Resolve merge conflict: add model HuggingFace link and remove HF_TOKEN

Author: Jamey O'Neill

.github/workflows/ci.yml

@@ -30,9 +30,6 @@ jobs:
       - name: Install dependencies
         run: make install
 
-      - name: Revert the changes to bin folder
-        run: chmod 644 ./bin/*
-
       # - name: Check code
       #   run: make check
 

.github/workflows/deploy-schemas.yml

@@ -1,10 +1,10 @@
-name: build
+name: Build and deploy documentation
 on:
   push:
     branches:
       - main
 jobs:
-  deploy:
+  build-and-deploy:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2

.github/workflows/docs.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.11]
+        python-version: [3.12]
 
     steps:
       - name: Checkout the repository

.github/workflows/publish-to-pypi-beta.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.11]
+        python-version: [3.12]
 
     steps:
       - name: Checkout the repository

.github/workflows/publish-to-pypi.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.11]
+        python-version: [3.12]
 
     steps:
       - name: Checkout the repository

.github/workflows/publish-to-test-pypi.yml

@@ -1,5 +1,20 @@
 # Changelog
 
-## [0.1.0] - Unreleased
+All notable changes to this project will be documented in this file.
 
-- Initial poster2json package (example structure).
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.1] - 2026-02-04
+
+### Added
+
+- Add documentation to the package.
+- Add tests to the package.
+- Update the logo for the package.
+
+## [0.1.0] - 2026-02-04
+
+### Added
+
+- Initial poster2json package.

CHANGELOG.md

@@ -48,15 +48,14 @@ endif
 
 # TEST ########################################################################
 
-RANDOM_SEED ?= $(shell date +%s)
 FAILURES := .cache/pytest/v/cache/lastfailed
 
-PYTEST_OPTIONS := --random --random-seed=$(RANDOM_SEED)
 ifndef DISABLE_COVERAGE
 PYTEST_OPTIONS += --cov=$(PACKAGE)
 endif
 ifdef CI
 PYTEST_OPTIONS += --cov-report=xml
+PYTEST_OPTIONS += -m "not gpu"
 endif
 PYTEST_RERUN_OPTIONS := --last-failed --exitfirst
 
@@ -68,27 +67,18 @@ test-unit: install
 	@ ( mv $(FAILURES) $(FAILURES).bak || true ) > /dev/null 2>&1
 	poetry run pytest $(PACKAGE) $(PYTEST_OPTIONS)
 	@ ( mv $(FAILURES).bak $(FAILURES) || true ) > /dev/null 2>&1
-ifndef DISABLE_COVERAGE
-	poetry run coveragespace update unit
-endif
 
 .PHONY: test-int
 test-int: install
 	@ if test -e $(FAILURES); then poetry run pytest tests $(PYTEST_RERUN_OPTIONS); fi
 	@ rm -rf $(FAILURES)
 	poetry run pytest tests $(PYTEST_OPTIONS)
-ifndef DISABLE_COVERAGE
-	poetry run coveragespace update integration
-endif
 
 .PHONY: test-all
 test-all: install
 	@ if test -e $(FAILURES); then poetry run pytest $(PACKAGE) tests $(PYTEST_RERUN_OPTIONS); fi
 	@ rm -rf $(FAILURES)
 	poetry run pytest $(PACKAGE) tests $(PYTEST_OPTIONS)
-ifndef DISABLE_COVERAGE
-	poetry run coveragespace update overall
-endif
 
 .PHONY: read-coverage
 read-coverage:

Makefile

@@ -1,6 +1,6 @@
 <div align="center">
 
-<img src="https://raw.githubusercontent.com/fairdataihub/poster2json/main/logo.svg" alt="logo" width="200" height="auto" />
+<img src="https://cdn.posters.science/logos/poster-fairy.png" alt="logo" width="200" height="auto" />
 
 <br />
 
@@ -58,6 +58,7 @@ Convert scientific posters (PDF/images) to structured JSON metadata using Large
 **poster2json** extracts structured metadata from scientific conference posters (PDF or image format) into machine-actionable JSON conforming to the [poster-json-schema](https://github.com/fairdataihub/poster-json-schema).
 
 The pipeline uses:
+
 - [**Llama-3.1-8B-Poster-Extraction**](https://huggingface.co/jimnoneill/Llama-3.1-8B-Poster-Extraction) for JSON structuring
 - **Qwen2-VL-7B** for vision-based OCR of image posters
 - **pdfalto** for layout-aware PDF text extraction
@@ -104,49 +105,56 @@ Output conforms to the [poster-json-schema](https://github.com/fairdataihub/post
 {
   "$schema": "https://posters.science/schema/v0.1/poster_schema.json",
   "creators": [
-    {"name": "Garcia, Sofia", "givenName": "Sofia", "familyName": "Garcia", "affiliation": ["University"]}
+    {
+      "name": "Garcia, Sofia",
+      "givenName": "Sofia",
+      "familyName": "Garcia",
+      "affiliation": ["University"]
+    }
+  ],
+  "titles": [
+    { "title": "Machine Learning Approaches to Diabetic Retinopathy Detection" }
   ],
-  "titles": [{"title": "Machine Learning Approaches to Diabetic Retinopathy Detection"}],
   "posterContent": {
     "sections": [
-      {"sectionTitle": "Abstract", "sectionContent": "..."},
-      {"sectionTitle": "Methods", "sectionContent": "..."},
-      {"sectionTitle": "Results", "sectionContent": "..."}
+      { "sectionTitle": "Abstract", "sectionContent": "..." },
+      { "sectionTitle": "Methods", "sectionContent": "..." },
+      { "sectionTitle": "Results", "sectionContent": "..." }
     ]
   },
-  "imageCaptions": [{"captions": ["Figure 1.", "ROC curves showing..."]}],
-  "tableCaptions": [{"captions": ["Table 1.", "Performance metrics"]}]
+  "imageCaptions": [{ "captions": ["Figure 1.", "ROC curves showing..."] }],
+  "tableCaptions": [{ "captions": ["Table 1.", "Performance metrics"] }]
 }
 ```
 
 ## System Requirements
 
-| Requirement | Specification |
-|-------------|---------------|
-| GPU | NVIDIA CUDA-capable, ≥16GB VRAM |
-| RAM | ≥32GB recommended |
-| Python | 3.10+ |
-| OS | Linux, macOS, Windows (via WSL2) |
+| Requirement | Specification                    |
+| ----------- | -------------------------------- |
+| GPU         | NVIDIA CUDA-capable, ≥16GB VRAM  |
+| RAM         | ≥32GB recommended                |
+| Python      | 3.10+                            |
+| OS          | Linux, macOS, Windows (via WSL2) |
 
 ## Performance
 
 Validated on 10 manually annotated scientific posters:
 
-| Metric | Score | Threshold |
-|--------|-------|-----------|
-| Word Capture | 0.96 | ≥0.75 |
-| ROUGE-L | 0.89 | ≥0.75 |
-| Number Capture | 0.93 | ≥0.75 |
-| Field Proportion | 0.99 | 0.30–2.50 |
+| Metric           | Score | Threshold |
+| ---------------- | ----- | --------- |
+| Word Capture     | 0.96  | ≥0.75     |
+| ROUGE-L          | 0.89  | ≥0.75     |
+| Number Capture   | 0.93  | ≥0.75     |
+| Field Proportion | 0.99  | 0.30–2.50 |
 
 **Pass Rate**: 10/10 (100%)
 
 ## Documentation
 
-| Document | Description |
-|----------|-------------|
+| Document                             | Description                     |
+| ------------------------------------ | ------------------------------- |
 | [Architecture](docs/architecture.md) | Technical details & methodology |
-| [Evaluation](docs/evaluation.md) | Validation metrics & results |
+| [Evaluation](docs/evaluation.md)     | Validation metrics & results    |
 
 ## Development Setup
 
@@ -155,15 +163,32 @@ Validated on 10 manually annotated scientific posters:
 git clone https://github.com/fairdataihub/poster2json.git
 cd poster2json
 
-# Install with Poetry
+# Create a virtual environment
+python -m venv .venv
+
+# Activate the virtual environment
+source venv/bin/activate
+.venv\Scripts\activate # On Windows
+
+# Install poetry
 pip install poetry
+
+# Install dependencies
 poetry install
 
 # Run tests
-poetry run pytest
+poe test
 
 # Format code
-poetry run poe format
+poe format
+```
+
+If you are on windows and have multiple python versions, you can use the following commands:
+
+```bash
+py -0p # list all python versions
+
+py -3.12 -m venv .venv
 ```
 
 ## License
@@ -175,7 +200,7 @@ MIT License - see [LICENSE](LICENSE.md) for details.
 ```bibtex
 @software{poster2json2026,
   title = {poster2json: Scientific Poster to JSON Metadata Extraction},
-  author = {O'Neill, James and Soundarajan, Sanjay and Patel, Bhavesh},
+  author = {O'Neill, James and Soundarajan, Sanjay and Portillo, Dorian and Patel, Bhavesh},
   year = {2026},
   url = {https://github.com/fairdataihub/poster2json},
   doi = {10.5281/zenodo.18320010}