Merge pull request #35 from traja-team/remove-rpy2

Remove rpy2, fix actogram plotting and test

.travis.yml

@@ -18,9 +18,6 @@ cache: pip
 
 before_install:
   - sudo apt-get update
-  - sudo mkdir -p /usr/local/lib/R/site-library
-  - echo 'R_LIBS=/usr/local/lib/R/library:/usr/local/lib/R/site-library/' > ~/.Renviron
-  - sudo chmod 2777 /usr/local/lib/R/site-library
 
 install:
 - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

docs/requirements.txt

@@ -13,5 +13,8 @@ networkx
 seaborn
 torch
 pytest
+pytest-cov
+codecov
+readline
 h5py
 ipython

docs/source/conf.py

@@ -68,7 +68,6 @@
     "doc_module": ("traja",),
     "reference_url": {
         "numpy": "http://docs.scipy.org/doc/numpy",
-        "scipy": "http://docs.scipy.org/doc/scipy/reference",
         "geopandas": "https://geopandas.readthedocs.io/en/latest/",
     },
     "sphinx_gallery": None,

environment.yml

@@ -2,7 +2,6 @@ name: traja
 channels:
   - conda-forge
   - pytorch
-  - r
 dependencies:
   - ipython
   - pytorch-cpu
@@ -17,5 +16,3 @@ dependencies:
   - scipy
   - sphinx
   - pillow
-  - r-essentials
-  - r-base

setup.py

@@ -25,7 +25,7 @@ def find_version(*file_paths):
 
 requirements = ["matplotlib", "pandas", "numpy", "shapely", "scipy", "tzlocal"]
 
-extras_requirements = {"all": ["torch", "rpy2", "tzlocal", "fastdtw"]}
+extras_requirements = {"all": ["torch", "tzlocal", "fastdtw"]}
 
 this_dir = os.path.abspath(os.path.dirname(__file__))
 with open(os.path.join(this_dir, "README.rst"), encoding="utf-8") as f:

traja/plotting.py

@@ -890,22 +890,29 @@ def _process_after_plot_args(**after_plot_args):
 
 
 def color_dark(
-    series: pd.Series, ax: matplotlib.axes.Axes, start: int = 19, end: int = 7
+    series: pd.Series, ax: matplotlib.axes.Axes = None, start: int = 19, end: int = 7
 ):
     """Color dark phase in plot."""
     assert is_datetime_or_timedelta_dtype(
         series.index
     ), f"Series must have datetime index but has {type(series.index)}"
 
+    if not ax:
+        ax = plt.gca()
+
+    # get boundaries for dark times
     dark_mask = (series.index.hour >= start) | (series.index.hour < end)
     run_values, run_starts, run_lengths = find_runs(dark_mask)
 
+    # highlighting    
     for idx, is_dark in enumerate(run_values):
         if is_dark:
             start = run_starts[idx]
             end = run_starts[idx] + run_lengths[idx] - 1
             ax.axvspan(series.index[start], series.index[end], alpha=0.5, color="gray")
 
+    return ax
+
 
 def find_runs(x: pd.Series) -> (np.ndarray, np.ndarray, np.ndarray):
     """Find runs of consecutive items in an array.
@@ -920,7 +927,6 @@ def find_runs(x: pd.Series) -> (np.ndarray, np.ndarray, np.ndarray):
     # handle empty array
     if n == 0:
         return np.array([]), np.array([]), np.array([])
-
     else:
         # find run starts
         loc_run_start = np.empty(n, dtype=bool)
@@ -984,10 +990,12 @@ def plot_actogram(
        Curr Protoc Mouse Biol. 2015;5(3):271-281. Published 2015 Sep 1. doi:10.1002/9780470942390.mo140229
 
     """
-    after_plot_args, _ = _get_after_plot_args(**kwargs)
+    assert isinstance(series, pd.Series)
     assert is_datetime_or_timedelta_dtype(
         series.index
     ), f"Series must have datetime index but has {type(series.index)}"
+
+    after_plot_args, _ = _get_after_plot_args(**kwargs)    
 
     ax = series.plot(ax=ax)
     ax.set_ylabel(series.name)

traja/tests/test_plotting.py

@@ -20,15 +20,6 @@ def test_stylize_axes():
     traja.plotting.stylize_axes(collection.axes)
 
 
-def test_color_dark():
-    df = traja.generate(n=10)
-    index = pd.DatetimeIndex(range(10))
-    df.index = index
-    traja.plot(df, interactive=False)
-    ax = plt.gca()
-    traja.color_dark(df.x, ax)
-
-
 def test_sans_serif():
     traja.plotting.sans_serif()
 
@@ -64,8 +55,8 @@ def test_label_axes():
 
 
 def test_plot_actogram():
-    df = traja.generate(n=10)
-    index = pd.DatetimeIndex(range(10))
+    df = traja.generate(n=1000)
+    index = pd.date_range("2018-01-01", periods=1000, freq="T")
     df.index = index
     activity = traja.calc_displacement(df)
     activity.name = "activity"