Make meta optional

Author: adelavega

autonima.egg-info/PKG-INFO

@@ -43,6 +43,10 @@ Requires-Dist: mypy>=1.0; extra == "dev"
 Requires-Dist: pre-commit>=3.0; extra == "dev"
 Provides-Extra: llm
 Requires-Dist: openai>=1.0; extra == "llm"
+Provides-Extra: readability
+Requires-Dist: readabilipy>=0.2.0; extra == "readability"
+Provides-Extra: meta
+Requires-Dist: nimare>=0.1.0; extra == "meta"
 Dynamic: author
 Dynamic: classifier
 Dynamic: description
@@ -90,6 +94,12 @@ Autonima enables end-to-end automation of systematic review steps:
    * Produces a final set of included studies for meta-analysis.
    * Uses function calling with Pydantic schemas for structured output.
 
+5. **Enhanced HTML Cleaning**
+
+   * Uses Mozilla's Readability algorithm via `readabilipy` to extract clean text content from HTML.
+   * Falls back to basic HTML cleaning when `readabilipy` is not available.
+   * Install with `pip install -e .[readability]` (requires Node.js).
+
 ---
 
 ## 📊 Benchmarking
@@ -127,6 +137,11 @@ cd autonima
 # install
 pip install -e .
 
+# install with enhanced HTML cleaning (requires Node.js)
+pip install -e .[readability]
+
+> Note: The enhanced HTML cleaning feature requires Node.js to be installed on your system.
+
 # run an example review pipeline
 python examples/run_pipeline.py --config examples/sample_config.yaml
 ```

autonima.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ autonima/__init__.py
 autonima/__main__.py
 autonima/cli.py
 autonima/config.py
+autonima/meta.py
 autonima/pipeline.py
 autonima/utils.py
 autonima.egg-info/PKG-INFO
@@ -12,6 +13,14 @@ autonima.egg-info/dependency_links.txt
 autonima.egg-info/entry_points.txt
 autonima.egg-info/requires.txt
 autonima.egg-info/top_level.txt
+autonima/coordinates/__init__.py
+autonima/coordinates/nimads_models.py
+autonima/coordinates/openai_client.py
+autonima/coordinates/parser.py
+autonima/coordinates/processor.py
+autonima/coordinates/schema.py
+autonima/llm/__init__.py
+autonima/llm/client.py
 autonima/models/__init__.py
 autonima/models/types.py
 autonima/retrieval/__init__.py

autonima.egg-info/requires.txt

@@ -21,3 +21,9 @@ pre-commit>=3.0
 
 [llm]
 openai>=1.0
+
+[meta]
+nimare>=0.1.0
+
+[readability]
+readabilipy>=0.2.0

autonima/__init__.py

@@ -34,7 +34,11 @@
 from .llm.client import GenericLLMClient
 
 # Import meta-analysis module components
-from .meta import run_meta_analyses
+try:
+    from .meta import run_meta_analyses
+    HAS_META = True
+except ImportError:
+    HAS_META = False
 
 __all__ = [
     "AutonimaPipeline",
@@ -47,6 +51,8 @@
     "ParseAnalysesOutput",
     "parse_tables",
     "CoordinateParsingClient",
-    "GenericLLMClient",
-    "run_meta_analyses"
-]
+    "GenericLLMClient"
+]
+
+if HAS_META:
+    __all__.append("run_meta_analyses")

autonima/cli.py

@@ -262,6 +262,19 @@ def meta(output_folder: str, estimator: str, estimator_args: str,
         import json
         from pathlib import Path
 
+        # Try to import NiMARE dependencies
+        try:
+            from .meta import run_meta_analyses
+        except ImportError as e:
+            log_error_with_debug(
+                logger,
+                "NiMARE is not installed. Please install with: pip install autonima[meta]"
+            )
+            if debug:
+                import pdb
+                pdb.post_mortem()
+            sys.exit(1)
+        
         # Parse estimator and corrector arguments
         try:
             estimator_args_dict = json.loads(estimator_args)
@@ -273,9 +286,6 @@ def meta(output_folder: str, estimator: str, estimator_args: str,
                 pdb.post_mortem()
             sys.exit(1)
 
-        # Import the meta-analysis function
-        from .meta import run_meta_analyses
-        
         # Run meta-analyses
         results = run_meta_analyses(
             output_folder,

autonima/meta.py

@@ -5,11 +5,22 @@
 from pathlib import Path
 import json
 import importlib
-from nimare.correct import FDRCorrector, FWECorrector
-from nimare.workflows import CBMAWorkflow
-from nimare.meta.cbma import MKDADensity, ALE, KDA
-from nimare.nimads import Studyset, Annotation
-from nimare.reports.base import run_reports
+
+# Try to import NiMARE dependencies
+try:
+    from nimare.correct import FDRCorrector, FWECorrector
+    from nimare.workflows import CBMAWorkflow
+    from nimare.meta.cbma import MKDADensity, ALE, KDA
+    from nimare.nimads import Studyset, Annotation
+    from nimare.reports.base import run_reports
+    NIMARE_AVAILABLE = True
+except ImportError:
+    NIMARE_AVAILABLE = False
+
+if not NIMARE_AVAILABLE:
+    raise ImportError(
+        "NiMARE is not installed. Please install with: pip install autonima[meta]"
+    )
 
 
 def create_estimator(estimator_name, estimator_args):

setup.py

@@ -53,8 +53,7 @@ def get_version():
         "biopython>=1.81",
         "pandas>=2.0",
         "matplotlib>=3.5",
-        "pubget>=0.0.8",
-        "nimare>=0.1.0"
+        "pubget>=0.0.8"
     ],
     extras_require={
         "dev": [
@@ -70,6 +69,9 @@ def get_version():
         ],
         "readability": [
             "readabilipy>=0.2.0"
+        ],
+        "meta": [
+            "nimare>=0.1.0"
         ]
     },
     entry_points={