GIT: merge changes from develop

.github/workflows/pypi-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/testing_python_app.yml

@@ -14,8 +14,13 @@ jobs:
 
     strategy:
       matrix:
+<<<<<<< HEAD
         os: [macos-12, ubuntu-latest]
         python-version: ["3.8", "3.9", "3.10"]
+=======
+        os: [macos-latest, ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+>>>>>>> develop
 
     steps:
       - uses: "actions/checkout@v3"

.github/workflows/testing_python_conda.yml

@@ -0,0 +1,46 @@
+name: CI conda
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+
+jobs:
+  tests:
+    name: "Python ${{ matrix.python-version }}"
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: "actions/checkout@v3"
+        with:
+          fetch-depth: 0
+
+      # Setup conda env
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: graphbin
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: "Setup graphbin on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      
+      - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          pip install pytest pytest-cov
+          pytest --cov=graphbin --cov-report=xml --cov-append
+          

README.md

@@ -1,15 +1,16 @@
 <p align="center">
-  <img src="https://raw.githubusercontent.com/metagentools/GraphBin/master/GraphBin_logo.png" width="400" title="GraphBin logo" alt="GraphBin logo">
+  <img src="https://raw.githubusercontent.com/metagentools/GraphBin/develop/GraphBin_logo_light.png#gh-light-mode-only" width="400" title="GraphBin logo" alt="GraphBin logo">
+  <img src="https://raw.githubusercontent.com/metagentools/GraphBin/develop/GraphBin_logo_dark.png#gh-dark-mode-only" width="400" title="GraphBin logo" alt="GraphBin logo">
 </p>
 
 # GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
 
 [![DOI](https://img.shields.io/badge/DOI-10.1093/bioinformatics/btaa180-informational)](https://doi.org/10.1093/bioinformatics/btaa180)
-[![Anaconda-Server Badge](https://anaconda.org/bioconda/graphbin/badges/version.svg)](https://anaconda.org/bioconda/graphbin)
-[![Anaconda-Server Badge](https://anaconda.org/bioconda/graphbin/badges/downloads.svg)](https://anaconda.org/bioconda/graphbin)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/graphbin/README.html)
+[![Conda](https://img.shields.io/conda/v/bioconda/graphbin)](https://anaconda.org/bioconda/graphbin)
+[![Conda](https://img.shields.io/conda/dn/bioconda/graphbin)](https://anaconda.org/bioconda/graphbin)
 [![PyPI version](https://badge.fury.io/py/graphbin.svg)](https://badge.fury.io/py/graphbin)
 [![Downloads](https://static.pepy.tech/badge/graphbin)](https://pepy.tech/project/graphbin)
-
 [![CI](https://github.com/metagentools/GraphBin/actions/workflows/testing_python_app.yml/badge.svg)](https://github.com/metagentools/GraphBin/actions/workflows/testing_python_app.yml)
 [![codecov](https://codecov.io/gh/metagentools/GraphBin/branch/develop/graph/badge.svg?token=0S310F6QXJ)](https://codecov.io/gh/metagentools/GraphBin)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
@@ -26,6 +27,7 @@ GraphBin installation requires python 3 to run. The following dependencies are r
 * [python-igraph](https://igraph.org/python/)
 * [cogent3](https://cogent3.org/)
 * [cairocffi](https://pypi.org/project/cairocffi/)
+* [click](https://click.palletsprojects.com/)
 
 ## Installing GraphBin
 
@@ -121,7 +123,7 @@ graphbin --assembler megahit --graph /path/to/graph_file.gfa --contigs /path/to/
 ## Citation
 If you use GraphBin in your work, please cite GraphBin as,
 
-Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin. GraphBin: Refined binning of metagenomic contigs using assembly graphs. Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3307–3313, DOI: [10.1093/bioinformatics/btaa180](http://dx.doi.org/10.1093/bioinformatics/btaa180)
+> Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin. GraphBin: Refined binning of metagenomic contigs using assembly graphs. Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3307–3313, DOI: [https://doi.org/10.1093/bioinformatics/btaa180](https://doi.org/10.1093/bioinformatics/btaa180)
 
 ```bibtex
 @article{10.1093/bioinformatics/btaa180,
@@ -143,8 +145,8 @@ Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin. GraphBin: Refined binn
 
 ## Funding
 
-GraphBin is funded by a [Essential Open Source Software for Science Grant](https://chanzuckerberg.com/eoss/proposals/cogent3-python-apis-for-iq-tree-and-graphbin-via-a-plug-in-architecture/) from the Chan Zuckerberg Initiative.
+GraphBin is funded by an [Essential Open Source Software for Science Grant](https://chanzuckerberg.com/eoss/proposals/cogent3-python-apis-for-iq-tree-and-graphbin-via-a-plug-in-architecture/) from the Chan Zuckerberg Initiative.
 
 <p align="left">
-  <img src="https://raw.githubusercontent.com/metagentools/GraphBin/master/images/czi-logo.png" width="300">
+  <img src="https://chanzuckerberg.com/wp-content/themes/czi/img/logo.svg" width="300">
 </p>

docs/requirements.txt

@@ -1,4 +1,4 @@
-jinja2==3.0.3
+jinja2==3.1.4
 mkdocs>=1.3.1
 babel>=2.9.0
 click>=7.0

docs/usage.md

@@ -41,8 +41,8 @@ Options:
 For the SPAdes version, `graphbin` takes in 3 files as inputs (required).
 
 * Assembly graph file (in `.gfa` format)
-* Contigs file (in FASTA format)
-* Paths of contigs (in `.paths` format)
+* Contigs file (`contigs.fasta` file in FASTA format)
+* Paths of contigs (`contigs.paths` file)
 * Binning output from an existing tool (in `.csv` format)
 
 For the SGA version, `graphbin` takes in 2 files as inputs (required).
@@ -57,6 +57,13 @@ For the MEGAHIT version, `graphbin` takes in 3 files as inputs (required).
 * Contigs file (in FASTA format)
 * Binning output from an existing tool (in `.csv` format)
 
+For the Flye version, `graphbin` takes in 3 files as inputs (required).
+
+* Assembly graph file (in `.gfa` format)
+* Contigs file (`assembly.fasta` file in FASTA format)
+* Paths of contigs (`assembly_info.txt` file)
+* Binning output from an existing tool (in `.csv` format)
+
 **Note:** Make sure that the initial binning result consists of contigs belonging to only one bin. GraphBin is designed to handle initial contigs which belong to only one bin. Multiple bins for the initial contigs are not supported.
 
 **Note:** You can specify the delimiter for the initial binning result file and the final output file using the delimiter paramter. Enter the following values for different delimiters; `,` for a comma, `;` for a semicolon, `$'\t'` for a tab, `" "` for a space and `|` for a pipe.
@@ -90,19 +97,44 @@ k99_18709,bin_1
 k99_15596,bin_2
 ...
 ```
+Example Flye binned input
+```
+contig_1,bin_1
+contig_2,bin_1
+contig_3,bin_2
+contig_4,bin_1
+contig_5,bin_2
+...
+```
+
 Make sure to follow the steps provided in the [preprocessing section](https://graphbin.readthedocs.io/en/latest/preprocess/) to prepare the initial binning result.
 
 ## Example Usage
 
 ```
+# metaSPAdes assembly
 graphbin --assembler spades --graph /path/to/graph_file.gfa --contigs /path/to/contigs.fasta --paths /path/to/paths_file.paths --binned /path/to/binning_result.csv --output /path/to/output_folder
 ```
 ```
+# SGA assembly
 graphbin --assembler sga --graph /path/to/graph_file.asqg --contigs /path/to/contigs.fa --binned /path/to/binning_result.csv --output /path/to/output_folder
 ```
 ```
+# MEGAHIT assembly
 graphbin --assembler megahit --graph /path/to/graph_file.gfa --contigs /path/to/contigs.fa --binned /path/to/binning_result.csv --output /path/to/output_folder
 ```
+```
+# metaFlye assembly
+graphbin --assembler flye --graph /path/to/assembly_graph.gfa --contigs /path/to/assembly.fasta --paths /path/to/assembly_info.txt --binned /path/to/binning_result.csv --output /path/to/output_folder
+```
+```
+# Canu assembly
+graphbin --assembler canu --graph /path/to/assembly.contigs.gfa --contigs /path/to/assembly.contigs.fasta --binned /path/to/binning_result.csv --output /path/to/output_folder
+```
+```
+# Miniasm assembly
+graphbin --assembler miniasm --graph /path/to/reads.gfa --contigs /path/to/unitigs.fasta --binned /path/to/binning_result.csv --output /path/to/output_folder
+```
 
 ## Output
 

environment.yml

@@ -1,11 +1,13 @@
 name: graphbin
 channels:
   - bioconda
-  - defaults
+  - conda-forge
+  - anaconda
 dependencies:
   - python>=3.7.1
+  - flit
+  - cairocffi
+  - python-igraph
+  - click
   - pip
-  - pip:
-    - cogent3
-    - cairocffi
-    - python-igraph>=0.7.1
+  - cogent3

pyproject.toml

@@ -5,15 +5,15 @@ build-backend = "flit_core.buildapi"
 [project]
 name = "graphbin"
 authors = [
-    { name = "Vijini Mallawaarachchi", email = "Vijini.Mallawaarachchi@anu.edu.au"},
-    { name = "Anuradha Wickramarachchi", email = "Anuradha.Wickramarachchi@anu.edu.au"},
+    { name = "Vijini Mallawaarachchi", email = "viji.mallawaarachchi@gmail.com"},
+    { name = "Anuradha Wickramarachchi", email = "anuradhawick@gmail.com"},
     { name = "Yu Lin", email = "yu.lin@anu.edu.au"},
 ]
 keywords = ["genomics", "bioinformatics"]
 readme = "README.md"
 license = { file = "LICENSE" }
 requires-python = ">=3.7"
-dependencies = ["python-igraph", "cogent3", "cairocffi"]
+dependencies = ["igraph", "cogent3", "cairocffi", "click"]
 classifiers = [
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Science/Research",
@@ -32,7 +32,7 @@ Documentation = "https://graphbin.readthedocs.io/en/latest/"
 "Source Code" = "https://github.com/metagentools/GraphBin/"
 
 [project.scripts]
-graphbin = "graphbin:main"
+graphbin = "graphbin.cli:main"
 
 [project.optional-dependencies]
 test = [

requirements.txt

@@ -1,3 +1,4 @@
 cogent3
-python-igraph>=0.7.1
-cairocffi
+igraph>=0.7.1
+cairocffi
+click