Merge branch 'release/0.2.0'

.github/workflows/run-tests.yml

@@ -5,12 +5,12 @@ on: [push]
 jobs:
   build-linux:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     strategy:
       max-parallel: 5
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9, "3.10"]
+        python-version: [3.7, 3.8, 3.9, "3.10"]
 
     steps:
     - uses: actions/checkout@v2

.travis.yml

@@ -1,10 +1,11 @@
+dist: focal
 language: python
 python:
   # We don't actually use the Travis Python, but this keeps it organized.
-  - "3.6"
   - "3.7"
   - "3.8"
   - "3.9"
+  - "3.10"
 notifications:
   email: false
 before_install:

README.rst

@@ -2,21 +2,27 @@
 VTAM - Validation and Taxonomic Assignation of Metabarcoding Data
 =============================================================================================
 
-.. image:: https://img.shields.io/pypi/v/vtam.svg
+.. image:: https://img.shields.io/pypi/v/vtam.svg?color=blue
     :target: https://pypi.python.org/pypi/vtam
 
 .. image:: https://img.shields.io/pypi/pyversions/vtam.svg
     :target: https://www.python.org
 
+.. image:: https://static.pepy.tech/personalized-badge/vtam?period=month&units=international_system&left_color=gray&right_color=blue&left_text=Downloads
+    :target: https://pepy.tech/project/vtam
+
+.. image:: https://codecov.io/gh/aitgon/vtam/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/aitgon/vtam
+
 .. image:: https://readthedocs.org/projects/vtam/badge/?version=latest
     :target: http://vtam.readthedocs.io/en/latest/?badge=latest
 
+.. image:: https://app.travis-ci.com/aitgon/vtam.svg?branch=master
+    :target: https://app.travis-ci.com/github/aitgon/vtam
+
 .. image:: https://github.com/aitgon/vtam/workflows/CI/badge.svg
     :target: https://github.com/aitgon/vtam/actions?query=branch%3Amaster+workflow%3ACI
 
-.. image:: https://codecov.io/gh/aitgon/vtam/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/aitgon/vtam
-
 VTAM is a metabarcoding package with various commands to process high throughput sequencing (HTS) data of amplicons of one or several metabarcoding markers in FASTQ format and produce a table of amplicon sequence variants (ASVs) assigned to taxonomic groups.
 If you use VTAM in scientific works, **please cite the following article**:
 

RELEASE.rst

@@ -1,3 +1,22 @@
+**Changes In Version 0.2.0 (May 12, 2022)**
+
+- Addressed issues 12, 14, and 19: refactored commands merge sortreads and filter to work with zipped files (.gz and .bz2 format).
+   * Merge and sortreads produce zipped files when zipped files are provided: issues
+   * filter can accept compressed input: issue 19,
+   * sortreads produce compressed output when provided with compressed inputs: issue 14,
+   * merge produce compressed output when provided with compressed: inputs 12.
+
+- Addressed issues 15, 16, 17, 18 (improved demultiplexing with sortreads):
+   * implemented --no_reverse option to check only on strand: issue 15,
+   * use cutadapt v3 to search all tags pairs in parallel: issue 16,
+   * added options --tag_to_end and --primer_to_end to search and trim for tags (issue 17) and primers (issue 18) only at the end of the strands.
+
+- Addressed issue 20:
+   * added command random_seq to produce random samples from a dataset
+
+- Addressed issue 1:
+    * Integrated the make_known_occurrences command to create a .tsv file with the known occurrences.
+
 **Changes In Version 0.1.22 (Jan 31, 2022)**
 
 - Updated and tested with python 3.9 and 3.10

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-description-file = README.rst
+description_file = README.rst
 author = Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz
 email = [email protected]
 copyright = Copyright (c) 2018-2022: Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz

setup.py

@@ -1,7 +1,7 @@
 # -*- coding: UTF-8 -*-
 
-__author__ = "Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz"
-__copyright__ = "Copyright 2018-2022, Aitor Gonzalez, Emese Meglecz"
+__author__ = "Aitor González, Raphael Hebert, Thomas Dechatre, Reda Mekdad, Ulysse Castet, Emese Meglecz"
+__copyright__ = "Copyright 2018-2022, Aitor González, Emese Meglecz"
 __email__ = "[email protected], [email protected]"
 __license__ = "MIT"
 
@@ -18,8 +18,9 @@
 email = config['metadata']['email']
 license = config['metadata']['license']
 
-if sys.version_info < (3, 6):
-    print("At least Python 3.6 is required.\n", file=sys.stderr)
+cutoff_version_info = (3, 7)
+if sys.version_info < cutoff_version_info:
+    print("At least Python {}.{} is required.\n".format(cutoff_version_info[0], cutoff_version_info[1]), file=sys.stderr)
     exit(1)
 
 try:
@@ -53,7 +54,6 @@ def get_version(rel_path):
 License :: OSI Approved :: MIT License
 Programming Language :: Python
 Programming Language :: Python :: 3
-Programming Language :: Python :: 3.6
 Programming Language :: Python :: 3.7
 Programming Language :: Python :: 3.8
 Programming Language :: Python :: 3.9

vtam/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.1.22"
+__version__ = "0.2.0"
 
 import os
 import pathlib