⬆️ Upgrade to aiida-core v1.4.0

- drop support for python<3.5
- remove six dependency
- fix deprecation warnings
- impore pre-commit code style
- add tox.ini and docker-compose.yml for improved test infrastructure

.gitignore

@@ -9,6 +9,7 @@ dist/
 *.egg*
 .DS_Store
 .idea/
+.tox/
 .pytest_cache/
 .idea/vcs.xml
 postgres*.log

.pre-commit-config.yaml

@@ -10,49 +10,50 @@ exclude: >
 repos:
 
   - repo: git://github.com/pre-commit/pre-commit-hooks
-    rev: v2.2.3
+    rev: v3.2.0
     hooks:
     - id: check-json
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.5.3
+    hooks:
+    - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+    - id: black
+
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.3
+    hooks:
     - id: flake8
+      # additional_dependencies:
+      # - flake8-bugbear==20.1.4
+      # - flake8-builtins==1.5.3
+      # - flake8-comprehensions==3.2.3
       exclude: >
         (?x)^(
           aiida_lammps/calculations/dynaphopy.py
         )$
 
-  - repo: https://github.com/psf/black
-    rev: stable
-    hooks:
-    - id: black
-
   - repo: local
     hooks:
-
     - id: version-number
       name: Check version numbers
-      entry: python ./.travis-data/check_version.py
-      language: system
+      entry: python ./.pre-commit/check_version.py version
+      language: python
       files: >-
         (?x)^(
           setup.json|
-          .travis-data/check_version.py|
+          .pre-commit/check_version.py|
           aiida_lammps/__init__.py
         )$
       pass_filenames: false
-
-    # - id: travis-linter
-    #   name: Travis Lint
-    #   entry: travis lint
-    #   files: .travis.yml
-    #   language: ruby
-    #   additional_dependencies: ['travis']
-
-    # - id: doc8
-    #   entry: doc8
-    #   language: system
-    #   types: [rst]
-    #   name: doc8 - Lint the documentation.
+      additional_dependencies:
+        - click
 
     # TODO could also add check-manifest

.pre-commit/check_version.py

@@ -0,0 +1,71 @@
+"""Validate consistency of versions and dependencies.
+
+Validates consistency of setup.json and
+
+ * environment.yml
+ * version in aiida_lammps/__init__.py
+"""
+import json
+import os
+import sys
+
+import click
+
+FILENAME_SETUP_JSON = "setup.json"
+SCRIPT_PATH = os.path.split(os.path.realpath(__file__))[0]
+ROOT_DIR = os.path.join(SCRIPT_PATH, os.pardir)
+FILEPATH_SETUP_JSON = os.path.join(ROOT_DIR, FILENAME_SETUP_JSON)
+
+
+def get_setup_json():
+    """Return the `setup.json` as a python dictionary."""
+    with open(FILEPATH_SETUP_JSON, "r") as handle:
+        setup_json = json.load(handle)  # , object_pairs_hook=OrderedDict)
+
+    return setup_json
+
+
+@click.group()
+def cli():
+    """Command line interface for pre-commit checks."""
+    pass
+
+
+@cli.command("version")
+def validate_version():
+    """Check that version numbers match.
+
+    Check version number in setup.json and aiida_lammos/__init__.py and make sure
+    they match.
+    """
+    # Get version from python package
+    sys.path.insert(0, ROOT_DIR)
+    import aiida_lammps  # pylint: disable=wrong-import-position
+
+    version = aiida_lammps.__version__
+
+    setup_content = get_setup_json()
+    if version != setup_content["version"]:
+        click.echo("Version number mismatch detected:")
+        click.echo(
+            "Version number in '{}': {}".format(
+                FILENAME_SETUP_JSON, setup_content["version"]
+            )
+        )
+        click.echo(
+            "Version number in '{}/__init__.py': {}".format("aiida_lammps", version)
+        )
+        click.echo(
+            "Updating version in '{}' to: {}".format(FILENAME_SETUP_JSON, version)
+        )
+
+        setup_content["version"] = version
+        with open(FILEPATH_SETUP_JSON, "w") as fil:
+            # Write with indentation of two spaces and explicitly define separators to not have spaces at end of lines
+            json.dump(setup_content, fil, indent=2, separators=(",", ": "))
+
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    cli()  # pylint: disable=no-value-for-parameter

aiida_lammps/calculations/dynaphopy.py

@@ -1,10 +1,10 @@
-from aiida.engine import CalcJob
-from aiida.orm import ArrayData, StructureData, TrajectoryData
-from aiida.common.exceptions import InputValidationError
 from aiida.common.datastructures import CalcInfo, CodeInfo
+from aiida.common.exceptions import InputValidationError
 from aiida.common.utils import classproperty
-
+from aiida.engine import CalcJob
+from aiida.orm import ArrayData, StructureData, TrajectoryData
 from aiida_phonopy.common.raw_parsers import get_force_constants, get_poscar_txt
+
 from aiida_lammps.common.generate_input_files import (
     get_trajectory_txt,
     parameters_to_input_file,

aiida_lammps/calculations/lammps/__init__.py

@@ -1,13 +1,12 @@
-from aiida.engine import CalcJob
-from aiida.common.exceptions import ValidationError
 from aiida.common import CalcInfo, CodeInfo
-from aiida.orm import StructureData, Dict
+from aiida.common.exceptions import ValidationError
+from aiida.engine import CalcJob
+from aiida.orm import Dict, StructureData
 from aiida.plugins import DataFactory
+import numpy as np
+
 from aiida_lammps.common.generate_structure import generate_lammps_structure
 from aiida_lammps.data.potential import EmpiricalPotential
-import six
-
-import numpy as np
 
 
 def get_supercell(structure, supercell_shape):
@@ -111,27 +110,27 @@ def define(cls, spec):
         spec.input("parameters", valid_type=Dict, help="the parameters", required=False)
         spec.input(
             "metadata.options.cell_transform_filename",
-            valid_type=six.string_types,
+            valid_type=str,
             default="cell_transform.npy",
         )
         spec.input(
             "metadata.options.output_filename",
-            valid_type=six.string_types,
+            valid_type=str,
             default=cls._DEFAULT_OUTPUT_FILE_NAME,
         )
         spec.input(
             "metadata.options.trajectory_suffix",
-            valid_type=six.string_types,
+            valid_type=str,
             default=cls._DEFAULT_TRAJECTORY_FILE_NAME,
         )
         spec.input(
             "metadata.options.system_suffix",
-            valid_type=six.string_types,
+            valid_type=str,
             default=cls._DEFAULT_SYSTEM_FILE_NAME,
         )
         spec.input(
             "metadata.options.restart_filename",
-            valid_type=six.string_types,
+            valid_type=str,
             default=cls._DEFAULT_RESTART_FILE_NAME,
         )
 

aiida_lammps/calculations/lammps/combinate.py

@@ -1,15 +1,15 @@
 # Not working with Aiida 1.0
 
 from aiida.common.exceptions import InputValidationError
+from aiida.orm import ArrayData, Dict
 from aiida_phonopy.common.raw_parsers import (
     get_force_constants,
-    get_poscar_txt,
     get_FORCE_SETS_txt,
+    get_poscar_txt,
 )
-from aiida_lammps.calculations.lammps import BaseLammpsCalculation
-from aiida.orm import Dict, ArrayData
 import numpy as np
-import six
+
+from aiida_lammps.calculations.lammps import BaseLammpsCalculation
 
 
 def generate_dynaphopy_input(
@@ -59,7 +59,7 @@ def define(cls, spec):
         super(CombinateCalculation, cls).define(spec)
         spec.input(
             "metadata.options.parser_name",
-            valid_type=six.string_types,
+            valid_type=str,
             default="dynaphopy",
         )
         spec.input("parameters_dynaphopy", valid_type=Dict, help="dynaphopy parameters")
@@ -68,7 +68,7 @@ def define(cls, spec):
         )
         spec.input("force_sets", valid_type=ArrayData, help="phonopy force sets")
 
-        # spec.input('settings', valid_type=six.string_types, default='lammps.optimize')
+        # spec.input('settings', valid_type=str, default='lammps.optimize')
 
     @staticmethod
     def create_main_input_content(
@@ -94,8 +94,10 @@ def create_main_input_content(
         lammps_input_file += "neighbor        0.3 bin\n"
         lammps_input_file += "neigh_modify    every 1 delay 0 check no\n"
 
-        lammps_input_file += "velocity        all create {0} {1} dist gaussian mom yes\n".format(
-            parameter_data.dict.temperature, random_number
+        lammps_input_file += (
+            "velocity        all create {0} {1} dist gaussian mom yes\n".format(
+                parameter_data.dict.temperature, random_number
+            )
         )
         lammps_input_file += "velocity        all scale {}\n".format(
             parameter_data.dict.temperature

aiida_lammps/calculations/lammps/force.py

@@ -1,8 +1,8 @@
 from aiida.plugins import DataFactory
+
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
-from aiida_lammps.validation import validate_against_schema
 from aiida_lammps.common.utils import convert_date_string
-import six
+from aiida_lammps.validation import validate_against_schema
 
 
 class ForceCalculation(BaseLammpsCalculation):
@@ -12,11 +12,11 @@ def define(cls, spec):
 
         spec.input(
             "metadata.options.parser_name",
-            valid_type=six.string_types,
+            valid_type=str,
             default="lammps.force",
         )
 
-        # spec.input('settings', valid_type=six.string_types, default='lammps.optimize')
+        # spec.input('settings', valid_type=str, default='lammps.optimize')
 
         spec.output(
             "arrays",

aiida_lammps/calculations/lammps/md.py

@@ -1,10 +1,10 @@
-import numpy as np
 from aiida.common.exceptions import InputValidationError
 from aiida.plugins import DataFactory
+import numpy as np
+
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
-from aiida_lammps.common.utils import convert_date_string, join_keywords, get_path
+from aiida_lammps.common.utils import convert_date_string, get_path, join_keywords
 from aiida_lammps.validation import validate_against_schema
-import six
 
 
 class MdCalculation(BaseLammpsCalculation):
@@ -14,7 +14,7 @@ def define(cls, spec):
 
         spec.input(
             "metadata.options.parser_name",
-            valid_type=six.string_types,
+            valid_type=str,
             default="lammps.md",
         )
         spec.default_output_port = "results"
@@ -96,8 +96,10 @@ def create_main_input_content(
             raise_error=False,
         )
         if initial_temp is not None:
-            lammps_input_file += "velocity        all create {0} {1} dist gaussian mom yes\n".format(
-                initial_temp, pdict.get("rand_seed", np.random.randint(10000000))
+            lammps_input_file += (
+                "velocity        all create {0} {1} dist gaussian mom yes\n".format(
+                    initial_temp, pdict.get("rand_seed", np.random.randint(10000000))
+                )
             )
             lammps_input_file += "velocity        all scale {}\n".format(initial_temp)
 

aiida_lammps/calculations/lammps/md_multi.py

@@ -1,9 +1,9 @@
 from aiida.common.exceptions import InputValidationError
 from aiida.plugins import DataFactory
+
 from aiida_lammps.calculations.lammps import BaseLammpsCalculation
-from aiida_lammps.common.utils import convert_date_string, join_keywords, get_path
+from aiida_lammps.common.utils import convert_date_string, get_path, join_keywords
 from aiida_lammps.validation import validate_against_schema
-import six
 
 
 class MdMultiCalculation(BaseLammpsCalculation):
@@ -15,7 +15,7 @@ def define(cls, spec):
 
         spec.input(
             "metadata.options.parser_name",
-            valid_type=six.string_types,
+            valid_type=str,
             default="lammps.md.multi",
         )
         spec.default_output_port = "results"