docs: adopt Diátaxis framework for user documentation by zircote · Pull Request #32 · zircote/nsip

zircote · 2026-02-16T21:41:55Z

Summary

Adopts the Diátaxis documentation framework to add structured learning paths for NSIP users. The repository had excellent technical reference docs but lacked learning materials for newcomers.

Changes

Tutorials: Getting Started guide (15-minute hands-on introduction)
How-To Guides: Configure Client, Compare Animals
Explanation: Understanding EBVs (breeding value concepts)
Reference: Error Handling (complete error type reference)
Infrastructure: Updated docs/README.md, added ADR-0003

New Documentation Structure

docs/
├── tutorials/          # Learning-oriented guides (NEW)
├── how-to/             # Problem-oriented guides (NEW)
├── explanation/        # Understanding-oriented discussions (NEW)
├── reference/          # Information-oriented technical docs (NEW)
├── runbooks/           # Operational procedures (existing)
├── template/           # Template adoption guides (existing)
└── workflows/          # CI/CD documentation (existing)

Closes #30

Generated by the Update Docs agentic workflow.

github-actions · 2026-02-16T21:42:27Z

Benchmark Results

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codecov · 2026-02-16T21:43:25Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.83%. Comparing base (2e68126) to head (73268ae).
⚠️ Report is 6 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #32   +/-   ##
=======================================
  Coverage   95.83%   95.83%           
=======================================
  Files           9        9           
  Lines        6499     6499           
=======================================
  Hits         6228     6228           
  Misses        271      271

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github-actions · 2026-02-16T21:44:45Z

Code Coverage Report

Overall Coverage: 0%

Summary

Filename                      Regions    Missed Regions     Cover   Functions  Missed Functions  Executed       Lines      Missed Lines     Cover    Branches   Missed Branches     Cover
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
client.rs                        1444                67    95.36%         118                13    88.98%         923                35    96.21%           0                 0         -
format.rs                        2172                 3    99.86%         132                 1    99.24%        1292                 1    99.92%           0                 0         -
main.rs                           326               241    26.07%          14                 8    42.86%         225               168    25.33%           0                 0         -
mcp/analytics.rs                  408                 2    99.51%          24                 0   100.00%         331                 0   100.00%           0                 0         -
mcp/mod.rs                        144                55    61.81%          23                15    34.78%         128                65    49.22%           0                 0         -
mcp/prompts.rs                   1908                33    98.27%         126                 6    95.24%        1043                12    98.85%           0                 0         -
mcp/resources.rs                 1317                20    98.48%          93                 1    98.92%         865                 6    99.31%           0                 0         -
mcp/tools.rs                     2146                90    95.81%         116                18    84.48%        1333                47    96.47%           0                 0         -
models.rs                        1079                31    97.13%          78                10    87.18%         762                14    98.16%           0                 0         -
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL                           10944               542    95.05%         724                72    90.06%        6902               348    94.96%           0                 0         -

Full HTML report available in CI artifacts.

Copilot

Pull request overview

This PR adopts the Diátaxis documentation framework to provide structured learning paths for NSIP users. The repository had comprehensive technical reference documentation but lacked beginner-friendly tutorials and conceptual explanations. This change adds four types of documentation: learning-oriented tutorials, problem-oriented how-to guides, understanding-oriented explanations, and information-oriented reference materials.

Changes:

Added initial documentation in all four Diátaxis quadrants (tutorials, how-to guides, explanations, reference)
Reorganized docs/README.md to use Diátaxis framework with clear navigation
Created ADR-0003 documenting the framework adoption decision

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
docs/README.md	Reorganized documentation index using Diátaxis quadrants with quick start section
docs/adr/0003-adopt-diataxis-documentation-framework.md	ADR documenting framework adoption rationale and implementation approach
docs/tutorials/GETTING-STARTED.md	15-minute hands-on tutorial for NSIP API basics
docs/how-to/CONFIGURE-CLIENT.md	Guide for customizing HTTP client timeout and retry settings
docs/how-to/COMPARE-ANIMALS.md	Guide for comparing genetic traits across multiple animals
docs/explanation/EBV-EXPLAINED.md	Conceptual explanation of Estimated Breeding Values
docs/reference/ERROR-HANDLING.md	Complete reference for error types and handling patterns

Copilot · 2026-02-16T21:47:50Z

docs/tutorials/GETTING-STARTED.md

+- [Working with EBV Traits](EBV-TRAITS.md) - Filter and rank animals by genetic traits
+- [MCP Integration](MCP-INTEGRATION.md) - Connect AI assistants to NSIP data


These tutorial links reference non-existent files. The files EBV-TRAITS.md and MCP-INTEGRATION.md do not exist in the docs/tutorials directory. Consider either creating these files or removing these links from the "Next Steps" section.

Suggested change

- [Working with EBV Traits](EBV-TRAITS.md) - Filter and rank animals by genetic traits

- [MCP Integration](MCP-INTEGRATION.md) - Connect AI assistants to NSIP data

- Working with EBV Traits — Coming soon: filter and rank animals by genetic traits

- MCP Integration — Coming soon: connect AI assistants to NSIP data

Copilot · 2026-02-16T21:47:50Z

docs/tutorials/GETTING-STARTED.md

+**How-To Guides:**
+- [How to Configure Timeout and Retries](../how-to/CONFIGURE-CLIENT.md)
+- [How to Compare Animals](../how-to/COMPARE-ANIMALS.md)
+- [How to Calculate Inbreeding Coefficient](../how-to/INBREEDING-CHECK.md)


This link references a non-existent file. The file INBREEDING-CHECK.md does not exist in the docs/how-to directory. Consider either creating this file or removing the link.

Suggested change

- [How to Calculate Inbreeding Coefficient](../how-to/INBREEDING-CHECK.md)

Copilot · 2026-02-16T21:47:50Z

docs/how-to/COMPARE-ANIMALS.md

+    .with_trait_range("Weight", TraitRangeFilter {
+        min: Some(10.0),
+        max: Some(50.0),
+    });


The TraitRangeFilter structure and method name are incorrect. According to crates/models.rs lines 71-77, TraitRangeFilter has fields min: f64 and max: f64 (not Option types). Additionally, the method is with_trait_ranges (plural) which takes a HashMap, not with_trait_range (singular). The correct usage would be: SearchCriteria::new().with_trait_ranges([("Weight".to_string(), TraitRangeFilter { min: 10.0, max: 50.0 })].into())

Suggested change

.with_trait_range("Weight", TraitRangeFilter {

min: Some(10.0),

max: Some(50.0),

});

.with_trait_ranges(

[(

"Weight".to_string(),

TraitRangeFilter {

min: 10.0,

max: 50.0,

},

)]

.into(),

);

Copilot · 2026-02-16T21:47:50Z

docs/how-to/CONFIGURE-CLIENT.md

+## See Also
+
+- [Error Handling Reference](../reference/ERROR-HANDLING.md)
+- [API Client Architecture](../explanation/CLIENT-ARCHITECTURE.md)


This link references a non-existent file. The file CLIENT-ARCHITECTURE.md does not exist in the docs/explanation directory. Consider either creating this file or removing the link.

Suggested change

- [API Client Architecture](../explanation/CLIENT-ARCHITECTURE.md)

- API Client Architecture (conceptual overview)

Copilot · 2026-02-16T21:47:51Z

docs/explanation/EBV-EXPLAINED.md

+## Further Reading
+
+- [How to Compare Animals](../how-to/COMPARE-ANIMALS.md) - Practical comparison techniques
+- [How to Rank Animals](../how-to/RANK-ANIMALS.md) - Multi-trait ranking


This link references a non-existent file. The file RANK-ANIMALS.md does not exist in the docs/how-to directory. Consider either creating this file or removing the link.

Suggested change

- [How to Rank Animals](../how-to/RANK-ANIMALS.md) - Multi-trait ranking

- How to Rank Animals - Multi-trait ranking (coming soon)

Copilot · 2026-02-16T21:47:51Z

docs/tutorials/GETTING-STARTED.md

+    // Search for Maternal breed animals (breed_id: 640)
+    let criteria = SearchCriteria::new()
+        .with_status("CURRENT")
+        .with_gender("M");  // Male animals only


The gender filter value should be "Male" (full word) instead of "M". According to the SearchCriteria documentation in crates/models.rs line 49, the gender field expects "Male", "Female", or "Both".

Suggested change

.with_gender("M"); // Male animals only

.with_gender("Male"); // Male animals only

Copilot · 2026-02-16T21:47:52Z

docs/how-to/COMPARE-ANIMALS.md

+
+    // Fetch all profiles concurrently
+    let futures = lpn_ids.iter()
+        .map(|id| client.search_by_lpn(id));
+
+    let profiles = futures::future::try_join_all(futures).await?;
+


This code example uses the futures crate which is not a dependency of the nsip project. The example should use tokio's join functionality instead. For example, use tokio::try_join! or iterate and await sequentially.

Suggested change

// Fetch all profiles concurrently

let futures = lpn_ids.iter()

.map(|id| client.search_by_lpn(id));

let profiles = futures::future::try_join_all(futures).await?;

// Fetch all profiles (one request per LPN)

let mut profiles = Vec::with_capacity(lpn_ids.len());

for id in &lpn_ids {

profiles.push(client.search_by_lpn(id).await?);

}

Copilot · 2026-02-16T21:47:52Z

docs/how-to/COMPARE-ANIMALS.md

+- [How to Calculate Inbreeding Coefficient](INBREEDING-CHECK.md)
+- [How to Rank Animals](RANK-ANIMALS.md)
+- [Understanding EBVs](../explanation/EBV-EXPLAINED.md)
+- [MCP Compare Tool Reference](../MCP.md#compare)


These links reference non-existent files. The files INBREEDING-CHECK.md and RANK-ANIMALS.md do not exist in the docs/how-to directory. Consider either creating these files or removing these links.

Suggested change

- [How to Calculate Inbreeding Coefficient](INBREEDING-CHECK.md)

- [How to Rank Animals](RANK-ANIMALS.md)

- [Understanding EBVs](../explanation/EBV-EXPLAINED.md)

- [MCP Compare Tool Reference](../MCP.md#compare)

- [Understanding EBVs](../explanation/EBV-EXPLAINED.md)

- [MCP Compare Tool Reference](../MCP.md#compare)

Copilot · 2026-02-16T21:47:52Z

docs/explanation/EBV-EXPLAINED.md

+
+### Multi-Trait Selection
+
+Use weighted trait scores (see [How to Rank Animals](../how-to/RANK-ANIMALS.md)).


This link references a non-existent file. The file RANK-ANIMALS.md does not exist in the docs/how-to directory. Consider either creating this file or removing the link.

Copilot · 2026-02-16T21:47:52Z

docs/how-to/CONFIGURE-CLIENT.md

+
+````rust
+let client = NsipClient::builder()
+    .base_url("http://nsipsearch.nsip.org/api")


The example NsipClient::builder().base_url("http://nsipsearch.nsip.org/api") configures the client to talk to the remote NSIP API over plain HTTP instead of HTTPS, exposing all requests and responses to interception and tampering on the network. If users copy this configuration into production code, an on-path attacker could read or modify genetic data and API responses. Update this example to use https:// for remote endpoints (keeping http://localhost only for local testing) so the recommended configuration uses encrypted transport by default.

Suggested change

.base_url("http://nsipsearch.nsip.org/api")

.base_url("https://nsipsearch.nsip.org/api")

Add structured learning paths using the Diátaxis framework: Tutorials (learning-oriented): - Getting Started - 15-minute hands-on introduction How-To Guides (problem-oriented): - Configure Client - Timeout and retry customization - Compare Animals - Side-by-side genetic trait comparisons Explanation (understanding-oriented): - Understanding EBVs - Breeding value concepts and usage Reference (information-oriented): - Error Handling - Complete error type reference Updated docs/README.md to organize all documentation by framework quadrants. Added ADR-0003 documenting the framework adoption decision. Addresses documentation gap identified in repository analysis. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

github-actions · 2026-02-16T21:54:34Z

Benchmark Results

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Full results available in CI artifacts.

github-actions · 2026-02-16T21:55:07Z

Benchmark Results

No benchmarks configured. Add benchmarks to benches/ directory.

Full results available in CI artifacts.

github-actions · 2026-02-16T21:57:07Z

Code Coverage Report

Overall Coverage: 0%

Summary

Filename                      Regions    Missed Regions     Cover   Functions  Missed Functions  Executed       Lines      Missed Lines     Cover    Branches   Missed Branches     Cover
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
client.rs                        1444                67    95.36%         118                13    88.98%         923                35    96.21%           0                 0         -
format.rs                        2172                 3    99.86%         132                 1    99.24%        1292                 1    99.92%           0                 0         -
main.rs                           326               241    26.07%          14                 8    42.86%         225               168    25.33%           0                 0         -
mcp/analytics.rs                  408                 2    99.51%          24                 0   100.00%         331                 0   100.00%           0                 0         -
mcp/mod.rs                        144                55    61.81%          23                15    34.78%         128                65    49.22%           0                 0         -
mcp/prompts.rs                   1908                33    98.27%         126                 6    95.24%        1043                12    98.85%           0                 0         -
mcp/resources.rs                 1317                20    98.48%          93                 1    98.92%         865                 6    99.31%           0                 0         -
mcp/tools.rs                     2146                90    95.81%         116                18    84.48%        1333                47    96.47%           0                 0         -
models.rs                        1079                31    97.13%          78                10    87.18%         762                14    98.16%           0                 0         -
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL                           10944               542    95.05%         724                72    90.06%        6902               348    94.96%           0                 0         -

Full HTML report available in CI artifacts.

Tutorials: - FIRST-API-QUERY.md, INTERPRETING-RESULTS.md, MCP-SERVER-SETUP.md How-To Guides: - BATCH-QUERY.md, EXPORT-JSON.md, FILTER-SEARCH-RESULTS.md - SCRIPTING-INTEGRATION.md, USE-MCP-TOOLS.md Explanation: - BREED-GROUPS-AND-TRAITS.md, DATA-TO-DECISIONS.md - GENETIC-EVALUATION.md, NSIP-DATA-MODEL.md Reference: - CLI.md, CONFIGURATION.md, LIBRARY-API.md, MCP-TOOLS.md Content sourced from NSIP.org research with accurate breed groups (USA Hair/Terminal/Maternal/Range), EBV traits, units (lbs for growth, mm for carcass, % for FEC/reproduction), and selection indexes (USA MAT-HAIR, USA Terminal).

- README.md: update index with all 22 Diátaxis documents - EBV-EXPLAINED.md: add MWWT, WFEC, PFEC, SC traits; fix units to lbs; add USA MAT-HAIR/Terminal index details - GETTING-STARTED.md: correct API field names and examples - COMPARE-ANIMALS.md: fix trait names and method signatures - CONFIGURE-CLIENT.md: fix cross-reference links - ERROR-HANDLING.md: expand examples, fix broken links All growth trait units corrected to lbs to match the NSIP Search API (crates/mcp/analytics.rs). Added note explaining LAMBPLAN uses kg internally while NSIP API reports in lbs.

github-actions · 2026-02-16T22:54:10Z

Benchmark Results

No benchmarks configured. Add benchmarks to benches/ directory.

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github-actions · 2026-02-16T22:55:57Z

Code Coverage Report

Overall Coverage: 0%

Summary

Filename                      Regions    Missed Regions     Cover   Functions  Missed Functions  Executed       Lines      Missed Lines     Cover    Branches   Missed Branches     Cover
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
client.rs                        1444                67    95.36%         118                13    88.98%         923                35    96.21%           0                 0         -
format.rs                        2172                 3    99.86%         132                 1    99.24%        1292                 1    99.92%           0                 0         -
main.rs                           326               241    26.07%          14                 8    42.86%         225               168    25.33%           0                 0         -
mcp/analytics.rs                  408                 2    99.51%          24                 0   100.00%         331                 0   100.00%           0                 0         -
mcp/mod.rs                        144                55    61.81%          23                15    34.78%         128                65    49.22%           0                 0         -
mcp/prompts.rs                   1908                33    98.27%         126                 6    95.24%        1043                12    98.85%           0                 0         -
mcp/resources.rs                 1317                20    98.48%          93                 1    98.92%         865                 6    99.31%           0                 0         -
mcp/tools.rs                     2146                90    95.81%         116                18    84.48%        1333                47    96.47%           0                 0         -
models.rs                        1079                31    97.13%          78                10    87.18%         762                14    98.16%           0                 0         -
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL                           10944               542    95.05%         724                72    90.06%        6902               348    94.96%           0                 0         -

Full HTML report available in CI artifacts.

- Add YAML frontmatter (status, date) to ADR-0001, ADR-0002, ADR-0003 - Narrow adrscope validation pattern to [0-9]*.md to skip README.md - Fix line-length lint on checkout action comment - Add ADR-0003 to README index

github-actions · 2026-02-16T23:00:45Z

Benchmark Results

No benchmarks configured. Add benchmarks to benches/ directory.

Full results available in CI artifacts.

github-actions · 2026-02-16T23:02:37Z

Code Coverage Report

Overall Coverage: 0%

Summary

Filename                      Regions    Missed Regions     Cover   Functions  Missed Functions  Executed       Lines      Missed Lines     Cover    Branches   Missed Branches     Cover
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
client.rs                        1444                67    95.36%         118                13    88.98%         923                35    96.21%           0                 0         -
format.rs                        2172                 3    99.86%         132                 1    99.24%        1292                 1    99.92%           0                 0         -
main.rs                           326               241    26.07%          14                 8    42.86%         225               168    25.33%           0                 0         -
mcp/analytics.rs                  408                 2    99.51%          24                 0   100.00%         331                 0   100.00%           0                 0         -
mcp/mod.rs                        144                55    61.81%          23                15    34.78%         128                65    49.22%           0                 0         -
mcp/prompts.rs                   1908                33    98.27%         126                 6    95.24%        1043                12    98.85%           0                 0         -
mcp/resources.rs                 1317                20    98.48%          93                 1    98.92%         865                 6    99.31%           0                 0         -
mcp/tools.rs                     2146                90    95.81%         116                18    84.48%        1333                47    96.47%           0                 0         -
models.rs                        1079                31    97.13%          78                10    87.18%         762                14    98.16%           0                 0         -
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL                           10944               542    95.05%         724                72    90.06%        6902               348    94.96%           0                 0         -

Full HTML report available in CI artifacts.

Add all required schema fields: title, description, type, category, tags, status, created, updated, author, project, technologies, and audience.

github-actions · 2026-02-16T23:14:44Z

Benchmark Results

No benchmarks configured. Add benchmarks to benches/ directory.

Full results available in CI artifacts.

github-actions · 2026-02-16T23:16:21Z

Code Coverage Report

Overall Coverage: 0%

Summary

Filename                      Regions    Missed Regions     Cover   Functions  Missed Functions  Executed       Lines      Missed Lines     Cover    Branches   Missed Branches     Cover
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
client.rs                        1444                67    95.36%         118                13    88.98%         923                35    96.21%           0                 0         -
format.rs                        2172                 3    99.86%         132                 1    99.24%        1292                 1    99.92%           0                 0         -
main.rs                           326               241    26.07%          14                 8    42.86%         225               168    25.33%           0                 0         -
mcp/analytics.rs                  408                 2    99.51%          24                 0   100.00%         331                 0   100.00%           0                 0         -
mcp/mod.rs                        144                55    61.81%          23                15    34.78%         128                65    49.22%           0                 0         -
mcp/prompts.rs                   1908                33    98.27%         126                 6    95.24%        1043                12    98.85%           0                 0         -
mcp/resources.rs                 1317                20    98.48%          93                 1    98.92%         865                 6    99.31%           0                 0         -
mcp/tools.rs                     2146                90    95.81%         116                18    84.48%        1333                47    96.47%           0                 0         -
models.rs                        1079                31    97.13%          78                10    87.18%         762                14    98.16%           0                 0         -
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL                           10944               542    95.05%         724                72    90.06%        6902               348    94.96%           0                 0         -

Full HTML report available in CI artifacts.

Copilot AI review requested due to automatic review settings February 16, 2026 21:41

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fix(ci): add structured MADR frontmatter to ADR files

5ac5164

- Add YAML frontmatter (status, date) to ADR-0001, ADR-0002, ADR-0003 - Narrow adrscope validation pattern to [0-9]*.md to skip README.md - Fix line-length lint on checkout action comment - Add ADR-0003 to README index

zircote temporarily deployed to copilot February 16, 2026 23:00 — with GitHub Actions Inactive

fix(ci): use full structured-MADR frontmatter in ADRs

73268ae

Add all required schema fields: title, description, type, category, tags, status, created, updated, author, project, technologies, and audience.

zircote temporarily deployed to copilot February 16, 2026 23:14 — with GitHub Actions Inactive

zircote merged commit a56b918 into main Feb 16, 2026
32 checks passed

zircote deleted the docs/diataxis-framework branch February 16, 2026 23:26

github-actions bot mentioned this pull request Feb 17, 2026

[repo-status] Daily Status Report - February 17, 2026 #34

Closed

		- [Working with EBV Traits](EBV-TRAITS.md) - Filter and rank animals by genetic traits
		- [MCP Integration](MCP-INTEGRATION.md) - Connect AI assistants to NSIP data

-    .with_trait_range("Weight", TraitRangeFilter {
-        min: Some(10.0),
-        max: Some(50.0),
-    });
+    .with_trait_ranges(
+        [(
+            "Weight".to_string(),
+            TraitRangeFilter {
+                min: 10.0,
+                max: 50.0,
+            },
+        )]
+        .into(),
+    );

	- [API Client Architecture](../explanation/CLIENT-ARCHITECTURE.md)
	- API Client Architecture (conceptual overview)

	- [How to Rank Animals](../how-to/RANK-ANIMALS.md) - Multi-trait ranking
	- How to Rank Animals - Multi-trait ranking (coming soon)

	.with_gender("M"); // Male animals only
	.with_gender("Male"); // Male animals only


		### Multi-Trait Selection

		Use weighted trait scores (see [How to Rank Animals](../how-to/RANK-ANIMALS.md)).

	.base_url("http://nsipsearch.nsip.org/api")
	.base_url("https://nsipsearch.nsip.org/api")

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zircote commented Feb 16, 2026

Summary

Changes

New Documentation Structure

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