Merge pull request #91 from bio-ontology-research-group/develop

Develop

.github/workflows/unittests.yml

@@ -0,0 +1,159 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python Unit Tests
+
+on:
+  push:
+    branches: [ "main", develop ]
+  pull_request:
+    branches: [ "main", develop ]
+
+jobs:
+  python-3-9:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.9"]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        activate-environment: anaconda-client-env
+        environment-file: envs/environment_3_9.yml
+        auto-activate-base: false
+        channels: conda-forge
+        use-mamba: true
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 nose pinocchio nose-exclude coverage
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
+    - name: Test with nose
+      run: |
+        nosetests tests
+
+  python-3-10:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        activate-environment: anaconda-client-env
+        environment-file: envs/environment_3_10.yml
+        auto-activate-base: false
+        channels: conda-forge
+        use-mamba: true
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest coverage pytest-faulthandler
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest -m "not slow" -p no:faulthandler
+
+
+  python-3-11:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.11"]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        activate-environment: anaconda-client-env
+        environment-file: envs/environment_3_11.yml
+        auto-activate-base: false
+        channels: conda-forge
+        use-mamba: true
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest coverage pytest-faulthandler
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest -m "not slow" -p no:faulthandler
+
+  python-3-12:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.12"]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        activate-environment: anaconda-client-env
+        environment-file: envs/environment_3_12.yml
+        auto-activate-base: false
+        channels: conda-forge
+        use-mamba: true
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest coverage pytest-faulthandler
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest -m "not slow" -p no:faulthandler

docs/source/conf.py

@@ -22,8 +22,8 @@
 copyright = '2023, Bio-Ontology Research Group'
 author = 'BORG'
 
-release = '1.0.1'
-version = '1.0.1'
+release = '1.0.2-dev'
+version = '1.0.2-dev'
 # -- General configuration
 
 extensions = [

docs/source/index.rst

@@ -27,7 +27,7 @@ Getting started
 **mOWL** can be installed from `source code <https://github.com/bio-ontology-research-group/mowl>`_ or from `PyPi <https://pypi.org/project/mowl-borg/>`_. For more details on installation check out the how to :doc:`install/index` section of the project.
 
 .. note::
-   This version of documentation corresponds to mOWL-1.0.1.
+   This version of documentation corresponds to mOWL-1.0.2-dev.
 
 
 mOWL, JPype and the JVM