Add frontend, more granulare cachine

README.md

@@ -20,6 +20,7 @@ Useful extras:
 pip install -e .[llm]          # screening and other LLM-backed workflows
 pip install -e .[meta]         # `autonima meta`
 pip install -e .[readability]  # enhanced HTML extraction
+pip install -e .[ui]           # `autonima ui` local web app
 pip install -e .[docs]         # local docs build
 ```
 
@@ -60,6 +61,12 @@ Run meta-analysis on the generated NiMADS outputs:
 autonima meta runs/my_review/outputs
 ```
 
+Launch the local web UI:
+
+```bash
+autonima ui --workspace .
+```
+
 ## Minimal Config Example
 
 ```yaml

autonima.egg-info/PKG-INFO

@@ -54,6 +54,9 @@ Requires-Dist: mkdocs>=1.6; extra == "docs"
 Requires-Dist: mkdocs-material>=9.5; extra == "docs"
 Requires-Dist: mkdocs-click>=0.8; extra == "docs"
 Requires-Dist: pymdown-extensions>=10.0; extra == "docs"
+Provides-Extra: ui
+Requires-Dist: fastapi>=0.115; extra == "ui"
+Requires-Dist: uvicorn>=0.30; extra == "ui"
 Dynamic: author
 Dynamic: classifier
 Dynamic: description
@@ -88,6 +91,7 @@ Useful extras:
 pip install -e .[llm]          # screening and other LLM-backed workflows
 pip install -e .[meta]         # `autonima meta`
 pip install -e .[readability]  # enhanced HTML extraction
+pip install -e .[ui]           # `autonima ui` local web app
 pip install -e .[docs]         # local docs build
 ```
 
@@ -128,6 +132,12 @@ Run meta-analysis on the generated NiMADS outputs:
 autonima meta runs/my_review/outputs
 ```
 
+Launch the local web UI:
+
+```bash
+autonima ui --workspace .
+```
+
 ## Minimal Config Example
 
 ```yaml

autonima.egg-info/SOURCES.txt

@@ -45,6 +45,15 @@ autonima/templates/sample_config.yml
 autonima/utils/__init__.py
 autonima/utils/base.py
 autonima/utils/criteria.py
+autonima/webui/__init__.py
+autonima/webui/app.py
+autonima/webui/progress.py
+autonima/webui/runs.py
+autonima/webui/secrets.py
+autonima/webui/state.py
+autonima/webui/static/app.jsx
+autonima/webui/static/index.html
+autonima/webui/static/styles.css
 tests/test_annotation_incremental_caching.py
 tests/test_annotation_multi_analysis_validation.py
 tests/test_annotation_retry.py
@@ -56,12 +65,16 @@ tests/test_docs.py
 tests/test_fulltext_incomplete_outputs.py
 tests/test_fulltext_loading.py
 tests/test_fulltext_screening.py
+tests/test_llm_client.py
 tests/test_multi_annotation.py
+tests/test_nimads_annotations.py
 tests/test_objective_in_prompt.py
 tests/test_parallel_screening.py
 tests/test_pipeline_retrieval.py
 tests/test_pipeline_stage_cutoff.py
 tests/test_pubmed.py
 tests/test_retrieval.py
 tests/test_screening.py
-tests/test_simplified_screening.py
+tests/test_simplified_screening.py
+tests/test_webui.py
+tests/test_webui_api.py

autonima.egg-info/requires.txt

@@ -35,3 +35,7 @@ nimare>=0.1.0
 
 [readability]
 readabilipy>=0.2.0
+
+[ui]
+fastapi>=0.115
+uvicorn>=0.30

autonima/annotation/processor.py

@@ -146,8 +146,15 @@ def process_studies(
             self._save_results_by_study(all_decisions, output_dir, existing_cached_results)
         self.annotation_results = all_decisions
 
-        # Return all cached results (existing + new)
-        return self._load_cached_results(output_dir) or []
+        # Return only results eligible for this execution. Cached decisions
+        # for studies that no longer pass current screening can remain on disk
+        # for reuse, but must not flow into current outputs.
+        return self._filter_cached_results_for_current_run(
+            self._load_cached_results(output_dir) or [],
+            included_studies=included_studies or [],
+            all_studies=all_studies or [],
+            all_abstract_studies=all_abstract_studies or [],
+        )
 
     def _create_all_analyses_annotations(
         self,
@@ -402,6 +409,33 @@ def _get_studies_with_complete_results(
                 studies_with_complete_results.add(study_id)
 
         return studies_with_complete_results
+
+    def _filter_cached_results_for_current_run(
+        self,
+        results: List[AnnotationDecision],
+        included_studies: List[Study],
+        all_studies: List[Study],
+        all_abstract_studies: List[Study],
+    ) -> List[AnnotationDecision]:
+        """Filter cached annotation decisions to the current eligibility graph."""
+        included_ids = {study.pmid for study in included_studies}
+        all_ids = {study.pmid for study in all_studies}
+        abstract_ids = {study.pmid for study in all_abstract_studies}
+        custom_names = {annotation.name for annotation in self.config.annotations}
+
+        filtered: List[AnnotationDecision] = []
+        for result in results:
+            name = result.annotation_name
+            if name == "all_studies" and result.study_id in all_ids:
+                filtered.append(result)
+            elif name == "all_abstract" and result.study_id in abstract_ids:
+                filtered.append(result)
+            elif name == "all_analyses" and result.study_id in included_ids:
+                filtered.append(result)
+            elif name in custom_names and result.study_id in included_ids:
+                filtered.append(result)
+
+        return filtered
 
     def _get_annotations_with_complete_results_for_study(
         self,

autonima/annotation/schema.py

@@ -54,6 +54,7 @@ class AnnotationDecision(BaseModel):
     # NEW: Track which criteria were applied
     inclusion_criteria_applied: List[str] = []
     exclusion_criteria_applied: List[str] = []
+    cache_signature: Optional[Dict[str, Any]] = None
 
 
 class TableMetadata(BaseModel):