Merge pull request #33 from traja-team/vae.rebase

Vae.rebase

.gitignore

@@ -77,6 +77,8 @@ target/
 
 .DS_Store
 
+# Visualstudio code file
+.vscode
 # celery beat schedule file
 celerybeat-schedule
 
@@ -111,8 +113,17 @@ _build/
 
 # BUILD FILES
 *.zip
+hypers.json
+model
 
 docs/source/gallery
 docs/source/savefig
 docs/source/reference
-docs/source/autoexamples
+
+# Editor files
+*.swp
+*.swo
+
+
+# Model parameter files
+*.pt

.travis.yml

@@ -5,8 +5,8 @@ dist: xenial
 language: python
 
 python:
- - '3.6'
  - '3.7'
+ - '3.8'
 
 git:
   depth: false
@@ -23,23 +23,22 @@ before_install:
   - sudo chmod 2777 /usr/local/lib/R/site-library
 
 install:
- - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- - bash miniconda.sh -b -p $HOME/miniconda
- - export PATH="$HOME/miniconda/bin:$PATH"
- - hash -r
- - conda config --set always_yes yes --set changeps1 no
- - conda update -q conda
-
- # Update dependencies
- - conda env create -n test-environment -f environment.yml python=$TRAVIS_PYTHON_VERSION
- - source activate test-environment
- # Doc/Test requirements
- - pip install -r docs/requirements.txt
- - pip install .
-
+- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  -O miniconda.sh
+- bash miniconda.sh -b -p $HOME/miniconda
+- export PATH="$HOME/miniconda/bin:$PATH"
+- hash -r
+- conda config --set always_yes yes --set changeps1 no
+- conda update -q conda
+- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION 
+- source activate test-environment
+- pip install -r requirements-dev.txt
+- pip install -r docs/requirements.txt
+- pip install --upgrade pytest flake8 sphinx
+- pip install .
 script:
  - cd docs && make doctest && cd ..
- - py.test . --cov-report term --cov=traja --ignore tests/test_rutils.py
+ - py.test .
 
 after_success:
  - codecov

docs/neuralnets/train_lstm.py

@@ -0,0 +1,17 @@
+
+"""
+Train LSTM model for time series forecasting
+"""
+import traja
+from traja.model import LSTM 
+from traja.datasets import dataset
+
+df = traja.TrajaDataFrame({"x": [0, 1, 2, 3, 4], "y": [1, 3, 2, 4, 5]})
+
+# Dataloader
+
+# Model instance
+
+# Trainer
+
+

docs/requirements.txt

@@ -1,17 +1,17 @@
-pandas
-ipython
-numpy
+pandas>=1.2.0
+numpy==1.18.5
 matplotlib
 shapely
 scipy
+sklearn
 sphinx
 sphinx-gallery
-fastdtw
-pillow
-tzlocal
 sphinx_rtd_theme
+fastdtw
+plotly
+networkx
+seaborn
+torch
 pytest
-pytest-cov
-codecov
-readline
-rpy2
+h5py
+ipython

docs/source/reference/traja.TrajaDataFrame.examples

@@ -1,40 +1,99 @@
 
 
 Examples using ``traja.TrajaDataFrame``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="3D Plotting with traja">
 
 .. only:: html
 
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_3d_thumb.png
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_3d_thumb.png
+     :alt: 3D Plotting with traja
 
-        :ref:`sphx_glr_gallery_plot_3d.py`
+     :ref:`sphx_glr_gallery_plot_3d.py`
 
 .. raw:: html
 
     </div>
 
 .. only:: not html
 
-    * :ref:`sphx_glr_gallery_plot_3d.py`
+ * :ref:`sphx_glr_gallery_plot_3d.py`
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Basic plotting with traja">
+    <div class="sphx-glr-thumbcontainer" tooltip="Average direction for each grid cell">
 
 .. only:: html
 
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_with_traja_thumb.png
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_average_direction_thumb.png
+     :alt: Average direction for each grid cell
 
-        :ref:`sphx_glr_gallery_plot_with_traja.py`
+     :ref:`sphx_glr_gallery_plot_average_direction.py`
 
 .. raw:: html
 
     </div>
 
 .. only:: not html
 
-    * :ref:`sphx_glr_gallery_plot_with_traja.py`
+ * :ref:`sphx_glr_gallery_plot_average_direction.py`
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Plotting Multiple Trajectories">
+
+.. only:: html
+
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_collection_thumb.png
+     :alt: Plotting Multiple Trajectories
+
+     :ref:`sphx_glr_gallery_plot_collection.py`
+
+.. raw:: html
+
+    </div>
+
+.. only:: not html
+
+ * :ref:`sphx_glr_gallery_plot_collection.py`
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Comparing">
+
+.. only:: html
+
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_comparing_thumb.png
+     :alt: Comparing
+
+     :ref:`sphx_glr_gallery_plot_comparing.py`
+
+.. raw:: html
+
+    </div>
+
+.. only:: not html
+
+ * :ref:`sphx_glr_gallery_plot_comparing.py`
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Plotting trajectories on a grid">
+
+.. only:: html
+
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_grid_thumb.png
+     :alt: Plotting trajectories on a grid
+
+     :ref:`sphx_glr_gallery_plot_grid.py`
+
+.. raw:: html
+
+    </div>
+
+.. only:: not html
+
+ * :ref:`sphx_glr_gallery_plot_grid.py`

docs/source/reference/traja.generate.examples

@@ -1,112 +1,99 @@
 
 
 Examples using ``traja.generate``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="3D Plotting with traja">
 
 .. only:: html
 
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_3d_thumb.png
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_3d_thumb.png
+     :alt: 3D Plotting with traja
 
-        :ref:`sphx_glr_gallery_plot_3d.py`
+     :ref:`sphx_glr_gallery_plot_3d.py`
 
 .. raw:: html
 
     </div>
 
 .. only:: not html
 
-    * :ref:`sphx_glr_gallery_plot_3d.py`
+ * :ref:`sphx_glr_gallery_plot_3d.py`
 
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="Average direction for each grid cell">
 
 .. only:: html
 
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_average_direction_thumb.png
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_average_direction_thumb.png
+     :alt: Average direction for each grid cell
 
-        :ref:`sphx_glr_gallery_plot_average_direction.py`
+     :ref:`sphx_glr_gallery_plot_average_direction.py`
 
 .. raw:: html
 
     </div>
 
 .. only:: not html
 
-    * :ref:`sphx_glr_gallery_plot_average_direction.py`
+ * :ref:`sphx_glr_gallery_plot_average_direction.py`
 
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="Plotting Multiple Trajectories">
 
 .. only:: html
 
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_collection_thumb.png
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_collection_thumb.png
+     :alt: Plotting Multiple Trajectories
 
-        :ref:`sphx_glr_gallery_plot_collection.py`
+     :ref:`sphx_glr_gallery_plot_collection.py`
 
 .. raw:: html
 
     </div>
 
 .. only:: not html
 
-    * :ref:`sphx_glr_gallery_plot_collection.py`
+ * :ref:`sphx_glr_gallery_plot_collection.py`
 
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="Comparing">
 
 .. only:: html
 
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_comparing_thumb.png
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_comparing_thumb.png
+     :alt: Comparing
 
-        :ref:`sphx_glr_gallery_plot_comparing.py`
+     :ref:`sphx_glr_gallery_plot_comparing.py`
 
 .. raw:: html
 
     </div>
 
 .. only:: not html
 
-    * :ref:`sphx_glr_gallery_plot_comparing.py`
+ * :ref:`sphx_glr_gallery_plot_comparing.py`
 
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="Plotting trajectories on a grid">
 
 .. only:: html
 
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_grid_thumb.png
+ .. figure:: /gallery/images/thumb/sphx_glr_plot_grid_thumb.png
+     :alt: Plotting trajectories on a grid
 
-        :ref:`sphx_glr_gallery_plot_grid.py`
+     :ref:`sphx_glr_gallery_plot_grid.py`
 
 .. raw:: html
 
     </div>
 
 .. only:: not html
 
-    * :ref:`sphx_glr_gallery_plot_grid.py`
-
-.. raw:: html
-
-    <div class="sphx-glr-thumbcontainer" tooltip="Basic plotting with traja">
-
-.. only:: html
-
-    .. figure:: /gallery/images/thumb/sphx_glr_plot_with_traja_thumb.png
-
-        :ref:`sphx_glr_gallery_plot_with_traja.py`
-
-.. raw:: html
-
-    </div>
-
-.. only:: not html
-
-    * :ref:`sphx_glr_gallery_plot_with_traja.py`
+ * :ref:`sphx_glr_gallery_plot_grid.py`

requirements-dev.txt

@@ -1,9 +1,14 @@
+pandas>=1.2.0
+numpy==1.18.5
+matplotlib
+shapely
+psutil
+scipy
+sklearn
+fastdtw
+plotly
+networkx
+seaborn
+torch
 pytest
-Sphinx
-sphinx_gallery
-sphinx_rtd_theme
-pillow
-black
-pre-commit
-pyinstaller
-pyqt5
+h5py