From f0e44312742a7031c4e932c3dcd1c1bebfb5acb4 Mon Sep 17 00:00:00 2001
From: Eike Caldeweyher <46899008+f3rmion@users.noreply.github.com>
Date: Mon, 31 Oct 2022 14:07:42 +0100
Subject: [PATCH] Patch SciPy import error and bump version to 1.0.8 (#43)

* Patch version of SciPy.

* Bump version to 1.0.8

* Remove python versions from GA test workflow.

* Remove python versions.

* Delete lock file.
---
 noxfile.py               |  7 +++++--
 pyproject.toml           | 14 +++++++-------
 src/kallisto/__init__.py |  2 +-
 src/kallisto/console.py  |  4 +++-
 src/kallisto/methods.py  | 23 ++++++++++++-----------
 src/kallisto/molecule.py |  6 +++++-
 src/kallisto/rmsd.py     | 14 +++++++++++---
 src/kallisto/units.py    |  2 +-
 tests/test_cli.py        | 12 ++++++++----
 tests/test_version.py    |  2 +-
 10 files changed, 54 insertions(+), 32 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index a651700..d055b08 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -11,7 +11,7 @@
 locations = "src", "tests", "noxfile.py"
 
 
-python_versions = ["3.9", "3.8", "3.7"]
+python_versions = ["3.9", "3.8"]
 
 
 @nox.session(python=python_versions)
@@ -19,7 +19,10 @@ def tests(session: Session) -> None:
     args = session.posargs or ["--cov", "-m", "not e2e"]
     session.run("poetry", "install", "--no-dev", external=True)
     install_with_constraints(
-        session, "coverage[toml]", "pytest", "pytest-cov",
+        session,
+        "coverage[toml]",
+        "pytest",
+        "pytest-cov",
     )
     session.run("pytest", *args)
 
diff --git a/pyproject.toml b/pyproject.toml
index 82c7d9f..2e2d6ca 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "kallisto"
-version = "1.0.7"
+version = "1.0.8"
 description = "The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented."
 license = "Apache 2.0"
 readme = "README.md"
@@ -10,19 +10,19 @@ keywords = ["chemistry", "computational-chemistry", "quantum-chemistry", "machin
 authors = ["Eike Caldeweyher <hello@eikecaldeweyher.de>", "Rocco Meli <rocco.meli@biodtp.ox.ac.uk>", "Philipp Pracht <pracht@thch.uni-bonn.de>"]
 
 [tool.poetry.dependencies]
-python = "^3.7"
-click = "^7.1.2"
+python = "^3.8"
+click = "^8.0.0"
 numpy = "^1.19.0"
-scipy = "^1.5.2"
+scipy = "1.9.2"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"
 pytest-cov = {version = "^2.10.0", extras = ["toml"]}
 coverage = {version = "^5.2", extras = ["toml"]}
-black = "^19.10b0"
+black = "^22.1.0"
 flake8 = "^3.8.3"
-flake8-bandit = "^2.1.2"
-flake8-black = "^0.2.0"
+flake8-bandit = "^3.0.0"
+flake8-black = "^0.3.0"
 flake8-bugbear = "^20.1.4"
 flake8-import-order = "^0.18.1"
 safety = "^1.9.0"
diff --git a/src/kallisto/__init__.py b/src/kallisto/__init__.py
index 9e604c0..e13bd59 100644
--- a/src/kallisto/__init__.py
+++ b/src/kallisto/__init__.py
@@ -1 +1 @@
-__version__ = "1.0.7"
+__version__ = "1.0.8"
diff --git a/src/kallisto/console.py b/src/kallisto/console.py
index 6aaacbc..c0d449a 100644
--- a/src/kallisto/console.py
+++ b/src/kallisto/console.py
@@ -423,7 +423,9 @@ def lig(config, inp: str, center: int, out: click.File):
     k = 0
     for path in substructures:
         silentPrinter(
-            config.silent, "Substructure {}: {}".format(k, path), out,
+            config.silent,
+            "Substructure {}: {}".format(k, path),
+            out,
         )
         k += 1
 
diff --git a/src/kallisto/methods.py b/src/kallisto/methods.py
index 3664579..793feb2 100644
--- a/src/kallisto/methods.py
+++ b/src/kallisto/methods.py
@@ -10,9 +10,9 @@ def getCoordinationNumbers(
 ):
     """A method to compute coordination numbers (cns).
 
-        CN values are calculated for a given structure and are returned as an
-        array. Choose functional type by "cn" defining standard (exp), covalent (cov),
-        or error (err)."""
+    CN values are calculated for a given structure and are returned as an
+    array. Choose functional type by "cn" defining standard (exp), covalent (cov),
+    or error (err)."""
 
     from kallisto.data import covalent_radius as rcov
     from kallisto.data import pauling_en
@@ -65,7 +65,7 @@ def getCoordinationNumbers(
         # Fitted to match Wiberg bond orders of diatomic molecules
         k4 = 4.10451
         k5 = 19.08857
-        k6 = 2 * 11.28174 ** 2
+        k6 = 2 * 11.28174**2
 
         kn = 7.50
         for i in range(nat):
@@ -107,7 +107,7 @@ def getProximityShells(
     # Fitted to match Wiberg bond orders of diatomic molecules
     k4 = 4.10451
     k5 = 19.08857
-    k6 = 2 * 11.28174 ** 2
+    k6 = 2 * 11.28174**2
 
     kn = 7.50
     threshold = 800.0
@@ -148,10 +148,10 @@ def getAtomicPartialCharges(
     at: np.ndarray, coords: np.ndarray, cns: np.ndarray, charge: int
 ):
     """A method to compute atomic electronegativity equilibration partial
-        charges (eeqs).
+    charges (eeqs).
 
-        EEQ values are calculated for a given structure and are returned as an
-        array."""
+    EEQ values are calculated for a given structure and are returned as an
+    array."""
 
     from kallisto.data import eeq_alp, eeq_cnfak, eeq_en, eeq_gamm
     from numpy import linalg as LA
@@ -269,7 +269,8 @@ def getPolarizabilities(at: np.ndarray, covcn: np.ndarray, qs: np.ndarray, charg
             cncount[int(icn)] += 1
             for jj in range(23):
                 alphar[jj][j][ia] = np.maximum(
-                    ascale[j][ia] * (alphaiw[jj][j][ia] - hcount[j][ia] * alpha[jj]), 0,
+                    ascale[j][ia] * (alphaiw[jj][j][ia] - hcount[j][ia] * alpha[jj]),
+                    0,
                 )
         for j in range(refn[ia]):
             icn = cncount[int(np.rint(refcn[j][ia]))]
@@ -379,8 +380,8 @@ def getVanDerWaalsRadii(
 ):
     """A method to compute environment and charge dependent van der Waals radii (vdws).
 
-        VDW values are calculated from atomic polarizabilities for a given structure
-        and are returned as an array."""
+    VDW values are calculated from atomic polarizabilities for a given structure
+    and are returned as an array."""
 
     from kallisto.data import chemical_symbols
     from kallisto.data.vdw import rahm, truhlar
diff --git a/src/kallisto/molecule.py b/src/kallisto/molecule.py
index a6f4040..e6a76cd 100644
--- a/src/kallisto/molecule.py
+++ b/src/kallisto/molecule.py
@@ -29,7 +29,11 @@ class Molecule(object):
         Atomic charges."""
 
     def __init__(
-        self, symbols=None, positions=None, numbers=None, charges=None,
+        self,
+        symbols=None,
+        positions=None,
+        numbers=None,
+        charges=None,
     ):
 
         molecule = None
diff --git a/src/kallisto/rmsd.py b/src/kallisto/rmsd.py
index b255fdd..eb68fcc 100644
--- a/src/kallisto/rmsd.py
+++ b/src/kallisto/rmsd.py
@@ -4,7 +4,7 @@
 from typing import Tuple
 
 import numpy as np
-from scipy.sparse.linalg.eigen.arpack import eigsh
+from scipy.sparse.linalg import eigsh
 from scipy.spatial import distance
 from scipy.spatial.transform import Rotation as R
 
@@ -199,7 +199,12 @@ def exchangeSubstructure(
             # get all bonding partner
             oldSubBonds = oldsub.get_bonds(partner="X")
             outxyz = matchSubstrates(
-                bonds, newsub, newSubBonds, oldsub, oldSubBonds, centralAtom,
+                bonds,
+                newsub,
+                newSubBonds,
+                oldsub,
+                oldSubBonds,
+                centralAtom,
             )
 
             # atoms from complex excluding old substrate
@@ -223,7 +228,10 @@ def exchangeSubstructure(
                 shift = outxyz[0, :] - refShift
                 for j in range(newnat):
                     outxyz2[j, :] = getRodriguezRotation(
-                        outxyz[j, :], origin, partner, theta,
+                        outxyz[j, :],
+                        origin,
+                        partner,
+                        theta,
                     )
                     outxyz2[j, :] += shift
 
diff --git a/src/kallisto/units.py b/src/kallisto/units.py
index 54a865e..5af09c7 100644
--- a/src/kallisto/units.py
+++ b/src/kallisto/units.py
@@ -78,7 +78,7 @@ def createUnits(version):
         units["_me"]
         * units["_e"] ** 3
         / 16
-        / pi ** 2
+        / pi**2
         / units["_eps0"] ** 2
         / units["_hbar"] ** 2
     )
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 7705bb5..f425f9a 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -176,7 +176,8 @@ def test_cli_vdw_angstrom(runner, pyridine_xyz):
 
 def test_cli_vdw_angstrom_truhlar(runner, pyridine_xyz):
     result = runner.invoke(
-        cli, ["vdw", "--angstrom", "--vdwtype", "truhlar", pyridine_xyz],
+        cli,
+        ["vdw", "--angstrom", "--vdwtype", "truhlar", pyridine_xyz],
     )
     assert result.exit_code == 0
 
@@ -258,7 +259,8 @@ def test_cli_exs_silent(runner, pyridine_xyz):
 
 def test_cli_exs(runner, pyridine_xyz):
     result = runner.invoke(
-        cli, ["exs", "--center", "0", "--subnr", "2", pyridine_xyz, pyridine_xyz],
+        cli,
+        ["exs", "--center", "0", "--subnr", "2", pyridine_xyz, pyridine_xyz],
     )
     assert result.exit_code == 0
     newstructure = "newstructure.xyz"
@@ -304,14 +306,16 @@ def test_cli_exs_with_rotation(runner, pyridine_xyz):
 # test cli part for stm
 def test_cli_stm_silent(runner, iridiumcat_xyz):
     result = runner.invoke(
-        cli, ["--silent", "stm", "--origin", "18", "--partner", "23", iridiumcat_xyz],
+        cli,
+        ["--silent", "stm", "--origin", "18", "--partner", "23", iridiumcat_xyz],
     )
     assert result.exit_code == 0
 
 
 def test_cli_stm(runner, iridiumcat_xyz):
     result = runner.invoke(
-        cli, ["stm", "--origin", "18", "--partner", "23", iridiumcat_xyz],
+        cli,
+        ["stm", "--origin", "18", "--partner", "23", iridiumcat_xyz],
     )
     assert result.exit_code == 0
 
diff --git a/tests/test_version.py b/tests/test_version.py
index 7856c6d..7d40084 100644
--- a/tests/test_version.py
+++ b/tests/test_version.py
@@ -4,4 +4,4 @@
 
 
 def test_version():
-    assert __version__ == "1.0.7"
+    assert __version__ == "1.0.8"