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Start adding docs to prior estimation.#17

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dcelisgarza merged 12 commits intomainfrom
docs
Oct 6, 2025
Merged

Start adding docs to prior estimation.#17
dcelisgarza merged 12 commits intomainfrom
docs

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Copilot AI review requested due to automatic review settings October 5, 2025 12:20
@dcelisgarza dcelisgarza marked this pull request as draft October 5, 2025 12:20
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Pull Request Overview

This PR adds comprehensive documentation to the base prior estimation module by adding detailed docstrings to all abstract types and functions in the prior estimation hierarchy. The documentation follows Julia's standard format with code snippets, descriptions, and cross-references.

Key changes:

  • Added comprehensive docstrings to all abstract types in the prior estimation hierarchy
  • Added documentation for core functions like prior, clusterise, centrality_vector, etc.
  • Updated the documentation index to include all documented types and functions

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File Description
src/13_Prior/1_Base_Prior.jl Added detailed docstrings to all abstract types and functions in the prior estimation module
docs/src/api/13_Prior/1_BasePrior.md Updated documentation index to include all newly documented types and functions

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codecov bot commented Oct 5, 2025

Codecov Report

❌ Patch coverage is 87.57764% with 20 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.49%. Comparing base (4cd4184) to head (95723be).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/19_Optimisation/8_JuMPConstraints.jl 71.15% 15 Missing ⚠️
...raintGeneration/3_PhylogenyConstraintGeneration.jl 50.00% 2 Missing ⚠️
src/13_Prior/1_Base_Prior.jl 96.55% 2 Missing ⚠️
src/19_Optimisation/17_RiskConstraints.jl 88.88% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #17      +/-   ##
==========================================
- Coverage   84.54%   84.49%   -0.05%     
==========================================
  Files         111      111              
  Lines       11918    11925       +7     
==========================================
  Hits        10076    10076              
- Misses       1842     1849       +7     

☔ View full report in Codecov by Sentry.
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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@dcelisgarza dcelisgarza marked this pull request as ready for review October 6, 2025 15:30
@dcelisgarza dcelisgarza requested a review from Copilot October 6, 2025 15:30
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Pull Request Overview

Copilot reviewed 30 out of 33 changed files in this pull request and generated 4 comments.

elseif i == 3
5e-4
elseif i == 4 || Sys.isapple() && i == 12
elseif i in (4, 12)
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[nitpick] Consider using a more descriptive approach for these magic numbers. Define constants or add comments explaining why indices 4 and 12 require special tolerance handling.

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@dcelisgarza dcelisgarza requested a review from Copilot October 6, 2025 17:05
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Pull Request Overview

Copilot reviewed 33 out of 36 changed files in this pull request and generated 2 comments.

@dcelisgarza dcelisgarza requested a review from Copilot October 6, 2025 18:07
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Pull Request Overview

Copilot reviewed 33 out of 36 changed files in this pull request and generated 3 comments.

@dcelisgarza dcelisgarza requested a review from Copilot October 6, 2025 18:27
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Pull Request Overview

Copilot reviewed 33 out of 36 changed files in this pull request and generated 1 comment.

@dcelisgarza dcelisgarza requested a review from Copilot October 6, 2025 18:39
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Pull Request Overview

Copilot reviewed 34 out of 37 changed files in this pull request and generated 1 comment.

@dcelisgarza dcelisgarza merged commit 0578b91 into main Oct 6, 2025
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@dcelisgarza dcelisgarza deleted the docs branch October 6, 2025 18:47
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