Make error

[HelloWorldLTY]

Hi, thank you for sharing this interesting project. I tried to run 'make validate' after cloning the github repo. However, this error is reported:

Did I miss anything? Thanks.

[Eurekashen]

Hi, thank you for sharing this interesting project. I tried to run 'make validate' after cloning the github repo. However, this error is reported:

Did I miss anything? Thanks.

Thank you for your interest. This issue arose because the make validate script failed to automatically create the necessary directories. We have since resolved this problem. You can now use make validate to validate the repo structure and then use make test to verify the compatibility of your current environment with the designed skills; this command will also automatically generate a concise report.

[HelloWorldLTY]

Hi, I tried the current framework again, and if I run 'make test', a new error will be generated:

========================================================
  SkillFoundry Test Report
========================================================

  Total:   167
  Passed:  72
  Failed:  7
  Errors:  88

--------------------------------------------------------
  Failures (7):
    x test_print_plan_shows_all_tasks_in_batches
      -> missing: experiments/sc_skills/batch_design_manifest.json
    x test_audit_skill_suite_reports_full_coverage
      -> AssertionError: 266 != 267
    x test_required_experiment_files_exist
      -> AssertionError: False is not true : Missing required experiment file: /SkillFoundry/experim
    x test_biosamples_sample_search_returns_expected_fields
      -> AssertionError: False is not true
    x test_validator_script_runs_on_subset
      -> missing: experiments/sc_skills/batch_design_manifest.json
    x test_scanpy_qc_runtime
      -> {SCANPY_PYTHON}")
    x test_scanpy_ranked_genes_runtime
      -> {SCANPY_PYTHON}")
...

I guess I must install related packages such as scanpy in my current environment?

If I skip this step, and try "python3 scripts/sciskill_framework.py --json status --focus-limit 10", an error will be generated:

Traceback (most recent call last):
  File "/SkillFoundry/scripts/sciskill_framework.py", line 14, in <module>
    from sciskill_framework.cli import main
  File "/SkillFoundry/scripts/sciskill_framework.py", line 14, in <module>
    from sciskill_framework.cli import main
ModuleNotFoundError: No module named 'sciskill_framework.cli'; 'sciskill_framework' is not a package

I think we somehow need to install this package? But i cannot find setup.py file in this repo. Thanks.

[Eurekashen]

Hi, I tried the current framework again, and if I run 'make test', a new error will be generated:

========================================================
  SkillFoundry Test Report
========================================================

  Total:   167
  Passed:  72
  Failed:  7
  Errors:  88

--------------------------------------------------------
  Failures (7):
    x test_print_plan_shows_all_tasks_in_batches
      -> missing: experiments/sc_skills/batch_design_manifest.json
    x test_audit_skill_suite_reports_full_coverage
      -> AssertionError: 266 != 267
    x test_required_experiment_files_exist
      -> AssertionError: False is not true : Missing required experiment file: /SkillFoundry/experim
    x test_biosamples_sample_search_returns_expected_fields
      -> AssertionError: False is not true
    x test_validator_script_runs_on_subset
      -> missing: experiments/sc_skills/batch_design_manifest.json
    x test_scanpy_qc_runtime
      -> {SCANPY_PYTHON}")
    x test_scanpy_ranked_genes_runtime
      -> {SCANPY_PYTHON}")
...

I guess I must install related packages such as scanpy in my current environment?

If I skip this step, and try "python3 scripts/sciskill_framework.py --json status --focus-limit 10", an error will be generated:

Traceback (most recent call last):
  File "/SkillFoundry/scripts/sciskill_framework.py", line 14, in <module>
    from sciskill_framework.cli import main
  File "/SkillFoundry/scripts/sciskill_framework.py", line 14, in <module>
    from sciskill_framework.cli import main
ModuleNotFoundError: No module named 'sciskill_framework.cli'; 'sciskill_framework' is not a package

I think we somehow need to install this package? But i cannot find setup.py file in this repo. Thanks.

Thank you for the information. I had made a mistake earlier, but I have now resolved the issue. The loop for designing skills should now be functioning correctly. It is normal to encounter failures and errors when running make test. This occurs because the agent is not yet active at that stage, and the environment is not automatically configured. However, when you actually utilize the corresponding skills, the agent will automatically configure the environment (or do so based on the provided prompts). Furthermore, certain skills such as those related to Slurm are only usable within a cluster environment. Therefore, we recommend that you either download and install only the specific skills you require (download links are available on the dashboard of our website) or utilize the framework to design the necessary skills yourself.

If you have any further questions, please feel free to ask. We will continue to fix and improve things!