WIP: move cluster.manual to cluster

cortex-lab · Nov 23, 2016 · 6a6e22e · 6a6e22e
1 parent 3f6ead3
commit 6a6e22e
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Showing 21 changed files with 19 additions and 26 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -5,7 +5,7 @@ recursive-include tests *
 recursive-include phy/electrode/probes *.prb
 recursive-include phy/plot/glsl *.vert *.frag *.glsl
 recursive-include phy/plot/static *.npy *.gz *.txt
-recursive-include phy/cluster/manual/static *.html *.css
+recursive-include phy/cluster/static *.html *.css
 recursive-include phy/gui/static *.html *.css *.js
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@
 
 **phy** contains the following subpackages:
 
-* **phy.cluster.manual**: an API for manual sorting, used to create graphical interfaces for neurophysiological data
+* **phy.cluster**: an API for manual sorting, used to create graphical interfaces for neurophysiological data
 * **phy.gui**: a generic API for creating desktop applications with PyQt.
 * **phy.plot**: a generic API for creating high-performance plots with VisPy (using the graphics processor via OpenGL)
 

diff --git a/docs/cluster-manual.md → docs/clustering.md b/docs/cluster-manual.md → docs/clustering.md
@@ -1,6 +1,6 @@
 # Manual clustering
 
-The `phy.cluster.manual` package provides manual clustering routines. The components can be used independently in a modular way.
+The `phy.cluster` package provides manual clustering routines. The components can be used independently in a modular way.
 
 ## Clustering
 
@@ -84,7 +84,7 @@ The `ClusterMeta` class implement the logic of assigning metadata to every clust
 Here is an example.
 
 ```python
->>> from phy.cluster.manual import ClusterMeta
+>>> from phy.cluster import ClusterMeta
 >>> cm = ClusterMeta()
 ```
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -3,7 +3,7 @@ pages:
 - Home: 'index.md'
 - GUI: 'gui.md'
 - Plotting: 'plot.md'
-- Manual clustering: 'cluster-manual.md'
+- Manual clustering: 'clustering.md'
 - Configuration and plugin system: 'config.md'
 - Command-line interface: 'cli.md'
 theme: readthedocs
diff --git a/phy/cluster/__init__.py b/phy/cluster/__init__.py
@@ -1,6 +1,9 @@
 # -*- coding: utf-8 -*-
 # flake8: noqa
 
-"""Automatic and manual clustering facilities."""
+"""Manual clustering facilities."""
 
-from . import manual
+from ._utils import ClusterMeta
+from .clustering import Clustering
+from .gui_component import ManualClustering
+from .views import WaveformView, TraceView, FeatureView, CorrelogramView
diff --git a/phy/cluster/manual/_history.py → phy/cluster/_history.py b/phy/cluster/manual/_history.py → phy/cluster/_history.py
diff --git a/phy/cluster/manual/_utils.py → phy/cluster/_utils.py b/phy/cluster/manual/_utils.py → phy/cluster/_utils.py
diff --git a/phy/cluster/manual/clustering.py → phy/cluster/clustering.py b/phy/cluster/manual/clustering.py → phy/cluster/clustering.py
diff --git a/phy/cluster/manual/controller.py → phy/cluster/controller.py b/phy/cluster/manual/controller.py → phy/cluster/controller.py
@@ -11,14 +11,14 @@
 
 import numpy as np
 
-from phy.cluster.manual.gui_component import ManualClustering
-from phy.cluster.manual.views import (WaveformView,
-                                      TraceView,
-                                      FeatureView,
-                                      CorrelogramView,
-                                      select_traces,
-                                      extract_spikes,
-                                      )
+from phy.cluster.gui_component import ManualClustering
+from phy.cluster.views import (WaveformView,
+                               TraceView,
+                               FeatureView,
+                               CorrelogramView,
+                               select_traces,
+                               extract_spikes,
+                               )
 from phy.gui import GUI
 from phy.io.array import _get_data_lim, concat_per_cluster, get_excerpts
 from phy.io import Context, Selector

diff --git a/phy/cluster/manual/gui_component.py → phy/cluster/gui_component.py b/phy/cluster/manual/gui_component.py → phy/cluster/gui_component.py
diff --git a/phy/cluster/manual/__init__.py b/phy/cluster/manual/__init__.py
diff --git a/phy/cluster/manual/tests/__init__.py b/phy/cluster/manual/tests/__init__.py
diff --git a/phy/cluster/manual/tests/conftest.py → phy/cluster/tests/conftest.py b/phy/cluster/manual/tests/conftest.py → phy/cluster/tests/conftest.py
@@ -10,7 +10,7 @@
 
 import numpy as np
 
-from phy.cluster.manual.controller import Controller
+from phy.cluster.controller import Controller
 from phy.electrode.mea import staggered_positions
 from phy.io.array import (get_closest_clusters,
                           _spikes_in_clusters,

diff --git a/phy/cluster/manual/tests/test_clustering.py → phy/cluster/tests/test_clustering.py b/phy/cluster/manual/tests/test_clustering.py → phy/cluster/tests/test_clustering.py
diff --git a/phy/cluster/manual/tests/test_controller.py → phy/cluster/tests/test_controller.py b/phy/cluster/manual/tests/test_controller.py → phy/cluster/tests/test_controller.py
diff --git a/...luster/manual/tests/test_gui_component.py → phy/cluster/tests/test_gui_component.py b/...luster/manual/tests/test_gui_component.py → phy/cluster/tests/test_gui_component.py
diff --git a/phy/cluster/manual/tests/test_history.py → phy/cluster/tests/test_history.py b/phy/cluster/manual/tests/test_history.py → phy/cluster/tests/test_history.py
diff --git a/phy/cluster/manual/tests/test_utils.py → phy/cluster/tests/test_utils.py b/phy/cluster/manual/tests/test_utils.py → phy/cluster/tests/test_utils.py
diff --git a/phy/cluster/manual/tests/test_views.py → phy/cluster/tests/test_views.py b/phy/cluster/manual/tests/test_views.py → phy/cluster/tests/test_views.py
diff --git a/phy/cluster/manual/views.py → phy/cluster/views.py b/phy/cluster/manual/views.py → phy/cluster/views.py
diff --git a/tools/api.py b/tools/api.py
@@ -315,7 +315,6 @@ def generate_api_doc(package, subpackages, path=None):
     package = 'phy'
     subpackages = [
                    'cluster',
-                   'cluster.manual',
                    'electrode',
                    'gui',
                    'io',