Cleaning up and fix the flake8 complains (#40)

* Cleaning up and fix the flake8 complains

* Add iosrt configurations

* Add `application-import-names`

* Fix the import order errors from flake8

Author: FanwangM

bfit/fit.py

@@ -26,7 +26,7 @@
 from timeit import default_timer as timer
 
 import numpy as np
-from scipy.optimize import NonlinearConstraint, minimize
+from scipy.optimize import minimize, NonlinearConstraint
 
 from bfit.measure import KLDivergence, Measure, SquaredDifference
 

bfit/greedy.py

@@ -27,7 +27,7 @@
 import numpy as np
 from scipy.optimize import nnls
 
-from bfit.fit import KLDivergenceFPI, ScipyFit, _BaseFit
+from bfit.fit import _BaseFit, KLDivergenceFPI, ScipyFit
 from bfit.measure import SquaredDifference
 from bfit.model import AtomicGaussianDensity
 

bfit/test/test_greedy.py

@@ -26,10 +26,10 @@
 import numpy.testing as npt
 
 from bfit.greedy import (
-    GreedyKLFPI,
-    GreedyLeastSquares,
     get_next_choices,
     get_two_next_choices,
+    GreedyKLFPI,
+    GreedyLeastSquares,
     pick_two_lose_one,
     remove_redundancies,
 )

bfit/test/test_grid.py

@@ -25,7 +25,7 @@
 import numpy as np
 from numpy.testing import assert_almost_equal, assert_raises
 
-from bfit.grid import ClenshawRadialGrid, CubicGrid, UniformRadialGrid, _BaseRadialGrid
+from bfit.grid import _BaseRadialGrid, ClenshawRadialGrid, CubicGrid, UniformRadialGrid
 
 
 def test_raises_base():

docs/conf.py

@@ -29,20 +29,20 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages',
-    'numpydoc',
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "numpydoc",
     # 'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
+    "sphinx.ext.doctest",
     # for adding “copy to clipboard” buttons to all text/code boxes
-    'sphinx_copybutton',
-    'autoapi.extension',
-    'nbsphinx',
-    #'sphinxcontrib.bibtex'
+    "sphinx_copybutton",
+    "autoapi.extension",
+    "nbsphinx",
+    # 'sphinxcontrib.bibtex',
 ]
 
 # Add any paths that contain templates here, relative to this directory.

examples/atomdb_db.py

@@ -11,24 +11,29 @@
 import numpy as np
 from atomdb import load
 
-from bfit.density import SlaterAtoms
-from bfit.fit import KLDivergenceFPI, ScipyFit
+from bfit.fit import KLDivergenceFPI
 from bfit.grid import ClenshawRadialGrid
-from bfit.measure import KLDivergence
 from bfit.model import AtomicGaussianDensity
 from bfit.parse_ugbs import get_ugbs_exponents
 
+# change the path to the location of the AtomDB data as needed
+DATAPATH = ("/home/ali-tehrani/SoftwareProjects/AtomDBdata",)
+
 results_final = {}
 atoms = ["H",  "C", "N", "O", "F", "P", "S", "Cl"]
-atomic_numbs = [1, 6, 7, 8, 9, 15, 16, 17] #[1 + i for i in range(0, len(atoms))]
+atomic_numbs = [1, 6, 7, 8, 9, 15, 16, 17]  # [1 + i for i in range(0, len(atoms))]
 mult = [2, 3, 4, 3, 2, 4, 3, 2]
 for k, element in enumerate(atoms):
     print("Start Atom %s" % element)
 
     # Construct a integration grid
     atomic_numb = atomic_numbs[k]
     grid = ClenshawRadialGrid(
-        atomic_numb, num_core_pts=10000, num_diffuse_pts=899, include_origin=True#, extra_pts=[50,75,100],
+        atomic_numb,
+        num_core_pts=10000,
+        num_diffuse_pts=899,
+        include_origin=True,
+        # extra_pts=[50,75,100],
     )
 
     # Initial Guess constructed from UGBS
@@ -41,15 +46,19 @@
     e_0 = np.array(exps_s + exps_p) * 2.0
 
     # Construct Atomic Density and Fitting Object
-    #density = SlaterAtoms(element=element).atomic_density(grid.points)
+    # density = SlaterAtoms(element=element).atomic_density(grid.points)
     # Use AtomDB to calculate the density
-    atom = load(elem=element, charge=0, mult=mult[k], dataset="hci", datapath="/home/ali-tehrani/SoftwareProjects/AtomDBdata")
+    atom = load(
+        elem=element,
+        charge=0,
+        mult=mult[k],
+        dataset="hci",
+        datapath=DATAPATH,
+    )
 
     dens = atom.dens_func()
     density = dens(grid.points)
 
-    import matplotlib.pyplot as plt
-
     # plt.plot(grid.points, density, "bo-")
     # plt.show()
     print(density[-1], grid.points[-1], grid.points[0:3])
@@ -69,7 +78,9 @@
     # measure = KLDivergence(mask_value=1e-18)
     # fit_KL_slsqp = ScipyFit(grid, density, model, measure=measure, method="SLSQP", spherical=True)
     # # Run the SLSQP optimization algorithm
-    # results = fit_KL_slsqp.run(coeffs, e_0, maxiter=10000, disp=True, with_constraint=True, tol=1e-14)
+    # results = fit_KL_slsqp.run(
+    # coeffs, e_0, maxiter=10000, disp=True, with_constraint=True, tol=1e-14
+    # )
 
     print("KL-FPI INFO")
     print("-----------")

examples/table/table_3.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from bfit.density import SlaterAtoms
-from bfit.fit import KLDivergenceFPI, ScipyFit
+from bfit.fit import ScipyFit
 from bfit.grid import ClenshawRadialGrid
 from bfit.measure import KLDivergence
 from bfit.model import AtomicGaussianDensity

pyproject.toml

@@ -127,15 +127,6 @@ line-length = 100
 # )
 # '''
 
-[tool.isort]
-profile = "black"
-known_first_party = ["bfit"]
-# If you need to exclude files from having their imports sorted
-#extend_skip_glob  = [
-#    "bfit/somefile.py",
-#    "bfit/somedir/*",
-#]
-
 # https://beta.ruff.rs/docs
 [tool.ruff]
 line-length = 100
@@ -329,4 +320,3 @@ disable=[
     "no-else-return",
     "too-many-statements",
 ]
-

tox.ini

@@ -26,6 +26,9 @@ commands =
 ignore_errors = true
 
 [testenv:linters]
+ignore_errors = true
+# allow for linters to fail
+# ignore_outcome = true
 deps =
     numpy
     scipy
@@ -39,15 +42,13 @@ deps =
     # black
     bandit
 commands =
-    flake8 bfit/ bfit/test
+    python -m flake8 --config=tox.ini bfit/ bfit/test
     pylint bfit --rcfile=pyproject.toml --disable=similarities
     # black -l 100 --check ./
     # black -l 100 --diff ./
     # Use bandit configuration file
     bandit -r bfit -c .bandit.yml
 
-ignore_errors = true
-
 [testenv:coverage-report]
 deps = coverage>=4.2
 skip_install = true
@@ -93,8 +94,10 @@ exclude =
     .eggs,
 
 max-line-length = 100
-import-order-style = google
-ignore =
+; import-order-style = google
+import-order-style = smarkets
+application-import-names = bfit
+extend-ignore =
     # E121 : continuation line under-indented for hanging indent
     E121,
     # E123 : closing bracket does not match indentation of opening bracket’s line
@@ -191,3 +194,4 @@ source =
    bfit
    .tox/*/lib/python*/site-packages/bfit
    .tox/pypy*/site-packages/bfit
+