Changes based on reviews from Galaxy usegalaxy tools team #18
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comments fixed
line added for lint
qchiujunhao
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qchiujunhao
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Jan 4, 2025
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Thank you, Paulo, for the changes—great work! Just a few adjustments are needed to pass the tests. Thank you! |
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How can I see the reason for the failure? |
qchiujunhao
requested changes
Jan 4, 2025
Noticed that there is a comment about this.
qchiujunhao
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Jan 6, 2025
qchiujunhao
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Jan 7, 2025
* Removed torch and Horovod in Dockerfile Since ludwig[full] will install torch and Ray. Ludwig has strong support for Ray, a framework for distributed computing, so we are not going to use Horovod. Ray doesn't support python 3.11 now. * Upgrading version * Updated version on macros.xml * Auto generate a config from a dataset * fixed new line issue for lint * delete the code for config edit functionality * updated the import for merge_with_defaults * fixed a typo * added a functionality - edit a config * changed to not sort by keys * removed render_config * Replace chars back * Removed this functionality since Galaxy provides this functionality * added a checked box for rendered config * added a dropdown for selecting the output feature * updated to 0.10.3 * job_conf change (#12) * job_conf change * Readme comments resolved_1 * expect_num_outputs (#13) * Readme comments and job_conf changes * expect_num_outputs added (test on xml files) * Gpu docker (#14) * Update README.md Specify that users should select the branch they want to install. * path for job_conf.yml * added a Dockerfile for GPU * Reorganized the Dockerfile * add unzip after testing * define the docker requirements for gpu * HTML & deploy (#16) * lint and tests * passed the tests * deleted the code for debugging * add a triggered branch * change to new version of actions * lint the import order * new html and assert_contents * update hyperopt test file * define the order and replace pwd * passed all tests locally * use the same docker image * Update temp_hyperopt_training.learning_rate.pdf after update_test_data * Removed tool declarations in actions. * Delete slash.yaml (#19) * Changes based on reviews from Galaxy usegalaxy tools team (#18) * comments fixed * Update ludwig_hyperopt.py line added for lint * fix_from_comments_Junhao * fix_#2 * Change discover_datasets pattern in viz outputs Noticed that there is a comment about this. --------- Co-authored-by: JunhaoQiu <56094690+qchiujunhao@users.noreply.github.com> * fixed issues after testing on the cancer server (#20) * fixed issues after testing on the cancer server 1. The Ray server requires `TMP` environment variables to start. 2. Sometimes datasets have spaces at the end of their filenames. During sanitization, these spaces cause the name to become `**.csv_`, which raises an issue. To fix this, spaces in the filename are replaced with nothing before sanitization. 3.Removed the table in the hyperopt HTML report since it was too visually unappealing. A JSON file output is provided instead. * test data updated * python lint * replace -> strip * Outputs changes (#21) * deleted table from html 1. deleted test stats table from experiment report html 2. change some output name * python lint --------- Co-authored-by: Paulo Cilas Morais Lyra Junior <58008200+paulocilasjr@users.noreply.github.com>
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Issues addressed:
$TMP*from the code.pwdwith.${dataset.element_identifier}.yaml.safe_dump().format = "auto"in Ludwig_visualize.xml.ludwig_modelwith thehtmlformat.minandmaxfor numeric parameters.