MNT Added action for building docs and fixed deprecated methods (#34)

* added action for updating doc and fixed deprecated methods

* fix pip

* bump up python version

* python version

.github/workflows/build_docs.yml

@@ -0,0 +1,52 @@
+name: Build docs
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y inkscape
+        sudo apt-get install -y ffmpeg
+        pip install --upgrade pip
+        pip install -q wheel numpy scipy Pillow==9.5.0 matplotlib opencv-python
+        pip install -q ipython Sphinx sphinx-gallery numpydoc sphinx-rtd-theme sphinx-bootstrap-theme
+        pip install -e . --no-build-isolation
+        python -c 'import moten; print(moten.__version__)'
+
+    - name: Build documents
+      run: |
+        cd docs && make githubio-docs && cd ..
+        touch docs/build/html/.nojekyll
+
+    - name: Publish to gh-pages if tagged
+      if: startsWith(github.ref, 'refs/tags')
+      uses: JamesIves/[email protected]
+      with:
+        branch: gh-pages
+        folder: docs/build/html

docs/source/conf.py

@@ -40,15 +40,15 @@
               'sphinx.ext.viewcode',
               'sphinx.ext.napoleon',
               'sphinx_gallery.gen_gallery',
-              'sphinx_rtd_theme',
-              ]
+              'sphinx_rtd_theme'              ]
 
 
 napoleon_use_ivar = True
 autosummary_generate = True
 numpydoc_class_members_toctree = True
 numpydoc_show_class_members = True
 
+
 # # Sphinx-gallery
 sphinx_gallery_conf = {
     # path to your examples scripts

docs/source/sg_execution_times.rst

@@ -0,0 +1,49 @@
+
+:orphan:
+
+.. _sphx_glr_sg_execution_times:
+
+
+Computation times
+=================
+**00:02.412** total execution time for 5 files **from all galleries**:
+
+.. container::
+
+  .. raw:: html
+
+    <style scoped>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
+    <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
+    </style>
+    <script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script>
+    <script type="text/javascript" class="init">
+    $(document).ready( function () {
+        $('table.sg-datatable').DataTable({order: [[1, 'desc']]});
+    } );
+    </script>
+
+  .. list-table::
+   :header-rows: 1
+   :class: table table-striped sg-datatable
+
+   * - Example
+     - Time
+     - Mem (MB)
+   * - :ref:`sphx_glr_auto_examples_introduction_demo_show_filters.py` (``../../examples/introduction/demo_show_filters.py``)
+     - 00:02.412
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_introduction_demo_batching.py` (``../../examples/introduction/demo_batching.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_introduction_demo_example.py` (``../../examples/introduction/demo_example.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_introduction_demo_gabor_filters.py` (``../../examples/introduction/demo_gabor_filters.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_introduction_demo_image_coordinates.py` (``../../examples/introduction/demo_image_coordinates.py``)
+     - 00:00.000
+     - 0.0

examples/introduction/demo_show_filters.py

@@ -28,7 +28,7 @@
 
 # %%
 # (*Ignore this code block. It is needed to display the animation as a video on this website*)
-output = '../../docs/build/html/_downloads/example_moten_filter.mp4'
+output = '../../docs/build/html/_downloads/example_moten_filter.gif'
 fig = animation._fig
 title = 'Example filter:\ndirection of motion=180, spatial fq=16cpi, temporal fq=4Hz'
 fig.suptitle(title)

moten/core.py

@@ -51,7 +51,7 @@ def raw_project_stimulus(stimulus,
     # checks for 2D stimuli
     assert stimulus.ndim == 2                             # (nimages, pixels)
     assert isinstance(vhsize, tuple) and len(vhsize) == 2 # (hdim, vdim)
-    assert np.prod(vhsize) == stimulus.shape[1]        # hdim*vdim == pixels
+    assert np.prod(vhsize) == stimulus.shape[1]           # hdim*vdim == pixels
 
     # Compute responses
     nfilters = len(filters)
@@ -103,7 +103,7 @@ def project_stimulus(stimulus,
     # checks for 2D stimuli
     assert stimulus.ndim == 2                             # (nimages, pixels)
     assert isinstance(vhsize, tuple) and len(vhsize) == 2 # (hdim, vdim)
-    assert np.prod(vhsize) == stimulus.shape[1]        # hdim*vdim == pixels
+    assert np.prod(vhsize) == stimulus.shape[1]           # hdim*vdim == pixels
 
     # Compute responses
     nfilters = len(filters)

moten/pyramids.py

@@ -26,8 +26,7 @@
 __all__ = ['MotionEnergyPyramid',
            'StimulusMotionEnergy',
            'StimulusStaticGaborPyramid',
-           'DefaultPyramids',
-           ]
+           'DefaultPyramids']
 
 ##############################
 #
@@ -42,6 +41,7 @@ class MotionEnergyPyramid(object):
     are constructed and each is centered at different locations
     in the image in order to tile the stimulus.
 
+    
     Parameters
     ----------
     stimulus_vhsize : tuple of ints