Update docs, squash bugs

Author: standage

README.md

@@ -4,17 +4,19 @@
 [![Install with bioconda][condabadge]](http://bioconda.github.io/recipes/microhapdb/README.html)
 [![BSD licensed][licensebadge]](https://github.com/bioforensics/MicroHapDB/blob/master/LICENSE.txt)
 
-NBFAC, 2018-2023
+NBFAC, 2018-2025
 https://github.com/bioforensics/microhapdb
 
 **MicroHapDB** is a comprehensive catalog of human microhaplotype variation.
 The database integrates marker and population frequency data from numerous published research articles.
 Allele frequency estimates and allelic diversity statistics ($A_e$) are computed for 26 global populations so that markers can be ranked and evaluated for various applications.
 
-MicroHapDB is designed to be user-friendly for researchers, technology developers, and forensic practitioners, supporting a range of access methods from browsing and simple text queries to complex queries and full programmatic access via a Python API.
-It is designed as a community resource requiring minimal infrastructure to use and maintain: the entire contents of the database are distributed in plain text with each copy of MicroHapDB.
+MicroHapDB is managed as a community resource requiring minimal infrastructure to maintain: the entire contents of the database are distributed in plain text with each copy of MicroHapDB.
+The primary interface to MicroHapDB is through the console command line, which provides methods for browsing, searching, and filtering the database contents.
+Full programmatic access is available via a Python API.
+Alternatively, users can access the database tables directly using a spreadsheet program (e.g. Microsoft Excel), 
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/bioforensics/MicroHapDB/master?labpath=binder%2Fdemo_v0.9.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/bioforensics/MicroHapDB/master?labpath=binder%2Fdemo_v0.11.ipynb)
 
 
 ## Installation
@@ -32,10 +34,6 @@ pytest --pyargs microhapdb --doctest-modules
 MicroHapDB provides several methods to access the contents of a locally installed database.
 The [MicroHapDB documentation](https://microhapdb.readthedocs.io/) includes a ["Getting started" guide](https://microhapdb.readthedocs.io/en/latest/starting.html) as well as a comprehensive reference for running MicroHapDB on the command line.
 
-> *A particularly intrepid and curious user may also be so bold as to download the core database tables directly from [GitHub](https://github.com/bioforensics/MicroHapDB/tree/master/microhapdb/data).*
-
-MicroHapDB includes [statistics for ranking markers](https://microhapdb.readthedocs.io/en/latest/ranking.html), tools for [panel design](targets), and instructions for [adding markers to a private local copy of the database](https://microhapdb.readthedocs.io/en/latest/extending.html).
-
 
 ## Citation
 
@@ -45,12 +43,10 @@ If you use this database, please cite our work.
 
 MicroHapDB was created and is maintained by the Bioinformatics Group at the National Bioforensic Anaylsis Center (NBFAC).
 
-Additional references are available [on this page](https://microhapdb.readthedocs.io/en/latest/install.html).
+Additional references are available [on this page](https://microhapdb.readthedocs.io/en/latest/citations.html).
 
 
-[alfred]: https://alfred.med.yale.edu/alfred/alfredDataDownload.asp
-[Pandas]: https://pandas.pydata.org
-[cibadge]: https://github.com/bioforensics/MicroHapDB/workflows/CI%20Build/badge.svg
+[cibadge]: https://github.com/bioforensics/MicroHapDB/workflows/CI%20Build/badge.svg?branch=master
 [pypibadge]: https://img.shields.io/pypi/v/microhapdb.svg
 [condabadge]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
 [licensebadge]: https://img.shields.io/badge/license-BSD-blue.svg

binder/demo_v0.9-run.ipynb binder/demo_v0.11-run.ipynbbinder/demo_v0.9-run.ipynb renamed to binder/demo_v0.11-run.ipynb

@@ -9,7 +9,8 @@
     "\n",
     "Daniel Standage  \n",
     "2023-08-29  \n",
-    "MicroHapDB version 0.9\n",
+    "MicroHapDB version 0.11  \n",
+    "Updated 2025-04-24\n",
     "\n",
     "## Overview\n",
     "\n",
@@ -77,7 +78,7 @@
    "source": [
     "## Markers\n",
     "\n",
-    "The `microhapdb marker` command is used to retrieve information about markers from the database. Running the command with no other configuration will dump the entire contents of the markers table onto the screen. Given that there are more than 3000 markers in the database, this usually isn't very useful."
+    "The `microhapdb marker` command is used to retrieve information about microhaps from the database. Running the command with no other configuration will dump the entire contents of the markers table onto the screen. Given that there are more than 3000 microhap allele definitions in the database, this usually isn't very useful."
    ]
   },
   {
@@ -95,7 +96,7 @@
    "id": "b164d065-905a-4dce-8db4-5919d5a0879f",
    "metadata": {},
    "source": [
-    "If we add a marker name, MicroHapDB will display info only for that marker."
+    "If we add a microhap identifier, MicroHapDB will display info only for that microhap."
    ]
   },
   {
@@ -113,7 +114,7 @@
    "id": "50cc952f-1815-4ac2-ad13-e68feff6c0e8",
    "metadata": {},
    "source": [
-    "Adding `--format=detail` will provide a richly detailed report for the selected marker(s)."
+    "Adding `--format=detail` will provide a richly detailed report for the selected microhap(s)."
    ]
   },
   {
@@ -131,7 +132,7 @@
    "id": "66f4f9a8-8cad-4e66-8f40-1b65cafb5c41",
    "metadata": {},
    "source": [
-    "If the user supplies a locus name, all markers defined at that locus will be displayed."
+    "If the provided identifier refers to a microhap locus with multiple allele definitions, all allele definitions will be displayed."
    ]
   },
   {

binder/demo_v0.9.ipynb binder/demo_v0.11.ipynbbinder/demo_v0.9.ipynb renamed to binder/demo_v0.11.ipynb

@@ -6,4 +6,4 @@ channels:
 dependencies:
   - bash_kernel
   - curl
-  - microhapdb==0.10
+  - microhapdb==0.11