Format files to prepare for pypi publish #10
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The linter error is due to being on a fork: wearerequired/lint-action#13 The analysis error is because random is a requirement that is not found in pypi anymore. Its not called random2. I will change the code to use numpy random in this case. |
…ession-compendia repo
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Based on discussion with @cgreene pulling out "extra" functions (i.e. functions specific to analysis performed in https://github.com/greenelab/simulate-expression-compendia) and leave only simulation functions (i.e dir setup, vae training, simulations). Closing it for now while I add those changes and will reopen when its ready for review |
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This PR is now ready to review. This PR complements: greenelab/simulate-expression-compendia#33 The ponyo repo included scripts to about the method to generate new simulated data as well as scripts specific to running the analysis found in this repo. This PR is removes those analysis-specific scripts. The main changes in this PR are:
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| # Check if analysis output directory exist otherwise create | ||
| for each_dir in output_dirs: |
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Does it make more sense to merge this for loop with the one on lines 55-59?
ponyo/utils.py
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| os.makedirs(new_dir, exist_ok=True) | ||
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| # Create results directories | ||
| output_dirs = [os.path.join(base_dir, dataset_name, "results")] |
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This list includes only one element. The for loops on lines 65 and 71 seem redundant. If you do want to use for loop, these two loops can be merged into one.
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If the linter is never going to work on PRs, you may want to switch to something like this part of the actions I use in saged/whistl.
Though to use flake8 as a linter instead of an error checker, you would probably want the command to be
- name: Lint with flake8
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$CONDA/bin/conda install flake8
$CONDA/bin/flake8 . --count --show-source --statistics
You can then add exceptions with --ignore as needed.
I approved the PR in case you want linter tinkering to be a different PR. Otherwise I can rereview it once the linter is working
ponyo/vae.py
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| @@ -106,7 +105,7 @@ def tybalt_2layer_model( | |||
| # The below is necessary for starting core Python generated random numbers | |||
| # in a well-defined state. | |||
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| rn.seed(12345) | |||
| np.random.seed(12345) | |||
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You're setting the numpy seed twice in this file, and the seed for the base random package is no longer set. The second thing may not matter since you're not importing random in this file, but the first one appears to be a copy number variation
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Thank you for your comments! @ben-heil about the linter, since the linter is working properly and its a permissions error with my fork I'll wait to see if this changes (since submitting feedback to them) |
This PR updates Readme and setup files to prepare for publishing this repo to pypi