Merge pull request #333 from dice-group/develop

Develop

.github/workflows/docs.yml

@@ -1,56 +1,56 @@
-name: Build docs
-
-on:
-  push:
-    branches:
-     - master
-     - develop
-  pull_request:
-
-jobs:
-  docs:
-    runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 5
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Install tox
-      id: install-tox
-      run: |
-        pip install tox
-        echo "tox_version=$(pip list | grep tox | tr -d ' ')" >> $GITHUB_OUTPUT
-    - name: prepare required software
-      run: |
-        # epstopdf & dot & noto-fonts
-        sudo apt update && sudo apt install texlive-font-utils graphviz fonts-noto
-    - uses: actions/cache@v3
-      with:
-        key: ${{ runner.os }}-${{ steps.install-tox.outputs.tox_version }}-docs-${{ hashFiles('environment.yml', 'tox.ini') }}
-        path: .tox
-    - name: Build docs with tox
-      run: |
-        tox -o -e docs
-    - name: Build latex docs with tox
-      run: |
-        tox -o -e docs -- latex
-    - name: Compile LaTeX document
-      uses: docker://texlive/texlive:latest
-      with:
-        args: make -C docs/_build/latex
-    - run: |
-        cp docs/_build/latex/ontolearn.pdf docs/_build/html/
-    - name: Deploy to netlify
-      uses: nwtgck/[email protected]
-      with:
-        publish-dir: 'docs/_build/html'
-        production-branch: develop
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        deploy-message: "Deploy from GitHub Actions ${{ github.sha }}"
-        alias: ${{ github.head_ref }}
-        enable-pull-request-comment: false
-        enable-commit-comment: false
-      env:
-        NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
-        NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
-      timeout-minutes: 5
+#name: Build docs
+#
+#on:
+#  push:
+#    branches:
+#     - master
+#     - develop
+#  pull_request:
+#
+#jobs:
+#  docs:
+#    runs-on: ubuntu-latest
+#    strategy:
+#      max-parallel: 5
+#
+#    steps:
+#    - uses: actions/checkout@v3
+#    - name: Install tox
+#      id: install-tox
+#      run: |
+#        pip install tox
+#        echo "tox_version=$(pip list | grep tox | tr -d ' ')" >> $GITHUB_OUTPUT
+#    - name: prepare required software
+#      run: |
+#        # epstopdf & dot & noto-fonts
+#        sudo apt update && sudo apt install texlive-font-utils graphviz fonts-noto
+#    - uses: actions/cache@v3
+#      with:
+#        key: ${{ runner.os }}-${{ steps.install-tox.outputs.tox_version }}-docs-${{ hashFiles('environment.yml', 'tox.ini') }}
+#        path: .tox
+#    - name: Build docs with tox
+#      run: |
+#        tox -o -e docs
+#    - name: Build latex docs with tox
+#      run: |
+#        tox -o -e docs -- latex
+#    - name: Compile LaTeX document
+#      uses: docker://texlive/texlive:latest
+#      with:
+#        args: make -C docs/_build/latex
+#    - run: |
+#        cp docs/_build/latex/ontolearn.pdf docs/_build/html/
+#    - name: Deploy to netlify
+#      uses: nwtgck/[email protected]
+#      with:
+#        publish-dir: 'docs/_build/html'
+#        production-branch: develop
+#        github-token: ${{ secrets.GITHUB_TOKEN }}
+#        deploy-message: "Deploy from GitHub Actions ${{ github.sha }}"
+#        alias: ${{ github.head_ref }}
+#        enable-pull-request-comment: false
+#        enable-commit-comment: false
+#      env:
+#        NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+#        NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+#      timeout-minutes: 5

.github/workflows/test.yml

@@ -7,22 +7,26 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9.18"]
       max-parallel: 5
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          environment-file: environment.yml
+      # - name: Set up Conda
+      #   uses: conda-incubator/setup-miniconda@v2
+      #   with:
+      #    environment-file: environment.yml
+        # conda run -n test pytest -p no:warnings -x
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
 
       - name: Test with pytest
         run: |
           wget https://files.dice-research.org/projects/Ontolearn/KGs.zip
           unzip KGs.zip
-          conda run -n test pytest -p no:warnings -x
+          pytest -p no:warnings -x

.gitignore

@@ -157,3 +157,4 @@ embeddings.zip
 KGs.zip
 /Fuseki/
 /KGs/
+/NCESData/

README.md

@@ -20,8 +20,8 @@ pip install ontolearn
 ```
 or
 ```shell
-git clone https://github.com/dice-group/Ontolearn.git && conda create --name onto python=3.8.18 && conda activate onto 
-pip3 install -e . && python -c "import ontolearn"
+git clone https://github.com/dice-group/Ontolearn.git 
+conda create --name onto python=3.9.18 && conda activate onto && pip3 install -e . && python -c "import ontolearn"
 wget https://files.dice-research.org/projects/Ontolearn/KGs.zip -O ./KGs.zip && unzip KGs.zip
 ```
 ```shell

deploy_cl.py

@@ -3,7 +3,7 @@
 from argparse import ArgumentParser
 import random
 import os
-
+from ontolearn.model_adapter import compute_quality
 from ontolearn.ea_algorithms import EASimple
 from ontolearn.ea_initialization import EARandomWalkInitialization, RandomInitMethod, EARandomInitialization
 from ontolearn.fitness_functions import LinearPressureFitness
@@ -32,18 +32,6 @@
 renderer = DLSyntaxObjectRenderer()
 
 
-def compute_quality(KB, solution, pos, neg, qulaity_func="F1"):
-    func = metrics[qulaity_func]().score2
-    instances = set(KB.individuals(solution))
-    if isinstance(list(pos)[0], str):
-        instances = {ind.get_iri().as_str().split("/")[-1] for ind in instances}
-    tp = len(pos.intersection(instances))
-    fn = len(pos.difference(instances))
-    fp = len(neg.intersection(instances))
-    tn = len(neg.difference(instances))
-    return func(tp=tp, fn=fn, fp=fp, tn=tn)[-1]
-
-
 def setup_prerequisites(individuals, pos_ex, neg_ex, random_ex: bool, size_of_ex):
 
     # start_time = time.time()
@@ -661,9 +649,11 @@ def run(args):
 
     if not os.path.exists("NCESData/") and args.model == "nces":
         print("\nWarning! You are trying to deploy NCES without the NCES data!")
-        print(f"Please download the necessary files first: see ./download_external_resources.sh\n")
+        print(f"Please download the necessary files first: see "
+              f"https://ontolearn-docs-dice-group.netlify.app/usage/02_installation#download-external-files\n")
     elif not os.path.exists("KGs") and "KGs/" in args.path_knowledge_base:
         print("\nWarning! There is no 'KGs' folder!")
-        print(f"Please download the datasets first: see ./download_external_resources.sh\n")
+        print(f"Please download the datasets first: "
+              f"see https://ontolearn-docs-dice-group.netlify.app/usage/02_installation#download-external-files\n")
     else:
         run(args)

environment.yml

@@ -4,14 +4,13 @@ channels:
   - conda-forge
   - pytorch
 dependencies:
-  - python=3.8
+  - python=3.9.18
   - matplotlib=3.3.4
   - pandas=1.2.3
   - pytorch=1.8.0
   - rdflib=6.0.2
   - scikit-learn=1.0.2
   - sortedcontainers=2.4.0
-  - owlready2=0.40
   - flask=1.1.2
   - deap=1.3.1
   - httpx=0.21.1
@@ -27,13 +26,15 @@ dependencies:
   # docs
   - sphinx=4.0.2
   - sphinx_rtd_theme=0.5.1
-  - myst-parser=0.15.2
+  - myst-parser==0.15.2
   # # building
   - build=0.6.0
   # PIP
   - pip=21.0.1
   - pip:
-    - owlapy == 0.1.0
+    - dicee==0.1.2
+    - owlready2==0.40
+    - owlapy==0.1.0
     - tokenizers==0.12.1
     - transformers==4.19.2
     # testing
@@ -43,3 +44,4 @@ dependencies:
     - sphinx-theme==1.0
     - sphinxcontrib-plantuml==0.21
     - plantuml-local-client==1.2021.10
+    - jinja2==3.1.2

examples/advanced-usage-NCES.ipynb

@@ -6,7 +6,7 @@
    "id": "immune-fluid",
    "metadata": {},
    "source": [
-    "From the main directory \"Ontolearn\", run the commands for NCES data in [`./download_external_resources.sh`](../download_external_resources.sh) to download pretrained models and datasets."
+    "From the main directory \"Ontolearn\", run the commands for NCES data mentioned [here](https://ontolearn-docs-dice-group.netlify.app/usage/02_installation#download-external-files) to download pretrained models and datasets."
    ]
   },
   {

examples/celoe_notebook.ipynb

@@ -8,7 +8,7 @@
    "source": [
     "# CELOE Notebook\n",
     "This is a jupyter notebook file to execute [CELOE](ontolearn.concept_learner.CELOE) and generate predictive results. We recommend you to see the [concept learners](../docs/usage/06_concept_learners.md) guide before continuing with the execution.\n",
-    "Also if you have not done it already, from the main directory \"Ontolearn\", run the commands for Datasets in [`./download_external_resources.sh`](../download_external_resources.sh) to download the datasets."
+    "Also if you have not done it already, from the main directory \"Ontolearn\", run the commands for Datasets mentioned [here](https://ontolearn-docs-dice-group.netlify.app/usage/02_installation#download-external-files) to download the datasets."
    ]
   },
   {