🔧 Updated README, setup.py, docs, etc...

.github/workflows/python-package_3_13.yml

@@ -0,0 +1,48 @@
+# 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 package
+
+on:
+  push:
+    branches: [ "main", develop ]
+  pull_request:
+    branches: [ "main", develop ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.13"]
+    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_13.yml
+        auto-activate-base: false
+        channels: conda-forge
+        use-mambda: 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

.gitignore

@@ -40,4 +40,6 @@ dist/
 *.zip
 *.log
 
-docs/source/api/mowl.*
+docs/source/api/mowl.*
+
+**/wandb

README.md

@@ -30,15 +30,17 @@ mainly in Python, but we have integrated the functionalities of [OWLAPI](https:/
 
 ### System dependencies
 
-  - JDK version >= 11
+  - JDK version >= 22.x.x
   - Python version: 3.9, 3.10, 3.11, 3.12
-  - Conda version >= 4.x.x
+  - Conda version >= 24.x.x
 
 ### Python requirements
 
-  - Gensim >= 4.x.x
-  - PyTorch >= 1.12.x
-  - PyKEEN >= 1.10.1
+  - torch
+  - gensim >= 4.3.0
+  - JPype1 == 1.5.0
+  - pykeen == 1.10.2
+  - scipy < 1.13.0
 
 ### Install from PyPi
 
@@ -60,6 +62,16 @@ pip install git+https://github.com/bio-ontology-research-group/mowl
 * [Evaluating Different Methods for Semantic Reasoning Over Ontologies](https://ceur-ws.org/Vol-3592/paper9.pdf)
 * [Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning](https://doi.org/10.1093/bioinformatics/btae301)
 
+### Authors
+
+**mOWL** is a project initiated and developed by the [Bio-Ontology Research Group](https://cemse.kaust.edu.sa/borg) from KAUST.
+Furthermore, mOWL had other collaboration by being part of:
+
+* [Biohackathon Japan 2024](http://2024.biohackathon.org/)
+* [Biohackathon MENA 2023](https://biohackathon-europe.org/) as project ``#20``.
+* [Biohackathon Europe 2022](https://2022.biohackathon-europe.org/) as project ``#18``.
+* [Biohackathon Europe 2021](https://2021.biohackathon-europe.org/) as project ``#27``.
+
 ## License
 This software library is distributed under the [BSD-3-Clause license](https://github.com/bio-ontology-research-group/mowl/blob/main/LICENSE)
 

docs/source/install/index.rst

@@ -1,38 +1,29 @@
 Installation and Setup
 ===================================
 
-System requirements
--------------------
-
-- JDK version 17
-- Python version 3.9, 3.10, 3.11, 3.12
-- Conda version >= 4.x.x
+System dependencies
+---------------------
 
+- JDK version >= 22.x.x
+- Python version: 3.9, 3.10, 3.11, 3.12
+- Conda version >= 24.x.x
 
 Python requirements
-----------------------
+-----------------------
 
-- Gensim >= 4.x.x
-- PyTorch >= 1.12.x
-- PyKEEN >= 1.10.1
+- torch
+- gensim >= 4.3.0
+- JPype1 == 1.5.0
+- pykeen == 1.10.2
+- scipy < 1.13.0
 
 
-
 Install from source code
 --------------------------
 
-Before installing from source, make sure to meet the dependencies.
-
-
-Installation can be done with the following commands:
-
 .. code:: bash
-	  
-   git clone https://github.com/bio-ontology-research-group/mowl.git
-   
-   cd mowl
 
-   pip install .
+   pip install git+https://github.com/bio-ontology-research-group/mowl
 
 Install from PyPi
 ------------------------------

envs/environment_3_13.yml

@@ -0,0 +1,23 @@
+name: mowl313
+channels:
+  - conda-forge
+dependencies:
+  - python=3.13
+  - click
+  - deprecated
+  - gensim>=4.3.0
+  - gradle
+  - JPype1=1.5.0
+  - pandas
+  - pytorch
+  - pyyaml
+  - requests
+  - scikit-learn
+  - scipy<1.13.0  
+  - tqdm
+  - urllib3
+  - pip
+  - pip:
+    - pykeen==1.10.2
+    - temp
+

envs/environment_dev_3_13.yml

@@ -0,0 +1,44 @@
+name: mowldev313
+channels:
+  - pytorch
+  - conda-forge
+  - anaconda
+dependencies:
+  - python=3.13
+  - cairo
+  - deprecated
+  - numpy
+  - networkx
+  - click
+  - grpcio
+  - JPype1=1.5.0
+  - pandas
+  - protobuf
+  - pyyaml
+  - requests
+  - scipy<1.13.0
+  - scikit-learn
+  - urllib3
+  - pytorch
+  - gensim>=4.3.0
+  - openjdk
+  - gradle
+  - pip
+  - pip:
+    - build
+    - pykeen==1.10.2
+    - sphinx-rtd-theme
+    - pytest
+    - pytest-faulthandler
+    - coverage
+    - flake8
+    - autopep8
+    - memory-profiler
+  - jupyter
+  - ipykernel
+  - sphinx
+  - sphinx-gallery
+  - nbsphinx
+  - mock
+
+

setup.py

@@ -24,7 +24,7 @@
     package_dir={"": "."},
     packages=setuptools.find_packages(where=".", exclude=("tests",)),
     package_data={"mowl": ["lib/*.jar"]},
-    python_requires=">=3.9"
+    python_requires=">=3.9",
     install_requires=[
         "click",
         "deprecated",