Merge 91465b4 into 6386ff5

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+extend-ignore =
+    E501
+    W503
+    E203

.github/workflows/publish.yml

@@ -38,4 +38,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
-        password: ${{ secrets.PYPI_TOKEN }}
+        password: ${{ secrets.PYPI_TOKEN }}

.pre-commit-config.yaml

@@ -1,11 +1,36 @@
-# Install pre-commit hooks via:
-# pre-commit install
-
-# yapf = yet another python formatter
+---
 repos:
-- repo: https://github.com/pre-commit/mirrors-yapf
-  rev: v0.28.0
-  hooks:
-  - id: yapf
-    name: yapf
-    args: ["-i"]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: end-of-file-fixer
+            exclude: ^.*data/
+          - id: trailing-whitespace
+          - id: check-yaml
+          - id: check-added-large-files
+    - repo: https://github.com/pycqa/isort
+      rev: 5.10.1
+      hooks:
+          - id: isort
+            args: [--profile, black, --filter-files]
+    - repo: https://github.com/PyCQA/autoflake
+      rev: v2.0.0
+      hooks:
+          - id: autoflake
+    - repo: https://github.com/asottile/pyupgrade
+      rev: v3.2.2
+      hooks:
+          - id: pyupgrade
+            args: [--py37-plus]
+    - repo: https://github.com/psf/black
+      rev: 22.12.0
+      hooks:
+          - id: black
+            language_version: python3
+    - repo: https://github.com/PyCQA/flake8
+      rev: 6.0.0
+      hooks:
+          - id: flake8
+            args: [--count, --show-source, --statistics]
+            additional_dependencies: [flake8-bugbear, flake8-builtins, flake8-comprehensions,
+                flake8-debugger, flake8-logging-format, pep8-naming, pyflakes, tryceratops]

README.md

@@ -32,7 +32,7 @@ parameters = {
     },
     'input_parameters': { # appended at the end of the input
         'output.wfx':None
-    }, 
+    },
 }
 ```
 In `route_parameters`, specifying `key: None` adds only `key` without the equals sign to the input script.
@@ -56,7 +56,7 @@ A quick demo of how to submit a calculation:
 verdi daemon start # make sure the daemon is running
 cd examples
 # Submit test calculation (argument is the label of gaussian code)
-verdi run example_01_opt.py gaussian09 
+verdi run example_01_opt.py gaussian09
 ```
 
 ## For maintainers

aiida_gaussian/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 aiida_gaussian
 

aiida_gaussian/calculations/__init__.py

@@ -1,6 +1,5 @@
-# -*- coding: utf-8 -*-
-from __future__ import absolute_import
-
-from .gaussian import GaussianCalculation
-from .formchk import FormchkCalculation
 from .cubegen import CubegenCalculation
+from .formchk import FormchkCalculation
+from .gaussian import GaussianCalculation
+
+__all__ = ["CubegenCalculation", "FormchkCalculation", "GaussianCalculation"]

aiida_gaussian/calculations/cubegen.py

@@ -1,10 +1,8 @@
-# -*- coding: utf-8 -*-
 """Gaussian input plugin."""
-from __future__ import absolute_import
 
-from aiida.orm import Dict, RemoteData, Str, Int, Bool, SinglefileData
 from aiida.common import CalcInfo, CodeInfo
 from aiida.engine import CalcJob
+from aiida.orm import Bool, Dict, Int, RemoteData, SinglefileData
 
 
 class CubegenCalculation(CalcJob):
@@ -42,20 +40,20 @@ class CubegenCalculation(CalcJob):
 
     @classmethod
     def define(cls, spec):
-        super(CubegenCalculation, cls).define(spec)
+        super().define(spec)
 
         spec.input(
             "parameters",
             valid_type=Dict,
             required=True,
-            help='dictionary containing entries for cubes to be printed.'
+            help="dictionary containing entries for cubes to be printed.",
         )
 
         spec.input(
-            'parent_calc_folder',
+            "parent_calc_folder",
             valid_type=RemoteData,
             required=True,
-            help='the folder of a containing the .fchk'
+            help="the folder of a containing the .fchk",
         )
 
         spec.input(
@@ -66,23 +64,23 @@ def define(cls, spec):
         )
 
         spec.input(
-            'retrieve_cubes',
+            "retrieve_cubes",
             valid_type=Bool,
             required=False,
             default=lambda: Bool(False),
-            help='should the cubes be retrieved?'
+            help="should the cubes be retrieved?",
         )
 
         spec.input(
             "gauss_memdef",
             valid_type=Int,
             required=False,
             default=lambda: Int(1024),
-            help="Set the GAUSS_MEMDEF env variable to set the max memory in MB."
+            help="Set the GAUSS_MEMDEF env variable to set the max memory in MB.",
         )
 
         # Turn mpi off by default
-        spec.input('metadata.options.withmpi', valid_type=bool, default=False)
+        spec.input("metadata.options.withmpi", valid_type=bool, default=False)
 
         spec.input(
             "metadata.options.parser_name",
@@ -122,7 +120,7 @@ def prepare_for_submission(self, folder):
 
         if "stencil" in self.inputs:
             calcinfo.local_copy_list.append(
-                (self.inputs.stencil.uuid, self.inputs.stencil.filename, 'stencil.txt')
+                (self.inputs.stencil.uuid, self.inputs.stencil.filename, "stencil.txt")
             )
 
         for key, params in self.inputs.parameters.get_dict().items():
@@ -136,15 +134,19 @@ def prepare_for_submission(self, folder):
 
             codeinfo.cmdline_params = []
             codeinfo.cmdline_params.append(
-                str(self.inputs.metadata.options.resources['tot_num_mpiprocs'])
+                str(self.inputs.metadata.options.resources["tot_num_mpiprocs"])
             )
             codeinfo.cmdline_params.append(kind_str)
-            codeinfo.cmdline_params.append(self.PARENT_FOLDER_NAME + "/" + self.DEFAULT_INPUT_FILE)
+            codeinfo.cmdline_params.append(
+                self.PARENT_FOLDER_NAME + "/" + self.DEFAULT_INPUT_FILE
+            )
             codeinfo.cmdline_params.append(cube_name)
 
             if npts == -1:
-                if 'stencil' not in self.inputs:
-                    self.report("Warning: npts: -1 set but no stencil provided, using -2")
+                if "stencil" not in self.inputs:
+                    self.report(
+                        "Warning: npts: -1 set but no stencil provided, using -2"
+                    )
                     codeinfo.cmdline_params.append("-2")
                 else:
                     codeinfo.cmdline_params.append(str(npts))

aiida_gaussian/calculations/formchk.py

@@ -1,10 +1,8 @@
-# -*- coding: utf-8 -*-
 """Gaussian formchk plugin."""
-from __future__ import absolute_import
 
-from aiida.orm import List, RemoteData, SinglefileData, Str, Bool
 from aiida.common import CalcInfo, CodeInfo
 from aiida.engine import CalcJob
+from aiida.orm import Bool, RemoteData, Str
 
 
 class FormchkCalculation(CalcJob):
@@ -18,31 +16,31 @@ class FormchkCalculation(CalcJob):
 
     @classmethod
     def define(cls, spec):
-        super(FormchkCalculation, cls).define(spec)
+        super().define(spec)
 
         spec.input(
-            'parent_calc_folder',
+            "parent_calc_folder",
             valid_type=RemoteData,
             required=True,
-            help='the folder of a containing the .chk'
+            help="the folder of a containing the .chk",
         )
         spec.input(
-            'chk_name',
+            "chk_name",
             valid_type=Str,
             required=False,
             default=lambda: Str(cls.DEFAULT_INPUT_FILE),
-            help="name of the checkpoint file"
+            help="name of the checkpoint file",
         )
         spec.input(
-            'retrieve_fchk',
+            "retrieve_fchk",
             valid_type=Bool,
             required=False,
             default=lambda: Bool(False),
-            help="retrieve the fchk file"
+            help="retrieve the fchk file",
         )
 
         # Turn mpi off by default
-        spec.input('metadata.options.withmpi', valid_type=bool, default=False)
+        spec.input("metadata.options.withmpi", valid_type=bool, default=False)
 
     # --------------------------------------------------------------------------
     def prepare_for_submission(self, folder):
@@ -51,7 +49,8 @@ def prepare_for_submission(self, folder):
         codeinfo = CodeInfo()
         codeinfo.code_uuid = self.inputs.code.uuid
         codeinfo.cmdline_params = [
-            self.PARENT_FOLDER_NAME + "/" + self.inputs.chk_name.value, self.DEFAULT_OUTPUT_FILE
+            self.PARENT_FOLDER_NAME + "/" + self.inputs.chk_name.value,
+            self.DEFAULT_OUTPUT_FILE,
         ]
         codeinfo.withmpi = self.inputs.metadata.options.withmpi
 
@@ -70,7 +69,9 @@ def prepare_for_submission(self, folder):
         comp_uuid = self.inputs.parent_calc_folder.computer.uuid
         remote_path = self.inputs.parent_calc_folder.get_remote_path()
         copy_info = (comp_uuid, remote_path, self.PARENT_FOLDER_NAME)
-        if self.inputs.code.computer.uuid == comp_uuid:  # if running on the same computer - make a symlink
+        if (
+            self.inputs.code.computer.uuid == comp_uuid
+        ):  # if running on the same computer - make a symlink
             # if not - copy the folder
             calcinfo.remote_symlink_list.append(copy_info)
         else:

aiida_gaussian/calculations/gaussian.py

@@ -1,23 +1,20 @@
-# -*- coding: utf-8 -*-
 """Gaussian input plugin."""
-from __future__ import absolute_import
 
-from aiida.orm import Dict, RemoteData, Float
+import pymatgen.io.gaussian as mgaus
 from aiida.common import CalcInfo, CodeInfo
 
 # from aiida.cmdline.utils import echo
 from aiida.engine import CalcJob
+from aiida.orm import Dict, Float, RemoteData
 from aiida.plugins import DataFactory
 
-import pymatgen.io.gaussian as mgaus
-
 StructureData = DataFactory("core.structure")
 
 
 class GaussianCalculation(CalcJob):
     """
     AiiDA calculation plugin wrapping Gaussian
-    
+
     Template:
 
     parameters = Dict(dict={
@@ -47,7 +44,7 @@ class GaussianCalculation(CalcJob):
 
     @classmethod
     def define(cls, spec):
-        super(GaussianCalculation, cls).define(spec)
+        super().define(spec)
 
         # Input parameters
         spec.input(
@@ -57,7 +54,9 @@ def define(cls, spec):
             help="Input structure; will be converted to pymatgen object",
         )
 
-        spec.input("parameters", valid_type=Dict, required=True, help="Input parameters")
+        spec.input(
+            "parameters", valid_type=Dict, required=True, help="Input parameters"
+        )
         spec.input(
             "settings",
             valid_type=Dict,
@@ -162,7 +161,7 @@ def prepare_for_submission(self, folder):
                            the plugin should put all its files.
         """
 
-        if 'structure' in self.inputs:
+        if "structure" in self.inputs:
             pmg_structure = self.inputs.structure.get_pymatgen_molecule()
         else:
             # If structure is not specified, it is read from the chk file
@@ -204,7 +203,7 @@ def prepare_for_submission(self, folder):
             comp_uuid = self.inputs.parent_calc_folder.computer.uuid
             remote_path = self.inputs.parent_calc_folder.get_remote_path()
             copy_info = (comp_uuid, remote_path, self.PARENT_FOLDER_NAME)
-            if (self.inputs.code.computer.uuid == comp_uuid):
+            if self.inputs.code.computer.uuid == comp_uuid:
                 # if running on the same computer - make a symlink
                 # if not - copy the folder
                 calcinfo.remote_symlink_list.append(copy_info)
@@ -229,13 +228,17 @@ def _render_input_string_from_params(cls, param_dict, pmg_structure):
             pmg_structure,
             title="input generated by the aiida-gaussian plugin",
             charge=param_dict.get("charge"),
-            spin_multiplicity=param_dict.get("multiplicity", param_dict.get("spin_multiplicity")),
+            spin_multiplicity=param_dict.get(
+                "multiplicity", param_dict.get("spin_multiplicity")
+            ),
             functional=param_dict.get("functional"),
             basis_set=param_dict.get("basis_set"),
             route_parameters=param_dict.get("route_parameters"),
             input_parameters=param_dict.get("input_parameters"),
             link0_parameters=param_dict.get("link0_parameters"),
-            dieze_tag=param_dict.get("dieze_tag", "#N"),  # normal print level by default
+            dieze_tag=param_dict.get(
+                "dieze_tag", "#N"
+            ),  # normal print level by default
         )
 
         return inp.to_string(cart_coords=True)