feature update: unit-test & header to scripts

.gitignore

@@ -159,6 +159,9 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+# Pytest cache
+test_output*/
+
 # PyCharm
 #  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore

ontoaligner/__init__.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 __version__ = "1.4.1"
 
 from .pipeline import OntoAlignerPipeline

ontoaligner/aligner/__init__.py

@@ -1,3 +1,16 @@
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from .fewshot.models import * # NOQA
 from .fewshot.dataset import * # NOQA
 from .icv.models import * # NOQA

ontoaligner/aligner/fewshot/__init__.py

@@ -1,2 +1,14 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from .fewshot import * # NOQA

ontoaligner/aligner/fewshot/dataset.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines dataset classes for few-shot learning tasks, particularly for concept comparison tasks.
 These classes inherit from the RAGDataset class and extend its functionality to handle few-shot learning

ontoaligner/aligner/fewshot/fewshot.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines the FewShotRAG class, an extension of the RAG model, designed for few-shot learning tasks.
 The FewShotRAG class uses retrieval-augmented generation techniques, combining information retrieval and

ontoaligner/aligner/fewshot/models.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines a collection of classes that extend the FewShotRAG model, each combining a specific
 retrieval model and language model (LLM) configuration. These specialized configurations are tailored

ontoaligner/aligner/icv/__init__.py

@@ -1,2 +1,14 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from .icv import * # NOQA

ontoaligner/aligner/icv/icv.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 Script for implementing ICV-based ontology matching using RAG and LLM architectures.
 

ontoaligner/aligner/icv/models.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 Script for integrating ICV-based language models with various retrieval mechanisms.
 

ontoaligner/aligner/lightweight/__init__.py

@@ -1,2 +1,14 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from .lightweight import * # NOQA

ontoaligner/aligner/lightweight/lightweight.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines models for ontology matching, specifically a lightweight model
 and an extension that uses fuzzy string matching via the RapidFuzz library.
@@ -108,7 +120,7 @@ def calculate_similarity(self, source: str, candidates: List) -> [int, float]:
         Returns:
             List: A list containing the index of the most similar candidate and the normalized similarity score.
         """
-        selected_candid = rapidfuzz.process_cpp.extractOne(
+        selected_candid = rapidfuzz.process.extractOne(
             source,
             candidates,
             scorer=self.ratio_estimate(),

ontoaligner/aligner/lightweight/models.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines different variants of the `FuzzySMLightweight` class, each implementing
 a different string similarity ratio estimation method using the RapidFuzz library.

ontoaligner/aligner/llm/__init__.py

@@ -1,2 +1,14 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from .llm import * # NOQA

ontoaligner/aligner/llm/dataset.py

@@ -1,5 +1,16 @@
-# -*- coding: utf-8 -*-
-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from typing import Any, Dict
 
 from torch.utils.data import Dataset

ontoaligner/aligner/llm/llm.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines several classes for interacting with large language models (LLMs) through
 various architectures, such as a generic LLM class, OpenAI-based LLMs, and encoder-decoder

ontoaligner/aligner/llm/models.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines various subclasses for different types of language models (LMs), including encoder-decoder
 models, decoder-only models, and models interfacing with OpenAI's GPT. These classes inherit from

ontoaligner/aligner/rag/__init__.py

@@ -1,2 +1,14 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from .rag import * # NOQA

ontoaligner/aligner/rag/dataset.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines a set of custom dataset classes for handling various types of data used in a real-world entity classification task.
 These datasets preprocess and format the input data to create structured prompts for a classification model, with variations

ontoaligner/aligner/rag/models.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines a series of Retrieval-Augmented Generation (RAG) classes that combine different retrieval models
 and language models (LLMs). Each class specializes in pairing a specific retrieval model (e.g., AdaRetrieval, BERTRetrieval)

ontoaligner/aligner/rag/rag.py

@@ -1,4 +1,16 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 """
 This script defines several classes that implement retrieval-augmented generation (RAG) architectures for natural language generation tasks.
 The architecture integrates retrieval models (such as AdaRetrieval and BERTRetrieval) and language models (such as AutoModelForCausalLM and OpenAI)

ontoaligner/aligner/retrieval/__init__.py

@@ -1,2 +1,14 @@
-# -*- coding: utf-8 -*-
+# Copyright 2025 Scientific Knowledge Organization (SciKnowOrg) Research Group. 
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 from .retrieval import * # NOQA