Merge pull request #528 from dice-group/develop

New release: 0.9.2

Author: Demirrr

.coveragerc

@@ -1,7 +1,6 @@
 [run]
 omit =
     tests/*
-    ontolearn/triple_store.py
 
 [report]
 exclude_lines =

.github/workflows/test.yml

@@ -1,20 +1,36 @@
 name: Python package
 
-on: [push,pull_request]
+on: [push, pull_request]
 
 jobs:
   build:
     runs-on: ubuntu-latest
+    services:
+      fuseki:
+        image: stain/jena-fuseki
+        ports:
+          - 3030:3030
+        options: >-
+          --health-cmd "curl --silent --fail http://localhost:3030 || exit 1"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        env:
+          ADMIN_PASSWORD: admin
+
     strategy:
       matrix:
         python-version: ["3.10.14"]
       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: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -32,8 +48,30 @@ jobs:
           wget https://files.dice-research.org/projects/NCES/NCES_Ontolearn_Data/NCESData.zip
           unzip KGs.zip && unzip LPs.zip && unzip NCESData.zip && unzip CLIPData.zip
 
+      - name: Wait for Fuseki to start
+        run: |
+          echo "Waiting for Fuseki to be ready..."
+          until curl -s http://localhost:3030; do
+            sleep 2
+          done
+          echo "Fuseki is up!"
+
+      - name: Create dataset (mutagenesis)
+        run: |
+          curl -X POST http://localhost:3030/$/datasets \
+            --user admin:admin \
+            --header "Content-Type: application/x-www-form-urlencoded" \
+            --data "dbName=mutagenesis&dbType=tdb"
+
+      - name: Load OWL data into Fuseki
+        run: |
+          curl -X PUT -H "Content-Type: application/rdf+xml" \
+            --data-binary @KGs/Mutagenesis/mutagenesis.owl \
+            http://localhost:3030/mutagenesis/data \
+            --user admin:admin
+
       - name: Testing and coverage report
         run: | 
           pip install coverage
           coverage run -m pytest -p no:warnings -x
-          coverage report -m
+          coverage report -m

.gitignore

@@ -163,3 +163,5 @@ KGs.zip
 **/CLIPData*
 **/LPs*
 LPs.zip
+/results/
+reports.csv

README.md

@@ -1,9 +1,10 @@
 [![Downloads](https://static.pepy.tech/badge/ontolearn)](https://pepy.tech/project/ontolearn)
 [![Downloads](https://img.shields.io/pypi/dm/ontolearn)](https://pypi.org/project/ontolearn/)
 [![Coverage](https://img.shields.io/badge/coverage-86%25-green)](https://ontolearn-docs-dice-group.netlify.app/usage/09_further_resources#code-coverage)
-[![Pypi](https://img.shields.io/badge/pypi-0.9.1-blue)](https://pypi.org/project/ontolearn/0.9.1/)
-[![Docs](https://img.shields.io/badge/documentation-0.9.1-yellow)](https://ontolearn-docs-dice-group.netlify.app/usage/01_introduction)
+[![Pypi](https://img.shields.io/badge/pypi-0.9.2-blue)](https://pypi.org/project/ontolearn/0.9.2/)
+[![Docs](https://img.shields.io/badge/documentation-0.9.2-yellow)](https://ontolearn-docs-dice-group.netlify.app/usage/01_introduction)
 [![Python](https://img.shields.io/badge/python-3.10.13+-4584b6)](https://www.python.org/downloads/release/python-31013/)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/dice-group/Ontolearn)
  
 
 ![Ontolearn](docs/_static/images/Ontolearn_logo.png)
@@ -244,6 +245,16 @@ To compute the test performance, we compute F1-score of H w.r.t. test positive a
 # To download learning problems and benchmark learners on the Family benchmark dataset with benchmark learning problems.
 python examples/concept_learning_cv_evaluation.py --kb ./KGs/Family/family-benchmark_rich_background.owl --lps ./LPs/Family/lps_difficult.json --path_of_nces_embeddings ./NCESData/family/embeddings/ConEx_entity_embeddings.csv --path_of_clip_embeddings ./CLIPData/family/embeddings/ConEx_entity_embeddings.csv --max_runtime 60 --report family_results.csv 
 ```
+
+```shell
+# To download learning problems and benchmark with selected learners on the Family benchmark dataset with benchmark learning problems.
+python examples/concept_learning_cv_evaluation.py --kb ./KGs/Family/family-benchmark_rich_background.owl --lps ./LPs/Family/lps_difficult.json --learner_types ocel drill tdl nces --path_of_nces_embeddings ./NCESData/family/embeddings/ConEx_entity_embeddings.csv --path_of_clip_embeddings ./CLIPData/family/embeddings/ConEx_entity_embeddings.csv --max_runtime 60 --report family_results.csv 
+```
+
+```shell
+# To download learning problems and benchmark with a single learner on the Family benchmark dataset with benchmark learning problems.
+python examples/concept_learning_cv_evaluation.py --kb ./KGs/Family/family-benchmark_rich_background.owl --lps ./LPs/Family/lps_difficult.json --learner_types nces --path_of_nces_embeddings ./NCESData/family/embeddings/ConEx_entity_embeddings.csv --path_of_clip_embeddings ./CLIPData/family/embeddings/ConEx_entity_embeddings.csv --max_runtime 60 --report family_results.csv 
+```
 In the following python script, the results are summarized and the markdown displayed below generated.
 ```python
 import pandas as pd

docs/usage/01_introduction.md

@@ -1,6 +1,6 @@
 # About Ontolearn
 
-**Version:** ontolearn 0.9.1
+**Version:** ontolearn 0.9.2
 
 **GitHub repository:** [https://github.com/dice-group/Ontolearn](https://github.com/dice-group/Ontolearn)
 

docs/usage/09_further_resources.md

@@ -139,7 +139,7 @@ You can also reach us privately in any of the emails below:
 
 ## Code Coverage
 
-The coverage report is generated using [coverage.py](https://coverage.readthedocs.io/en) for Ontolearn v0.9.1.
+The coverage report is generated using [coverage.py](https://coverage.readthedocs.io/en) for Ontolearn v0.9.2.
 
 
 ```
@@ -167,7 +167,7 @@ ontolearn/learners/__init__.py                    5      0   100%
 ontolearn/learners/celoe.py                     167     25    85%   158, 183, 237, 241, 314-318, 332, 335-360
 ontolearn/learners/drill.py                      31      0   100%
 ontolearn/learners/ocel.py                       21      0   100%
-ontolearn/learners/tree_learner.py              193     28    85%   160, 243-273, 361, 368, 370-374, 390, 393, 414, 423
+ontolearn/learners/tree_learner.py              193     27    86%   160, 243-273, 361, 368, 370-374, 390, 393, 414
 ontolearn/learning_problem.py                    55      9    84%   98, 119, 129, 135-140
 ontolearn/learning_problem_generator.py          16      0   100%
 ontolearn/lp_generator/__init__.py                2      0   100%
@@ -177,16 +177,17 @@ ontolearn/metrics.py                             50      0   100%
 ontolearn/nces_architectures.py                  73      0   100%
 ontolearn/nces_modules.py                       143     29    80%   44-45, 68-69, 72, 200-203, 213-242, 245-246
 ontolearn/nces_trainer.py                       196     12    94%   72, 76, 85, 89, 174, 181-183, 204, 219-221
-ontolearn/nces_utils.py                          99     62    37%   58-59, 64-82, 89-141, 147, 156
+ontolearn/nces_utils.py                          99     60    39%   64-82, 89-141, 147, 156
 ontolearn/owl_neural_reasoner.py                178     22    88%   72-94, 101, 121, 127, 133, 137, 165-173, 196, 240, 251, 256, 271, 399-402
 ontolearn/quality_funcs.py                       39     27    31%   32-56, 60-69
-ontolearn/refinement_operators.py               519     26    95%   165-166, 296, 397-398, 444, 538, 562, 596-598, 743, 779, 885, 913, 932, 958-960, 967, 988-990, 992, 994, 1062, 1084
+ontolearn/refinement_operators.py               519     25    95%   165-166, 296, 397-398, 444, 538, 562, 596-598, 743, 779, 885, 913, 958-960, 967, 988-990, 992, 994, 1062, 1084
 ontolearn/search.py                             293     43    85%   69, 132, 163-170, 195, 215, 264, 302, 306, 309, 338, 391, 411, 428, 432, 440, 451-452, 455-463, 466, 481, 483, 508, 510, 575-576, 665-666, 761, 765, 769
+ontolearn/triple_store.py                       501    237    53%   102-103, 121-122, 134-135, 151, 154-160, 167, 215-218, 225-230, 233-235, 242, 248-254, 284-286, 289, 304, 307-311, 323-327, 330-334, 339-341, 350-353, 364-368, 371-373, 376-385, 388-390, 397-398, 402-411, 454-456, 484-495, 503-515, 518-522, 525-529, 532-533, 536-537, 541-549, 553-561, 567, 571, 586-590, 594, 642, 646, 652, 663-667, 712, 738, 751, 795, 798, 809-811, 814, 818-830, 833, 836, 839, 842-844, 856-860, 889-890, 893, 896-897, 900-901, 904-905, 909, 912-913, 917, 921, 924, 928-933, 937-951, 959-965, 974-981, 985-991, 994, 997, 1000, 1003, 1006, 1009, 1012, 1015, 1020-1025, 1030-1035, 1041-1046, 1052-1057, 1060, 1068, 1072-1073, 1076-1077, 1082, 1087
 ontolearn/utils/__init__.py                      33      2    94%   58, 98
 ontolearn/utils/log_config.py                    19      0   100%
 ontolearn/utils/oplogging.py                      8      0   100%
 ontolearn/utils/static_funcs.py                 111     26    77%   53, 64, 138, 170-175, 216-217, 232-249
 ontolearn/value_splitter.py                     159      6    96%   111-113, 118, 127, 130
 ---------------------------------------------------------------------------
-TOTAL                                          5005    775    85%
+TOTAL                                          5506   1008    82%
 ```