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feat: DIAMOnD #247

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@tristan-f-r tristan-f-r commented May 30, 2025 •
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Another disease module mining algorithm to complement #240 (#109). Closes #244.

Note that, in compliance with #246, DIAMOnD is MIT licensed.

@tristan-f-r tristan-f-r added the algorithm Pathway reconstruction algorithm to add to SPRAS label May 30, 2025
@tristan-f-r tristan-f-r marked this pull request as ready for review May 30, 2025 22:12
@tristan-f-r tristan-f-r marked this pull request as draft May 30, 2025 22:14
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tristan-f-r commented May 30, 2025

Moving this back to a draft because I need to handle rank information.

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tristan-f-r commented May 30, 2025
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@tristan-f-r tristan-f-r added the discussion Further information is requested label May 30, 2025
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tristan-f-r commented Jun 13, 2025

This will be updated after #261 gets merged.

@tristan-f-r tristan-f-r marked this pull request as ready for review July 8, 2025 16:33
@tristan-f-r tristan-f-r removed the discussion Further information is requested label Jul 11, 2025
@tristan-f-r tristan-f-r mentioned this pull request Jul 16, 2025
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tristan-f-r commented Jul 24, 2025 •
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@agitter this only needs a docker push and further review on some pandas calls in parse_output and its correctness, but the rest of this is a straightforward PRM implementation from what I remember. (DIAMOnD.parse_outputs turns node rankings into edge rankings.)

@tristan-f-r tristan-f-r mentioned this pull request Jul 28, 2025
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read-the-docs-community bot commented Sep 21, 2025 •
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Documentation build overview

📚 spras | 🛠️ Build #31377403 | 📁 Comparing f499fd5 against latest (18f2cf8)


🔍 Preview build

Show files changed (6 files in total): 📝 5 modified | ➕ 1 added | ➖ 0 deleted
File Status
genindex.html 📝 modified
fordevs/modules.html 📝 modified
fordevs/spras.config.html 📝 modified
fordevs/spras.html 📝 modified
prms/diamond.html ➕ added
prms/prms.html 📝 modified

@github-actions github-actions bot added the merge-conflict This PR has merge conflicts. label Jan 9, 2026
@github-actions github-actions bot removed the merge-conflict This PR has merge conflicts. label Jan 10, 2026
@tristan-f-r tristan-f-r added the awaiting-author Author of the PR needs to fix something from a review / etc. label Jan 10, 2026
@tristan-f-r tristan-f-r removed the awaiting-author Author of the PR needs to fix something from a review / etc. label Jan 10, 2026
@tristan-f-r tristan-f-r added awaiting-author Author of the PR needs to fix something from a review / etc. and removed awaiting-author Author of the PR needs to fix something from a review / etc. labels Jan 23, 2026
@github-actions github-actions bot added the merge-conflict This PR has merge conflicts. label Jan 31, 2026
@github-actions github-actions bot removed the merge-conflict This PR has merge conflicts. label Jan 31, 2026
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