Can you also update the input/readme with information about the dummy file and dummy column in the prizes file

If I try to use an updated dummy nodes file (dummy-1.txt) with the original sources, targets, and node-prizes files, I get this error:

Running docker containers
RuleException:
ValueError in file /Users/nehatalluri/Desktop/research/spras/Snakefile, line 159:
You are trying to merge on object and float64 columns. If you wish to proceed you should use pd.concat
  File "/Users/nehatalluri/Desktop/research/spras/Snakefile", line 159, in __rule_merge_input
  File "/Users/nehatalluri/Desktop/research/spras/spras/runner.py", line 42, in merge_input
  File "/Users/nehatalluri/Desktop/research/spras/spras/dataset.py", line 27, in __init__
  File "/Users/nehatalluri/Desktop/research/spras/spras/dataset.py", line 124, in load_files_from_dict
  File "/Users/nehatalluri/anaconda3/envs/spras/lib/python3.11/site-packages/pandas/core/frame.py", line 10093, in merge
  File "/Users/nehatalluri/anaconda3/envs/spras/lib/python3.11/site-packages/pandas/core/reshape/merge.py", line 110, in merge
  File "/Users/nehatalluri/anaconda3/envs/spras/lib/python3.11/site-packages/pandas/core/reshape/merge.py", line 707, in __init__
  File "/Users/nehatalluri/anaconda3/envs/spras/lib/python3.11/site-packages/pandas/core/reshape/merge.py", line 1340, in _maybe_coerce_merge_keys
[Fri Oct 11 15:43:19 2024]
Error in rule merge_input:
    jobid: 0
    input: input/node-prizes.txt, input/sources.txt, input/targets.txt, input/dummy-1.txt, input/network.txt
    output: output/dummy/data0-merged.pickle

this is what my config file looks like for the datasets

datasets:
    -
      # Labels can only contain letters, numbers, or underscores
      label: data0
      node_files: ["node-prizes.txt", "sources.txt", "targets.txt", "dummy-1.txt"]
      # DataLoader.py can currently only load a single edge file, which is the primary network
      edge_files: ["network.txt"]
      # Placeholder
      other_files: []
      # Relative path from the spras directory
      data_dir: "input"

this is what I updated dummy-1.txt to be:
A

Could you also add tests to the OI1 testing sweep that test's the run function using the dummy nodes

There is a chance you will need to update the generate inputs test sweep as well (still need to think through if you really do).

If I try to use an updated dummy nodes file (dummy-1.txt) with the original sources, targets, and node-prizes files, I get this error:

@ntalluri
I think the error is because the file it titled dummy-1.txt instead of dummy.txt because wouldn't having the file title as dummy-1 cause the node.data_table dummy column to be called dummy-1 too? and in the oi1 code it looks for dummy in the node_table columns

Can you also run pre-commit run --all-files locally and push those changes. The 'Run pre-commit checks' test keeps failing.

Can you also run pre-commit run --all-files locally and push those changes. The 'Run pre-commit checks' test keeps failing.
@ntalluri

Running that gave me this:

'[INFO] Initializing environment for https://github.com/charliermarsh/ruff-pre-commit.
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/charliermarsh/ruff-pre-commit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
check yaml...............................................................Passed
check toml...............................................................Passed
trim trailing whitespace.................................................Failed

• hook id: trailing-whitespace
• exit code: 1
• files were modified by this hook

Fixing spras/omicsintegrator1.py
Fixing config/config.yaml

ruff.....................................................................Failed

• hook id: ruff
• files were modified by this hook

Found 1 error (1 fixed, 0 remaining).'

what's the hook id: ruff refering to?

hook id: ruff

I think this is referring to this https://docs.astral.sh/ruff/, which is a linter and code formatter that pre-commit will use that was specified in the .pre-commit-config.yaml file

but that pre-commit message looks good due to this message Found 1 error (1 fixed, 0 remaining) which I always interpret that pre-commit was able to clean up the code.