diff --git a/README.md b/README.md
index 86259a6..99d1414 100644
--- a/README.md
+++ b/README.md
@@ -1,30 +1,31 @@
+
 # AutoFL
 
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![DOI](https://zenodo.org/badge/644095707.svg)](https://zenodo.org/doi/10.5281/zenodo.10255367)
-[![Docker](https://img.shields.io/badge/Docker-blue.svg)](https://img.shields.io/badge/Docker-blue)
+[![Docker](https://img.shields.io/badge/Docker-blue.svg)](https://hub.docker.com/r/cezarsas/autofl/)
+
+Automatic source code file annotation using weak labeling.
 
-Automatic source code file annotation using weak labelling.
+## Overview
+
+AutoFL is a tool designed for automatic annotation of source code files through weak labeling techniques. It provides both an API and a web-based UI for easy analysis of projects across different languages.
 
 ## Setup
 
-Clone the repository and the UI submodule [autofl-ui](https://github.com/SasCezar/autofl-ui) by running the following
-command:
+To set up the repository along with its UI submodule, clone it using:
 
 ```bash
 git clone --recursive git@github.com:SasCezar/AutoFL.git AutoFL
 ```
 
-### Optional Setup
+### Optional Model Setup
 
-To make use of certain feature like semantic based labelling functions, you need to download the model.
-For example, for **w2v-so**, you can download the model from [here](https://github.com/vefstathiou/SO_word2vec), and
-place it in the [data/models/w2v-so](data/models/w2v-so) folder, or a custom
-path that you can use in the configs.
+For advanced features like semantic-based labeling, download models as required. For example, to use **w2v-so**, download the model from [here](https://github.com/vefstathiou/SO_word2vec) and place it in the `data/models/w2v-so` folder. Alternatively, you can provide a custom path in the configuration files.
 
 ## Usage
 
-Run docker compose in the project folder (where the [docker-compose.yaml](docker-compose.yaml) is located) by executing:
+To run the tool using Docker, navigate to the project directory (where the `docker-compose.yaml` file is located) and execute:
 
 ```shell
 docker compose up
@@ -32,57 +33,45 @@ docker compose up
 
 ### API Endpoint
 
-You can analyze the files of project by making a request to the endpoint:
+To analyze the files of a project, make a POST request to the following endpoint:
 
 ```shell
-curl -X POST -d '{"name": "<PROJECT_NAME>", "remote": "<PROJECT_REMOTE>", "languages": ["<PROGRAMMING_LANGUAGE>"]}' localhost:8000/label/files  -H "content-type: application/json"
+curl -X POST -d '{"name": "<PROJECT_NAME>", "remote": "<PROJECT_REMOTE>", "languages": ["<PROGRAMMING_LANGUAGE>"]}' localhost:8000/label/files -H "content-type: application/json"
 ```
 
-For example, to analyze the files
-of [https://github.com/mickleness/pumpernickel](https://github.com/mickleness/pumpernickel), you can make the following
-request:
+For instance, to analyze the project at [https://github.com/mickleness/pumpernickel](https://github.com/mickleness/pumpernickel), use:
 
 ```shell
-curl -X POST -d '{"name": "pumpernickel", "remote": "https://github.com/mickleness/pumpernickel", "languages": ["java"]}' localhost:8000/label/files  -H "content-type: application/json"
+curl -X POST -d '{"name": "pumpernickel", "remote": "https://github.com/mickleness/pumpernickel", "languages": ["java"]}' localhost:8000/label/files -H "content-type: application/json"
 ```
 
-### UI
+### Web UI
 
-The tool also offers a web UI that is available at the following page (when running locally):
-[http://localhost:8501](http://localhost:8501)
+AutoFL provides a web-based UI accessible locally at [http://localhost:8501](http://localhost:8501):
 
 ![UI](resources/ui-screenshots/landing-page.png)
 
-For more details, check the [UI repo](https://github.com/SasCezar/autofl-ui).
-
-[//]: # (For more details, check the [UI repo]&#40;https://github.com/SasCezar/autofl-ui&#41;)
+For more details, check the [UI repository](https://github.com/SasCezar/autofl-ui).
 
 ## Configuration
 
-AutoFL uses [Hydra](https://hydra.cc/) to manage the configuration. The configuration files are located in
-the [config](config) folder.
-The main configuration file is [main.yaml](./config/main.yaml), which contains the following options:
+AutoFL uses [Hydra](https://hydra.cc/) to manage configurations. The configuration files can be found in the `config` folder. The main configuration file, `main.yaml`, allows you to customize various options:
 
-- **local**: which environment to use, either local or docker. [Docker](./config/local/docker.yaml) is default.
-- **taxonomy**: which taxonomy to use. Currently only [gitranking](./config/taxonomy/gitranking.yaml) is supported, but
-  custom taxonomies can be added.
-- **annotator**: which annotators to use. Default is [simple](./config/annotator/simple.yaml), which allows good results
-  without extra dependencies on language models.
-- **version_strategy**: which version strategy to use. Default is [latest](./config/version_strategy/latest.yaml), which
-  will only analyze the latest version of the project.
-- **dataloader**: which dataloader to use. Default is [postgres](./config/dataloader/postgres.yaml) which allows the API
-  to fetch already analysed projects.
-- **writer**: which writer to use. Default is [postgres](./config/writer/postgres.yaml) which allows the API to store
-  the results in a database.
+- **local**: Choose between local or Docker environments. [Docker](config/environment/docker.yaml) is the default.
+- **taxonomy**: Set the taxonomy for labeling. Currently supports [gitranking](./config/taxonomy/gitranking.yaml). You can add custom taxonomies.
+- **annotator**: Specify the annotators to use. The default is [simple](./config/annotator/simple.yaml), offering good results without dependencies on language models.
+- **version_strategy**: Select the versioning strategy. The default is [latest](./config/version_strategy/latest.yaml).
+- **dataloader**: Choose the dataloader. The default is [postgres](./config/dataloader/postgres.yaml).
+- **writer**: Set the writer for storing results. The default is [postgres](./config/writer/postgres.yaml).
 
-Other configuration can be defined by creating a new file in the folder of the specific component.
+Additional configurations can be added by creating new files in the corresponding component folders.
 
 ## Functionalities
 
 - Annotation (UI/API/Script)
-    - File
-    - Package
-    - Project
+  - File-Level
+  - Package-Level
+  - Project-Level
 - Batch Analysis (Script Only)
 - Temporal Analysis (**TODO**)
 - Classification (**TODO**)
@@ -97,26 +86,23 @@ Other configuration can be defined by creating a new file in the folder of the s
 
 ## Development
 
-The tool is composed of multiple components, their interaction is shown in the following diagram:
+AutoFL is composed of multiple components, as shown in the architecture diagram below:
 
 ![Architecture](resources/architecture/architecture.png)
 
-### Add New Languages
+### Adding Support for New Languages
 
-In order to support more languages, a new language specific parser is needed.
-We can create one quickly by using [tree-sitter](https://tree-sitter.github.io/tree-sitter/),
-and a custom parser.
+To add support for additional languages, a language-specific parser is required. You can use [tree-sitter](https://tree-sitter.github.io/tree-sitter/) to develop a parser quickly.
 
-#### Parser
+#### Parser Details
 
-The parser needs to be in the [parser/languages](./src/parser/languages) folder.
-It has to extend the ```BaseParser``` class, which has the following interface.
+The parser needs to be located in the `parser/languages` folder. It should extend the `BaseParser` class, which follows this structure:
 
 ```python
 class ParserBase(ABC):
-    """
-    Abstract class for a programming language parser.
-    """
+"""
+Abstract class for a programming language parser.
+"""
 
     def __init__(self, library_path: Path | str):
         """
@@ -126,92 +112,73 @@ class ParserBase(ABC):
         ...
 ```
 
-And the language specific class has to contain the logic to parse the language to get the identifiers.
-For example for Python, the class will look like this:
+To implement the parsing logic, create a class that handles extracting identifiers. For Python, the parser might look like:
 
 ```python
-class PythonParser(ParserBase,
-                   lang=Extension.python.name):  # The lang argument is used to register the parser in the ParserFactory class.
+class PythonParser(ParserBase, lang=Extension.python.name):
     """
-    Python specific parser. Uses a generic grammar for multiple versions of python. Uses tree_sitter to get the AST
+    Python-specific parser using a generic grammar for multiple versions. Utilizes tree-sitter for AST extraction.
     """
 
     def __init__(self, library_path: Path | str):
-        super().__init__(library_path)
-        self.language: Language = Language(library_path,
-                                           Extension.python.name)  # Creates the tree-sitter language for python
-        self.parser.set_language(self.language)  # Sets tree-sitter parser to parse the language
-
-        # Pattern used to match the identifiers, it depends on the Lanugage. Check tree-sitter
-        self.identifiers_pattern: str = """
-                                        ((identifier) @identifier)
-                                        """
-
-        # Creates the query used to find the identifiers in the AST produced by tree-sitter
-        self.identifiers_query = self.language.query(self.identifiers_pattern)
-
-        # Keyword that will be ignored, in this case, the language specific keywords as the query extracts them as well. 
-        self.keywords = set(keyword.kwlist)  # Use python's built in keyword list
-        self.keywords.update(['self', 'cls'])
+        ...
 ```
 
-A custom class that does not rely on [tree-sitter](https://github.com/tree-sitter/tree-sitter) can be also used,
-however, there are more methods from ParserBase that need to be
-changed. Check the implementation of [ParserBase](src/parser/parser.py).
+A custom parser independent of tree-sitter can also be developed. For more details, refer to the implementation of [ParserBase](src/parser/parser.py).
 
-## Know Issues
+## Known Issues
+
+- **Dependency Installation**: The setup process may take significant time (~10 minutes), and dependency installations might fail due to timeouts. This appears to be a network-related issue, and retrying often resolves it. Future updates will aim to simplify dependencies.
+- **~~Indefinite Analysis Loops~~**: ~~In some projects, the analysis may loop indefinitely. This issue is currently under investigation.~~ Seems solved in the latest version. Will monitor for further occurrences.
+
+## Docker Image Availability
+
+AutoFL is also available as a Docker image. You can pull the image from Docker Hub using:
+
+```shell
+docker pull cezarsas/autofl
+```
 
-- The installation of the dependencies requires quite some time (~10 minutes), and might fail due to timout.
-  Unfortunately, this issue is hard to reproduce, as it
-  seems to be related to the network connection. If you encounter this issue, please try again. Future versions will try
-  to fix this issue by
-  cleaning up the dependencies and reducing the number of dependencies.
-- For some projects, the analysis might loop indefinitely. We are still investigating the cause of this issue.
+Find more details and updates at the [Docker Hub page](https://hub.docker.com/r/cezarsas/autofl/).
 
 ## Disclaimer
 
-The project is offered as is, it still in development, and it might not work as expected in some cases.
-It has been developed and tested on Docker 24.0.7 and 25.0.0 for  ```Ubuntu 22.04```. While minor testing has been done
-on ```Windows``` and ```MacOS```, not all functionalities might work due to differences in Docker for these OSs (e.g.
-Windows uses WSL 2).
+This tool is in active development and may not function as expected in some cases. It has been tested primarily on Docker versions `24.0.7` and `25.0.0` for `Ubuntu 22.04`. Limited testing has been performed on `Windows` and `MacOS`, where functionality may vary.
 
-In case of any problems, please open an issue, make a pull request, or contact me at ```c.a.sas@rug.nl```.
+If you encounter any issues, please open an issue on GitHub, make a pull request, or contact me at `c.a.sas@rug.nl`.
 
-## Cite
+## Citation
 
-If you use this work please cite us:
+If you find this tool useful, please cite our work:
 
 ### Paper
 
-```text
+```bibtex
 @article{sas2024multigranular,
-         title     = {Multi-granular Software Annotation using File-level Weak Labelling}, 
-         author    = {Cezar Sas and Andrea Capiluppi},
-         journal   = {Empirical Software Engineering},
-         volume    = {29},
-         number    = {1},
-         pages     = {12},
-         year      = {2024},
-         url       = {https://doi.org/10.1007/s10664-023-10423-7},
-         doi       = {10.1007/s10664-023-10423-7}
+title     = {Multi-granular Software Annotation using File-level Weak Labelling},
+author    = {Cezar Sas and Andrea Capiluppi},
+journal   = {Empirical Software Engineering},
+volume    = {29},
+number    = {1},
+pages     = {12},
+year      = {2024},
+url       = {https://doi.org/10.1007/s10664-023-10423-7},
+doi       = {10.1007/s10664-023-10423-7}
 }
 ```
 
-**Note**: The code used in the paper is available in
-the [https://github.com/SasCezar/CodeGraphClassification](https://github.com/SasCezar/CodeGraphClassification)
-repository.
-However, this tool is more up to date, easier to use, more configurable, and also offers a UI.
+**Note**: The code used in this paper is available at [CodeGraphClassification](https://github.com/SasCezar/CodeGraphClassification). However, AutoFL provides enhanced features, is more user-friendly, and includes a UI.
 
 ### Tool
 
-```text
+```bibtex
 @software{sas2023autofl,
           author    = {Sas, Cezar and Capiluppi, Andrea},
-          month     = dec,
+          month     = oct,
           title     = {{AutoFL}},
           url       = {https://github.com/SasCezar/AutoFL},
-          version   = {0.4.1},
-          year      = {2023},
+          version   = {0.5.0},
+          year      = {2024},
           url       = {https://doi.org/10.5281/zenodo.10255368},
           doi       = {10.5281/zenodo.10255368}
 }
diff --git a/config/local/docker.yaml b/config/environment/docker.yaml
similarity index 100%
rename from config/local/docker.yaml
rename to config/environment/docker.yaml
diff --git a/config/local/local.yaml b/config/environment/local.yaml
similarity index 100%
rename from config/local/local.yaml
rename to config/environment/local.yaml
diff --git a/config/main.yaml b/config/main.yaml
index 9103a43..6222e42 100644
--- a/config/main.yaml
+++ b/config/main.yaml
@@ -1,7 +1,7 @@
 # @package _global_
 defaults:
   - _self_
-  - local: docker
+  - environment: docker
   - taxonomy: gitranking
   - annotator: default
   - version_strategy: latest
diff --git a/config/runs.yaml b/config/runs.yaml
index cd518e2..92e3bb2 100644
--- a/config/runs.yaml
+++ b/config/runs.yaml
@@ -1,7 +1,7 @@
 # @package _global_
 defaults:
   - _self_
-  - local: local
+  - environment: docker
   - run: batch_annotation
 
 package_annotation: True
diff --git a/config/test.yaml b/config/test.yaml
index af6aae8..9ad573a 100644
--- a/config/test.yaml
+++ b/config/test.yaml
@@ -1,7 +1,7 @@
 # @package _global_
 defaults:
   - _self_
-  - local: local
+  - environment: docker
   - taxonomy: small
   - annotator: default
   - version_strategy: latest
diff --git a/data/grammars/languages.so b/data/grammars/languages.so
deleted file mode 100755
index 50ff2de..0000000
Binary files a/data/grammars/languages.so and /dev/null differ
diff --git a/docs/index.md b/docs/index.md
index 442ccb8..16ac2c8 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,69 +1,77 @@
+
 # AutoFL
+
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![DOI](https://zenodo.org/badge/644095707.svg)](https://zenodo.org/doi/10.5281/zenodo.10255367)
-[![Docker](https://img.shields.io/badge/Docker-blue.svg)](https://img.shields.io/badge/Docker-blue)
+[![Docker](https://img.shields.io/badge/Docker-blue.svg)](https://hub.docker.com/r/cezarsas/autofl/)
+
+Automatic source code file annotation using weak labeling.
+
+## Overview
 
-Automatic source code file annotation using weak labelling.
+AutoFL is a tool designed for automatic annotation of source code files through weak labeling techniques. It provides both an API and a web-based UI for easy analysis of projects across different languages.
 
 ## Setup
-Clone the repository and the UI submodule [autofl-ui](https://github.com/SasCezar/autofl-ui) by running the following command:
+
+To set up the repository along with its UI submodule, clone it using:
+
 ```bash
 git clone --recursive git@github.com:SasCezar/AutoFL.git AutoFL
 ```
 
-### Optional Setup
-To make use of certain feature like semantic based labelling functions, you need to download the model.
-For example, for **w2v-so**, you can download the model from [here](https://github.com/vefstathiou/SO_word2vec), and place it in the [data/models/w2v-so](data/models/w2v-so) folder, or a custom
-path that you can use in the configs.
+### Optional Model Setup
+
+For advanced features like semantic-based labeling, download models as required. For example, to use **w2v-so**, download the model from [here](https://github.com/vefstathiou/SO_word2vec) and place it in the `data/models/w2v-so` folder. Alternatively, you can provide a custom path in the configuration files.
 
 ## Usage
 
-Run docker the docker compose file [docker-compose.yaml](docker-compose.yaml) by executing:
+To run the tool using Docker, navigate to the project directory (where the `docker-compose.yaml` file is located) and execute:
+
 ```shell
 docker compose up
 ```
-in the project folder.
 
 ### API Endpoint
-You can analyze the files of project by making a request to the endpoint:
+
+To analyze the files of a project, make a POST request to the following endpoint:
+
 ```shell
-curl -X POST -d '{"name": "<PROJECT_NAME>", "remote": "<PROJECT_REMOTE>", "languages": ["<PROGRAMMING_LANGUAGE>"]}' localhost:8000/label/files  -H "content-type: application/json"
+curl -X POST -d '{"name": "<PROJECT_NAME>", "remote": "<PROJECT_REMOTE>", "languages": ["<PROGRAMMING_LANGUAGE>"]}' localhost:8000/label/files -H "content-type: application/json"
 ```
-For example, to analyze the files of [https://github.com/mickleness/pumpernickel](https://github.com/mickleness/pumpernickel), you can make the following request:
+
+For instance, to analyze the project at [https://github.com/mickleness/pumpernickel](https://github.com/mickleness/pumpernickel), use:
+
 ```shell
-curl -X POST -d '{"name": "pumpernickel", "remote": "https://github.com/mickleness/pumpernickel", "languages": ["java"]}' localhost:8000/label/files  -H "content-type: application/json"
+curl -X POST -d '{"name": "pumpernickel", "remote": "https://github.com/mickleness/pumpernickel", "languages": ["java"]}' localhost:8000/label/files -H "content-type: application/json"
 ```
 
-### UI
+### Web UI
 
-The tool also offers a web UI that is available at the following page (when running locally):
-[http://localhost:8501](http://localhost:8501)
+AutoFL provides a web-based UI accessible locally at [http://localhost:8501](http://localhost:8501):
 
-![UI](resources/ui-screenshots/landing-page.png)
+![UI](/resources/ui-screenshots/landing-page.png)
 
-For more details, check the [UI repo](https://github.com/SasCezar/autofl-ui).
-
-[//]: # (For more details, check the [UI repo]&#40;https://github.com/SasCezar/autofl-ui&#41;)
+For more details, check the [UI repository](https://github.com/SasCezar/autofl-ui).
 
 ## Configuration
-AutoFL uses [Hydra](https://hydra.cc/) to manage the configuration. The configuration files are located in the [config](config) folder.
-The main configuration file is [main.yaml](./config/main.yaml), which contains the following options:
 
-- **local**: which environment to use, either local or docker. [Docker](./config/local/docker.yaml) is default.
-- **taxonomy**: which taxonomy to use. Currently only [gitranking](./config/taxonomy/gitranking.yaml) is supported.
-- **annotator**: which annotators to use. Default is [simple](./config/annotator/simple.yaml), which allows good results without extra dependencies on models.
-- **version_strategy**: which version strategy to use. Default is [latest](./config/version_strategy/latest.yaml), which will only analyze the latest version of the project.
-- **dataloader**: which dataloader to use. Default is [postgres](./config/dataloader/postgres.yaml) which allows the API to fetch already analysed projects.
-- **writer**: which writer to use. Default is [postgres](./config/writer/postgres.yaml) which allows the API to store the results in a database.
+AutoFL uses [Hydra](https://hydra.cc/) to manage configurations. The configuration files can be found in the `config` folder. The main configuration file, `main.yaml`, allows you to customize various options:
+
+- **local**: Choose between local or Docker environments. [Docker](config/environment/docker.yaml) is the default.
+- **taxonomy**: Set the taxonomy for labeling. Currently supports [gitranking](./config/taxonomy/gitranking.yaml). You can add custom taxonomies.
+- **annotator**: Specify the annotators to use. The default is [simple](./config/annotator/simple.yaml), offering good results without dependencies on language models.
+- **version_strategy**: Select the versioning strategy. The default is [latest](./config/version_strategy/latest.yaml).
+- **dataloader**: Choose the dataloader. The default is [postgres](./config/dataloader/postgres.yaml).
+- **writer**: Set the writer for storing results. The default is [postgres](./config/writer/postgres.yaml).
 
-Other configuration can be defined by creating a new file in the folder of the specific component.
+Additional configurations can be added by creating new files in the corresponding component folders.
 
 ## Functionalities
 
 - Annotation (UI/API/Script)
-    - File
-    - Package
-    - Project
+  - File-Level
+  - Package-Level
+  - Project-Level
 - Batch Analysis (Script Only)
 - Temporal Analysis (**TODO**)
 - Classification (**TODO**)
@@ -78,21 +86,23 @@ Other configuration can be defined by creating a new file in the folder of the s
 
 ## Development
 
-### Add New Languages
+AutoFL is composed of multiple components, as shown in the architecture diagram below:
+
+![Architecture](resources/architecture/architecture.png)
+
+### Adding Support for New Languages
 
-In order to support more languages, a new language specific parser is needed.
-We can create one quickly by using [tree-sitter](https://tree-sitter.github.io/tree-sitter/),
-and a custom parser.
+To add support for additional languages, a language-specific parser is required. You can use [tree-sitter](https://tree-sitter.github.io/tree-sitter/) to develop a parser quickly.
 
-#### Parser
-The parser needs to be in the [parser/languages](./src/parser/languages) folder.
-It has to extend the ```BaseParser``` class, which has the following interface.
+#### Parser Details
+
+The parser needs to be located in the `parser/languages` folder. It should extend the `BaseParser` class, which follows this structure:
 
 ```python
 class ParserBase(ABC):
-    """
-    Abstract class for a programming language parser.
-    """
+"""
+Abstract class for a programming language parser.
+"""
 
     def __init__(self, library_path: Path | str):
         """
@@ -101,75 +111,74 @@ class ParserBase(ABC):
         """
         ...
 ```
-And the language specific class has to contain the logic to parse the language to get the identifiers.
-For example for Python, the class will look like this:
+
+To implement the parsing logic, create a class that handles extracting identifiers. For Python, the parser might look like:
 
 ```python
-class PythonParser(ParserBase, lang=Extension.python.name):  # The lang argument is used to register the parser in the ParserFactory class.
+class PythonParser(ParserBase, lang=Extension.python.name):
     """
-    Python specific parser. Uses a generic grammar for multiple versions of python. Uses tree_sitter to get the AST
+    Python-specific parser using a generic grammar for multiple versions. Utilizes tree-sitter for AST extraction.
     """
 
     def __init__(self, library_path: Path | str):
-        super().__init__(library_path)
-        self.language: Language = Language(library_path, Extension.python.name)   # Creates the tree-sitter language for python
-        self.parser.set_language(self.language)                                   # Sets tree-sitter parser to parse the language
-        
-        # Pattern used to match the identifiers, it depends on the Lanugage. Check tree-sitter
-        self.identifiers_pattern: str = """
-                                        ((identifier) @identifier)
-                                        """
-        
-        # Creates the query used to find the identifiers in the AST produced by tree-sitter
-        self.identifiers_query = self.language.query(self.identifiers_pattern)
-
-        # Keyword that will be ignored, in this case, the language specific keywords as the query extracts them as well. 
-        self.keywords = set(keyword.kwlist)  # Use python's built in keyword list
-        self.keywords.update(['self', 'cls'])
+        ...
 ```
 
-A custom class that does not rely on [tree-sitter](https://github.com/tree-sitter/tree-sitter) can be also used, however, there are more methods from ParserBase that need to be
-changed. Check the implementation of [ParserBase](src/parser/parser.py).
+A custom parser independent of tree-sitter can also be developed. For more details, refer to the implementation of [ParserBase](src/parser/parser.py).
+
+## Known Issues
+
+- **Dependency Installation**: The setup process may take significant time (~10 minutes), and dependency installations might fail due to timeouts. This appears to be a network-related issue, and retrying often resolves it. Future updates will aim to simplify dependencies.
+- **~~Indefinite Analysis Loops~~**: ~~In some projects, the analysis may loop indefinitely. This issue is currently under investigation.~~ Seems solved in the latest version. Will monitor for further occurrences.
+
+## Docker Image Availability
+
+AutoFL is also available as a Docker image. You can pull the image from Docker Hub using:
+
+```shell
+docker pull cezarsas/autofl
+```
+
+Find more details and updates at the [Docker Hub page](https://hub.docker.com/r/cezarsas/autofl/).
 
 ## Disclaimer
 
-The project is still in development, and it might not work as expected in some cases.
-It has been developed and tested on Docker 24.0.7 for  ```Ubuntu 22.04```. While minor testing has been done on ```Windows``` and ```MacOS```,
-not all functionalities might work due to differences in Docker for these OSs (e.g. Windows uses WSL 2).
+This tool is in active development and may not function as expected in some cases. It has been tested primarily on Docker versions `24.0.7` and `25.0.0` for `Ubuntu 22.04`. Limited testing has been performed on `Windows` and `MacOS`, where functionality may vary.
 
-In case of any problems, please open an issue, make a pull request, or contact me at ```c.a.sas@rug.nl```.
+If you encounter any issues, please open an issue on GitHub, make a pull request, or contact me at `c.a.sas@rug.nl`.
 
-## Cite
+## Citation
 
-If you use this work please cite us:
+If you find this tool useful, please cite our work:
 
 ### Paper
-```text
+
+```bibtex
 @article{sas2024multigranular,
-         title     = {Multi-granular Software Annotation using File-level Weak Labelling}, 
-         author    = {Cezar Sas and Andrea Capiluppi},
-         journal   = {Empirical Software Engineering},
-         volume    = {29},
-         number    = {1},
-         pages     = {12},
-         year      = {2024},
-         url       = {https://doi.org/10.1007/s10664-023-10423-7},
-         doi       = {10.1007/s10664-023-10423-7}
+title     = {Multi-granular Software Annotation using File-level Weak Labelling},
+author    = {Cezar Sas and Andrea Capiluppi},
+journal   = {Empirical Software Engineering},
+volume    = {29},
+number    = {1},
+pages     = {12},
+year      = {2024},
+url       = {https://doi.org/10.1007/s10664-023-10423-7},
+doi       = {10.1007/s10664-023-10423-7}
 }
 ```
 
-**Note**: The code used in the paper is available in the [https://github.com/SasCezar/CodeGraphClassification](https://github.com/SasCezar/CodeGraphClassification) repository.
-However, this tool is more up to date, is easier to use, configurable, and also offers a UI.
+**Note**: The code used in this paper is available at [CodeGraphClassification](https://github.com/SasCezar/CodeGraphClassification). However, AutoFL provides enhanced features, is more user-friendly, and includes a UI.
 
 ### Tool
-```text
+
+```bibtex
 @software{sas2023autofl,
           author    = {Sas, Cezar and Capiluppi, Andrea},
-          month     = dec,
+          month     = oct,
           title     = {{AutoFL}},
           url       = {https://github.com/SasCezar/AutoFL},
-          version   = {0.3.0},
-          year      = {2023},
+          version   = {0.5.0},
+          year      = {2024},
           url       = {https://doi.org/10.5281/zenodo.10255368},
           doi       = {10.5281/zenodo.10255368}
 }
diff --git a/pyproject.toml b/pyproject.toml
index a3ce6bd..8b16bc8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,18 +1,18 @@
 [tool.poetry]
 name = "autofl"
-version = "0.4.1"
+version = "0.5.0"
 description = ""
 authors = ["Cezar Sas <cezar.sas@gmail.com>"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
 python = ">=3.10,<3.13"
-fastapi = "^0.109.0"
-gunicorn = "^21.2.0"
-uvicorn = "^0.27.0"
+fastapi = "^0.115.0"
+gunicorn = "^23.0.0"
+uvicorn = "^0.31.0"
 pandas = "^2.2.0"
 hydra-core = "^1.3.2"
-setuptools = "^69.0.3"
+setuptools = "^75.1.0"
 multiset = "^3.0.2"
 scikit-learn = "^1.4.0"
 pydantic = "^2.5.3"
@@ -22,24 +22,30 @@ tqdm = "^4.66.1"
 # yake = { git = "git@github.com:LIAAD/yake.git" }
 python-rake = "^1.5.0"
 more-itertools = "^10.2.0"
-tree-sitter = "^0.20.4"
+tree-sitter = "^0.23.0"
 sqlalchemy = "^2.0.25"
 psycopg = {extras = ["binary"], version = "^3.1.17"}
 gensim = "^4.3.3"
 fasttext-wheel = "^0.9.2"
 transformers = "^4.37.1"
-sentence-transformers = "^2.2.2"
+sentence-transformers = "3.1.1"
+tree-sitter-python = "^0.23.2"
+tree-sitter-java = "^0.23.2"
+tree-sitter-cpp = "^0.23.1"
+tree-sitter-c-sharp = "^0.23.0"
+tree-sitter-c = "^0.23.1"
+
 
 [tool.poetry.group.dev.dependencies]
 notebook = "^6.5.4"
 jupyter = "^1.0.0"
-mkdocs = "^1.5.3"
-mkdocstrings = "^0.24.0"
+mkdocs = "^1.6.1"
+mkdocstrings = "^0.26.1"
 mkdocs-gen-files = "^0.5.0"
-mkdocstrings-python = "^1.7.5"
+mkdocstrings-python = "^1.11.1"
 mkdocs-literate-nav = "^0.6.1"
-mkdocs-section-index = "^0.3.8"
-mkdocs-material = "^9.4.14"
+mkdocs-section-index = "^0.3.9"
+mkdocs-material = "^9.5.39"
 
 
 [build-system]
diff --git a/scripts/python/build_tree_sitter_library.py b/scripts/python/build_tree_sitter_library.py
deleted file mode 100644
index 97f29ba..0000000
--- a/scripts/python/build_tree_sitter_library.py
+++ /dev/null
@@ -1,22 +0,0 @@
-from os.path import join
-
-import hydra
-from omegaconf import DictConfig
-from tree_sitter import Language
-
-
-@hydra.main(config_path="../../config", config_name="main", version_base="1.3")
-def build_library(cfg: DictConfig):
-    languages = ['java', 'python', 'cpp', 'c-sharp', 'c']
-    repositories = [join(cfg.grammars_path, f'tree-sitter-{pl}') for pl in languages]
-    Language.build_library(
-        # Store the library in the `build` directory
-        cfg.languages_library,
-
-        # Include one or more languages
-        repositories
-    )
-
-
-if __name__ == '__main__':
-    build_library()
diff --git a/src/parser/languages/c.py b/src/parser/languages/c.py
index 2de7d60..752cc02 100644
--- a/src/parser/languages/c.py
+++ b/src/parser/languages/c.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 
-from tree_sitter import Language
-
+from tree_sitter import Language, Parser
+import tree_sitter_c as tsc
 from parser.extensions import Extension
 from parser.parser import ParserBase
 
@@ -13,12 +13,12 @@ class CParser(ParserBase, lang=Extension.c.name):
 
     def __init__(self, library_path: Path | str):
         super().__init__(library_path)
-        self.language: Language = Language(library_path, Extension.c.name)
-        self.parser.set_language(self.language)
+        self.language: Language = Language(tsc.language())
+        self.parser: Parser = Parser(self.language)
         self.identifiers_pattern: str = """
                                         ((identifier) @identifier)
                                         ((type_identifier) @type)
                                         """
-        self.identifiers_query = self.language.query(self.identifiers_pattern)\
+        self.identifiers_query = self.language.query(self.identifiers_pattern)
 
         self.keywords = {'malloc'}
diff --git a/src/parser/languages/cpp.py b/src/parser/languages/cpp.py
index 03a85a8..c1e4522 100644
--- a/src/parser/languages/cpp.py
+++ b/src/parser/languages/cpp.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 
-from tree_sitter import Language
-
+from tree_sitter import Language, Parser
+import tree_sitter_cpp as tscpp
 from parser.extensions import Extension
 from parser.parser import ParserBase
 
@@ -13,8 +13,8 @@ class CPPParser(ParserBase, lang=Extension.cpp.name):
 
     def __init__(self, library_path: Path | str):
         super().__init__(library_path)
-        self.language: Language = Language(library_path, Extension.cpp.name)
-        self.parser.set_language(self.language)
+        self.language: Language = Language(tscpp.language())
+        self.parser: Parser = Parser(self.language)
         # TODO Fix, doesn't work - It doesn't find the namespaced identifiers
         self.identifiers_pattern: str = """
                                         ((identifier) @identifier)
diff --git a/src/parser/languages/csharp.py b/src/parser/languages/csharp.py
index 139dd89..c26c66f 100644
--- a/src/parser/languages/csharp.py
+++ b/src/parser/languages/csharp.py
@@ -1,7 +1,7 @@
 from pathlib import Path
 
-from tree_sitter import Language
-
+from tree_sitter import Language, Parser
+import tree_sitter_c_sharp as tscs
 from parser.extensions import Extension
 from parser.parser import ParserBase
 
@@ -13,8 +13,8 @@ class CSharpParser(ParserBase, lang=Extension.c_sharp.name):
 
     def __init__(self, library_path: Path | str):
         super().__init__(library_path)
-        self.language: Language = Language(library_path, Extension.c_sharp.name)
-        self.parser.set_language(self.language)
+        self.language: Language = Language(tscs.language())
+        self.parser: Parser = Parser(self.language)
         self.identifiers_pattern: str = """
                                         ((identifier) @identifier)
                                         """
diff --git a/src/parser/languages/java.py b/src/parser/languages/java.py
index 3e6055e..97d1f61 100644
--- a/src/parser/languages/java.py
+++ b/src/parser/languages/java.py
@@ -1,7 +1,8 @@
 from pathlib import Path
+from typing import Dict, List
 
-from tree_sitter import Language, Tree
-
+from tree_sitter import Language, Tree, Parser, Node
+import tree_sitter_java as tsjava
 from parser.extensions import Extension
 from parser.parser import ParserBase
 
@@ -13,8 +14,8 @@ class JavaParser(ParserBase, lang=Extension.java.name):
 
     def __init__(self, library_path: Path | str):
         super().__init__(library_path)
-        self.language: Language = Language(library_path, Extension.java.name)
-        self.parser.set_language(self.language)
+        self.language: Language = Language(tsjava.language())
+        self.parser: Parser = Parser(self.language)
         self.identifiers_pattern: str = """
                                         ((identifier) @identifier)
                                         ((type_identifier) @type)
diff --git a/src/parser/languages/python.py b/src/parser/languages/python.py
index 3237af3..58fe63a 100644
--- a/src/parser/languages/python.py
+++ b/src/parser/languages/python.py
@@ -1,8 +1,8 @@
 import keyword
 from pathlib import Path
 
-from tree_sitter import Language
-
+from tree_sitter import Language, Parser
+import tree_sitter_python as tsp
 from parser.extensions import Extension
 from parser.parser import ParserBase
 
@@ -14,8 +14,8 @@ class PythonParser(ParserBase, lang=Extension.python.name):
 
     def __init__(self, library_path: Path | str):
         super().__init__(library_path)
-        self.language: Language = Language(library_path, Extension.python.name)
-        self.parser.set_language(self.language)
+        self.language: Language = Language(tsp.language())
+        self.parser: Parser = Parser(self.language)
         self.identifiers_pattern: str = """
                                         ((identifier) @identifier)
                                         """
diff --git a/src/parser/parser.py b/src/parser/parser.py
index b1c7a73..4980c00 100644
--- a/src/parser/parser.py
+++ b/src/parser/parser.py
@@ -39,11 +39,12 @@ def parse(self, file: File) -> Tuple[List[str], str]:
         return identifiers, package
 
     @staticmethod
-    def get_node_text(code: bytes, identifiers_nodes: List[Tuple[Node, str]]) -> List[str]:
+    def get_node_text(code: bytes, identifiers_nodes: dict[str, list[Node]]) -> List[str]:
         identifiers = []
-        for node, _ in identifiers_nodes:
-            token = code[node.start_byte:node.end_byte]
-            identifiers.append(token.decode())
+        for type in identifiers_nodes:
+            for node in identifiers_nodes[type]:
+                token = code[node.start_byte:node.end_byte]
+                identifiers.append(token.decode())
 
         return identifiers
 
diff --git a/test/test_parser/test_c_parser.py b/test/test_parser/test_c_parser.py
index 59f43b5..f1d0cf3 100644
--- a/test/test_parser/test_c_parser.py
+++ b/test/test_parser/test_c_parser.py
@@ -39,7 +39,8 @@ def setUp(self) -> None:
 
     def test_identifiers(self):
         identifiers, _ = self.parser.parse(self.file)
-        self.assertListEqual(identifiers, self.gt)
+        self.assertEqual(len(identifiers), len(self.gt))
+        self.assertSetEqual(set(identifiers), set(self.gt))
 
     @staticmethod
     def load_file(path):
diff --git a/test/test_parser/test_cpp_parser.py b/test/test_parser/test_cpp_parser.py
index 8e002ff..89f0512 100644
--- a/test/test_parser/test_cpp_parser.py
+++ b/test/test_parser/test_cpp_parser.py
@@ -23,10 +23,9 @@ def setUp(self) -> None:
     def test_identifiers(self):
         # TODO
         identifiers, _ = self.parser.parse(self.file)
-        print(identifiers)
-        print(len(identifiers))
-        print(self.gt)
-        self.assertListEqual(identifiers, self.gt)
+        self.assertEqual(len(identifiers), len(self.gt))
+        self.assertSetEqual(set(identifiers), set(self.gt))
+
 
     def test_packages(self):
         # TODO
diff --git a/test/test_parser/test_csharp_parser.py b/test/test_parser/test_csharp_parser.py
index b334b69..3f60d2d 100644
--- a/test/test_parser/test_csharp_parser.py
+++ b/test/test_parser/test_csharp_parser.py
@@ -23,10 +23,9 @@ def setUp(self) -> None:
     def test_identifiers(self):
         # TODO
         identifiers, _ = self.parser.parse(self.file)
-        print(identifiers)
-        print(len(identifiers))
-        print(self.gt)
-        self.assertListEqual(identifiers, self.gt)
+        self.assertEqual(len(identifiers), len(self.gt))
+        self.assertSetEqual(set(identifiers), set(self.gt))
+
 
     def test_packages(self):
         # TODO
diff --git a/test/test_parser/test_java_parser.py b/test/test_parser/test_java_parser.py
index 1d2d427..2675172 100644
--- a/test/test_parser/test_java_parser.py
+++ b/test/test_parser/test_java_parser.py
@@ -2,6 +2,7 @@
 from pathlib import Path
 
 from hydra import initialize, compose
+from sympy import pprint
 
 from entity.file import File
 from parser.parser import ParserFactory, ParserBase
@@ -25,7 +26,8 @@ def setUp(self) -> None:
 
     def test_identifiers(self):
         identifiers, _ = self.parser.parse(self.file)
-        self.assertListEqual(identifiers, self.gt)
+        self.assertEqual(len(identifiers), len(self.gt))
+        self.assertSetEqual(set(identifiers), set(self.gt))
 
     def test_packages(self):
         # TODO
diff --git a/test/test_parser/test_python_parser.py b/test/test_parser/test_python_parser.py
index 7e5f2bb..d93732a 100644
--- a/test/test_parser/test_python_parser.py
+++ b/test/test_parser/test_python_parser.py
@@ -29,7 +29,8 @@ def setUp(self) -> None:
 
     def test_identifiers(self):
         identifiers, _ = self.parser.parse(self.file)
-        self.assertListEqual(identifiers, self.gt)
+        self.assertEqual(len(identifiers), len(self.gt))
+        self.assertSetEqual(set(identifiers), set(self.gt))
 
     def test_packages(self):
         # TODO