pytest-runner requirement removed for conda build

doc/index.rst

@@ -3,12 +3,10 @@
 TRamWAy
 =======
 
-|tramway| is a tool to analyse single molecule dynamics from their locations or trajectories.
+|tramway| is a tool to analyse single molecule dynamics using their locations or trajectories.
+Parameters of single molecule dynamics such as diffusivity, drift, force and potential energy are resolved in space and time.
 
-Parameters of single molecule dynamics such as diffusivity, drift, force and potential energy can be estimated across space and time.
-Maps of these parameters are thus generated and additional tools such as curl calculation for force maps may extract further information about the dynamics.
-
-|tramway| has been designed as a modular Python library that may accomodate additional plugins for the main processing steps, namely the tessellation and inference steps.
+|tramway| has been designed as a modular Python library that may accomodate additional plugins to sample the localization microscopy data and infer model parameters in microdomains.
 
 The full code is distributed under :ref:`CeCILL license <license>` and is available at `github`_.
 
@@ -19,19 +17,19 @@ Features
 
 .. * :ref:`deconvolution <deconvolution>` of stacks of images
 
-* tracking of localization data
+* tracking of localization microscopy data
 * spatial :ref:`tessellation <tessellation>` and temporal segmentation
-* :ref:`inference <inference>` of diffusivity, drift, force and potential energy
+* :ref:`inference <inference>` of diffusivity, drift, force, potential energy, etc.
 * analyses of the estimated force, such as curl calculation and :ref:`Bayes factor <inference_bayes_factor>` calculation to distinguish between interactions and spurious forces
-* and more: generation of random-walk trajectories, plotting utilities, etc
+* and more: generation of random walk trajectories, plotting utilities, etc
 
 
 
 -------------
 Quick example
 -------------
 
-Maps of diffusivity and potential energy estimates can be generated from molecule trajectories with as few as three commands:
+Maps of diffusivity and effective potential estimates can be generated from molecule trajectories with as few as three commands:
 
 .. code-block:: shell
 	:linenos:
@@ -43,9 +41,9 @@ Maps of diffusivity and potential energy estimates can be generated from molecul
 * Single molecule locations and/or trajectories are usually stored in text files.
   In the above example, such an input file is named *trajectories.txt*.
 * The first step (``1``) consists of importing these location data and tessellating the space into cells of adequate size. 
-  The *GWR* method grows a graph that fits closely the molecule density.
-* All the analyses derivating from a same dataset are stored in a single *.rwa* file.
-* The second step (``2``) consists of infering parameters of the molecule dynamics,
+  The *GWR* method grows a graph that fits molecule density.
+* All the analysis results derived from a same dataset are stored in a single *.rwa* file.
+* The second step (``2``) consists of inferring parameters of the molecule dynamics,
   for example local diffusivities and potential energies (*DV* mode).
   This may take a while and recruit most of the processing units of the host.
 * The estimated values can now be visualized as 2D maps (``3``).
@@ -71,7 +69,6 @@ The equivalent Python code is:
 	map_plot('my_analyses.rwa')
 
 
-
 --------------
 Where to start
 --------------

meta.yaml

@@ -0,0 +1,54 @@
+
+{% set name = "tramway" %}
+{% set version = "0.5rc4" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  #url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  #sha256: 80226d3949c210f1c9b22ecb884080f34869a033c3491f40c540cec094bfae7f
+  git_url: https://github.com/decbaycomp/tramway.git
+
+build:
+  noarch: python
+  number: 0
+  script: "{{ PYTHON }} -m pip install .[roi,animate] -vv"
+
+requirements:
+  #build:
+  #  - pytest-runner
+  host:
+    - pip
+    - python >=3.6
+  run:
+    - hdf5
+    - python >=3.6
+    - rwa-python
+
+test:
+  imports:
+    - tramway
+  requires:
+    - pytest
+  commands:
+    - pytest tests/test_core.py
+    - pytest tests/test_analyzer.py
+    - pytest tests/test_analyzer_pipeline.py::test_LocalHost
+  source_files:
+    - tests/test_core.py
+    - tests/test_analyzer.py
+    - tests/test_analyzer_pipeline.py
+
+about:
+  home: https://github.com/DecBayComp/TRamWAy
+  license: CECILL-2.1
+  license_family: GPL
+  license_file: LICENSE
+  summary: 'The RAndom Walk AnalYzer: analysis toolbox for localization microscopy data'
+  doc_url: https://tramway.readthedocs.io/
+
+extra:
+  recipe-maintainers:
+    - DecBayComp

setup.py

@@ -10,7 +10,6 @@
         'animate':  ['opencv-python', 'scikit-image', 'tqdm'],
         'roi':  ['polytope', 'cvxopt', 'tqdm'],
         'webui':    ['bokeh>=2.0.2', 'selenium']}
-setup_requires = ['pytest-runner']
 tests_require = ['pytest']
 
 
@@ -32,7 +31,6 @@
     classifiers = [
         'Intended Audience :: Science/Research',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',

tramway/analyzer/env/environments.py

@@ -1585,7 +1585,10 @@ def scratch(cls, username):
         raise NotImplementedError
     def __init__(self, **kwargs):
         SlurmOverSSH.__init__(self, **kwargs)
-        self.interpreter = 'singularity exec -H $HOME -B /pasteur tramway-hpc-210114.sif python3.6 -s'
+        if os.path.isdir('/pasteur'):
+            self.interpreter = 'singularity exec -H $HOME -B /pasteur tramway-hpc-210114.sif python3.6 -s'
+        else:
+            self.interpreter = 'singularity exec -H $HOME tramway-hpc-210114.sif python3.6 -s'
         self.ssh.host = self.hostname()
     @property
     def username(self):