Merge pull request #85 from yupidevs/develop

Develop
yupidevs · Nov 21, 2021 · 369fc8d · 369fc8d
2 parents d88a5e5 + 5ae4a7d
commit 369fc8d
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diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -15,8 +15,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
+      with:
+        python-version: '3.8.6'
     - name: Install Poetry
-      run: curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
+      run: curl -sSL https://install.python-poetry.org | python -
     - name: Add Poetry to path
       run: echo "${HOME}/.poetry/bin" >> $GITHUB_PATH
     - name: Config pypi token

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -14,8 +14,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
+      with:
+        python-version: '3.8.6'
     - name: Install Poetry
-      run: curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
+      run: curl -sSL https://install.python-poetry.org | python -
     - name: Add Poetry to path
       run: echo "${HOME}/.poetry/bin" >> $GITHUB_PATH
     - name: Install yupi on venv

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -28,7 +28,7 @@
 author = 'Gustavo Viera-López, Alfredo Reyes, Jorge Morgado, Ernesto Altshuler'
 
 # The full version, including alpha/beta/rc tags
-release = '0.8.1'
+release = '0.8.2'
 
 
 # -- General configuration ---------------------------------------------------
@@ -70,4 +70,4 @@
 html_static_path = ['_static']
 
 
-master_doc = 'index'
+master_doc = 'index'
diff --git a/docs/source/examples/example1.rst b/docs/source/examples/example1.rst
@@ -91,7 +91,7 @@ Langevin Generator:
 .. code-block:: python
 
    tau = (alpha / m)**-1                   # relaxation time
-   noise_scale = np.sqrt(2 / tau) * v_eq   # scale parameter of noise pdf
+   sigma = np.sqrt(2 / tau) * v_eq   # scale parameter of noise pdf
 
 
 Finally, we define general simulation parameters:
@@ -113,7 +113,7 @@ we just need to instantiate the class and generate the Trajectories:
 
 .. code-block:: python
 
-   lg = LangevinGenerator(tt, dim, N, dt, tau, noise_scale)
+   lg = LangevinGenerator(tt, dim, N, dt, tau, sigma)
    trajs = lg.generate()
 
 

diff --git a/docs/source/examples/example6.rst b/docs/source/examples/example6.rst
@@ -33,7 +33,7 @@ Import all the dependencies:
 .. code-block:: python
 
    import numpy as np
-   from yupi.stats import collect_at
+   from yupi.stats import collect
    from yupi.graphics import plot_hists
    from yupi.generators import DiffDiffGenerator
 
@@ -89,7 +89,7 @@ time instants:
 
 .. code-block:: python
 
-   r = [collect_at(trajs, 'rx', time=t) for t in time_instants]
+   r = [collect(trajs, at=float(t)) for t in time_instants]
 
 Then, we can plot the results:
 
@@ -118,4 +118,4 @@ Then, we can plot the results:
 -------------
 
 | [1] Chechkin, Aleksei V., et al. "Brownian yet non-Gaussian diffusion: from superstatistics to subordination of diffusing diffusivities." Physical Review X 7.2 (2017): 021002.
-| [2] Thapa, Samudrajit, et al. "Bayesian analysis of single-particle tracking data using the nested-sampling algorithm: maximum-likelihood model selection applied to stochastic-diffusivity data." Physical Chemistry Chemical Physics 20.46 (2018): 29018-29037.
+| [2] Thapa, Samudrajit, et al. "Bayesian analysis of single-particle tracking data using the nested-sampling algorithm: maximum-likelihood model selection applied to stochastic-diffusivity data." Physical Chemistry Chemical Physics 20.46 (2018): 29018-29037.