📝 fix library versioning

HamedBabaei · HamedBabaei · commit fcfc02dae524 · 2025-03-17T16:31:01.000+01:00
diff --git a/docs/source/copy.rst b/docs/source/copy.rst
@@ -0,0 +1,124 @@
+OntoLearner Documentation
+==================================
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Introduction
+
+   introduction.rst
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: A. Benchmarking Ontologies
+
+    benchmarking/conference.rst
+    benchmarking/icon_ontology.rst
+    benchmarking/life_ontology.rst
+    benchmarking/dbpedia_ontology.rst
+    benchmarking/emotion_ontology.rst
+    benchmarking/plant_ontology.rst
+    benchmarking/sweet_ontology.rst
+    benchmarking/human_disease_ontology.rst
+    benchmarking/computer_science_ontology.rst
+    benchmarking/food_ontology.rst
+    benchmarking/environment_ontology.rst
+    benchmarking/gene_ontology.rst
+    benchmarking/chebi_ontology.rst
+    benchmarking/relations_ontology.rst
+    benchmarking/basic_formal_ontology.rst
+    benchmarking/gist_ontology.rst
+    benchmarking/eurio.rst
+    benchmarking/metadata4ing.rst
+    benchmarking/materials_mechanics_ontology.rst
+    benchmarking/units_of_measure_ontology.rst
+    benchmarking/saref_ontology.rst
+    benchmarking/heat_pump_ontology.rst
+    benchmarking/material_information.rst
+    benchmarking/materials_ontology.rst
+    benchmarking/emmo_ontology.rst
+    benchmarking/mdo_ontology.rst
+    benchmarking/dolce_ontology.rst
+    benchmarking/digital_buildings_ontology.rst
+    benchmarking/industrial_ontology_foundry.rst
+    benchmarking/nfdi_ontology.rst
+    benchmarking/music_ontology.rst
+    benchmarking/timeline_ontology.rst
+    benchmarking/chord_ontology.rst
+    benchmarking/sioc_ontology.rst
+    benchmarking/foaf_ontology.rst
+    benchmarking/dublin_core_ontology.rst
+    benchmarking/marine_tlo_ontology.rst
+    benchmarking/atol.rst
+    benchmarking/aiiso.rst
+    benchmarking/bio_ontology.rst
+    benchmarking/voaf_ontology.rst
+    benchmarking/cape_ontology.rst
+    benchmarking/tubes_ontology.rst
+    benchmarking/fso_ontology.rst
+    benchmarking/ssn_ontology.rst
+    benchmarking/bibframe_ontology.rst
+    benchmarking/good_relations_ontology.rst
+    benchmarking/dcat_ontology.rst
+    benchmarking/geonames_ontology.rst
+    benchmarking/yago_ontology.rst
+    benchmarking/product_types_ontology.rst
+    benchmarking/schema_org.rst
+    benchmarking/doap_vocabulary.rst
+    benchmarking/copyright_ontology.rst
+    benchmarking/agrovoc.rst
+    benchmarking/geographical_entity_ontology.rst
+    benchmarking/owl_time.rst
+    benchmarking/icalendar.rst
+    benchmarking/citation_typing_ontology.rst
+    benchmarking/fbrroo.rst
+    benchmarking/lex_info.rst
+    benchmarking/as2.rst
+    benchmarking/sio.rst
+    benchmarking/umbel.rst
+    benchmarking/bio_pax.rst
+    benchmarking/nomisma_ontology.rst
+    benchmarking/hydra.rst
+    benchmarking/doco.rst
+    benchmarking/qudt.rst
+    benchmarking/bbc_ontology.rst
+    benchmarking/bbc_politics.rst
+    benchmarking/bbc_programmes.rst
+    benchmarking/bbc_provenance.rst
+    benchmarking/bbc_sport.rst
+    benchmarking/bbc_storyline.rst
+    benchmarking/bbc_wildlife.rst
+    benchmarking/frapo.rst
+    benchmarking/contact.rst
+    benchmarking/chmo.rst
+    benchmarking/geologic_timescale_model.rst
+    benchmarking/premon.rst
+    benchmarking/datacite.rst
+    benchmarking/juso.rst
+    benchmarking/obi_ontology.rst
+    benchmarking/protein_ontology.rst
+    benchmarking/rxno.rst
+    benchmarking/sumo.rst
+    benchmarking/enm_ontology.rst
+    benchmarking/prov_ontology.rst
+    benchmarking/bto_ontology.rst
+    benchmarking/rex.rst
+    benchmarking/duo.rst
+    benchmarking/ncit.rst
+    benchmarking/edam.rst
+    benchmarking/uo.rst
+    benchmarking/cheminf.rst
+    benchmarking/nmrcv.rst
+    benchmarking/oboe.rst
+    benchmarking/pato.rst
+    benchmarking/ontokin.rst
+    benchmarking/swo.rst
+    integration/huggingface_hub.rst
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Learning Models
+
+   models/rag
diff --git a/docs/source/images/logo.ico b/docs/source/images/logo.ico
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -13,108 +13,13 @@ OntoLearner Documentation
    :maxdepth: 1
    :caption: A. Benchmarking Ontologies
 
-    benchmarking/conference.rst
-    benchmarking/icon_ontology.rst
-    benchmarking/life_ontology.rst
-    benchmarking/dbpedia_ontology.rst
-    benchmarking/emotion_ontology.rst
-    benchmarking/plant_ontology.rst
-    benchmarking/sweet_ontology.rst
-    benchmarking/human_disease_ontology.rst
-    benchmarking/computer_science_ontology.rst
-    benchmarking/food_ontology.rst
-    benchmarking/environment_ontology.rst
-    benchmarking/gene_ontology.rst
-    benchmarking/chebi_ontology.rst
-    benchmarking/relations_ontology.rst
-    benchmarking/basic_formal_ontology.rst
-    benchmarking/gist_ontology.rst
-    benchmarking/eurio.rst
-    benchmarking/metadata4ing.rst
-    benchmarking/materials_mechanics_ontology.rst
-    benchmarking/units_of_measure_ontology.rst
-    benchmarking/saref_ontology.rst
-    benchmarking/heat_pump_ontology.rst
-    benchmarking/material_information.rst
-    benchmarking/materials_ontology.rst
-    benchmarking/emmo_ontology.rst
-    benchmarking/mdo_ontology.rst
-    benchmarking/dolce_ontology.rst
-    benchmarking/digital_buildings_ontology.rst
-    benchmarking/industrial_ontology_foundry.rst
-    benchmarking/nfdi_ontology.rst
-    benchmarking/music_ontology.rst
-    benchmarking/timeline_ontology.rst
-    benchmarking/chord_ontology.rst
-    benchmarking/sioc_ontology.rst
-    benchmarking/foaf_ontology.rst
-    benchmarking/dublin_core_ontology.rst
-    benchmarking/marine_tlo_ontology.rst
-    benchmarking/atol.rst
-    benchmarking/aiiso.rst
-    benchmarking/bio_ontology.rst
-    benchmarking/voaf_ontology.rst
-    benchmarking/cape_ontology.rst
-    benchmarking/tubes_ontology.rst
-    benchmarking/fso_ontology.rst
-    benchmarking/ssn_ontology.rst
-    benchmarking/bibframe_ontology.rst
-    benchmarking/good_relations_ontology.rst
-    benchmarking/dcat_ontology.rst
-    benchmarking/geonames_ontology.rst
-    benchmarking/yago_ontology.rst
-    benchmarking/product_types_ontology.rst
-    benchmarking/schema_org.rst
-    benchmarking/doap_vocabulary.rst
-    benchmarking/copyright_ontology.rst
-    benchmarking/agrovoc.rst
-    benchmarking/geographical_entity_ontology.rst
-    benchmarking/owl_time.rst
-    benchmarking/icalendar.rst
-    benchmarking/citation_typing_ontology.rst
-    benchmarking/fbrroo.rst
-    benchmarking/lex_info.rst
-    benchmarking/as2.rst
-    benchmarking/sio.rst
-    benchmarking/umbel.rst
-    benchmarking/bio_pax.rst
-    benchmarking/nomisma_ontology.rst
-    benchmarking/hydra.rst
-    benchmarking/doco.rst
-    benchmarking/qudt.rst
-    benchmarking/bbc_ontology.rst
-    benchmarking/bbc_politics.rst
-    benchmarking/bbc_programmes.rst
-    benchmarking/bbc_provenance.rst
-    benchmarking/bbc_sport.rst
-    benchmarking/bbc_storyline.rst
-    benchmarking/bbc_wildlife.rst
-    benchmarking/frapo.rst
-    benchmarking/contact.rst
-    benchmarking/chmo.rst
-    benchmarking/geologic_timescale_model.rst
-    benchmarking/premon.rst
-    benchmarking/datacite.rst
-    benchmarking/juso.rst
-    benchmarking/obi_ontology.rst
-    benchmarking/protein_ontology.rst
-    benchmarking/rxno.rst
-    benchmarking/sumo.rst
-    benchmarking/enm_ontology.rst
-    benchmarking/prov_ontology.rst
-    benchmarking/bto_ontology.rst
-    benchmarking/rex.rst
-    benchmarking/duo.rst
-    benchmarking/ncit.rst
-    benchmarking/edam.rst
-    benchmarking/uo.rst
-    benchmarking/cheminf.rst
-    benchmarking/nmrcv.rst
-    benchmarking/oboe.rst
-    benchmarking/pato.rst
-    benchmarking/ontokin.rst
-    benchmarking/swo.rst
-    integration/huggingface_hub.rst
+   benchmarking/conference.rst
+   benchmarking/icon_ontology.rst
+   benchmarking/life_ontology.rst
+   benchmarking/dbpedia_ontology.rst
+   benchmarking/emotion_ontology.rst
+
+   integration/huggingface_hub.rst
 
 
 .. toctree::
diff --git a/pyproject.toml b/pyproject.toml
@@ -20,7 +20,7 @@ matplotlib="3.9.4"
 tqdm="4.67.1"
 pydantic="2.10.5"
 pathlib="1.0.1"
-logging="0.4.9.6"
+logging=">=0.4.9.6"
 
 [tool.poetry.dev-dependencies]
 ruff = "*"
diff --git a/requirements.txt b/requirements.txt
@@ -1,19 +1,19 @@
 
-rdflib~=7.1.1
-networkx~=3.2.1
+rdflib==7.1.1
+networkx==3.2.1
 
-seaborn~=0.13.2
-numpy~=1.26.4 # to update
-pandas~=2.0.3 # to update
+seaborn==0.13.2
+numpy==1.26.4 # to update
+pandas==2.0.3 # to update
 
 # Plot and Data Visualization
-matplotlib~=3.9.4
+matplotlib==3.9.4
 
 # Progress Bar
-tqdm~=4.67.1
+tqdm==4.67.1
 
 # Pydantic
-pydantic~=2.10.5
+pydantic==2.10.5
 
 logging
 pathlib
diff --git a/setup.py b/setup.py
@@ -23,7 +23,7 @@
         "tqdm==4.67.1",
         "pydantic==2.10.5",
         "pathlib==1.0.1",
-        "logging==0.4.9.6"
+        "logging>=0.4.9.6"
     ],
     classifiers=[
         "Development Status :: 5 - Production/Stable",
