analysis docs #681
analysis docs #681
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created doc for analysis
added box plot link
docs/tutorials/analysing_runs.md
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| haddock3-analyse -r my-run-folder -m 2 5 6 -p reference_fname my_ref.pdb receptor_chain F | ||
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| Here the `-p` key tells the code that you are about to insert caprieval parameters, whose name should match the parameter name. |
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parameter name and corresponding value must be separated by space.
| run_dir = "my-run-folder" | ||
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| # postprocess the run | ||
| postprocess = true |
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Open question (that should be discussed):
shoudn't the value of the postprocess parameter be true by default ?
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I agree. I think we discussed this with @amjjbonvin in the past and decided to set it to false by default, but I am more than open to re-discuss it!
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What about placing the post-processing section in first ? and then explaining the haddock3-analyse and haddock3-traceback ?
Also adding internal links to the 3 sections that will be later presented ?
Dedicated analyses modules are made available, allowing to investigate the different steps of a HADDOCK3 workflow, even after it has been completed.
* [Post-processing](#the-postprocess-option)
* [Analyse](#haddock3-analyse)
* [Traceback](#haddock3-traceback)
``` ?
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i agree about the bindings but I would not change the order..it's complicated to describe the postprocess option without saying anything about the commands it executes
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actually I would not modify the titles, I think that it's beneficial to have "haddock3-analyse" as a title for the user
Codecov ReportPatch and project coverage have no change.
Additional details and impacted files@@ Coverage Diff @@
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Hits 5944 5944
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What you are proposing is user documentation, but the docs that are built automatically are related to code documentation.
I would not mix these two in the same codebase because user access can be limited by documentation build issues that are unrelated to the information provided in those docs.
User information should fit together with the rest of the material at bonvinlab.org. However this is not for me to decide since I'm not the lead on the project.
I know this is user documentation, of course. It was thought as a technical guide for people that want to approach the haddock3-specific analysis, as it's done in the other docs/tutorials/ markdown files. |
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toxtests pass. Runtoxcommand inside the repository folder-test.cfgexamples execute without errors. Insideexamples/runpython run_tests.py -bCloses #628 by adding a new .md file in the
docs/tutorialsfolder, namelyanalysing_runs.md. It describes the basic usage ofhaddock3-analyseandhaddock3-traceback. I also added a couple of example plots forhaddock3-analyse