default container updated

doc/conf.py

@@ -85,7 +85,7 @@ def __getattr__(cls, name):
 # The short X.Y version.
 version = u'0.6'
 # The full version, including alpha/beta/rc tags.
-release = u'0.6'
+release = u'0.6.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

meta.yaml

@@ -1,20 +1,20 @@
 
 {% set name = "tramway" %}
-{% set version = "0.5" %}
+{% set version = "0.6" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/DecBayComp/TRamWAy/archive/v{{ version }}.tar.gz
-  sha256: 6e26acc4280dfb6d93f1d5009009927dd1fa2e63f18a2c4e160b9a1e40534bc6
+  sha256: 3a6bb7359ee58a247bf8b4b8bb7efb29a99599c2ce8aea78a6f269f3818bbe41
 
 build:
   skip: True  # [py<36]
   number: 0
   # remove polytope as soon as the package is available in some conda channel, if it ever is
-  script: "{{ PYTHON }} -m pip install --no-deps https://pypi.io/packages/source/p/polytope/polytope-0.2.3.tar.gz . -vv"
+  script: "{{ PYTHON }} -m pip install --no-deps . -vv"
 
 requirements:
   host:
@@ -24,8 +24,9 @@ requirements:
     - hdf5
     - python
     - rwa-python
-    - matplotlib
+    - matplotlib-base
     - cvxopt
+    - polytope
     - tqdm
     - scikit-image
     - stopit  # [not win]

setup.py

@@ -21,7 +21,7 @@
 
 setup(
     name = 'tramway',
-    version = '0.6',
+    version = '0.6.1',
     description = 'TRamWAy',
     long_description = long_description,
     url = 'https://github.com/DecBayComp/TRamWAy',

tramway/analyzer/env/environments.py

@@ -1244,7 +1244,7 @@ def dispatch(self, **kwargs):
             return True
     @classmethod
     def remote_dependencies(cls):
-        return None
+        return ''
     def exec_inline_python(self, inline_code):
         python = []
         if self.remote_dependencies():
@@ -1814,7 +1814,7 @@ def get_container_url(self, container=None):
                 }.get(container, None)
     @classmethod
     def default_container(cls):
-        return 'tramway-hpc-210715.sif'
+        return 'tramway-hpc-210720.sif'
     def setup(self, *argv, **kwargs):
         SlurmOverSSH.setup(self, *argv, **kwargs)
         if self.submit_side:

tramway/analyzer/images/__init__.py

@@ -140,6 +140,15 @@ def cropping_bounds(self, bounding_box, relative=True):
         Pixels are assumed to be centered on their indices in the array,
         when plotted.
 
+        .. note::
+
+            `cropping_bounds` is supposed to work well in combination with
+            `crop_frames`.
+            However, a notable exception is out-of-bounds indices.
+            `crop_frames` adjusts the size of the pixel matrix wrt the image,
+            while `cropping_bounds` does not min-max the returned indices wrt
+            the natural bounds of the image.
+
         Arguments:
 
             bounding_box (tuple): pair of ndarrays (lower bound, upper bound).
@@ -164,6 +173,10 @@ def crop_frames(self, bounding_box, index=None, return_time=False):
         Generator function; iterates and crops the image frames, similarly to
         :meth:`as_frames`.
 
+        .. note::
+
+            Time bounds are not supported yet.
+
         Arguments:
 
             bounding_box (tuple): pair of NumPy arrays (lower bound, upper bound).
@@ -173,10 +186,6 @@ def crop_frames(self, bounding_box, index=None, return_time=False):
 
             return_time (bool): return time along with cropped image frames, as first item.
 
-        .. note::
-
-            Time bounds are not supported yet.
-
         """
         lb, ub = bounding_box
         if 2<lb.size:
@@ -241,7 +250,7 @@ def to_color_movie(self, output_file=None, fourcc='VP80', colormap='gray',
             linecolor (*str* or 3-column float array): color for trajectories;
                 value :const:`None` defaults to red.
 
-            linewidth (int or float): trajectory line width
+            linewidth (*int* or *float*): trajectory line width.
 
             magnification (*int* or *str*): the original image pixels can be represented as
                 square-patches of `magnification` video pixel side;