Merge branch 'master' into poetry

.github/workflows/build.yml

@@ -3,10 +3,10 @@ name: Python package
 on:
   push:
     branches:
-    - main
+    - master
   pull_request:
     branches:
-    - main
+    - master
 
 jobs:
 
@@ -17,11 +17,11 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Python info
@@ -31,32 +31,32 @@ jobs:
           python --version
       - name: Upgrade pip and install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install .[dev,publishing]
+          python -m pip install --upgrade pip poetry
+          poetry install
       - name: Run unit tests
-        run: python -m pytest -v
+        run: poetry run pytest
       - name: Verify that we can build the package
-        run: python -m build
+        run: poetry build
 
   lint:
     name: Linting build
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Python info
         shell: bash -e {0}
         run: |
           which python
           python --version
       - name: Upgrade pip and install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install .[dev,publishing]
+          python -m pip install --upgrade pip poetry
+          poetry install --with dev
       - name: Check style against standards using ruff
-        run: ruff .
+        run: poetry run ruff check .

.github/workflows/cffconvert.yml

@@ -3,18 +3,18 @@ name: cffconvert
 on:
   push:
     branches:
-    - main
+    - master
   pull_request:
     branches:
-    - main
+    - master
 
 jobs:
 
   verify:
     name: "cffconvert"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out a copy of the repository
 
       - name: Check whether the citation metadata from CITATION.cff is valid

.github/workflows/documentation.yml

@@ -3,10 +3,10 @@ name: documentation
 on:
   push:
     branches:
-    - main
+    - master
   pull_request:
     branches:
-    - main
+    - master
 
 jobs:
   build-documentation:
@@ -15,22 +15,22 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Python info
         shell: bash -e {0}
         run: |
           which python
           python --version
       - name: Upgrade pip and install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install .[dev,publishing]
+          python -m pip install --upgrade pip poetry
+          poetry install --with dev
       - name: Install pandoc using apt
-        run: sudo apt install pandoc        
+        run: sudo apt install pandoc
       - name: Build documentation
         run: make coverage doctest html
         working-directory: docs

.github/workflows/markdown-link-check.yml

@@ -3,18 +3,18 @@ name: markdown-link-check
 on:
   push:
     branches:
-    - main
+    - master
   pull_request:
     branches:
-    - main
+    - master
 
 jobs:
 
   markdown-link-check:
     name: Check markdown links
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: gaurav-nelson/github-action-markdown-link-check@v1
       with:
         config-file: '.mlc-config.json'

.github/workflows/sonarcloud.yml

@@ -3,23 +3,23 @@ name: sonarcloud
 on:
   push:
     branches:
-    - main
+    - master
   pull_request:
     types: [opened, synchronize, reopened]
     branches:
-    - main
+    - master
 
 jobs:
 
   sonarcloud:
     name: SonarCloud
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
       - name: Python info
@@ -28,9 +28,10 @@ jobs:
           which python
           python --version
       - name: Install dependencies
-        run: python -m pip install .[dev]
+          python -m pip install --upgrade pip poetry
+          poetry install
       - name: Run unit tests with coverage
-        run: python -m pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/
+        run: poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/
       - name: Correct coverage paths
         run: sed -i "s+$PWD/++g" coverage.xml
       - name: SonarCloud Scan

.gitignore

@@ -29,3 +29,6 @@ env
 env3
 venv
 venv3
+
+# poetry
+poetry.lock

CITATION.cff

@@ -7,8 +7,7 @@ authors:
     family-names: Ahmad
     given-names: Zargham
     orcid: "https://orcid.org/0000-0000-0000-0000"
-date-released: 20??-MM-DD
-doi: <insert your DOI here>
+date-released: 2024-06-19
 version: "0.1.0"
 repository-code: "https://github.com/RECETOX/rcx-tk"
 keywords:

docs/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
+SPHINXBUILD   = poetry run sphinx-build
 SPHINXPROJ    = rcx_tk
 SOURCEDIR     = .
 BUILDDIR      = _build

docs/conf.py

@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = u"rcx_tk"
-copyright = u"2024, Netherlands eScience Center"
+copyright = u"2024, RECETOX, Masaryk University"
 author = u"Zargham Ahmad"
 
 # The version info for the project you're documenting, acts as replacement for

docs/make.bat

@@ -5,7 +5,7 @@ pushd %~dp0
 REM Command file for Sphinx documentation
 
 if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
+	set SPHINXBUILD=poetry run sphinx-build
 )
 set SOURCEDIR=.
 set BUILDDIR=_build