docs: update citations, readme, changelog and add API key guide for v0.1.6

Author: aritraroy24

CHANGELOG.md

@@ -1,26 +1,42 @@
-## [0.1.5] - 08-02-2026
+## [0.1.6] - 2026-04-02
+
+### Changed
+
+- Updated [README.md](README.md), [CITATION.cff](CITATION.cff) and docs with the published version (advance article) of the ComProScanner paper in _Digital Discovery_ as fully open access:
+  - [ComProScanner: a multi-agent based framework for composition-property structured data extraction from scientific literature](https://doi.org/10.1039/D5DD00521C)
 
 ### Added
+
+- Guide for API key creation for various LLM providers and publisher APIs added to the documentation at `docs/getting-started/api-key-guide.md` with detailed instructions for each provider.
+
+### Fixed
+
+- Model prefix handling in `rag_tool.py` standardized to reflect the docs.
+- `HF_TOKEN` documentation clarified as optional — only required for gated or private Hugging Face models.
+
+---
+
+## [0.1.5] - 2026-02-08
+
+### Added
+
 - Data related to comparison with other agentic data extraction frameworks added for the ComProScanner paper in the `examples/piezo_test/comparing_existing_frameworks` folder.
 
 - New parameter `apply_advanced_cleaning` added to data cleaning methods in `data_cleaner.py`. When set to `True`, it triggers the advanced cleaning pipeline.
 
 - Advanced composition cleaning methods in `data_cleaner.py`:
-
   - `_remove_miller_indices()` - Removes crystal plane notations from chemical formulas
   - `_remove_zero_coefficient_elements()` - Removes elements with zero coefficients
   - `_normalize_coefficients()` - Removes trailing zeros from coefficients
   - `_expand_leading_and_trailing_coefficients()` - Expands leading/trailing coefficient patterns
   - `_expand_parenthetical_coefficients()` - Expands nested bracket coefficients
 
 - Enhanced documentation in `docs/usage/data-cleaning.md`:
-
   - Added `apply_advanced_cleaning` parameter documentation
   - Added Mermaid process flow diagram showing cleaning stages
   - Added advanced cleaning examples with tables for each transformation type
 
 - Template for GitHub issues added to [.github/ISSUE_TEMPLATE](https://github.com/slimeslab/ComProScanner/tree/main/.github/ISSUE_TEMPLATE) for the following topics:
-
   - bug reports
   - feature requests
   - documentation improvements
@@ -29,24 +45,22 @@
 - [Changelog page](https://slimeslab.github.io/ComProScanner/about/changelog/) added in the documentation. Also, [CHANGELOG.md](https://github.com/slimeslab/ComProScanner/blob/main/CHANGELOG.md) linked in [README.md](https://github.com/slimeslab/ComProScanner/blob/main/README.md).
 
 - DeepWiki integration badge added to README.md for community Q&A support:
-
   - [Ask DeepWiki](https://deepwiki.com/slimeslab/ComProScanner)
 
 - arXiv preprint badge added to README.md:
-
   - [arXiv:2510.20362](https://arxiv.org/abs/2510.20362)
 
 - [CITATION.cff](https://github.com/slimeslab/ComProScanner/blob/main/CITATION.cff) added for standardized citation information based on the latest release and arXiv preprint.
 
 ### Fixed
+
 - OAWorks API is replaced with OpenAlex API as OAWorks is no longer available.
 
 - Empty/corrupted PDF handled in `pdf_processor.py` and `wiley_processor.py` to avoid having GLYPH errors during text extraction.
 
 - Data extraction failures fixed if composition-property text data is empty.
 
 - CSV progress tracking in `elsevier_processor.py`:
-
   - DtypeWarning resolved by adding `dtype=str, low_memory=False` to `pd.read_csv()`
   - Data loss issue fixed with immediate CSV persistence for processed articles
   - Sleep delays optimized for batch writes
@@ -69,19 +83,19 @@
 
 - README badges section converted from HTML to markdown format for better compatibility across platforms.
 
-## [0.1.4] - 02-12-2025
+---
+
+## [0.1.4] - 2025-12-02
 
 ### Added
 
 - New function `clean_data()` added for improved data cleaning and preprocessing instead of integrating it into data extraction function.
 
 - New documentation page for Data Cleaning added:
-
   - docs/usage/data-cleaning.md
   - Added to mkdocs.yml navigation.
 
 - New API overview documentation page added:
-
   - docs/api.md
   - Added to mkdocs.yml navigation.
   - New mkdocstrings configuration added to mkdocs.yml for automatic API documentation generation.
@@ -104,30 +118,38 @@
   - [ComProScanner Logo](https://raw.githubusercontent.com/aritraroy24/ComProScanner/main/assets/comproscanner_logo.png)
   - [ComProScanner Workflow](https://raw.githubusercontent.com/aritraroy24/ComProScanner/main/assets/overall_workflow.png)
 
-## [0.1.3] - 04-11-2025
+---
+
+## [0.1.3] - 2025-11-04
 
 ### Fixed
 
 - **RecursiveCharacterTextSplitter** importing updated for latest _langchain_ version to avoid import errors:
   - Changed from `from langchain.text_splitter import RecursiveCharacterTextSplitter`
   - To `from langchain.text_splitter.recursive_character import RecursiveCharacterTextSplitter`
 
-## [0.1.2] - 24-10-2025
+---
+
+## [0.1.2] - 2025-10-24
 
 ### Added
 
 - Link to ComProScanner preprint on arXiv in the documentation index page and README.md:
   - [arXiv:2510.20362](https://arxiv.org/abs/2510.20362)
 
-## [0.1.1] - 22-10-2025
+---
+
+## [0.1.1] - 2025-10-22
 
 ### Fixed
 
 - README images updated with external image link to fix PyPI rendering issue.
   - [ComProScanner Logo](https://i.ibb.co/whHSbGvT/comproscanner-logo.png)
   - [ComProScanner Workflow](https://i.ibb.co/QWd2qd3/overall-workflow.png)
 
-## [0.1.0] - 22-10-2025
+---
+
+## [0.1.0] - 2025-10-22
 
 ### Added
 

CITATION.cff

@@ -16,7 +16,7 @@ contact:
   - family-names: Roy
     given-names: Aritra
     orcid: "https://orcid.org/0000-0002-4928-2935"
-message: If you use this software, please cite our article on arXiv.
+message: If you use this software, please cite our article in Digital Discovery.
 preferred-citation:
   authors:
     - family-names: Roy
@@ -31,21 +31,28 @@ preferred-citation:
     - family-names: Gattinoni
       given-names: Chiara
       orcid: "https://orcid.org/0000-0002-3376-6374"
-  date-published: 2025-10-23
+  doi: "10.1039/D5DD00521C"
   identifiers:
+    - type: doi
+      value: "10.1039/D5DD00521C"
+      description: "Peer-reviewed article"
     - type: other
       value: "arXiv:2510.20362"
       description: "arXiv preprint"
-  title: "ComProScanner: A multi-agent based framework for composition-property structured data extraction from scientific literature"
+  journal: "Digital Discovery"
+  publisher:
+    name: "RSC"
+  status: advance-online
+  title: "ComProScanner: a multi-agent based framework for composition-property structured data extraction from scientific literature"
   type: article
-  url: "https://arxiv.org/abs/2510.20362"
+  url: "https://doi.org/10.1039/D5DD00521C"
 repository-code: "https://github.com/slimeslab/ComProScanner"
 license: MIT
 title: "ComProScanner: A multi-agent based framework for composition-property structured data extraction from scientific literature"
 type: software
 url: "https://slimeslab.github.io/ComProScanner/"
-version: "0.1.4"
-date-released: 2025-12-03
+version: "0.1.6"
+date-released: 2026-04-02
 keywords:
   - materials science
   - data extraction

README.md

@@ -169,14 +169,15 @@ eval_visualizer.plot_multiple_radar_charts(
 If you use ComProScanner in your research, please cite:
 
 ```bibtex
-@misc{roy2025comproscannermultiagentbasedframework,
-      title={ComProScanner: A multi-agent based framework for composition-property structured data extraction from scientific literature},
-      author={Aritra Roy and Enrico Grisan and John Buckeridge and Chiara Gattinoni},
-      year={2025},
-      eprint={2510.20362},
-      archivePrefix={arXiv},
-      primaryClass={physics.comp-ph},
-      url={https://arxiv.org/abs/2510.20362},
+@Article{roy2026comproscannermultiagentbasedframework,
+author ="Roy, Aritra and Grisan, Enrico and Buckeridge, John and Gattinoni, Chiara",
+title  ="ComProScanner: a multi-agent based framework for composition-property structured data extraction from scientific literature",
+journal  ="Digital Discovery",
+year  ="2026",
+pages  ="Accepted",
+publisher  ="RSC",
+doi  ="10.1039/D5DD00521C",
+url  ="https://doi.org/10.1039/D5DD00521C"
 }
 ```
 

docs/about/changelog.md

@@ -1,25 +1,42 @@
-## Unreleased
+## [0.1.6] - 2026-04-02
+
+### Changed
+
+- Updated [README.md](README.md), [CITATION.cff](CITATION.cff) and docs with the published version (advance article) of the ComProScanner paper in _Digital Discovery_ as fully open access:
+  - [ComProScanner: a multi-agent based framework for composition-property structured data extraction from scientific literature](https://doi.org/10.1039/D5DD00521C)
 
 ### Added
 
+- Guide for API key creation for various LLM providers and publisher APIs added to the documentation at `docs/getting-started/api-key-guide.md` with detailed instructions for each provider.
+
+### Fixed
+
+- Model prefix handling in `rag_tool.py` standardized to reflect the docs.
+- `HF_TOKEN` documentation clarified as optional — only required for gated or private Hugging Face models.
+
+---
+
+## [0.1.5] - 2026-02-08
+
+### Added
+
+- Data related to comparison with other agentic data extraction frameworks added for the ComProScanner paper in the `examples/piezo_test/comparing_existing_frameworks` folder.
+
 - New parameter `apply_advanced_cleaning` added to data cleaning methods in `data_cleaner.py`. When set to `True`, it triggers the advanced cleaning pipeline.
 
 - Advanced composition cleaning methods in `data_cleaner.py`:
-
   - `_remove_miller_indices()` - Removes crystal plane notations from chemical formulas
   - `_remove_zero_coefficient_elements()` - Removes elements with zero coefficients
   - `_normalize_coefficients()` - Removes trailing zeros from coefficients
   - `_expand_leading_and_trailing_coefficients()` - Expands leading/trailing coefficient patterns
   - `_expand_parenthetical_coefficients()` - Expands nested bracket coefficients
 
 - Enhanced documentation in `docs/usage/data-cleaning.md`:
-
   - Added `apply_advanced_cleaning` parameter documentation
   - Added Mermaid process flow diagram showing cleaning stages
   - Added advanced cleaning examples with tables for each transformation type
 
 - Template for GitHub issues added to [.github/ISSUE_TEMPLATE](https://github.com/slimeslab/ComProScanner/tree/main/.github/ISSUE_TEMPLATE) for the following topics:
-
   - bug reports
   - feature requests
   - documentation improvements
@@ -28,19 +45,22 @@
 - [Changelog page](https://slimeslab.github.io/ComProScanner/about/changelog/) added in the documentation. Also, [CHANGELOG.md](https://github.com/slimeslab/ComProScanner/blob/main/CHANGELOG.md) linked in [README.md](https://github.com/slimeslab/ComProScanner/blob/main/README.md).
 
 - DeepWiki integration badge added to README.md for community Q&A support:
-
   - [Ask DeepWiki](https://deepwiki.com/slimeslab/ComProScanner)
 
 - arXiv preprint badge added to README.md:
-
   - [arXiv:2510.20362](https://arxiv.org/abs/2510.20362)
 
 - [CITATION.cff](https://github.com/slimeslab/ComProScanner/blob/main/CITATION.cff) added for standardized citation information based on the latest release and arXiv preprint.
 
 ### Fixed
 
-- CSV progress tracking in `elsevier_processor.py`:
+- OAWorks API is replaced with OpenAlex API as OAWorks is no longer available.
+
+- Empty/corrupted PDF handled in `pdf_processor.py` and `wiley_processor.py` to avoid having GLYPH errors during text extraction.
 
+- Data extraction failures fixed if composition-property text data is empty.
+
+- CSV progress tracking in `elsevier_processor.py`:
   - DtypeWarning resolved by adding `dtype=str, low_memory=False` to `pd.read_csv()`
   - Data loss issue fixed with immediate CSV persistence for processed articles
   - Sleep delays optimized for batch writes
@@ -63,19 +83,19 @@
 
 - README badges section converted from HTML to markdown format for better compatibility across platforms.
 
-## [0.1.4] - 02-12-2025
+---
+
+## [0.1.4] - 2025-12-02
 
 ### Added
 
 - New function `clean_data()` added for improved data cleaning and preprocessing instead of integrating it into data extraction function.
 
 - New documentation page for Data Cleaning added:
-
   - docs/usage/data-cleaning.md
   - Added to mkdocs.yml navigation.
 
 - New API overview documentation page added:
-
   - docs/api.md
   - Added to mkdocs.yml navigation.
   - New mkdocstrings configuration added to mkdocs.yml for automatic API documentation generation.
@@ -94,29 +114,42 @@
 
 ### Changed
 
-- README images updated with raw GitHub links for better reliability: [ComProScanner Logo](https://raw.githubusercontent.com/aritraroy24/ComProScanner/main/assets/comproscanner_logo.png), [ComProScanner Workflow](https://raw.githubusercontent.com/aritraroy24/ComProScanner/main/assets/overall_workflow.png)
+- README images updated with raw GitHub links for better reliability:
+  - [ComProScanner Logo](https://raw.githubusercontent.com/aritraroy24/ComProScanner/main/assets/comproscanner_logo.png)
+  - [ComProScanner Workflow](https://raw.githubusercontent.com/aritraroy24/ComProScanner/main/assets/overall_workflow.png)
 
-## [0.1.3] - 04-11-2025
+---
+
+## [0.1.3] - 2025-11-04
 
 ### Fixed
 
 - **RecursiveCharacterTextSplitter** importing updated for latest _langchain_ version to avoid import errors:
   - Changed from `from langchain.text_splitter import RecursiveCharacterTextSplitter`
   - To `from langchain.text_splitter.recursive_character import RecursiveCharacterTextSplitter`
 
-## [0.1.2] - 24-10-2025
+---
+
+## [0.1.2] - 2025-10-24
 
 ### Added
 
-- Link to ComProScanner preprint on arXiv in the documentation index page and README.md: [arXiv:2510.20362](https://arxiv.org/abs/2510.20362)
+- Link to ComProScanner preprint on arXiv in the documentation index page and README.md:
+  - [arXiv:2510.20362](https://arxiv.org/abs/2510.20362)
+
+---
 
-## [0.1.1] - 22-10-2025
+## [0.1.1] - 2025-10-22
 
 ### Fixed
 
-- README images updated with external image link to fix PyPI rendering issue. [ComProScanner Logo](https://i.ibb.co/whHSbGvT/comproscanner-logo.png), [ComProScanner Workflow](https://i.ibb.co/QWd2qd3/overall-workflow.png)
+- README images updated with external image link to fix PyPI rendering issue.
+  - [ComProScanner Logo](https://i.ibb.co/whHSbGvT/comproscanner-logo.png)
+  - [ComProScanner Workflow](https://i.ibb.co/QWd2qd3/overall-workflow.png)
+
+---
 
-## [0.1.0] - 22-10-2025
+## [0.1.0] - 2025-10-22
 
 ### Added
 

docs/about/citation.md

@@ -3,13 +3,14 @@
 If you use ComProScanner in your research, please cite our related paper:
 
 ```bibtex
-@misc{roy2025comproscannermultiagentbasedframework,
-      title={ComProScanner: A multi-agent based framework for composition-property structured data extraction from scientific literature},
-      author={Aritra Roy and Enrico Grisan and John Buckeridge and Chiara Gattinoni},
-      year={2025},
-      eprint={2510.20362},
-      archivePrefix={arXiv},
-      primaryClass={physics.comp-ph},
-      url={https://arxiv.org/abs/2510.20362},
+@Article{roy2026comproscannermultiagentbasedframework,
+author ="Roy, Aritra and Grisan, Enrico and Buckeridge, John and Gattinoni, Chiara",
+title  ="ComProScanner: a multi-agent based framework for composition-property structured data extraction from scientific literature",
+journal  ="Digital Discovery",
+year  ="2026",
+pages  ="Accepted",
+publisher  ="RSC",
+doi  ="10.1039/D5DD00521C",
+url  ="https://doi.org/10.1039/D5DD00521C"
 }
 ```