Merge remote-tracking branch 'origin/master' into dev/util

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+
+extend-ignore = E221,E211,E222,E202,F541,E201,E203,E501

.github/workflows/testsuite.yml

@@ -0,0 +1,101 @@
+name: Test suite
+
+on:
+
+  workflow_dispatch:
+
+  pull_request:
+
+    branches:
+      - develop
+      - master
+
+    paths:
+      - .github/workflows/testsuite.yml
+      - giatools/*.py
+      - setup.py
+      - tests/*.py
+      - tests/data/**
+      - requirements.txt
+
+  push:
+
+    branches:
+      - master
+
+permissions:
+  contents: read
+  issues: write
+  pull-requests: write
+
+jobs:
+
+  python_lint:
+
+    name: Linting
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 isort
+
+      - name: Run flake8
+        shell: bash
+        run: |
+          flake8 giatools
+          flake8 tests
+
+      - name: Run isort
+        shell: bash
+        run: |
+          isort giatools --check-only
+          isort tests --check-only
+
+  run_testsuite:
+
+    name: Tests
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version:
+        - "3.8"
+        - "3.9"
+        - "3.10"
+        - "3.11"
+        - "3.12"
+
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        shell: bash
+        run: |
+          sudo apt install -y libopenblas-dev
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Run tests
+        uses: kostrykin/[email protected]
+        with:
+          report: ${{ strategy.job-index == 0 }}
+          gist-id: 07509ac0c0aa1d5a65ca03806bd3600b
+          github-auth: ${{ secrets.GITHUB_TOKEN }}
+          gist-auth: ${{ secrets.GIST_SECRET }}
+          gist-filename: giatools.json

README.rst

@@ -0,0 +1,15 @@
+.. raw:: html
+
+  <div align="center">
+    <h6>Tools required for Galaxy Image Analysis</h6>
+    <h1>
+      <a href="https://github.com/BMCV/giatools">giatools</a><br>
+      <a href="https://github.com/BMCV/giatools/actions/workflows/testsuite.yml"><img src="https://github.com/BMCV/giatools/actions/workflows/testsuite.yml/badge.svg" /></a>
+      <a href="https://github.com/BMCV/giatools/actions/workflows/testsuite.yml"><img src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/kostrykin/07509ac0c0aa1d5a65ca03806bd3600b/raw/giatools.json" /></a>
+      <a href="https://anaconda.org/bioconda/giatools"><img src="https://img.shields.io/badge/Install%20with-conda-%2387c305" /></a>
+      <a href="https://anaconda.org/bioconda/giatools"><img src="https://img.shields.io/conda/v/bioconda/giatools.svg?label=Version" /></a>
+      <a href="https://anaconda.org/bioconda/giatools"><img src="https://img.shields.io/conda/dn/bioconda/giatools.svg?label=Downloads" /></a>
+    </h1>
+  </div>
+
+Use ``python -m unittest`` in the root directory of the repository to run the test suite.

giatools/__init__.py

@@ -3,4 +3,3 @@
 VERSION_PATCH = 2
 
 VERSION = '%d.%d%s' % (VERSION_MAJOR, VERSION_MINOR, '.%d' % VERSION_PATCH if VERSION_PATCH > 0 else '')
-