Update documentation and release issues (#35)

* Add epilog to classify help statement

- This was causing the printing of the help statement to break.

* Make description and epilog more informative

* Add logos for RTD

* Add gtnet commands to coverage tests

* Fix typo

* Add background to logo

* Only display logo on home page

* Tweak logos

* Shorten logo

* Move Github README to RST

* Add CodeCov badge

.github/workflows/run_coverage.yml

@@ -55,6 +55,9 @@ jobs:
       - name: Run tests and generate coverage report
         run: |
           pytest --cov
+          gtnet predict data/small.fna > data/small.raw.test.csv
+          gtnet filter --fpr 0.05 data/small.raw.csv > data/small.tax.test.csv
+          gtnet classify --fpr 0.05 data/small.fna > data/small.tax.test.csv
           python -m coverage xml  # codecov uploader requires xml format
           python -m coverage report -m
 

README.md → README.rst

@@ -1,42 +1,29 @@
+=====
 GTNet
 =====
-The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences
-
-## Getting started
-Installing GTNet from PyPI
-```bash
-pip install gtnet
-```
-
-Installing GTNet from source
-```bash
-pip install git+https://github.com/exabiome/gtnet.git
-```
-
-## Running GTNet
-Getting taxonomic classifications for all sequences in a Fasta file.
-```bash
-gtnet classify data/small.fna > data/small.tax.csv
-```
-
-### GTNet steps
-GTNet consists of two main steps: 1) get scored predictions of taxonoimc assignments and 2) filter
-scored predictions. The previous command combines these two commands into a single command with a 
-default false-positive rate. The two steps have been separated into two commands for those who
-want to experiment with different false-positive rates.
-
-Getting predictions for all sequences in a Fasta file.
-```bash
-gtnet predict data/small.fna > data/small.tax.raw.csv
-```
-The first time you run `predict`, the model file will be downloaded and stored in the
-same directory that the `gtnet` package is installed in. Therefore, for the this to be successful,
-you must have write privileges on the directory that `gtnet` is installed in.
-
-Filtering predictions 
-```bash
-gtnet filter --fpr 0.05 data/small.tax.raw.csv > data/small.tax.csv
-```
+The Genome Taxonomy Network for assigning GTDB microbial taxonomy to DNA sequences.
+
+Documentation can be found at https://gtnet.readthedocs.io.
+
+Latest Release
+==============
+
+.. image:: https://badge.fury.io/py/gtnet.svg
+    :target: https://badge.fury.io/py/gtnet
+
+Overall Health
+==============
+
+.. image:: https://codecov.io/gh/exabiome/gtnet/branch/main/graph/badge.svg?token=AFJH59YZ3U
+    :target: https://codecov.io/gh/exabiome/gtnet
+
+.. image:: https://readthedocs.org/projects/hdmf/badge/?version=stable
+    :target: https://hdmf.readthedocs.io/en/stable/?badge=stable
+
+Installation
+============
+
+See the `GTNet documentation <https://gtnet.readthedocs.io/en/stable/installation.html>`_.
 
 LICENSE
 =======
@@ -101,5 +88,5 @@ NOTICE.  This Software was developed under funding from the U.S. Department
 of Energy and the U.S. Government consequently retains certain rights.  As
 such, the U.S. Government has been granted for itself and others acting on
 its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the
-Software to reproduce, distribute copies to the public, prepare derivative 
+Software to reproduce, distribute copies to the public, prepare derivative
 works, and perform publicly and display publicly, and to permit others to do so.

docs/source/conf.py

@@ -136,6 +136,10 @@
 # documentation.
 # html_theme_options = {}
 
+html_theme_options = {
+    'logo_only': True,
+}
+
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
 
@@ -148,12 +152,13 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-# html_logo = None
+html_logo = "gtnet.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-# html_favicon = None
+html_favicon = "gtnet-favicon.png"
+
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

src/gtnet/classify.py

@@ -20,8 +20,9 @@ def classify(argv=None):
     argv : Namespace, default=sys.argv
         The command-line arguments to use for running this command
     """
-    desc = "Get taxonomic classification for each sequence in a Fasta file."
-    epi = ()
+    desc = "Get filtered taxonomic classification for each sequence in a Fasta file."
+    epi = ("This command will output a taxonomic classification filtered to a specified false-positive rate "
+           "for each sequence")
 
     parser = argparse.ArgumentParser(description=desc, epilog=epi)
     parser.add_argument('fasta', type=str, help='the Fasta files to do taxonomic classification on')