ContextLab · jeremymanning · Dec 10, 2025 · Dec 8, 2025 · Dec 9, 2025 · Dec 9, 2025
diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,4 @@ dist/*
 .pytest_cache/*
 venv/
 docs/_build
+docs/sg_execution_times.rst
diff --git a/README.md b/README.md
@@ -59,12 +59,12 @@ This will work on clean systems, but if you encounter issues you may need to run
 <h2>Requirements</h2>
 
 + python>=3.6
-+ pandas>=0.18.0
-+ seaborn>=0.7.1
-+ matplotlib>=1.5.1
-+ scipy>=0.17.1
-+ numpy>=1.10.4
-+ future
++ pandas>=2.0.0
++ seaborn>=0.12.0
++ matplotlib>=3.5.0
++ scipy>=1.10.0
++ numpy>=2.0.0
++ joblib>=1.3.0
 + pytest (for development)
 
 If installing from github (instead of pip), you must also install the requirements:

diff --git a/benchmark_cluster.py b/benchmark_cluster.py
@@ -0,0 +1,37 @@
+import quail
+import time
+import numpy as np
+import pandas as pd
+
+def run_benchmark():
+    print("Generating data...")
+    # 20 subjects, 10 lists each, 16 items
+    n_subj = 20
+    n_lists = 10
+    list_len = 16
+
+    # Create random items
+    # Pres: ints
+    pres = [[[str(k) for k in range(list_len)] for j in range(n_lists)] for i in range(n_subj)]
+    # Rec: random shuffle of pres
+    rec = [[[str(k) for k in np.random.permutation(range(list_len))] for j in range(n_lists)] for i in range(n_subj)]
+
+    # Features: Scalar 'val'
+    features = [{'item': str(k), 'val': float(k)} for k in range(list_len)]
+    # Expand features to 3D
+    pres_feat = [[features for j in range(n_lists)] for i in range(n_subj)]
+
+    egg = quail.Egg(pres=pres, rec=rec, features=pres_feat)
+
+    print("Starting fingerprint analysis...")
+    start = time.time()
+    # Compute fingerprint with permutations (expensive part)
+    # 10 perms
+    res = egg.analyze('fingerprint', n_perms=10, permute=True, parallel=False)
+    end = time.time()
+
+    print(f"Analysis complete in {end - start:.2f} seconds.")
+    print(f"Result shape: {res.data.shape}")
+
+if __name__ == '__main__':
+    run_benchmark()
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diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
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diff --git a/docs/_build/doctrees/tutorial/.ipynb_checkpoints/optimal presenter-checkpoint.doctree b/docs/_build/doctrees/tutorial/.ipynb_checkpoints/optimal presenter-checkpoint.doctree
diff --git a/docs/_build/doctrees/tutorial/.ipynb_checkpoints/speech_decoding-checkpoint.doctree b/docs/_build/doctrees/tutorial/.ipynb_checkpoints/speech_decoding-checkpoint.doctree
diff --git a/docs/_build/doctrees/tutorial/advanced_plotting.doctree b/docs/_build/doctrees/tutorial/advanced_plotting.doctree
diff --git a/docs/_build/doctrees/tutorial/basic_analyze_and_plot.doctree b/docs/_build/doctrees/tutorial/basic_analyze_and_plot.doctree
diff --git a/docs/_build/doctrees/tutorial/egg.doctree b/docs/_build/doctrees/tutorial/egg.doctree
diff --git a/docs/_build/doctrees/tutorial/fingerprint.doctree b/docs/_build/doctrees/tutorial/fingerprint.doctree
diff --git a/docs/_build/doctrees/tutorial/optimal presenter.doctree b/docs/_build/doctrees/tutorial/optimal presenter.doctree
diff --git a/docs/_build/doctrees/tutorial/speech_decoding.doctree b/docs/_build/doctrees/tutorial/speech_decoding.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c7fe727da017c84d722f3c6469a0ea04
+config: 06f8dbfe2189432395f7cdc548d7e758
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_downloads/auto_examples_jupyter.zip b/docs/_build/html/_downloads/auto_examples_jupyter.zip
diff --git a/docs/_build/html/_downloads/auto_examples_python.zip b/docs/_build/html/_downloads/auto_examples_python.zip
diff --git a/docs/_build/html/_downloads/crack_egg.ipynb b/docs/_build/html/_downloads/crack_egg.ipynb
diff --git a/docs/_build/html/_downloads/crack_egg.py b/docs/_build/html/_downloads/crack_egg.py
diff --git a/docs/_build/html/_downloads/create_egg.ipynb b/docs/_build/html/_downloads/create_egg.ipynb
diff --git a/docs/_build/html/_downloads/create_egg.py b/docs/_build/html/_downloads/create_egg.py
diff --git a/docs/_build/html/_downloads/create_multisubject_egg.ipynb b/docs/_build/html/_downloads/create_multisubject_egg.ipynb
diff --git a/docs/_build/html/_downloads/create_multisubject_egg.py b/docs/_build/html/_downloads/create_multisubject_egg.py