ends up running like (truncated)

docker compose "-f compose-service1.yml -f compose-service2.yml..." up -d

So docker tries to find one file called

 compose-service1.yml -f compose-service2.yml -f compose-service3.yml -f compose-service4.yml -f compose-service5.yml

(with the leading space!)

Unlike bash, fish doesn't split this on spaces. This is generally a good idea, because people use filenames that include spaces. Your bash example is broken if a .yml file has spaces in the name.

But because you want each -f and each filename to be a separate argument to docker compose, you need to ensure that the -f and the filename end up on separate lines.

for file in *.yml; printf '%s\n' -f $file; end

or

for file in *.yml; string join \n -- -f $file; end

is probably the simplest way to do that. This would print

-f
compose-service1.yml
-f
compose-service2.yml
-f
compose-service3.yml
-f
compose-service4.yml
-f
compose-service5.yml

which fish would then turn into one argument per line.

Alternatively:

Docker's option parsing is reasonably standard, so you can also pass a compose file as -fcompose.yml, directly attached to the -f option. (this also explains your error - docker sees a -f and then uses the rest of the argument as the filename)

That would allow using echo:

for file in *.yml; echo -- "-f$file"; end

This just prepends the -f and then prints it with a newline (no echo -n), which ends up printing

-fcompose-service1.yml
-fcompose-service2.yml

(and so on)

As an aside, if you really really really need a command substitution to be split on spaces, you can use string split " ". This is common with pkg-config and other *-config tools inspired by it.

pkg-config --cflags --libs gio-2.0

prints (truncated as an example)

-pthread -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/glib-2.0

which is meant to be used as-if copy-pasted into the commandline. (this means that pkg-config paths can't include spaces, btw)

In that case you would use

g++ example_01.cpp (pkg-config --cflags --libs gio-2.0 | string split -n " ")

(the -n/--no-empty flag makes it ignore empty elements, which effectively means it treats runs of spaces as one thing).

So, if you wanted to re-do your bash command like it is, with broken spaces in filenames, you could also use

docker compose (for file in *.yml; echo -n -- "-f $file "; end | string split -n " ") up -d

I'd do

for f in *.yml; set opts $opts "-f" $f; end
docker compose $opts up d

Suppose you have 10 files. The opts list will have 20 entries. Then the docker compose command receives the -f option and the file as separate parameters.

The for loop, whilst perfectly fine, isn't strictly necessary:

fs=*.yml docker compose {-f,$fs} up -d