v0.1.1

.github/workflows/sierras_ci.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.9", "3.10"]
 
     steps:
       - uses: actions/checkout@master

docs/source/api.rst

@@ -25,10 +25,10 @@ Submodules
    :show-inheritance:
    :member-order: bysource
 
-``sierras.diffusion`` module
-----------------------------
+``sierras.get_diffusion_coefficient`` module
+--------------------------------------------
 
-.. automodule:: sierras.diffusion
+.. automodule:: sierras.get_diffusion_coefficient
    :members:
    :undoc-members:
    :show-inheritance:

sierras/__init__.py

@@ -37,12 +37,12 @@
 
 __author__ = "Francisco Fernandez"
 __email__ = "fernandezfrancisco2195@gmail.com"
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 
 
 # ============================================================================
 # IMPORTS
 # ============================================================================
 
 from .arrhenius import ArrheniusDiffusion  # noqa
-from .diffusion import get_diffusion_coefficient  # noqa
+from .get_diffusion_coefficient import from_msd, from_vacf  # noqa

sierras/diffusion.py → sierras/get_diffusion_coefficient.py

@@ -10,7 +10,7 @@
 # DOCS
 # ============================================================================
 
-"""Function to fit the mean square displacement."""
+"""Functions to obtain the diffusion coefficient."""
 
 # ============================================================================
 # IMPORTS
@@ -25,7 +25,7 @@
 # ============================================================================
 
 
-def get_diffusion_coefficient(
+def from_msd(
     time, msd, start=0, stop=None, ndim=3, sample_weight=None, lr_kws=None
 ):
     """To obtain the trace diffusion coefficient from mean square displacement.
@@ -77,3 +77,8 @@ def get_diffusion_coefficient(
     dcoef = reg.coef_[0] / (2 * ndim)
 
     return dcoef, reg
+
+
+def from_vacf():
+    """To obtain it from the velocity autocorrelation function."""
+    raise NotImplementedError

tests/test_diffusion.py

@@ -14,7 +14,7 @@
 
 import pytest
 
-import sierras.diffusion
+import sierras.get_diffusion_coefficient
 
 # ============================================================================
 # TESTS
@@ -31,7 +31,7 @@
         (0, 50, (0.70261868, (4.215712, -0.1003175))),
     ],
 )
-def test_get_diffusion_coefficient(start, stop, reference):
+def test_get_diffusion_coefficient_from_msd(start, stop, reference):
     """Test the linear regression to get the trace diffusion coefficient.
 
     This test uses data of a Lennard-Jones fluid in its liquid phase.
@@ -242,7 +242,7 @@ def test_get_diffusion_coefficient(start, stop, reference):
         ]
     )
 
-    dcoeff, reg = sierras.diffusion.get_diffusion_coefficient(
+    dcoeff, reg = sierras.get_diffusion_coefficient.from_msd(
         time_data, msd_data, start=start, stop=stop
     )
 

tox.ini

@@ -7,19 +7,14 @@ envlist = style, docstyle, check-manifest, docs, py39, coverage
 
 [gh-actions]
 python =
-    3.9: style, docstyle, check-manifest, docs, py39, coverage
+    3.9: py39
+    3.10: style, docstyle, check-manifest, docs, py310, coverage
 
 # =============================================================================
 # ENVS
 # =============================================================================
 
 
-[testenv]
-deps =
-    pytest
-commands =
-    pytest tests/ {posargs}
-
 [testenv:style]
 skip_install = True
 usedevelop = False
@@ -31,16 +26,6 @@ deps = flake8
 commands =
         flake8 setup.py tests/ sierras/ {posargs}
 
-[testenv:coverage]
-deps =
-    {[testenv]deps}
-    coverage
-    pytest-cov
-commands =
-    coverage erase
-    pytest -q tests/ --cov=sierras/ --cov-append --cov-report=
-    coverage report --fail-under=90 -m
-
 [testenv:docstyle]
 deps = pydocstyle
 commands =
@@ -62,3 +47,19 @@ deps =
     -r {toxinidir}/docs/requirements.txt
 commands =
     sphinx-build -W -b html -d {envtmpdir}/doctrees source {envtmpdir}/html
+
+[testenv]
+deps =
+    pytest
+commands =
+    pytest tests/ {posargs}
+
+[testenv:coverage]
+deps =
+    {[testenv]deps}
+    coverage
+    pytest-cov
+commands =
+    coverage erase
+    pytest -q tests/ --cov=sierras/ --cov-append --cov-report=
+    coverage report --fail-under=90 -m