Duplicated error message upon project load

[nsheff]

Using the example pep in the dnameth pipeline, I see:

looper check
No project config defined (peppy), using: {'config_file': 'test_config.yaml', 'output_dir': '.', 'sample_pipeline_interfaces': None, 'project_pipeline_interfaces': None}. Read from dotfile (/home/nsheff/code/dnameth_pipelines/examples/.looper.yaml).
Config file does not have version key. Defaulting to 2.1.0
Looper version: 1.5.2-dev
Command: check
Config file does not have version key. Defaulting to 2.1.0
Not all environment variables were populated in derived attribute source: $CODE/microtest/data/{filename}
Not all environment variables were populated in derived attribute source: $CODE/microtest/data/{filename}
Not all environment variables were populated in derived attribute source: $CODE/microtest/data/{filename}
Not all environment variables were populated in derived attribute source: $CODE/microtest/data/{filename}
Traceback (most recent call last):
  File "/home/nsheff/.local/bin/looper", line 8, in <module>
    sys.exit(main())
  File "/home/nsheff/.local/lib/python3.8/site-packages/looper/looper.py", line 1125, in main
    p = Project(
  File "/home/nsheff/.local/lib/python3.8/site-packages/looper/project.py", line 118, in __init__
    setattr(self[EXTRA_KEY], attr_name, kwargs[attr_name])
  File "/home/nsheff/.local/lib/python3.8/site-packages/peppy/project.py", line 1365, in __getitem__
    return self._project_data[item]
KeyError: '_cli_extra'

Why does it say: Config file does not have version key. Defaulting to 2.1.0 two times?

is looper loading the PEP twice?

[nsheff]

Ok, I don't think it's loading twice, I just think there are two error message for some reason -- also, one is not running through logmuse.

looper --verbosity 5 check
No project config defined (peppy), using: {'config_file': 'test_config.yaml', 'output_dir': '.', 'sample_pipeline_interfaces': None, 'project_pipeline_interfaces': None}. Read from dotfile (/home/nsheff/code/dnameth_pipelines/examples/.looper.yaml).
Config file does not have version key. Defaulting to 2.1.0
DEBU 11:41:39 | root:est:310 > Configured logger 'root' using logmuse v0.2.7 
INFO 11:41:39 | root:looper:1092 > Looper version: 1.5.2-dev
Command: check 
DEBU 11:41:39 | peppy:project:110 > Creating Project from file test_config.yaml 
DEBU 11:41:39 | peppy.utils:utils:148 > Creating a Project from a YAML file: test_config.yaml 
DEBU 11:41:39 | peppy:project:335 > Raw (test_config.yaml) config data: {'sample_table': 'microtest_annotation.csv', 'looper': {'output_dir': '$HOME/dnameth'}, 'sample_modifiers': {'append': {'pipeline_interfaces': '../piface_rrbs.yaml'}, 'imply': [{'if': {'organism': 'human'}, 'then': {'genome': 'hg38'}}, {'if': {'organism': 'mouse'}, 'then': {'genome': 'mm10'}}], 'derive': {'attributes': ['read1', 'read2'], 'sources': {'test_data_R1': 'examples/test_data/{sample_name}_R1.fastq.gz', 'test_data_R2': 'examples/test_data/{sample_name}_R2.fastq.gz', 'microtest': '$CODE/microtest/data/{filename}'}}}} 
DEBU 11:41:39 | peppy:project:368 > Adding attributes: sample_table, looper, sample_modifiers 
WARN 11:41:39 | peppy:project:1281 > Config file does not have version key. Defaulting to 2.1.0 
...

see how the first of the message lacks any logmuse styling?

[nsheff]

Also, it should specify which config (that's a peppy thing)

[donaldcampbelljr]

~~Could you clarify the exact issue? It appears that the original title is not the actual issue.~~

~~Is it ensuring all information is displayed in the terminal via logmuse?~~

~~Running with newest version:~~

(venv) drc@databio:~/GITHUB/hello_looper/hello_looper$ looper --verbosity 5 check --looper-config .looper_pipestat.yaml
DEBU 14:10:08 | root:est:310 > Configured logger 'root' using logmuse v0.2.7 
INFO 14:10:08 | root:cli_looper:614 > Looper version: 1.6.0
Command: check 
DEBU 14:10:08 | peppy:project:113 > Creating Project from file /home/drc/GITHUB/hello_looper/hello_looper/./project/project_config.yaml 
DEBU 14:10:08 | peppy.utils:utils:172 > Creating a Project from a YAML file: /home/drc/GITHUB/hello_looper/hello_looper/./project/project_config.yaml 

Etc.

[saanikat]

After discussion, it was discovered that this issue lies in peppy.

[khoroshevskyi]

This issue should be solved together with #465