Merge pull request #43 from PlasmaPy/pre-commit-ci-update-config

.codecov.yaml

@@ -4,4 +4,4 @@ coverage:
   status:
     project:
       default:
-        threshold: 0.2%
+        threshold: 0.2%

.codemeta.json

@@ -72,4 +72,4 @@
             }
         }
     ]
-}
+}

.coveragerc

@@ -8,4 +8,4 @@ omit =
 exclude_lines =
     coverage: ignore
     ImportError
-    ModuleNotFoundError
+    ModuleNotFoundError

.github/workflows/testing.yml

@@ -57,7 +57,7 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
- 
+
     - name: Create LFS file list
       run: git lfs ls-files -l | cut -d ' ' -f1 | sort > .lfs-assets-id
 

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v3.4.0
     hooks:
     -   id: check-yaml
     -   id: check-json
@@ -9,8 +9,8 @@ repos:
     -   id: trailing-whitespace
     -   id: check-ast
     -   id: requirements-txt-fixer
--   repo: https://github.com/timothycrosley/isort
-    rev: 4.3.21-2
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.7.0
     hooks:
     -   id: isort
         name: isort
@@ -20,11 +20,11 @@ repos:
         types: [python]
         args: [-m=3, -tc]
 -   repo: https://github.com/psf/black
-    rev: 19.3b0
+    rev: 20.8b1
     hooks:
     -   id: black
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: '3.7.9'
+    rev: '3.8.4'
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-docstrings]

LICENSE.md

@@ -12,8 +12,8 @@ modification, are permitted provided that the following conditions are met:
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 
-* Neither the name of PlasmaPy nor the names of its contributors may be used 
-  to endorse or promote products derived from this software without specific 
+* Neither the name of PlasmaPy nor the names of its contributors may be used
+  to endorse or promote products derived from this software without specific
   prior written permission.
 
 Subject to the terms and conditions of this license, each copyright
@@ -44,8 +44,8 @@ expressly, by implication, estoppel or otherwise.
 ## Disclaimer
 
 This software is provided by the copyright holders and contributors "as is"
-and any express or implied warranties, including, but not limited to, the 
-implied warranties of merchantability and fitness for a particular purpose are 
+and any express or implied warranties, including, but not limited to, the
+implied warranties of merchantability and fitness for a particular purpose are
 disclaimed. In no event shall the copyright holder or contributors be liable
 for any direct, indirect, incidental, special, exemplary, or consequential
 damages (including, but not limited to, procurement of substitute goods or

README.md

@@ -35,7 +35,7 @@ Smithsonian Institution.
 We love contributions! PlasmaPy-NEI is open source,
 built on open source, and we'd love to have you in our community.
 
-### Imposter syndrome disclaimer 
+### Imposter syndrome disclaimer
 
 We want your help. No, really.
 

docs/requirements.txt

@@ -2,9 +2,9 @@
 
 numpydoc
 pillow
+pytest
+setuptools-scm
 sphinx <= 2.4.4
 sphinx-automodapi
 sphinx-gallery
 sphinx_rtd_theme
-pytest
-setuptools-scm

licenses/PlasmaPy_license.md

@@ -12,8 +12,8 @@ modification, are permitted provided that the following conditions are met:
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 
-* Neither the name of PlasmaPy nor the names of its contributors may be used 
-  to endorse or promote products derived from this software without specific 
+* Neither the name of PlasmaPy nor the names of its contributors may be used
+  to endorse or promote products derived from this software without specific
   prior written permission.
 
 Subject to the terms and conditions of this license, each copyright
@@ -44,8 +44,8 @@ expressly, by implication, estoppel or otherwise.
 ## Disclaimer
 
 This software is provided by the copyright holders and contributors "as is"
-and any express or implied warranties, including, but not limited to, the 
-implied warranties of merchantability and fitness for a particular purpose are 
+and any express or implied warranties, including, but not limited to, the
+implied warranties of merchantability and fitness for a particular purpose are
 disclaimed. In no event shall the copyright holder or contributors be liable
 for any direct, indirect, incidental, special, exemplary, or consequential
 damages (including, but not limited to, procurement of substitute goods or

plasmapy_nei/__init__.py

@@ -11,5 +11,4 @@
 finally:
     del warnings
 
-from . import eigen
-from . import nei
+from . import eigen, nei

plasmapy_nei/eigen/eigenclass.py

@@ -5,12 +5,13 @@
 
 __all__ = ["EigenData", "eigen_data_dict"]
 
+import warnings
+
+import astropy.units as u
 import h5py
 import numpy as np
-from numpy import linalg as LA
 import pkg_resources
-import warnings
-import astropy.units as u
+from numpy import linalg as LA
 
 try:
     from plasmapy.particles import Particle, particle_input
@@ -169,11 +170,13 @@ def _load_data(self):
         )
 
         self._eigenvectors = np.ndarray(
-            shape=(self.ntemp, self.nstates, self.nstates), dtype=np.float64,
+            shape=(self.ntemp, self.nstates, self.nstates),
+            dtype=np.float64,
         )
 
         self._eigenvector_inverses = np.ndarray(
-            shape=(self.ntemp, self.nstates, self.nstates), dtype=np.float64,
+            shape=(self.ntemp, self.nstates, self.nstates),
+            dtype=np.float64,
         )
 
         self._ionization_rate[:, :] = c_rate[:, :]
@@ -196,7 +199,9 @@ def _load_data(self):
             rarr = r_rate[temperature_index, :]
 
             eqi = _get_equilibrium_charge_states(
-                carr, rarr, self.element.atomic_number,
+                carr,
+                rarr,
+                self.element.atomic_number,
             )
 
             for ion in range(1, self.nstates - 1):

plasmapy_nei/eigen/tests/test_eigenclass.py

@@ -5,9 +5,10 @@
 except ImportError:
     from plasmapy import particles as atomic
 
-from plasmapy_nei.eigen import EigenData
-import pytest
 import numpy as np
+import pytest
+
+from plasmapy_nei.eigen import EigenData
 
 
 @pytest.mark.parametrize("atomic_numb", np.arange(1, 30))
@@ -54,12 +55,12 @@ def time_advance_solver_for_testing(natom, te, ne, dt, f0, table):
 @pytest.mark.parametrize("natom", [1, 2, 6, 7, 8])
 def test_reachequlibrium_state(natom):
     """
-        Starting the random initial distribution, the charge states will reach
-        to equilibrium cases after a long time.
-        In this test, we set the ionization and recombination rates at
-        Te0=2.0e6 K and plasma density ne0=1.0e+7. A random charge states
-        distribution will be finally closed to equilibrium distribution at
-        2.0e6K.
+    Starting the random initial distribution, the charge states will reach
+    to equilibrium cases after a long time.
+    In this test, we set the ionization and recombination rates at
+    Te0=2.0e6 K and plasma density ne0=1.0e+7. A random charge states
+    distribution will be finally closed to equilibrium distribution at
+    2.0e6K.
     """
     #
     # Initial conditions, set plasma temperature, density and dt

plasmapy_nei/nei/nei.py

@@ -3,10 +3,12 @@
 __all__ = ["NEI", "NEIError", "SimulationResults"]
 
 
-import numpy as np
-from typing import Union, Optional, List, Dict, Callable
+from typing import Callable, Dict, List, Optional, Union
+
 import astropy.units as u
+import numpy as np
 from scipy import interpolate, optimize
+
 from plasmapy_nei.eigen import EigenData, eigen_data_dict
 
 try:
@@ -16,7 +18,6 @@
 
 import warnings
 
-
 # TODO: Allow this to keep track of velocity and position too, and
 # eventually to have density and temperature be able to be functions of
 # position.  (and more complicated expressions for density and
@@ -478,7 +479,11 @@ def __init__(
             n_init = self.hydrogen_number_density(self.time_start)
 
             self.initial = IonizationStates(
-                inputs=inputs, abundances=abundances, T_e=T_e_init, n=n_init, tol=tol,
+                inputs=inputs,
+                abundances=abundances,
+                T_e=T_e_init,
+                n=n_init,
+                tol=tol,
             )
 
             self.tol = tol
@@ -524,7 +529,9 @@ def __init__(
             ) from e
 
     def equil_ionic_fractions(
-        self, T_e: u.Quantity = None, time: u.Quantity = None,
+        self,
+        T_e: u.Quantity = None,
+        time: u.Quantity = None,
     ) -> Dict[str, np.ndarray]:
         """
         Return the equilibrium ionic fractions for a temperature or at
@@ -1178,7 +1185,13 @@ def _set_adaptive_timestep(self):
 
         try:
             new_dt = (
-                optimize.brentq(T_val, *dt_bounds, xtol=1e-14, maxiter=1000, disp=True,)
+                optimize.brentq(
+                    T_val,
+                    *dt_bounds,
+                    xtol=1e-14,
+                    maxiter=1000,
+                    disp=True,
+                )
                 * u.s
             )
         except Exception as exc:

plasmapy_nei/nei/tests/test_nei.py

@@ -6,11 +6,13 @@
     from plasmapy.atomic import IonizationStates, particle_symbol
 except ImportError:
     from plasmapy.particles import IonizationStates, particle_symbol
-from plasmapy_nei.nei import NEI
-from plasmapy_nei.eigen import EigenData
+
 import numpy as np
 import pytest
 
+from plasmapy_nei.eigen import EigenData
+from plasmapy_nei.nei import NEI
+
 inputs_dict = {"H": [0.9, 0.1], "He": [0.5, 0.3, 0.2]}
 abundances = {"H": 1, "He": 0.1}
 

requirements.txt

@@ -3,6 +3,6 @@ astropy >= 3.2
 h5py >= 2.9
 matplotlib >= 3.0
 numpy >= 1.16
+plasmapy >= 0.3.1
 scipy >= 1.0
 setuptools >= 41.2
-plasmapy >= 0.3.1

setup.cfg

@@ -14,7 +14,7 @@ packages = find:
 python_requires = >=3.7
 setup_requires =
     setuptools_scm
-install_requires = 
+install_requires =
     astropy>=3.2
     h5py
     numpy>=1.16