Merge pull request #11 from cokelaer/main

update/add workflows

.github/workflows/main.yml

@@ -4,36 +4,51 @@ on:
   push:
     branches:
       - main
+      - dev
   pull_request:
     branches-ignore: []
+  schedule:
+    - cron: '0 0 * * SUN'
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
+      matrix:
+        python: [3.7, 3.8, 3.9, '3.10']
+      fail-fast: false
 
     steps:
+
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+
+    - name: Setup python 3.X
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
+        python-version: ${{ matrix.python }}
+
+    - name: install package itself
       run: |
-        conda install -c conda-forge mamba --quiet
-        mamba install -c conda-forge --quiet -y --file=requirements.txt --file=requirements_dev.txt
+        pip install .[testing]
+
     - name: Lint with flake8
       run: |
-        mamba install flake8
+        pip install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest
       run: |
-        pytest
+        pytest --cov-report term-missing --cov=mergegi
+
+    - name: coveralls
+      run: |
+        echo $COVERALLS_REPO_TOKEN
+        coveralls --service=github
+      env:
+          GITHUB_TOKEN: ${{ github.token }}
+
+

.github/workflows/pypi.yml

@@ -0,0 +1,39 @@
+name: Publish to PyPI
+on: 
+  workflow_dispatch:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  build-n-publish:
+    name: Build and publish to PyPI and TestPyPI
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@main
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+
+    - name: Install package
+      run: |
+          pip install build
+
+    - name: Build source tarball
+      run: |
+          rm -rf dist;
+          python setup.py sdist
+
+    - name: Publish distribution to Test PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+    - name: Publish distribution to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

MANIFEST.in

@@ -0,0 +1,3 @@
+recursive-exclude * __pycache__
+recursive-exclude * *pyc
+recursive-exclude tests *

README.md

@@ -2,6 +2,9 @@
 
 [![Tests](https://github.com/sequana/MergeGI/actions/workflows/main.yml/badge.svg)](https://github.com/sequana/MergeGI/actions/workflows/main.yml)
 
+
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mergegi)
+
 **MergeGI** provides a single command line to merge and select barcoded raw data from [MGI](https://en.mgi-tech.com/products/) sequencing runs into a set of FastQ files ready for subsequent bioinformatics analysis. 
 
 
@@ -18,6 +21,14 @@ We provide **MergeGI** as a Python library available on [Pypi](https://pypi.pyth
 
 There is no dependencies except for **click** package so that installation should be straightforward. 
 
+
+For developers:
+
+    git clone git@github.com:sequana/MergeGI.git
+    cd MergeGI
+    pip install -e .[testing]
+
+
 ## Overview
 
 The main goal of **MergeGI** is to select and merge the FastQ files generated by a MGI sequencer into a list of FastQ files directly usable for subsequent bioinformatics analysis. Why do we need to do this preprocessing ? 
@@ -84,6 +95,16 @@ By default, lanes are merged. If this is not what you want you may disable this
 mergegi --samplesheet samplesheet.csv --input-directory mgi_raw_data --output-directory merge_data --paired --no-merge
 ```
 
+## Changelog
+
+
+========= ==========================================================================
+Version   Description
+========= ==========================================================================
+0.1.0     * simplify the CI action workflow and setup
+0.0.1     * first release
+
+
 ## Barcode distribution example
 
 <img src="doc/bccode.png" width="50%">

pyproject.toml

@@ -0,0 +1,37 @@
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "MergeGI"
+version= "0.1.0"
+authors=[
+    { name="Sequana Team" }
+]
+description="Merge MGI fastq files"
+readme="README.md"
+requires-python = ">=3.7"
+classifiers = [
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: Unix"
+]
+license = {text="BSD-4-Clause"}
+keywords = ["fastq", "MGI", "merger"]
+dependencies = [
+    "click"
+]
+
+[project.optional-dependencies]
+testing = ["pytest", "pytest-cov", "coveralls", "pytest-xdist"]
+
+[project.urls]
+"Homepage"= "https://github.com/sequana/MergeGI"
+"Bug Tracker"= "https://github.com/sequana/MergeGI/issues"
+
+[project.scripts]
+mergegi = "mergegi:main"