Remove aiida tools dependency (#54)

* Remove dependency on `aiida-tools`, vendoring the code instead
* Update pre-commit hooks:
  * Switch to `black` for formatting
  * Add `isort`
  * Move `mypy` to run in main environment

Add some type hints and a sprinkle of `# type: ignore` to make the updated mypy version happy.

.github/system_tests/test_daemon.py

@@ -1,17 +1,17 @@
 """Tests to run with a running daemon."""
+import operator
 import subprocess
 import sys
-import operator
 import time
-import numpy as np
 
 from aiida import orm
-from aiida.engine.daemon.client import get_daemon_client
-from aiida.engine import launch
 from aiida.common import exceptions
+from aiida.engine import launch
+from aiida.engine.daemon.client import get_daemon_client
+import numpy as np
 
-from aiida_optimize.engines import Bisection
 from aiida_optimize import OptimizationWorkChain
+from aiida_optimize.engines import Bisection
 import sample_processes
 
 TIMEOUTSECS = 4 * 60  # 4 minutes
@@ -24,12 +24,14 @@ def print_daemon_log():
 
     print(f"Output of 'cat {daemon_log}':")
     try:
-        print(subprocess.check_output(
-            ['cat', f'{daemon_log}'],
-            stderr=subprocess.STDOUT,
-        ))
+        print(
+            subprocess.check_output(
+                ["cat", f"{daemon_log}"],
+                stderr=subprocess.STDOUT,
+            )
+        )
     except subprocess.CalledProcessError as exception:
-        print(f'Note: the command failed, message: {exception}')
+        print(f"Note: the command failed, message: {exception}")
 
 
 def wait_for(proc, time_elapsed=5):
@@ -46,8 +48,8 @@ def check_optimization(
     x_exact,
     f_exact,
     evaluate=None,
-    input_getter=operator.attrgetter('x'),
-    output_port_names=None
+    input_getter=operator.attrgetter("x"),
+    output_port_names=None,
 ):  # pylint: disable=too-many-arguments
     """submit launch and check optimization"""
     func_workchain = getattr(sample_processes, func_workchain_name)
@@ -63,7 +65,7 @@ def check_optimization(
 
     wait_for(result_node)
 
-    assert 'optimal_process_uuid' in result_node.outputs
+    assert "optimal_process_uuid" in result_node.outputs
     assert np.isclose(result_node.outputs.optimal_process_output.value, f_exact, atol=ftol)
 
     calc = orm.load_node(result_node.outputs.optimal_process_uuid.value)
@@ -99,14 +101,14 @@ def launch_all():
         engine=Bisection,
         engine_kwargs=dict(
             lower=-1.1,
-            upper=1.,
+            upper=1.0,
             tol=tol,
         ),
-        func_workchain_name='Echo',
+        func_workchain_name="Echo",
         xtol=tol,
         ftol=tol,
-        x_exact=0.,
-        f_exact=0.,
+        x_exact=0.0,
+        f_exact=0.0,
     )
 
 
@@ -119,5 +121,5 @@ def main():
     sys.exit(0)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

.gitignore

@@ -7,3 +7,4 @@
 dist
 .vscode
 .mypy_cache
+build

.pre-commit-config.yaml

@@ -1,19 +1,16 @@
 repos:
 
-- repo: https://github.com/pre-commit/mirrors-yapf
-  rev: v0.30.0
+- repo: https://github.com/psf/black
+  rev: 22.3.0
   hooks:
-  - id: yapf
-    language: system
-
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.780
+  - id: black
+- repo: https://github.com/pycqa/isort
+  rev: 5.10.1
   hooks:
-  - id: mypy
-    exclude: '^(doc/)|(examples/)'
+  - id: isort
 
 - repo: https://github.com/PyCQA/pylint
-  rev: pylint-2.5.0
+  rev: v2.14.4
   hooks:
   - id: pylint
     language: system
@@ -33,3 +30,11 @@ repos:
         aiida_optimize/__init__.py
       )$
     pass_filenames: false
+
+  - id: mypy
+    name: mypy
+    entry: mypy
+    language: python
+    types: [python]
+    require_serial: true
+    files: '^(aiida_optimize/)'

.pylintrc

@@ -50,7 +50,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=too-few-public-methods,too-many-public-methods,bad-continuation,wrong-import-position,line-too-long,locally-disabled,wildcard-import,locally-enabled,too-many-instance-attributes,fixme,len-as-condition,useless-object-inheritance,wrong-import-order
+disable=too-few-public-methods,too-many-public-methods,bad-continuation,wrong-import-position,line-too-long,wildcard-import,too-many-instance-attributes,fixme,len-as-condition,useless-object-inheritance,wrong-import-order,duplicate-code
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
@@ -92,46 +92,28 @@ max-nested-blocks=5
 
 [BASIC]
 
-# Naming hint for argument names
-argument-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
 # Regular expression matching correct argument names
 argument-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
 
-# Naming hint for attribute names
-attr-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
 # Regular expression matching correct attribute names
 attr-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
 
 # Bad variable names which should always be refused, separated by a comma
 bad-names=foo,bar,baz,toto,tutu,tata
 
-# Naming hint for class attribute names
-class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
-
 # Regular expression matching correct class attribute names
 class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
 
-# Naming hint for class names
-class-name-hint=[A-Z_][a-zA-Z0-9]+$
-
 # Regular expression matching correct class names
 class-rgx=[A-Z_][a-zA-Z0-9]+$
 
-# Naming hint for constant names
-const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
 # Regular expression matching correct constant names
 const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
 
 # Minimum line length for functions/classes that require docstrings, shorter
 # ones are exempt.
 docstring-min-length=5
 
-# Naming hint for function names
-function-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
 # Regular expression matching correct function names
 function-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
 
@@ -141,21 +123,12 @@ good-names=i,j,k,ex,Run,_, _INPUT_FILE_NAME, _OUTPUT_FILE_NAME,t,x,y,z,f,Paramet
 # Include a hint for the correct naming format with invalid-name
 include-naming-hint=no
 
-# Naming hint for inline iteration names
-inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
-
 # Regular expression matching correct inline iteration names
 inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
 
-# Naming hint for method names
-method-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
 # Regular expression matching correct method names
 method-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*)|(setUp)|(tearDown))$
 
-# Naming hint for module names
-module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
 # Regular expression matching correct module names
 module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
 
@@ -171,9 +144,6 @@ no-docstring-rgx=^[_,setUp,tearDown]
 # to this list to register other decorators that produce valid properties.
 property-classes=abc.abstractproperty
 
-# Naming hint for variable names
-variable-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
-
 # Regular expression matching correct variable names
 variable-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
 
@@ -199,12 +169,6 @@ max-line-length=140
 # Maximum number of lines in a module
 max-module-lines=1000
 
-# List of optional constructs for which whitespace checking is disabled. `dict-
-# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
-# `trailing-comma` allows a space between comma and closing bracket: (a, ).
-# `empty-line` allows space-only lines.
-no-space-check=trailing-comma,dict-separator
-
 # Allow the body of a class to be on the same line as the declaration if body
 # contains single statement.
 single-line-class-stmt=no

aiida_optimize/__init__.py

@@ -7,11 +7,9 @@
 engines and wrappers for .
 """
 
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
+from . import engines, helpers, process_inputs, wrappers
 from ._optimization_workchain import OptimizationWorkChain
-from . import helpers
-from . import engines
-from . import wrappers
 
-__all__ = ["OptimizationWorkChain", "helpers", "engines", "wrappers"]
+__all__ = ["OptimizationWorkChain", "helpers", "engines", "wrappers", "process_inputs"]