Latest version works local perfect

breimanntools · Sep 20, 2023 · b1451f0 · b1451f0
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diff --git a/aaanalysis/data_loader/__pycache__/data_loader.cpython-39.pyc b/aaanalysis/data_loader/__pycache__/data_loader.cpython-39.pyc
diff --git a/aaanalysis/data_loader/data_loader.py b/aaanalysis/data_loader/data_loader.py
@@ -153,7 +153,7 @@ def load_dataset(name: str = "INFO",
     Load protein benchmarking datasets.
 
     The benchmarks are categorized into amino acid ('AA'), domain ('DOM'), and sequence ('SEQ') level
-    datasets. Use default settings (``name='INFO'``) for an overview table. Detailed analysis is in .
+    datasets. Use default settings (``name='INFO'``) for an overview table. Detailed analysis is in [Breimann23a]_.
 
     Parameters
     ----------
@@ -186,8 +186,8 @@ def load_dataset(name: str = "INFO",
 
     See also
     --------
-    See an overview of all benchmarks in  and a detailed usage tutorial in the
-    data loader tutorial.
+    See an overview of all benchmarks in :ref:`1_overview_benchmarks` and a detailed usage tutorial in the
+    `data loader tutorial <tutorials/tutorial2_data_loader.ipynb>`_.
 
     Examples
     --------
@@ -242,7 +242,7 @@ def load_scales(name="scales", just_aaindex=False, unclassified_in=True):
     """
     Load amino acid scales, scale classification (AAontology), or scale evaluation.
 
-    A thorough analysis of the residue and sequence datasets can be found in.
+    A thorough analysis of the residue and sequence datasets can be found in [Breimann23a]_.
 
     Parameters
     ----------

diff --git a/docs/build/doctrees/api.doctree b/docs/build/doctrees/api.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/generated/aaanalysis.AAclust.doctree b/docs/build/doctrees/generated/aaanalysis.AAclust.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.CPP.doctree b/docs/build/doctrees/generated/aaanalysis.CPP.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.CPPPlot.doctree b/docs/build/doctrees/generated/aaanalysis.CPPPlot.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.SequenceFeature.doctree b/docs/build/doctrees/generated/aaanalysis.SequenceFeature.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.dPULearn.doctree b/docs/build/doctrees/generated/aaanalysis.dPULearn.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.load_dataset.doctree b/docs/build/doctrees/generated/aaanalysis.load_dataset.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.load_scales.doctree b/docs/build/doctrees/generated/aaanalysis.load_scales.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.plot_gcfs.doctree b/docs/build/doctrees/generated/aaanalysis.plot_gcfs.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.plot_get_cdict.doctree b/docs/build/doctrees/generated/aaanalysis.plot_get_cdict.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.plot_get_cmap.doctree b/docs/build/doctrees/generated/aaanalysis.plot_get_cmap.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.plot_set_legend.doctree b/docs/build/doctrees/generated/aaanalysis.plot_set_legend.doctree
diff --git a/docs/build/doctrees/generated/aaanalysis.plot_settings.doctree b/docs/build/doctrees/generated/aaanalysis.plot_settings.doctree
diff --git a/docs/build/doctrees/index/tables.doctree b/docs/build/doctrees/index/tables.doctree
diff --git a/docs/build/doctrees/index/usage_principles/xai.doctree b/docs/build/doctrees/index/usage_principles/xai.doctree
diff --git a/docs/build/doctrees/usage_principles.doctree b/docs/build/doctrees/usage_principles.doctree
diff --git a/docs/build/html/_downloads/fe02006031f96dc9a3a8b158e5899dae/aaanalysis-CPPPlot-1.py b/docs/build/html/_downloads/fe02006031f96dc9a3a8b158e5899dae/aaanalysis-CPPPlot-1.py
@@ -0,0 +1,6 @@
+import matplotlib.pyplot as plt
+import aaanalysis as aa
+sf = aa.SequenceFeature()
+df_seq = aa.load_dataset(name='SEQ_DISULFIDE', min_len=100)
+labels = list(df_seq["label"])
+df_parts = sf.get_df_parts(df_seq=df_seq, jmd_n_len=10, jmd_c_len=10)
diff --git a/.../html/_images/social_previews/summary_generated_aaanalysis.AAclust_20fb7a30.png b/.../html/_images/social_previews/summary_generated_aaanalysis.AAclust_20fb7a30.png
diff --git a/.../html/_images/social_previews/summary_generated_aaanalysis.CPPPlot_5461b2c2.png b/.../html/_images/social_previews/summary_generated_aaanalysis.CPPPlot_5461b2c2.png
diff --git a/...uild/html/_images/social_previews/summary_generated_aaanalysis.CPP_6a66faaa.png b/...uild/html/_images/social_previews/summary_generated_aaanalysis.CPP_6a66faaa.png
diff --git a/...mages/social_previews/summary_generated_aaanalysis.SequenceFeature_6c1c9b33.png b/...mages/social_previews/summary_generated_aaanalysis.SequenceFeature_6c1c9b33.png
diff --git a/...html/_images/social_previews/summary_generated_aaanalysis.dPULearn_44ddb18b.png b/...html/_images/social_previews/summary_generated_aaanalysis.dPULearn_44ddb18b.png
diff --git a/.../_images/social_previews/summary_generated_aaanalysis.load_dataset_c5bd8cb0.png b/.../_images/social_previews/summary_generated_aaanalysis.load_dataset_c5bd8cb0.png
diff --git a/...l/_images/social_previews/summary_generated_aaanalysis.load_scales_65ee1b77.png b/...l/_images/social_previews/summary_generated_aaanalysis.load_scales_65ee1b77.png
diff --git a/...tml/_images/social_previews/summary_generated_aaanalysis.plot_gcfs_c60ff7c4.png b/...tml/_images/social_previews/summary_generated_aaanalysis.plot_gcfs_c60ff7c4.png
diff --git a/...images/social_previews/summary_generated_aaanalysis.plot_get_cdict_7e3963aa.png b/...images/social_previews/summary_generated_aaanalysis.plot_get_cdict_7e3963aa.png
diff --git a/..._images/social_previews/summary_generated_aaanalysis.plot_get_cmap_6e0e4868.png b/..._images/social_previews/summary_generated_aaanalysis.plot_get_cmap_6e0e4868.png
diff --git a/...mages/social_previews/summary_generated_aaanalysis.plot_set_legend_0daa943e.png b/...mages/social_previews/summary_generated_aaanalysis.plot_set_legend_0daa943e.png
diff --git a/..._images/social_previews/summary_generated_aaanalysis.plot_settings_070d72d4.png b/..._images/social_previews/summary_generated_aaanalysis.plot_settings_070d72d4.png
diff --git a/...ld/html/_images/social_previews/summary_index_usage_principles_xai_c236df6c.png b/...ld/html/_images/social_previews/summary_index_usage_principles_xai_c236df6c.png
diff --git a/...ld/html/_images/social_previews/summary_index_usage_principles_xai_c56d9fa3.png b/...ld/html/_images/social_previews/summary_index_usage_principles_xai_c56d9fa3.png
diff --git a/docs/build/html/_images/social_previews/summary_usage_principles_25466335.png b/docs/build/html/_images/social_previews/summary_usage_principles_25466335.png
diff --git a/docs/build/html/_images/social_previews/summary_usage_principles_94300a05.png b/docs/build/html/_images/social_previews/summary_usage_principles_94300a05.png
diff --git a/docs/build/html/_sources/api.rst.txt b/docs/build/html/_sources/api.rst.txt
@@ -21,8 +21,8 @@ Data
 .. autosummary::
     :toctree: generated/
 
-    .. aaanalysis.load_dataset
-    .. aaanalysis.load_scales
+    aaanalysis.load_dataset
+    aaanalysis.load_scales
 
 .. _feature_engineering_api:
 
@@ -31,10 +31,10 @@ Feature Engineering
 .. autosummary::
     :toctree: generated/
 
-    .. aaanalysis.AAclust
-    .. aaanalysis.SequenceFeature
-    .. aaanalysis.CPP
-    .. aaanalysis.CPPPlot
+    aaanalysis.AAclust
+    aaanalysis.SequenceFeature
+    aaanalysis.CPP
+    aaanalysis.CPPPlot
 
 .. _pu_learning_api:
 
@@ -43,7 +43,7 @@ PU Learning
 .. autosummary::
     :toctree: generated/
 
-    .. aaanalysis.dPULearn
+    aaanalysis.dPULearn
 
 .. _plot_api:
 
@@ -61,9 +61,9 @@ Plot Utilities
 .. autosummary::
     :toctree: generated/
 
-    .. aaanalysis.plot_settings
-    .. aaanalysis.plot_set_legend
-    .. aaanalysis.plot_gcfs
-    .. aaanalysis.plot_get_cmap
-    .. aaanalysis.plot_get_cdict
+    aaanalysis.plot_settings
+    aaanalysis.plot_set_legend
+    aaanalysis.plot_gcfs
+    aaanalysis.plot_get_cmap
+    aaanalysis.plot_get_cdict
 
diff --git a/docs/build/html/_sources/generated/aaanalysis.AAclust.rst.txt b/docs/build/html/_sources/generated/aaanalysis.AAclust.rst.txt
@@ -0,0 +1,28 @@
+aaanalysis.AAclust
+==================
+
+.. currentmodule:: aaanalysis
+
+.. autoclass:: AAclust
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~AAclust.__init__
+      ~AAclust.cluster_naming
+      ~AAclust.correlation
+      ~AAclust.eval
+      ~AAclust.fit
+      ~AAclust.get_cluster_centers
+      ~AAclust.get_cluster_medoids
+
+
+
+
+
+
diff --git a/docs/build/html/_sources/generated/aaanalysis.CPP.rst.txt b/docs/build/html/_sources/generated/aaanalysis.CPP.rst.txt
@@ -0,0 +1,24 @@
+aaanalysis.CPP
+==============
+
+.. currentmodule:: aaanalysis
+
+.. autoclass:: CPP
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CPP.__init__
+      ~CPP.eval
+      ~CPP.run
+
+
+
+
+
+
diff --git a/docs/build/html/_sources/generated/aaanalysis.CPPPlot.rst.txt b/docs/build/html/_sources/generated/aaanalysis.CPPPlot.rst.txt
@@ -0,0 +1,25 @@
+aaanalysis.CPPPlot
+==================
+
+.. currentmodule:: aaanalysis
+
+.. autoclass:: CPPPlot
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CPPPlot.__init__
+      ~CPPPlot.heatmap
+      ~CPPPlot.profile
+      ~CPPPlot.update_seq_size
+
+
+
+
+
+
diff --git a/docs/build/html/_sources/generated/aaanalysis.SequenceFeature.rst.txt b/docs/build/html/_sources/generated/aaanalysis.SequenceFeature.rst.txt
@@ -0,0 +1,30 @@
+aaanalysis.SequenceFeature
+==========================
+
+.. currentmodule:: aaanalysis
+
+.. autoclass:: SequenceFeature
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~SequenceFeature.__init__
+      ~SequenceFeature.add_dif
+      ~SequenceFeature.add_feat_value
+      ~SequenceFeature.add_position
+      ~SequenceFeature.feat_matrix
+      ~SequenceFeature.feat_names
+      ~SequenceFeature.get_df_parts
+      ~SequenceFeature.get_features
+      ~SequenceFeature.get_split_kws
+
+
+
+
+
+
diff --git a/docs/build/html/_sources/generated/aaanalysis.dPULearn.rst.txt b/docs/build/html/_sources/generated/aaanalysis.dPULearn.rst.txt
@@ -0,0 +1,24 @@
+aaanalysis.dPULearn
+===================
+
+.. currentmodule:: aaanalysis
+
+.. autoclass:: dPULearn
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~dPULearn.__init__
+      ~dPULearn.eval
+      ~dPULearn.fit
+
+
+
+
+
+
diff --git a/docs/build/html/_sources/generated/aaanalysis.load_dataset.rst.txt b/docs/build/html/_sources/generated/aaanalysis.load_dataset.rst.txt
@@ -0,0 +1,6 @@
+aaanalysis.load\_dataset
+========================
+
+.. currentmodule:: aaanalysis
+
+.. autofunction:: load_dataset
diff --git a/docs/build/html/_sources/generated/aaanalysis.load_scales.rst.txt b/docs/build/html/_sources/generated/aaanalysis.load_scales.rst.txt
@@ -0,0 +1,6 @@
+aaanalysis.load\_scales
+=======================
+
+.. currentmodule:: aaanalysis
+
+.. autofunction:: load_scales
diff --git a/docs/build/html/_sources/generated/aaanalysis.plot_gcfs.rst.txt b/docs/build/html/_sources/generated/aaanalysis.plot_gcfs.rst.txt
@@ -0,0 +1,6 @@
+aaanalysis.plot\_gcfs
+=====================
+
+.. currentmodule:: aaanalysis
+
+.. autofunction:: plot_gcfs
diff --git a/docs/build/html/_sources/generated/aaanalysis.plot_get_cdict.rst.txt b/docs/build/html/_sources/generated/aaanalysis.plot_get_cdict.rst.txt
@@ -0,0 +1,6 @@
+aaanalysis.plot\_get\_cdict
+===========================
+
+.. currentmodule:: aaanalysis
+
+.. autofunction:: plot_get_cdict
diff --git a/docs/build/html/_sources/generated/aaanalysis.plot_get_cmap.rst.txt b/docs/build/html/_sources/generated/aaanalysis.plot_get_cmap.rst.txt
@@ -0,0 +1,6 @@
+aaanalysis.plot\_get\_cmap
+==========================
+
+.. currentmodule:: aaanalysis
+
+.. autofunction:: plot_get_cmap
diff --git a/docs/build/html/_sources/generated/aaanalysis.plot_set_legend.rst.txt b/docs/build/html/_sources/generated/aaanalysis.plot_set_legend.rst.txt
@@ -0,0 +1,6 @@
+aaanalysis.plot\_set\_legend
+============================
+
+.. currentmodule:: aaanalysis
+
+.. autofunction:: plot_set_legend
diff --git a/docs/build/html/_sources/generated/aaanalysis.plot_settings.rst.txt b/docs/build/html/_sources/generated/aaanalysis.plot_settings.rst.txt
@@ -0,0 +1,6 @@
+aaanalysis.plot\_settings
+=========================
+
+.. currentmodule:: aaanalysis
+
+.. autofunction:: plot_settings