Updating to Poetry

Author: Roberto Vera Alvarez

.github/workflows/python-app.yml

@@ -5,31 +5,24 @@ name: Python application
 
 on:
   push:
-    branches: [ master ]
+    branches: ["**"]
   pull_request:
-    branches: [ master ]
+    branches: ["**"]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.12
+    - name: Install Poetry
+      run: pip install poetry tox
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8
-        if [ -f requirements/test.txt ]; then pip install -r requirements/test.txt; fi
-    - name: Lint with flake8
-      run: |
-        flake8 src/ --count --select=E9,F63,F7,F82 --show-source --statistics
-        flake8 src/ --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        python setup.py install
-        pytest
+      run: poetry install
+    - name: Test with tox
+      run: poetry run tox

.github/workflows/python-package.yml

@@ -1,4 +1,4 @@
-# This workflows will upload a Python Package using Twine when a release is created
+# This workflows will upload a Python Package using Poetry when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
 name: Upload Python Package
@@ -14,19 +14,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+    - name: Install Poetry
+      run: pip install poetry
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        poetry build
+        poetry publish

.github/workflows/python-publish.yml

@@ -1,5 +1,5 @@
 python:
-  version: 3.7
+  version: 3.12
   pip_install: true
   install:
       - requirements: docs/requirements.txt

.readthedocs.yaml

@@ -0,0 +1,85 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "pm4ngs"
+version = "0.0.0"   # Replace with the correct version or use a plugin for scm
+description = "PM4NGS generates a standard organizational structure for Next Generation Sequencing (ngs) data analysis"
+license = "Public Domain"
+authors = ["Vera Alvarez, Roberto <[email protected]>"]
+maintainers = ["Vera Alvarez, Roberto <[email protected]>"]
+readme = "README.md"
+homepage = "https://github.com/ncbi/pm4ngs"
+repository = "https://github.com/ncbi/pm4ngs"
+documentation = "https://pm4ngs.readthedocs.io/"
+keywords = ["Biocontainers", "Bioinformatics", "NGS", "Genomics"]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: Public Domain",
+    "Natural Language :: English",
+    "Operating System :: Unix",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+packages = [
+    { include = "pm4ngs", from = "src" },
+]
+
+[tool.poetry.dependencies]
+python = ">=3.7,<4.0"
+docutils = "*"
+bioconda2biocontainer = "*"
+biopython = "*"
+cookiecutter = "*"
+cwltool = "*"
+docker = "*"
+galaxy-tool-util = "*"
+GitPython = "*"
+goenrichment = "*"
+jupyter = "*"
+matplotlib = "*"
+networkx = "*"
+numpy = "*"
+pandas = "*"
+pdf2image = "*"
+PyYAML = "*"
+requests = "*"
+scipy = "*"
+seaborn = "*"
+statsmodels = "*"
+urllib3 = "*"
+xmltodict = "*"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "*"
+pytest-cov = "*"
+flake8 = "*"
+
+
+[tool.poetry.scripts]
+pm4ngs-server = "pm4ngs.main:start_server_main"
+pm4ngs-create = "pm4ngs.main:create_project"
+pm4ngs-rnaseq = "pm4ngs.main:rnaseq"
+pm4ngs-rnaseq-demo = "pm4ngs.main:rnaseq_demo"
+pm4ngs-chipseq = "pm4ngs.main:chipseq"
+pm4ngs-chipseq-demo = "pm4ngs.main:chipseq_demo"
+pm4ngs-chipexo = "pm4ngs.main:chipexo"
+pm4ngs-chipexo-demo = "pm4ngs.main:chipexo_demo"
+pm4ngs-transcriptome-annotation = "pm4ngs.main:transcriptome_annotation"
+pm4ngs-transcriptome-annotation-demo = "pm4ngs.main:transcriptome_annotation_demo"
+
+[tool.poetry.urls]
+Tracker = "https://github.com/ncbi/pm4ngs/issues"
+
+[tool.poetry-dynamic-versioning]
+enable = true
+vcs = "git"
+style = "semver"

pyproject.toml

@@ -1,8 +0,0 @@
-from pkg_resources import DistributionNotFound
-
-try:
-    _distribution = __import__('pkg_resources').get_distribution("pm4ngs")
-except DistributionNotFound:  # Likely, running from working dir without installed dist
-    __version__ = 'SNAPSHOT'
-else:
-    __version__ = _distribution.version if _distribution else 'SNAPSHOT'

requirements/base.txt

@@ -1,47 +1,19 @@
-; Tox configuration file - http://tox.readthedocs.io/en/latest/config.html
 [tox]
-envlist = py{37,38,39},flake8
+envlist = py{39,310,311,312},flake8
 
 
 [testenv]
-; Configuration to put in all test environments (unless overridden)
-;
-; Install pm4ngs, its test dependencies, and
-; teamcity-messages (so it can tell TC which tests passed).
-
-deps =
-    -rrequirements/test.txt
-
-; Coverage options are not in `addopts` because PyCharm doesn't stop on breakpoints inside tests
-commands = py.test {posargs:--cov pm4ngs --cov tests --cov-report term-missing --cov-report html --cov-report xml:coverage.xml}
-
-; usedevelop: if true, use `setup.py develop` to install pm4ngs
-; inside Tox's test environment.  If false, use `setup.py install`.
-;
-; Set `usedevelop = True` if you want your tests to run faster.
-;
-; Set `usedevelop = False` if your tests rely on data files or executable
-; binaries being installed correctly, or if your package is a namespace package
-; (like ncbi.*) AND it uses another package in the same namespace.
-usedevelop = True
-
-; If your application needs some external configuration values in environment
-; variables, uncomment these lines and list the variables here, separated by
-; whitespace, wildcards work:
-;passenv =
-;    MY_DATABASE_URL
+skip_install = true
+allowlist_externals = poetry
+commands_pre = poetry install
+commands = poetry run pytest {posargs:--cov bioconda2biocontainer --cov tests --cov-report term-missing --cov-report html --cov-report xml:coverage.xml}
 
 
 [testenv:flake8]
-; Flake8 test environment, don't install the package or its deps, instead just
-; install & run flake8.
-
 skip_install = True
-deps = flake8
-commands = flake8 src/ tests/
-
-; This should correspond to the lowest Python interpreter version supported by the package
-basepython = python3.7
+allowlist_externals = poetry
+commands_pre = poetry install --no-root
+commands = poetry run flake8 src/
 
 
 [pytest]