WIP contributing guide docs

Author: Dahlia Li

docs/development/contributing/index.md

@@ -1,5 +1,30 @@
 # Contributing
 
-We welcome contributions to TaxonoPy. More detailed guidance will be added here.
+We welcome contributions to TaxonoPy.
+
+---
+
+
+## Contribution Opportunities
+
+Documented failure cases are valuable inputs for improving TaxonoPy.
+Contributions may include:
+
+* documenting additional failure patterns
+* proposing secondary tie-breaking heuristics
+* extending existing resolution profiles
+* adding dataset-specific disambiguation rules
+
+Clear documentation of *why* a resolution fails is often as important as
+resolving it.
+
+If you encounter recurring failure modes, consider opening an issue with:
+
+* example UUIDs
+* trace output
+* GNVerifier results
+* proposed resolution logic
+
+---
 
 If you have suggestions or run into a bug, please open an issue at [https://github.com/Imageomics/TaxonoPy/issues](https://github.com/Imageomics/TaxonoPy/issues).

docs/development/failure_analysis_workflow/index.md

@@ -0,0 +1,143 @@
+# Failure Analysis Workflow
+
+A significant portion of TaxonoPy development involves understanding *why* certain taxonomic resolutions fail and whether those failures are expected, data-driven, or indicative of missing strategy coverage.
+
+This workflow was developed during large-scale resolution of the **EOL dataset**, but applies broadly to other sources.
+
+---
+
+## 1. Identify Failed Resolution Entries
+
+Start by locating entries marked as failed in resolved Parquet outputs.
+A common failure status encountered during analysis is:
+
+* `FAILED_FORCED_INPUT`
+
+Example command:
+
+```bash
+parquet cat <resolved_parquet_files> \
+  | grep FAILED_FORCED_INPUT \
+  | head \
+  | jq
+```
+
+This step yields candidate UUIDs for deeper inspection.
+
+---
+
+## 2. Compare Raw Input vs. Final Resolution
+
+For each failed UUID, compare the **raw input taxonomy** with the **final resolved output**.
+
+Typical fields to inspect include:
+
+* `scientific_name`
+* `kingdom` → `genus`
+* `source_dataset`
+* `resolution_status`
+* `resolution_strategy`
+
+This comparison often reveals inconsistencies in the input taxonomy (e.g., genus assignments that differ from authoritative sources).
+
+---
+
+## 3. Trace Resolution Decisions
+
+Use the `trace` command to inspect how TaxonoPy attempted to resolve the entry and why it failed.
+
+Example:
+
+```bash
+taxonopy --cache-dir <cache_directory> \
+  trace entry \
+  --uuid "<UUID>" \
+  --from-input <source_dataset_directory> \
+  --verbose
+```
+
+The trace output provides:
+
+* grouping information
+* query plan (term, rank, source)
+* resolution strategies attempted
+* explicit failure reasons
+* metadata used for match selection
+
+---
+
+## 4. Verify Against External Authorities (GNVerifier)
+
+To determine whether a failure is due to missing data or genuine ambiguity,
+independently verify the same taxonomic name using **Global Names Verifier**.
+
+=== "CLI / Alias Usage"
+
+    ```bash
+    gnverifier -j 1 \
+      --format compact \
+      --capitalize \
+      --all_matches \
+      --sources 11 \
+      "<scientific_name>" | jq
+    ```
+
+    This approach uses the GNVerifier command-line tool directly and is
+    suitable for shell-based workflows and batch inspection.
+
+=== "API Usage (Programmatic)"
+
+    ```bash
+    curl -X POST "https://verifier.globalnames.org/api/v1/verifications" \
+      -H "Content-Type: application/json" \
+      -d '{
+            "names": ["<scientific_name>"],
+            "capitalize": true,
+            "sources": [11]
+          }' | jq
+    ```
+
+    This method uses the GNVerifier HTTP API and is appropriate for
+    integration into automated pipelines or custom applications.
+
+---
+
+This step confirms whether multiple accepted records exist in authoritative
+sources such as GBIF.
+
+## 5. Common Failure Pattern: Multi-Accepted Match Tie
+
+Across analyzed EOL cases, the most frequent failure pattern observed was:
+
+> **Tie between multiple accepted results with equal taxonomic matches**
+
+These failures are typically produced by the strategy:
+
+* `ExactMatchPrimarySourceMultiAcceptedTaxonomicMatch`
+
+Example failure reason from trace output:
+
+```json
+{
+  "failure_reason": "Tie between N results with equal taxonomic matches"
+}
+```
+
+---
+
+## 6. Why This Strategy Fails
+
+This strategy is intentionally conservative:
+
+* it prioritizes correctness over forced resolution
+* it fails when multiple equally valid “best” matches exist
+* it avoids arbitrary selection without clear disambiguation signals
+
+However, analysis shows that many tied matches differ subtly in ways not currently used for secondary discrimination, such as:
+
+* author or publication year suffixes
+* infra-specific placeholders (e.g., `spec`)
+* rank depth differences
+* minor spelling or canonical variations
+
+---

mkdocs.yml

@@ -8,7 +8,10 @@ nav:
   - TaxonoPy:
       - User guide: index.md
       - Quick reference: user-guide/quick-reference.md
-      - CLI help reference: command_line_usage/help.md
+      - CLI help reference: 
+          - command_line_usage/help.md
+          - command_line_usage/tutorial.md
+
       - Installation: user-guide/installation.md
       - IO:
           - user-guide/io/index.md
@@ -18,7 +21,13 @@ nav:
       - Development:
           - Contributing:
               - development/contributing/index.md
+<<<<<<< HEAD
       - Acknowledgments: acknowledgments.md
+=======
+          - Failure Analysis Workflow: 
+              - development/failure_analysis_workflow/index.md
+      - Acknowledgements: acknowledgements.md
+>>>>>>> 01fb7a8 (WIP contributing guide docs)
 
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