Draft: MkDocs documentation site

docs/acknowledgements.md

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+# Acknowledgments
+
+The [Imageomics Institute](https://imageomics.org/) is supported by the National Science Foundation under [Award No. 2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) "HDR Institute: Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning." Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

docs/command_line_usage/help.md

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+# Help
+You may view the help for the command line interface by running:
+
+```bash
+taxonopy --help
+```
+This will show you the available commands and options:
+
+```
+usage: taxonopy [-h] [--cache-dir CACHE_DIR] [--show-cache-path] [--cache-stats] [--clear-cache] [--show-config] [--version] {resolve,trace,common-names} ...
+
+TaxonoPy: Resolve taxonomic names using GNVerifier and trace data provenance.
+
+positional arguments:
+  {resolve,trace,common-names}
+    resolve             Run the taxonomic resolution workflow
+    trace               Trace data provenance of TaxonoPy objects
+    common-names        Merge vernacular names (post-process) into resolved outputs
+
+options:
+  -h, --help            show this help message and exit
+  --cache-dir CACHE_DIR
+                        Directory for TaxonoPy cache (can also be set with TAXONOPY_CACHE_DIR environment variable) (default: None)
+  --show-cache-path     Display the current cache directory path and exit (default: False)
+  --cache-stats         Display statistics about the cache and exit (default: False)
+  --clear-cache         Clear the TaxonoPy object cache. May be used in isolation. (default: False)
+  --show-config         Show current configuration and exit (default: False)
+  --version             Show version number and exit
+```

docs/command_line_usage/tutorial.md

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+# Command Line Tutorial
+
+**Command ```resolve```:**
+The ```resolve``` command is used to perform taxonomic resolution on a dataset. It takes a directory of Parquet partitions as input and outputs a directory of resolved Parquet partitions.
+```
+usage: taxonopy resolve [-h] -i INPUT -o OUTPUT_DIR [--output-format {csv,parquet}] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--log-file LOG_FILE] [--force-input] [--batch-size BATCH_SIZE] [--all-matches]
+                        [--capitalize] [--fuzzy-uninomial] [--fuzzy-relaxed] [--species-group] [--refresh-cache]
+
+options:
+  -h, --help            show this help message and exit
+  -i, --input INPUT     Path to input Parquet or CSV file/directory
+  -o, --output-dir OUTPUT_DIR
+                        Directory to save resolved and unsolved output files
+  --output-format {csv,parquet}
+                        Output file format
+  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
+                        Set logging level
+  --log-file LOG_FILE   Optional file to write logs to
+  --force-input         Force use of input metadata without resolution
+
+GNVerifier Settings:
+  --batch-size BATCH_SIZE
+                        Max number of name queries per GNVerifier API/subprocess call
+  --all-matches         Return all matches instead of just the best one
+  --capitalize          Capitalize the first letter of each name
+  --fuzzy-uninomial     Enable fuzzy matching for uninomial names
+  --fuzzy-relaxed       Relax fuzzy matching criteria
+  --species-group       Enable group species matching
+
+Cache Management:
+  --refresh-cache       Force refresh of cached objects (input parsing, grouping) before running.
+```
+It is recommended to keep GNVerifier settings at their defaults.
+
+**Command ```trace```**:
+The ```trace``` command is used to trace the provenance of a taxonomic entry. It takes a UUID and an input path as arguments and outputs the full path of the entry through TaxonoPy.
+```
+usage: taxonopy trace [-h] {entry} ...
+
+positional arguments:
+  {entry}
+    entry     Trace an individual taxonomic entry by UUID
+
+options:
+  -h, --help  show this help message and exit
+
+usage: taxonopy trace entry [-h] --uuid UUID --from-input FROM_INPUT [--format {json,text}] [--verbose]
+
+options:
+  -h, --help            show this help message and exit
+  --uuid UUID           UUID of the taxonomic entry
+  --from-input FROM_INPUT
+                        Path to the original input dataset
+  --format {json,text}  Output format
+  --verbose             Show full details including all UUIDs in group
+```
+
+**Command ```common-names```:**
+The ```common-names``` command is used to merge vernacular names into the resolved output. It takes a directory of resolved Parquet partitions as input and outputs a directory of resolved Parquet partitions with common names.
+
+```
+usage: taxonopy common-names [-h] --resolved-dir ANNOTATION_DIR --output-dir OUTPUT_DIR
+
+options:
+  -h, --help            show this help message and exit
+  --resolved-dir ANNOTATION_DIR
+                        Directory containing your *.resolved.parquet files
+  --output-dir OUTPUT_DIR
+                        Directory to write annotated .parquet files
+```
+
+Note that the ```common-names``` command is a post-processing step and should be run after the ```resolve``` command.
+
+## Example Usage
+To perform taxonomic resolution on a dataset with subsequent common name annotation, run:
+```
+taxonopy resolve \
+    --input /path/to/formatted/input \
+    --output-dir /path/to/resolved/output
+```
+```
+taxonopy common-names \
+    --resolved-dir /path/to/resolved/output \
+    --output-dir /path/to/resolved_with_common-names/output
+```
+TaxonoPy creates a cache of the objects associated with input entries for use with the ```trace``` command. By default, this cache is stored in the ```~/.cache/taxonopy``` directory.
+
+## Development
+
+See the [Wiki Development Page](https://github.com/Imageomics/TaxonoPy/wiki/Development) for development instructions.

docs/index.md

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+# TaxonoPy
+
+Welcome! This is the initial MkDocs site for the TaxonoPy project. 
+
+TaxonoPy (taxon-o-py) is a command-line tool for creating an internally consistent taxonomic hierarchy using the [Global Names Verifier (gnverifier)](https://github.com/gnames/gnverifier)
+. See below for the structure of inputs and outputs.
+
+## Purpose
+The motivation for this package is to create an internally consistent and standardized classification set for organisms in a large biodiversity dataset composed from different data providers that may use very similar and overlapping but not identical taxonomic hierarchies.
+
+Its development has been driven by its application in the TreeOfLife-200M (TOL) dataset. This dataset contains over 200 million samples of organisms from four core data providers:
+
+- [The Global Biodiversity Information Facility (GBIF)](https://www.gbif.org/)
+- [BIOSCAN-5M](https://biodiversitygenomics.net/projects/5m-insects/)
+- [FathomNet](https://www.fathomnet.org/)
+- [The Encyclopedia of Life (EOL)](https://eol.org/)
+
+The names (and classification) of taxa may be (and often are) inconsistent across these resources. This package addresses this problem by creating an internally consistent classification set for such taxa.
+
+## Input
+A directory containing Parquet partitions of the seven-rank Linnaean taxonomic metadata for organisms in the dataset. Labels should include:
+
+- **uuid**: a unique identifier for each sample (required).
+- **kingdom, phylum, class, order, family, genus, species**: the taxonomic ranks of the organism (required, may have sparsity).
+- **scientific_name**: the scientific name to the most specific rank available (optional).
+- **common_name**: the common (i.e. vernacular) name of the organism (optional).
+
+
+
+See the example data in:
+```
+
+- `examples/input/sample.parquet`
+- `examples/resolved/sample.resolved.parquet` (generated with `taxonopy resolve`)
+- `examples/resolved_with_common_names/sample.resolved.parquet` (generated with `taxonopy common-names`)
+
+```
+
+
+## Challenges
+This taxonomy information is provided by each data provider and original sources, but the classification can be:
+
+- **Inconsistent** — between and within sources (e.g., kingdom *Metazoa* vs. *Animalia*)
+- **Incomplete** — missing ranks or containing "holes"
+- **Incorrect** — spelling errors, nonstandard terms, or outdated classifications
+- **Ambiguous** — homonyms, synonyms, and terms with multiple interpretations
+
+Taxonomic authorities exist to standardize classification, but:
+
+- There are multiple authorities  
+- They may disagree  
+- A given organism may be missing from some  
+
+## Solution
+TaxonoPy uses the taxonomic hierarchies provided by the TOL core data providers to query GNVerifier and create a standardized classification for each sample in the TOL dataset. It prioritizes the [GBIF Backbone Taxonomy](https://verifier.globalnames.org/data_sources/11), since this represents the largest part of the TOL dataset. Where GBIF misses, backup sources such as the [Catalogue of Life](https://verifier.globalnames.org/data_sources/1) and [Open Tree of Life (OTOL) Reference Taxonomy](https://verifier.globalnames.org/data_sources/179) are used.
+
+## Installation
+TaxonoPy can be installed with pip after setting up a virtual environment.
+
+### User Installation with pip
+To install the latest version of TaxonoPy, run:
+
+``` bash
+
+pip install taxonopy
+
+```
+

mkdocs.yml

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+site_name: TaxonoPy
+site_description: Documentation for the TaxonoPy package
+
+repo_url: https://github.com/Imageomics/taxonopy
+repo_name: Imageomics/taxonopy
+
+nav:
+  - Home: index.md
+  - Command Line Usage:
+      - Tutorial: command_line_usage/tutorial.md
+      - Help: command_line_usage/help.md
+  - Acknowledgements: acknowledgements.md
+
+theme: 
+  name: material
+  features:
+  - navigation.tabs
+  - navigation.tabs.sticky
+  - content.code.copy
+  - content.code.annotate
+
+plugins:
+- search
+- mkdocstrings:
+    handlers:
+      python:
+        paths: [src]  # search packages in the src folder
+        options:
+          docstring_style: google
+          merge_init_into_class: true
+markdown_extensions:
+  - admonition
+  - attr_list
+  - md_in_html
+  - pymdownx.blocks.caption
+  - pymdownx.details
+  - pymdownx.superfences

pyproject.toml

@@ -52,6 +52,12 @@ nb = [
     "jupyterlab",
     "marimo[recommended]"
 ]
+docs = [
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocs-material-extensions",
+    "mkdocstrings-python"
+]
 
 [project.urls]
 Documentation = "https://github.com/Imageomics/TaxonoPy"