Merge pull request #746 from janosh/fix-pypi-page

Fix PyPI page

Author: itsduowang

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
         args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
 
   - repo: https://github.com/psf/black
-    rev: 21.11b1
+    rev: 22.1.0
     hooks:
       - id: black
 
@@ -19,7 +19,7 @@ repos:
         args: [--max-line-length=125]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.1.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer

atomate/qchem/firetasks/critic2.py

@@ -114,7 +114,7 @@ def run_task(self, fw_spec):
                 coords.append((val + centering_vector[jj]) * bohr_to_ang)
             if str(molecule[ii].specie) != specie:
                 raise RuntimeError("Atom ordering different!")
-            if molecule[ii].distance_from_point(coords) > 1 * 10 ** -5:
+            if molecule[ii].distance_from_point(coords) > 1 * 10**-5:
                 raise RuntimeError("Atom position " + str(ii) + " inconsistent!")
 
         if (

atomate/qchem/workflows/tests/test_FF_and_critic.py

@@ -51,12 +51,8 @@ def test_FFopt_and_critic(self):
         # use powerup to replace run with fake run
         alph_formula = initial_mol.composition.alphabetical_formula
         ref_dirs = {
-            f"{alph_formula}:FFopt_testing": os.path.join(
-                test_files, "FFopt"
-            ),
-            f"{alph_formula}:CC2_testing": os.path.join(
-                test_files, "critic_example"
-            ),
+            f"{alph_formula}:FFopt_testing": os.path.join(test_files, "FFopt"),
+            f"{alph_formula}:CC2_testing": os.path.join(test_files, "critic_example"),
         }
         fake_wf = use_fake_qchem(real_wf, ref_dirs)
         self.lp.add_wf(fake_wf)

atomate/vasp/analysis/linear_response.py

@@ -269,7 +269,7 @@ def det_deriv(matrix, i, j):
                         kk, ll = k - 1 if k > j else k, l - 1 if l > i else l
                         minor_p = (-1) ** (i + j) * det_deriv(mji, kk, ll)
 
-                    j_matrix[k, l] = (minor_p * det - minor * det_p) / det ** 2
+                    j_matrix[k, l] = (minor_p * det - minor * det_p) / det**2
 
             jacobians[i].append(j_matrix)
 
@@ -312,7 +312,7 @@ def chi_inverse(chi, chi_err, method="full"):
         )
 
     # Assume cross-covariances are zero
-    chi_covar = np.diag(np.reshape(chi_err_block ** 2, [n_response * n_response]))
+    chi_covar = np.diag(np.reshape(chi_err_block**2, [n_response * n_response]))
 
     (chi_inv, chi_inv_var, chi_inv_jacobs) = inverse_matrix_uncertainty(
         chi_block, chi_covar
@@ -359,12 +359,12 @@ def compute_uj_simple_two_by_two(
     umat_err = f_matrix_err[2 * i : 2 * (i + 1), 2 * i : 2 * (i + 1)]
 
     uval = 0.25 * np.sum(umat)
-    uval_err = 0.25 * np.sqrt(np.sum(umat_err ** 2))
+    uval_err = 0.25 * np.sqrt(np.sum(umat_err**2))
 
     jmat = np.array([[-1, 1], [1, -1]]) * umat.copy()
     jmat_err = umat_err.copy()
     jval = 0.25 * np.sum(jmat)
-    jval_err = 0.25 * np.sqrt(np.sum(jmat_err ** 2))
+    jval_err = 0.25 * np.sqrt(np.sum(jmat_err**2))
 
     return uval, uval_err, jval, jval_err
 
@@ -439,7 +439,7 @@ def fmat_deriv_nscf(kk, ll, ik, il):
     uval_err = uval_err + np.sum(
         np.dot(
             np.transpose(jacob_vec),
-            np.dot(np.diag(np.reshape(chi_sub_scf_err ** 2, [4])), jacob_vec),
+            np.dot(np.diag(np.reshape(chi_sub_scf_err**2, [4])), jacob_vec),
         )
     )
     # nscf component
@@ -460,7 +460,7 @@ def fmat_deriv_nscf(kk, ll, ik, il):
     uval_err = uval_err + np.sum(
         np.dot(
             np.transpose(jacob_vec),
-            np.dot(np.diag(np.reshape(chi_sub_nscf_err ** 2, [4])), jacob_vec),
+            np.dot(np.diag(np.reshape(chi_sub_nscf_err**2, [4])), jacob_vec),
         )
     )
     # compute std
@@ -501,7 +501,7 @@ def fmat_deriv_nscf(kk, ll, ik, il):
     jval_err = jval_err + np.sum(
         np.dot(
             np.transpose(jacob_vec),
-            np.dot(np.diag(np.reshape(chi_sub_scf_err ** 2, [4])), jacob_vec),
+            np.dot(np.diag(np.reshape(chi_sub_scf_err**2, [4])), jacob_vec),
         )
     )
     # nscf component
@@ -522,7 +522,7 @@ def fmat_deriv_nscf(kk, ll, ik, il):
     jval_err = jval_err + np.sum(
         np.dot(
             np.transpose(jacob_vec),
-            np.dot(np.diag(np.reshape(chi_sub_nscf_err ** 2, [4])), jacob_vec),
+            np.dot(np.diag(np.reshape(chi_sub_nscf_err**2, [4])), jacob_vec),
         )
     )
     # compute std

atomate/vasp/builders/bandgap_estimation.py

@@ -48,12 +48,12 @@ def run(self):
                 ]  # electronic portion of eps ("eps_static") approximates eps_inf
                 n = math.sqrt(eps)  # sqrt(eps_inf) to get refractive index
                 d = {}
-                d["gap_moss"] = (95 / n ** 4) if n > 0 else None
+                d["gap_moss"] = (95 / n**4) if n > 0 else None
                 d["gap_gupta-ravindra"] = (4.16 - n) / 0.85 if n <= 4.16 else None
                 d["gap_reddy-anjaneyulu"] = 36.3 / math.exp(n)
-                d["gap_reddy-ahamed"] = 154 / n ** 4 + 0.365 if n > 0 else None
+                d["gap_reddy-ahamed"] = 154 / n**4 + 0.365 if n > 0 else None
                 d["gap_herve_vandamme"] = (
-                    13.47 / math.sqrt(n ** 2 - 1) - 3.47 if n > 1 else None
+                    13.47 / math.sqrt(n**2 - 1) - 3.47 if n > 1 else None
                 )
 
                 d = {"bandgap_estimation": d}

atomate/vasp/firetasks/tests/test_copy.py

@@ -8,6 +8,7 @@
 __email__ = "[email protected]"
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
+test_files = os.path.join(module_dir, "..", "..", "test_files")
 
 DEBUG_MODE = False
 
@@ -16,31 +17,16 @@ class TestCopyVaspOutputs(AtomateTest):
     @classmethod
     def setUpClass(cls):
         cls.plain_outdir = os.path.join(
-            module_dir,
-            "..",
-            "..",
-            "test_files",
-            "Si_structure_optimization_plain",
-            "outputs",
+            test_files, "Si_structure_optimization_plain", "outputs"
         )
         cls.gzip_outdir = os.path.join(
-            module_dir, "..", "..", "test_files", "Si_structure_optimization", "outputs"
+            test_files, "Si_structure_optimization", "outputs"
         )
         cls.relax2_outdir = os.path.join(
-            module_dir,
-            "..",
-            "..",
-            "test_files",
-            "Si_structure_optimization_relax2",
-            "outputs",
+            test_files, "Si_structure_optimization_relax2", "outputs"
         )
         cls.nokpts_outdir = os.path.join(
-            module_dir,
-            "..",
-            "..",
-            "test_files",
-            "Si_structure_optimization",
-            "outputs_no_kpts",
+            test_files, "Si_structure_optimization", "outputs_no_kpts"
         )
 
     def test_unittestsetup(self):

dev_scripts/plot_raman.py

@@ -44,8 +44,8 @@ def lorentzian(w, wj, delta_w=4.0):
     return (
         4.0
         / np.pi
-        * (w ** 2 * delta_w)
-        / ((w ** 2 - wj ** 2) ** 2 + 4 * delta_w ** 2 * w ** 2)
+        * (w**2 * delta_w)
+        / ((w**2 - wj**2) ** 2 + 4 * delta_w**2 * w**2)
     )
     # wolfram
     # return 1./np.pi * (delta_w/2)/ ( (w - wj)**2 + (delta_w/2)**2 )

setup.py

@@ -11,6 +11,7 @@
         version="1.0.3",
         description="atomate has implementations of FireWorks workflows for Materials Science",
         long_description=open(join(module_dir, "README.md")).read(),
+        long_description_content_type="text/markdown",
         url="https://github.com/hackingmaterials/atomate",
         author="Anubhav Jain, Kiran Mathew",
         author_email="[email protected], [email protected]",