Merge pull request #109 from zargham-ahmad/issue105

updated to poetry

.github/workflows/publish_pypi.yaml

@@ -6,21 +6,11 @@ on:
   workflow_dispatch:
 
 jobs:
-  publish:
+  build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.7'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-        python setup.py sdist bdist_wheel
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@release/v1.5
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - uses: actions/checkout@v3
+      - name: Build and publish to pypi
+        uses: JRubics/[email protected]
+        with:
+          pypi_token: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/python-package.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2
@@ -25,8 +25,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        pip install --user -r requirements.txt
+        python -m pip install flake8 pytest poetry
+        poetry install --no-root
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -35,4 +35,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with coverage
       run: |
-        pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
+        poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml

README.md

@@ -24,7 +24,7 @@ Hecht et al., (2022). RIAssigner: A package for gas chromatographic retention in
 ```
 git clone https://github.com/RECETOX/RIAssigner.git
 cd RIAssigner
-python -m pip install -e .
+poetry install
 ```
 (2) Install via [bioconda](https://anaconda.org/bioconda/riassigner) in your existing evironment.
 ```
@@ -115,3 +115,10 @@ classDiagram
 
 ### Testing
 All functionality is tested with the [pytest](https://docs.pytest.org/en/6.2.x/contents.html) framework. Make sure to run your IDE in the `riassigner-dev` conda environment (or make sure to use the respective python interpreter when developing) to follow formatting guidelines and to be able to execute the tests.
+
+For testing, install the package dependencies as follows:
+```
+git clone https://github.com/RECETOX/RIAssigner.git
+cd RIAssigner
+poetry install --no-root
+```

poetry.toml

@@ -0,0 +1,3 @@
+[virtualenvs]
+create = false
+prefer-active-python = true

pyproject.toml

@@ -0,0 +1,47 @@
+[tool.poetry]
+name = "RIAssigner"
+version = '0.3.3'
+description = "Python library for retention index calculation."
+authors = ["Helge Hecht <[email protected]>", "Maksym Skoryk <[email protected]>"]
+
+license = "MIT License"
+readme = "README.md"
+repository = "https://github.com/RECETOX/RIAssigner"
+keywords=[ 
+    "gas chromatography",
+    "mass spectrometry",
+    "retention index"
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8"
+]
+
+packages = [
+    { include = "RIAssigner" },
+]
+
+[tool.poetry.dependencies]
+python = "^3.8"
+matchms = "^0.14.0, <0.18.0"
+numpy = "*"
+pandas = "*"
+pint = "^0.17, <0.20"
+scipy = "*"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "*"
+pytest-cov = "*"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry_bumpversion.file."RIAssigner/__version__.py"]