Merge pull request #43 from GavinHuttley/main

DOC: simplify the README

README.md

@@ -4,45 +4,16 @@
 [![CodeQL](https://github.com/HuttleyLab/DiverseSeq/actions/workflows/codeql.yml/badge.svg)](https://github.com/HuttleyLab/DiverseSeq/actions/workflows/codeql.yml)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
-# DiverseSeq identifies the most diverse biological sequences from a collection
+# `diverse_seq` identifies the most diverse biological sequences from a collection
 
-`diverse_seq` provides tools for selecting a representative subset of sequences from a larger collection. It is an alignment-free method which scales linearly with the number of sequences.  It identifies the subset of sequences that maximize diversity as measured using Jensen-Shannon divergence. `DiverseSeq` provides a command-line tool (`dvs`) and plugins to the Cogent3 app system (prefixed by `dvs_`) allowing users to embed code in their own scripts. The command-line tools can be run in parallel.
+`diverse_seq` provides tools for selecting a representative subset of sequences from a larger collection. It is an alignment-free method which scales linearly with the number of sequences. It identifies the subset of sequences that maximize diversity as measured using Jensen-Shannon divergence. `diverse_seq` provides a command-line tool (`dvs`) and plugins to the Cogent3 app system (prefixed by `dvs_`) allowing users to embed code in their own scripts. The command-line tools can be run in parallel.
 
-## The available commands
-
-<!-- [[[cog
-import cog
-from diverse_seq.cli import main
-from click.testing import CliRunner
-runner = CliRunner()
-result = runner.invoke(main, ["--help"])
-help = result.output.replace("Usage: main", "Usage: dvs")
-cog.out(
-    "```\n{}\n```".format(help)
-)
-]]] -->
-```
-Usage: dvs [OPTIONS] COMMAND [ARGS]...
-
-  dvs -- alignment free detection of the most diverse sequences using JSD
-
-Options:
-  --version  Show the version and exit.
-  --help     Show this message and exit.
-
-Commands:
-  prep   Writes processed sequences to a <HDF5 file>.dvseqs.
-  max    Identify the seqs that maximise average delta JSD
-  nmost  Identify n seqs that maximise average delta JSD
-
-```
-<!-- [[[end]]] -->
-
-### `dvs prep`: Preparing the sequence data
+### `dvs prep`: preparing the sequence data
 
 Convert sequence data into a more efficient format for the diversity assessment. This must be done before running either the `nmost` or `max` commands.
 
-#### Usage:
+<details>
+    <summary>CLI options for dvs prep</summary>
 
 <!-- [[[cog
 import cog
@@ -75,14 +46,17 @@ Options:
 ```
 <!-- [[[end]]] -->
 
-### `dvs nmost`: Select the n-most diverse sequences
+</details>
+
+### `dvs nmost`: select the n-most diverse sequences
 
-We recommend using `nmost` for large datasets.
+Selects the n sequences that maximise the total JSD. We recommend using `nmost` for large datasets.
 
 > **Note**
 > A fuller explanation is coming soon!
 
-#### Command line usage:
+<details>
+    <summary>Options for command line dvs nmost</summary>
 
 <!-- [[[cog
 import cog
@@ -116,7 +90,10 @@ Options:
 ```
 <!-- [[[end]]] -->
 
-#### As a cogent3 plugin:
+</details>
+
+<details>
+    <summary>Options for cogent3 app dvs_select_nmost</summary>
 
 The `dvs nmost` is also available as the [cogent3 app](https://cogent3.org/doc/app/index.html) `dvs_select_nmost`. The result of using `cogent3.app_help("dvs_select_nmost")` is shown below.
 
@@ -173,23 +150,26 @@ named sequences are added to the final result.
 
 Input type
 ----------
-ArrayAlignment, Alignment, SequenceCollection
+SequenceCollection, Alignment, ArrayAlignment
 
 Output type
 -----------
-ArrayAlignment, Alignment, SequenceCollection
+SequenceCollection, Alignment, ArrayAlignment
 
 ```
 <!-- [[[end]]] -->
+</details>
+
 
-### `dvs max`: Maximise average delta JSD
+### `dvs max`: maximise variance in the selected sequences
 
-The result of the `max` command is typically a set that are modestly more diverse than that fron `nmost`.
+The result of the `max` command is typically a set that are modestly more diverse than that from `nmost`.
 
 > **Note**
 > A fuller explanation is coming soon!
 
-#### Command line usage:
+<details>
+    <summary>Options for command line dvs max</summary>
 
 <!-- [[[cog
 import cog
@@ -226,10 +206,12 @@ Options:
 ```
 <!-- [[[end]]] -->
 
+</details>
 
-#### As a cogent3 plugin:
+<details>
+<summary>Options for cogent3 app dvs_select_max</summary>
 
-The `dvs max` is also available as the [cogent3 app](https://cogent3.org/doc/app/index.html) `dvs_select_max`. The result of using `cogent3.app_help("dvs_select_max")` is shown below.
+The `dvs max` is also available as the [cogent3 app](https://cogent3.org/doc/app/index.html) `dvs_select_max`. 
 
 <!-- [[[cog
 import cog
@@ -256,8 +238,8 @@ Options for making the app
 --------------------------
 dvs_select_max_app = get_app(
     'dvs_select_max',
-    min_size=3,
-    max_size=10,
+    min_size=5,
+    max_size=30,
     stat='stdev',
     moltype='dna',
     include=None,
@@ -291,11 +273,12 @@ named sequences are added to the final result.
 
 Input type
 ----------
-ArrayAlignment, Alignment, SequenceCollection
+SequenceCollection, Alignment, ArrayAlignment
 
 Output type
 -----------
-ArrayAlignment, Alignment, SequenceCollection
+SequenceCollection, Alignment, ArrayAlignment
 
 ```
 <!-- [[[end]]] -->
+</details>