--quiet expecting an argument is a breaking change

[victorlin]

Snakemake version
7.7.0

Describe the bug

The new version 7.7.0 breaks scripts that use --quiet with a target name following the flag (e.g. snakemake --cores 1 --quiet myrule).

Previously, with version 7.6.2, --quiet was a standalone boolean flag:

usage: snakemake [-h] [--dry-run] [--profile PROFILE] [--cache [RULE ...]] [--snakefile FILE] [--cores [N]] [--jobs [N]]
                 ...
                 [--quiet] [--print-compilation]
                 ...
                 [target ...]

Now, with a change in --quiet behavior introduced in c8d81d0 and released in version 7.7.0, it will try to read any arguments:

usage: snakemake [-h] [--dry-run] [--profile PROFILE] [--cache [RULE ...]] [--snakefile FILE] [--cores [N]] [--jobs [N]]
                 ...
                 [--quiet [{progress,rules,all} ...]]
                 ...
                 [target ...]

Logs

See example below.

Minimal example

Setup:

cat >Snakefile << ~~
rule myrule:
    shell: "echo \"Hello world\""
~~

pip install snakemake==7.6.2
snakemake --cores 1 --quiet myrule
# Job stats:
# ...
# Hello world

pip install snakemake==7.7.0
snakemake --cores 1 --quiet myrule
# usage: snakemake [-h] [--dry-run] [--profile PROFILE] [--cache [RULE ...]] [--snakefile FILE] [--cores [N]] [--jobs [N]]
# ...
# snakemake: error: argument --quiet/-q: invalid choice: 'myrule' (choose from 'progress', 'rules', 'all')

Workarounds

Note that this only breaks when the target is specified directly following --quiet. So these still work with 7.7.0:

snakemake --cores 1 myrule --quiet
snakemake --quiet --cores 1 myrule
snakemake --cores 1 --quiet -- myrule

Additional context

N/A

[dariober]

If it helps, this should work but I haven't tried it:

snakemake --cores 1 --quiet -- myrule

The -- separates the list of optional arguments from the list of positional arguments. It's fairly standard behavior of command line parsers so I wouldn't consider it a bug even if it breaks backward compatibility (e.g. to grep --foo in a file you would do grep -- --foo my.file).

[victorlin]

@dariober thanks, that is a good practice to follow that I wasn't aware of until now. I've added your working example to the list in the issue description.

I agree that this isn't really a bug and there is no easy fix. Just having this here for anyone else who might come across the same thing, especially since the change in --quiet was not added to 7.7.0 release notes so it took some digging to understand.

[jdblischak]

I just got bit by this change in behavior, and I was also surprised it wasn't included in the changelog.

The -- workaround is sufficient for the minimal example in this Issue, but I'm not getting the expected behavior when I use it with my own Snakefiles (ie it's still printing all the rules despite passing --quiet). I'll try to create a minimal example to better pinpoint the problem.

[jdblischak]

I think I figured it out. I can't use the -- workaround when I also define command-line arguments via a profile.

# using the same Snakefile above
mkdir profile
echo "cores: 1" > profile/config.yaml

# works
snakemake --cores 1 --quiet -- myrule

# works
snakemake --profile profile/ myrule

# fails
snakemake --profile profile/ --quiet -- myrule

Error: you need to specify the maximum number of CPU cores to be used at the same time. If you want to use N cores, say --cores N or -cN. For all cores on your system (be sure that this is appropriate) use --cores all. For no parallelization use --cores 1 or -c1.

# fails
snakemake --profile profile/ --quiet all myrule

snakemake: error: argument --quiet/-q: invalid choice: 'myrule' (choose from 'progress', 'rules', 'all')

# works
snakemake --quiet --profile profile/ myrule

Essentially, it appears that now I have to specify --quiet prior to --profile. This is inconvenient, unexpected, and arbitrary. Am I missing something obvious?

[jdblischak]

Another strange behavior I noticed. The default behavior of --quiet is affected by the use of --profile. Again, using the same Snakefile and profile/config.yaml as above:

# 7.6.2

# expected
$ snakemake -nq
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1

# expected - same as above
$ snakemake --profile profile/ -nq
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1

# 7.7.0

# expected
$ snakemake -nq
Building DAG of jobs...
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1

# unexpected! Why is the rule shown?
$ snakemake --profile profile/ -nq
Building DAG of jobs...
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1


[Mon May 23 19:14:46 2022]
rule myrule:
    jobid: 0
    resources: tmpdir=/local/38306425

Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1

This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.

# expected - explicitly quieting the rules still works
$ snakemake --profile profile/ -nq rules
Building DAG of jobs...
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1

[pvandyken]

@jdblischak The bug preventing the mixing of --profile and --quiet is fixed with #1764.

[jdblischak]

@pvandyken Thanks for fixing the bug! I confirmed it is fixed in 7.9.0:

snakemake --version
## 7.9.0

cat > Snakefile << EOF
rule myrule:
    shell: "echo \"Hello world\""
EOF

mkdir profile
echo "cores: 1" > profile/config.yaml

# all of the following produce the same output
snakemake -nq
snakemake --profile profile/ -nq
snakemake --profile profile/ -nq rules
snakemake -nq --profile profile/
snakemake -nq rules --profile profile/

## Building DAG of jobs...
## Job stats:
## job       count    min threads    max threads
## ------  -------  -------------  -------------
## myrule        1              1              1
## total         1              1              1

[jdblischak]

@victorlin Thanks for reporting this bug. I think you can close the Issue now

[jdblischak]

Actually, looking back at the original post, I realize the issue was the change in behavior of the --quiet flag accepting arguments. This still requires the -- workaround (or specifying --quiet after the target), and I agree could be better documented since the --quiet flag has been around a long time as a standalone flag.

% snakemake --cores 1 --quiet myrule
snakemake: error: argument --quiet/-q: invalid choice: 'myrule' (choose from 'progress', 'rules', 'all')

% snakemake --cores 1 --quiet -- myrule
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1

Select jobs to execute...
Hello world
Complete log: .snakemake/log/2022-07-19T121336.050016.snakemake.log

% snakemake --cores 1 myrule --quiet
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
myrule        1              1              1
total         1              1              1

Select jobs to execute...
Hello world
Complete log: .snakemake/log/2022-07-19T121647.506241.snakemake.log

@victorlin It's your call as far as closing this Issue or leaving it open

[victorlin]

I think it's safe to close this as "won't fix", since there is an easy workaround and I doubt --quiet will be changed back to a standalone boolean flag.

[pvandyken]

I think I figured it out. I can't use the -- workaround when I also define command-line arguments via a profile.

@jdblischak Is this still an issue?

[jdblischak]

Is this still an issue?

@pvandyken No, your PR fixed that issue. That is what I confirmed above in #1660 (comment)

My comments after that were related to the subject of @victorlin's original post in this Issue, which is the fact that the ordering of --quiet and a target require more care now that --quiet can accept arguments