Merge pull request #14 from js2264/master

Improve install stability

.codecov.yml

@@ -0,0 +1,9 @@
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        if_ci_failed: ignore #success, failure, error, ignore
+        informational: false
+        only_pulls: false

.dockerignore

@@ -1,8 +1,11 @@
 *
+Dockerfile*
+.dockerignore
 !metator/*
 !setup.py
 !setup.cfg
+!metator.yaml
 !requirements.txt
 !MANIFEST.in
 !README.md
-!external
+!external

.github/workflows/python-package.yml

@@ -17,21 +17,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.8', '3.9', '3.10']
 
     steps:
 
     - uses: actions/checkout@v3
 
-
-
-    - name: Install Conda environment from metator.yaml
-      uses: mamba-org/provision-with-micromamba@main
-      with:
-        environment-file: metator.yaml
-        extra-specs: |
-          python=${{ matrix.python-version }}
-
     - name: Load apt packages
       run: |
         sudo apt-get update
@@ -52,13 +43,19 @@ jobs:
         ./gradlew build
         cd ..
 
+    - name: Install Conda environment from metator.yaml
+      uses: mamba-org/setup-micromamba@v1
+      with:
+          environment-file: metator.yaml
+          generate-run-shell: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+
     - name: Test with pytest
       run: |
         micromamba activate metator
         export LOUVAIN_PATH=external/gen-louvain
         export LEIDEN_PATH=networkanalysis/build/libs/networkanalysis-1.2.0.jar
-        PWD=$(pwd)
-        export PATH="$PATH:$PWD/bwa:$PWD/pairix/bin/:$PWD/pairix/util:$PWD/pairix/util/bam2pairs:/root/.local/bin"
         pytest --pylint --pylint-error-types=EF --pylint-rcfile=.pylintrc --doctest-modules metator
         pytest --cov=metator
         codecov

.gitignore

@@ -4,6 +4,7 @@ tests_data/assembly.fa.fxi
 tests_data/outdir/cam.pdf
 nohup.out
 codecov*
+!.codecov.yml
 
 # vscode
 .vscode

Dockerfile

@@ -1,60 +1,39 @@
 # syntax=docker/dockerfile:1
 
-FROM adoptopenjdk/openjdk12
+FROM mambaorg/micromamba:latest
 
 LABEL Name=metator Version=1.3.2
 
-WORKDIR /app
-COPY ./ /app
+COPY --chown=$MAMBA_USER:$MAMBA_USER . ./
 
 # Install 3rd party packages
-RUN \
-    apt-get update && \
-    apt-get install -y --no-install-recommends git make g++ curl
-
-# Install miniconda to /miniconda
-RUN curl -LO http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-RUN bash Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b
-RUN rm Miniconda3-latest-Linux-x86_64.sh
-ENV PATH=/miniconda/bin:${PATH}
-RUN conda update -y conda
-RUN conda config --add channels bioconda
-
-# # Get 3rd party package
-RUN conda install -c conda-forge -y python=3.8\
-    pip \
-    bowtie2 \
-    samtools \
-    pairix \
-    checkm-genome && conda clean -afy
-
-# Install bwa
-RUN git clone https://github.com/lh3/bwa.git && \
-    cd bwa && \
-    make &&\
-    cd /app
-ENV PATH="$PATH:/app/bwa"
+USER root
+RUN apt update && \
+    apt install -y --no-install-recommends git make g++ curl default-jre default-jdk zlib1g-dev
 
 # Install Louvain 
-RUN cd /app/external && \
+RUN cd ./external && \
     tar -xzf louvain-generic.tar.gz && \
     cd gen-louvain && \
     make && \
-    cd /app
-ENV LOUVAIN_PATH=/app/external/gen-louvain
+    cd ../
+ENV LOUVAIN_PATH=./external/gen-louvain
 
 # Install Leiden through Network analysis repo
 RUN git clone https://github.com/vtraag/networkanalysis.git && \
-    cd /app/networkanalysis && \
+    cd ./networkanalysis && \
     ./gradlew build && \
-    cd /app
-ENV LEIDEN_PATH=/app/networkanalysis/build/libs/networkanalysis-1.2.0.jar
+    cd ../
+ENV LEIDEN_PATH=$(pwd)/networkanalysis/build/libs/networkanalysis-1.2.0.jar
 
-
-# Install python dependencies
-RUN pip3 install -Ur requirements.txt
+## Install dependencies
+USER mambauser
+RUN micromamba install -y -n base --file metator.yaml && \
+    micromamba install -y -n base pip && \
+    micromamba clean --all --yes
 
 # Install metator
-RUN pip3 install .
+RUN micromamba run -n base python3 -m pip install -e .
 
-ENTRYPOINT ["metator"]
+WORKDIR /home/mambauser/
+ENTRYPOINT [ "/bin/bash" ]

README.md

@@ -17,41 +17,45 @@ Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that
 
 ## Table of contents
 
-* [Installation](#Installation)
-  * [Requirements](#Requirements)
-  * [Using pip](#Using-pip)
-  * [Using docker container](#Using-docker-container)
-* [Usage](#Usage)
-* [Output files](#Output-files)
-* [References](#References)
-* [Contact](#Contact)
+1. [MetaTOR](#metator)
+   1. [Table of contents](#table-of-contents)
+   2. [Installation](#installation)
+      1. [Requirements](#requirements)
+      2. [Using pip](#using-pip)
+      3. [Using conda](#using-conda)
+      4. [Louvain or Leiden dependency](#louvain-or-leiden-dependency)
+      5. [Using docker container](#using-docker-container)
+   3. [Usage](#usage)
+   4. [Output files](#output-files)
+   5. [References](#references)
+   6. [Contact](#contact)
+      1. [Authors](#authors)
+      2. [Research lab](#research-lab)
 
 ## Installation
 
 ### Requirements
 
-* Python 3.6 or later is required.
-* The following librairies are required but will be automatically installed with the pip installation: `numpy`, `scipy`, `sklearn`, `pandas`, `docopt`, `networkx` `biopython` `pyfastx` and `pysam`.
+* Python `3.8` to `3.10` or later is required.
+* The following librairies are required but will be automatically installed with the pip installation: `numpy`, `scipy`, `sklearn`, `pandas`, `docopt`, `networkx` `biopython` `pyfastx`, `pysam`, `micomplete` and `pairix`.
 * The following software should be installed separately if you used the pip installation:
   * [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
   * [samtools](http://www.htslib.org/)
   * [louvain](https://sourceforge.net/projects/louvain/) (original
         implementation).
   * [networkanalysis](https://github.com/vtraag/networkanalysis) (not
     necessary only if you want to use Leiden algorithm to partition the network)
-  * [micomplete](https://bitbucket.org/evolegiolab/micomplete/src/master/)
-  * [pairix](https://github.com/4dn-dcic/pairix) (not necessary if you do not use metator contact map)
 
 ### Using pip
 
 ```sh
-   pip3 install metator
+pip3 install metator
 ```
 
 or, to use the latest version:
 
 ```sh
-   pip3 install -e git+https://github.com/koszullab/metator.git@master#egg=metator
+pip3 install -e git+https://github.com/koszullab/metator.git@master#egg=metator
 ```
 
 ### Using conda
@@ -85,13 +89,13 @@ export LEIDEN_PATH=/networkanalysis_repository_path/build/libs/networkanalysis-1
 A dockerfile is also available if that is of interest. You may fetch the image by running the following:
 
 ```sh
-    docker pull koszullab/metator
+docker pull koszullab/metator
 ```
 
 ## Usage
 
 ```sh
-    metator {network|partition|validation|pipeline} [parameters]
+metator {network|partition|validation|pipeline} [parameters]
 ```
 
 A metaTOR command takes the form `metator action --param1 arg1 --param2

metator.yaml

@@ -7,6 +7,7 @@ dependencies:
   - requests
   - pip
   - git
+  - biopython=1.80
   - bowtie2=2.5.1
   - bwa=0.7.17
   - samtools=1.17
@@ -15,17 +16,15 @@ dependencies:
   - pysam=0.21.0
   - pairix=0.3.7
   - pairtools=1.0.2
+  - pyfastx==0.8.4
+  - cooler==0.9.1
+  - pandas==1.5.3
+  - hicstuff
   - pip:
-    - pyfastx==0.8.4
     - micomplete==1.1.1
-    - cooler==0.9.1
-    - pandas==1.5.3
-    - git+https://github.com/koszullab/hicstuff.git
     - metator
     - pytest
     - pylint
+    - codecov
     - pytest-cov
-    - pylint
     - pytest-pylint
-    - codecov
-

requirements.txt

@@ -1,10 +1,10 @@
-biopython
+biopython==1.80
 cdlib
 checkv
 docopt
 hicstuff
 looseversion
-micomplete
+micomplete==1.1.1
 networkx
 numpy
 pairtools

setup.py

@@ -57,7 +57,7 @@
     classifiers=CLASSIFIERS,
     url=URL,
     packages=find_packages(),
-    python_requires=">=3.6",
+    python_requires=">=3.8,<=3.10",
     include_package_data=True,
     long_description_content_type="text/markdown",
     install_requires=REQUIREMENTS,