updates for aiida 1.1.0 (#32)

* modify setting of default port values

Reuse existing port definitions so that default validators are reused
without having to specify them again.

* update to aiida 1.1.0 and skip testing on python 2.7

* remove postgresql github action

should not be needed for temporary postgres cluster

* docs: use load_documentation_profile

use new load_documentation_profile function from aiida-core.

 * re-introduce helper scripts (now tested via example)
 * remove python-modernize hook
 * remove python2-compatibility leftovers
 * remove leftover travis setup

.github/workflows/ci.yml

@@ -9,16 +9,10 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: [2.7, 3.7]
+        python-version: [3.7]
         backend: ['django']
     steps:
-    - uses: actions/checkout@v1
-    - uses: harmon758/postgresql-action@v1
-      with:
-        postgresql version: '11'
-        postgresql db: test_${{ matrix.backend }}
-        postgresql user: 'postgres'
-        postgresql password: ''
+    - uses: actions/checkout@v2
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
@@ -32,7 +26,7 @@ jobs:
         echo 'deb https://dl.bintray.com/rabbitmq/debian bionic main' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
         sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
         sudo apt update
-        sudo apt install postgresql postgresql-server-dev-all postgresql-client rabbitmq-server graphviz
+        sudo apt install postgresql-10 rabbitmq-server graphviz
         sudo systemctl status rabbitmq-server.service
 
     - name: Install python dependencies

.pre-commit-config.yaml

@@ -1,16 +1,6 @@
 # Install pre-commit hooks via:
 # pre-commit install
 
-# modernizer: make sure our code-base is Python 3 ready
-- repo: https://github.com/python-modernize/python-modernize.git
-  rev: b8e29d95ed6e0f03ab82280ec0ab36136472e9c4
-  hooks:
-  - id: python-modernize
-    exclude: ^docs/
-    args:
-      - --write
-      - --nobackups
-
 # yapf = yet another python formatter
 - repo: https://github.com/pre-commit/mirrors-yapf
   rev: v0.28.0

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 The AiiDA Team.
+Copyright (c) 2020 The AiiDA Team.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -63,10 +63,10 @@ Here goes a complete example of how to submit a test calculation using this plug
 
 A quick demo of how to submit a calculation:
 ```shell
-verdi daemon start         # make sure the daemon is running
+verdi daemon start     # make sure the daemon is running
 cd examples
-verdi run submit.py        # submit test calculation
-verdi process list -a  # check status of calculation
+./example_01.py        # run test calculation
+verdi process list -a  # check record of calculation
 ```
 
 The plugin also includes verdi commands to inspect its data types:

aiida_diff/__init__.py

@@ -4,6 +4,4 @@
 AiiDA demo plugin that wraps the `diff` executable for computing the difference between two files.
 """
 
-from __future__ import absolute_import
-
 __version__ = "1.0.0"

aiida_diff/calculations.py

@@ -3,10 +3,6 @@
 
 Register calculations via the "aiida.calculations" entry point in setup.json.
 """
-from __future__ import absolute_import
-
-import six
-
 from aiida.common import datastructures
 from aiida.engine import CalcJob
 from aiida.orm import SinglefileData
@@ -26,9 +22,16 @@ def define(cls, spec):
         """Define inputs and outputs of the calculation."""
         # yapf: disable
         super(DiffCalculation, cls).define(spec)
-        spec.input('metadata.options.resources', valid_type=dict, default={'num_machines': 1, 'num_mpiprocs_per_machine': 1})
-        spec.input('metadata.options.parser_name', valid_type=six.string_types, default='diff')
-        spec.input('metadata.options.output_filename', valid_type=six.string_types, default='patch.diff')
+
+        # set default values for AiiDA options
+        spec.inputs['metadata']['options']['resources'].default = {
+                'num_machines': 1,
+                'num_mpiprocs_per_machine': 1,
+                }
+        spec.inputs['metadata']['options']['parser_name'].default = 'diff'
+
+        # new ports
+        spec.input('metadata.options.output_filename', valid_type=str, default='patch.diff')
         spec.input('parameters', valid_type=DiffParameters, help='Command line parameters for diff')
         spec.input('file1', valid_type=SinglefileData, help='First file to be compared.')
         spec.input('file2', valid_type=SinglefileData, help='Second file to be compared.')

aiida_diff/cli.py

@@ -6,7 +6,6 @@
 "aiida.cmdline.data" (both in the setup.json file).
 """
 
-from __future__ import absolute_import
 import sys
 import click
 from aiida.cmdline.utils import decorators

aiida_diff/data/__init__.py

@@ -7,7 +7,6 @@
 
 # You can directly use or subclass aiida.orm.data.Data
 # or any other data type listed under 'verdi data'
-from __future__ import absolute_import
 from aiida.orm import Dict
 from voluptuous import Schema, Optional
 

aiida_diff/helpers.py

@@ -0,0 +1,96 @@
+""" Helper functions for automatically setting up computer & code.
+Helper functions for setting up 
+
+ 1. An AiiDA localhost computer
+ 2. A "diff" code on localhost
+ 
+Note: Point 2 is made possible by the fact that the ``diff`` executable is
+available in the PATH on almost any UNIX system.
+"""
+import tempfile
+import shutil
+
+LOCALHOST_NAME = 'localhost-test'
+
+executables = {
+    'diff': 'diff',
+}
+
+
+def get_path_to_executable(executable):
+    """ Get path to local executable.
+    :param executable: Name of executable in the $PATH variable
+    :type executable: str
+    :return: path to executable
+    :rtype: str
+    """
+    path = shutil.which(executable)
+    if path is None:
+        raise ValueError(
+            "'{}' executable not found in PATH.".format(executable))
+    return path
+
+
+def get_computer(name=LOCALHOST_NAME, workdir=None):
+    """Get AiiDA computer.
+    Loads computer 'name' from the database, if exists.
+    Sets up local computer 'name', if it isn't found in the DB.
+    
+    :param name: Name of computer to load or set up.
+    :param workdir: path to work directory 
+        Used only when creating a new computer.
+    :return: The computer node 
+    :rtype: :py:class:`aiida.orm.Computer` 
+    """
+    from aiida.orm import Computer
+    from aiida.common.exceptions import NotExistent
+
+    try:
+        computer = Computer.objects.get(name=name)
+    except NotExistent:
+        if workdir is None:
+            workdir = tempfile.mkdtemp()
+
+        computer = Computer(
+            name=name,
+            description='localhost computer set up by aiida_diff tests',
+            hostname=name,
+            workdir=workdir,
+            transport_type='local',
+            scheduler_type='direct')
+        computer.store()
+        computer.set_minimum_job_poll_interval(0.)
+        computer.configure()
+
+    return computer
+
+
+def get_code(entry_point, computer):
+    """Get local code.
+    Sets up code for given entry point on given computer.
+    
+    :param entry_point: Entry point of calculation plugin
+    :param computer: (local) AiiDA computer
+    :return: The code node 
+    :rtype: :py:class:`aiida.orm.Code` 
+    """
+    from aiida.orm import Code
+
+    try:
+        executable = executables[entry_point]
+    except KeyError:
+        raise KeyError(
+            "Entry point '{}' not recognized. Allowed values: {}".format(
+                entry_point, list(executables.keys())))
+
+    codes = Code.objects.find(filters={'label': executable})  # pylint: disable=no-member
+    if codes:
+        return codes[0]
+
+    path = get_path_to_executable(executable)
+    code = Code(
+        input_plugin_name=entry_point,
+        remote_computer_exec=[computer, path],
+    )
+    code.label = executable
+    return code.store()

aiida_diff/parsers.py

@@ -1,11 +1,8 @@
-# -*- coding: utf-8 -*-
 """
 Parsers provided by aiida_diff.
 
 Register parsers via the "aiida.parsers" entry point in setup.json.
 """
-from __future__ import absolute_import
-
 from aiida.engine import ExitCode
 from aiida.parsers.parser import Parser
 from aiida.plugins import CalculationFactory

aiida_diff/tests/__init__.py

@@ -3,8 +3,6 @@
 Includes both tests written in unittest style (test_cli.py) and tests written
 in pytest style (test_calculations.py).
 """
-from __future__ import absolute_import
-from __future__ import print_function
 import os
 
 TEST_DIR = os.path.dirname(os.path.realpath(__file__))

aiida_diff/tests/test_calculations.py

@@ -1,9 +1,6 @@
 """ Tests for calculations
 
 """
-from __future__ import print_function
-from __future__ import absolute_import
-
 import os
 from aiida_diff import tests
 

aiida_diff/tests/test_cli.py

@@ -1,9 +1,6 @@
 """ Tests for command line interface.
 
 """
-from __future__ import print_function
-from __future__ import absolute_import
-
 from aiida.manage.tests.unittest_classes import PluginTestCase
 
 

docs/source/conf.py

@@ -16,36 +16,26 @@
 import time
 import aiida_diff
 
-from aiida.manage import configuration
-from aiida.manage.manager import get_manager
+from aiida.manage.configuration import load_documentation_profile
 
 # -- AiiDA-related setup --------------------------------------------------
 
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
+# Load the dummy profile even if we are running locally, this way the documentation will succeed even if the current
+# default profile of the AiiDA installation does not use a Django backend.
+load_documentation_profile()
 
-# Enable rtd mode via `export READTHEDOCS=True`
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
-
-if on_rtd:  # let RTD set the theme
-    pass
-else:
+# If we are not on READTHEDOCS load the Sphinx theme manually
+if not os.environ.get('READTHEDOCS', None):
     import sphinx_rtd_theme
     html_theme = 'sphinx_rtd_theme'
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
-# Back-end settings for readthedocs online documentation.
-configuration.IN_RT_DOC_MODE = True
-configuration.BACKEND = "django"
-
-configuration.reset_config()  # empty config was created when importing aiida
-configuration.load_profile()  # load dummy config for RTD
-# load DB backend (no schema check since no DB)
-get_manager()._load_backend(schema_check=False)  # pylint: disable=protected-access
-
 # -- General configuration ------------------------------------------------
 
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
 # If your documentation needs a minimal Sphinx version, state it here.
 needs_sphinx = '1.5'
 
@@ -83,7 +73,7 @@
 
 # General information about the project.
 project = u'aiida-diff'
-copyright_first_year = "2019"
+copyright_first_year = "2020"
 copyright_owners = "The AiiDA Team"
 
 current_year = str(time.localtime().tm_year)