added nox, minor changes

README.md

@@ -1,14 +1,20 @@
+[![PyPI](https://img.shields.io/pypi/v/blast2galaxy?color=blue&label=PyPI.org)](https://pypi.org/project/blast2galaxy/)
+[![Docker Image Version (latest semver)](https://img.shields.io/docker/v/ipkbit/blast2galaxy?color=blue&label=DockerHub)](https://hub.docker.com/r/ipkbit/blast2galaxy)
+![GitHub release (latest SemVer)](https://img.shields.io/github/v/release/IPK-BIT/blast2galaxy?color=blue&label=Github)
+
+
+
+[![Python](https://img.shields.io/pypi/pyversions/blast2galaxy.svg?color=green)](https://badge.fury.io/py/blast2galaxy)
+[![PyPI Downloads](https://img.shields.io/pypi/dm/blast2galaxy.svg?label=PyPI%20downloads)](https://pypi.org/project/blast2galaxy/)
+![License](https://img.shields.io/github/license/IPK-BIT/divbrowse)
+
+
 # blast2galaxy
 
+
 ## About
 blast2galaxy is a Python package that provides a NCBI BLAST like CLI to perform BLAST searches against BLAST databases installed on Galaxy servers.
 
-## Installation
-
-```
-pip install blast2galaxy
-```
-
 ## Documentation
 
-tbd
+See https://ipk-bit.github.io/blast2galaxy/

docs/index.md

@@ -1,6 +1,6 @@
 # Welcome to blast2galaxy
 
-blast2galaxy provides a Python API and CLI to perform BLAST and DIAMOND queries against Galaxy servers that have the NCBI BLAST+ tools [[1]](#1 and DIAMOND installed.
+blast2galaxy provides a Python API and CLI to perform BLAST and DIAMOND queries against Galaxy servers that have the NCBI BLAST+ tools [[1]](#1) and DIAMOND [[2]](#2) installed.
 
 
 ![Screenshot](figure_1_v3.png)
@@ -13,4 +13,6 @@ or read the [API Reference](api.md) if you want to use blast2galaxy inside a Pyt
 
 <h2>References</h2>
 
-<a id="1">[1]</a> Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo, NCBI BLAST+ integrated into Galaxy, GigaScience, Volume 4, Issue 1, December 2015, s13742-015-0080-7, [https://doi.org/10.1186/s13742-015-0080-7](https://doi.org/10.1186/s13742-015-0080-7)
+<a id="1">[1]</a> Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo, NCBI BLAST+ integrated into Galaxy, GigaScience, Volume 4, Issue 1, December 2015, s13742-015-0080-7, [https://doi.org/10.1186/s13742-015-0080-7](https://doi.org/10.1186/s13742-015-0080-7)
+
+<a id="2">[2]</a> Buchfink, B., Reuter, K. & Drost, HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods 18, 366–368 (2021). [https://doi.org/10.1038/s41592-021-01101-x](https://doi.org/10.1038/s41592-021-01101-x)

noxfile.py

@@ -0,0 +1,17 @@
+import nox
+from nox_poetry import session
+
+nox.options.sessions = ["tests"]
+nox.options.default_venv_backend = "mamba"
+nox.options.reuse_venv = True
+
+@session(python=["3.10", "3.11", "3.12"], reuse_venv=True)
+def tests(session):
+    session.conda_install("python=" + session.python)
+
+    #session.install("poetry")
+    #session.run("poetry", "install")
+    #session.run("poetry", "run", "pytest")
+
+    session.install("pytest", ".")
+    session.run("pytest")