🐛 Move pipeline import earlier in configuration process

[shnizzedy]

Fixes

Fixes

Running the 'fmriprep-options' pre-configured pipeline.
Traceback (most recent call last):
  File "/code/run.py", line 524, in <module>
    c['pipeline_setup']['system_config']['max_cores_per_participant'], int(c['pipeline_setup']['system_config']['num_ants_threads'])
KeyError: 'num_ants_threads'

by @shnizzedy

Related to #1435 by @shnizzedy

Description

1. Moves the conversion of a pipeline config dict to a Configruration object from after

   C-PAC/dev/docker_data/run.py

   Lines 484 to 525 in 1cbbdaf

   	# get the aws_input_credentials, if any are specified
   	if args.aws_input_creds:
   	c['awsCredentialsFile'] = resolve_aws_credential(args.aws_input_creds)
   	if args.aws_output_creds:
   	c['pipeline_setup']['Amazon-AWS']['aws_output_bucket_credentials'] = resolve_aws_credential(
   	args.aws_output_creds
   	)
   	c['pipeline_setup']['output_directory']['path'] = os.path.join(args.output_dir, "output")
   	if "s3://" not in args.output_dir.lower():
   	c['pipeline_setup']['log_directory']['path'] = os.path.join(args.output_dir, "log")
   	else:
   	c['pipeline_setup']['log_directory']['path'] = os.path.join(DEFAULT_TMP_DIR, "log")
   	if args.mem_gb:
   	c['pipeline_setup']['system_config']['maximum_memory_per_participant'] = float(args.mem_gb)
   	elif args.mem_mb:
   	c['pipeline_setup']['system_config']['maximum_memory_per_participant'] = float(args.mem_mb) / 1024.0
   	else:
   	c['pipeline_setup']['system_config']['maximum_memory_per_participant'] = 6.0
   	# Preference: n_cpus if given, override if present, else from config if
   	# present, else n_cpus=3
   	if args.n_cpus == 0:
   	c['pipeline_setup']['system_config']['max_cores_per_participant'] = int(c['pipeline_setup']['system_config'].get('max_cores_per_participant', 3))
   	args.n_cpus = 3
   	else:
   	c['pipeline_setup']['system_config']['max_cores_per_participant'] = args.n_cpus
   	c['pipeline_setup']['system_config']['num_participants_at_once'] = int(c['pipeline_setup']['system_config'].get('num_participants_at_once', 1))
   	# Reduce cores per participant if cores times particiapants is more than
   	# available CPUS. n_cpus is a hard upper limit.
   	if (c['pipeline_setup']['system_config']['max_cores_per_participant'] * c['pipeline_setup']['system_config']['num_participants_at_once']) > int(
   	args.n_cpus
   	):
   	c['pipeline_setup']['system_config']['max_cores_per_participant'] = int(
   	args.n_cpus
   	) // c['pipeline_setup']['system_config']['num_participants_at_once']
   	c['pipeline_setup']['system_config']['num_ants_threads'] = min(
   	c['pipeline_setup']['system_config']['max_cores_per_participant'], int(c['pipeline_setup']['system_config']['num_ants_threads'])
   	)

   to before.
2. Sets imported pipleine base to 'anat-only' if args.anat_only

Technical details

I overshot where to do this type conversion in #1435

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop_v1.8_convergence branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no
  visible errors.

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