add cli options for config file management (#33)

* add cli options for config file management

Add cli options:

  --testing-config-action: Read config file if present ('read'), require config file ('require') or generate new config file ('generate').
  --regenerate-test-data: Regenerate test data

* add tests for new cli options

* add documentation of new cli options

* fix: check that the data directory path is absolute and exists

* fix: add quotation marks to exported environment variables

Paths may contain spaces etc.

.github/workflows/ci.yml

@@ -12,14 +12,7 @@ jobs:
         python-version: [3.6, 3.8]
         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
       with:
@@ -32,7 +25,7 @@ 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

aiida_testing/__init__.py

@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 """A pytest plugin for testing AiiDA plugins."""
 
-__version__ = '0.1.0.dev0'
+__version__ = '0.1.0.dev1'

aiida_testing/_config.py

@@ -1,30 +1,87 @@
 # -*- coding: utf-8 -*-
 """
-Defines a helper for loading the ``.aiida-testing-config.yml``
-configuration file.
+Helpers for managing the ``.aiida-testing-config.yml`` configuration file.
 """
 
 import os
 import pathlib
 import typing as ty
+import collections
+from voluptuous import Schema
+from enum import Enum
 
 import yaml
 
+CONFIG_FILE_NAME = '.aiida-testing-config.yml'
 
-def get_config() -> ty.Dict[str, str]:
+
+class ConfigActions(Enum):
     """
-    Reads the configuration file ``.aiida-testing-config.yml``. The
-    file is searched in the current working directory and all its parent
-    directories.
+    An enum containing the actions to perform on the config file.
     """
-    cwd = pathlib.Path(os.getcwd())
-    config: ty.Dict[str, str]
-    for dir_path in [cwd, *cwd.parents]:
-        config_file_path = (dir_path / '.aiida-testing-config.yml')
-        if config_file_path.exists():
-            with open(config_file_path) as config_file:
-                config = yaml.load(config_file, Loader=yaml.SafeLoader)
-                break
-    else:
-        config = {}
-    return config
+    READ = 'read'
+    GENERATE = 'generate'
+    REQUIRE = 'require'
+
+
+class Config(collections.abc.MutableMapping):
+    """Configuration of aiida-testing package."""
+
+    schema = Schema({'mock_code': Schema({str: str})})
+
+    def __init__(self, config=None):
+        self._dict = config or {}
+        self.validate()
+
+    def validate(self):
+        """Validate configuration dictionary."""
+        return self.schema(self._dict)
+
+    @classmethod
+    def from_file(cls):
+        """
+        Parses the configuration file ``.aiida-testing-config.yml``.
+
+        The file is searched in the current working directory and all its parent
+        directories.
+        """
+        cwd = pathlib.Path(os.getcwd())
+        config: ty.Dict[str, str]
+        for dir_path in [cwd, *cwd.parents]:
+            config_file_path = (dir_path / CONFIG_FILE_NAME)
+            if config_file_path.exists():
+                with open(config_file_path) as config_file:
+                    config = yaml.load(config_file, Loader=yaml.SafeLoader)
+                    break
+        else:
+            config = {}
+
+        return cls(config)
+
+    def to_file(self):
+        """Write configuration to file in yaml format.
+
+        Writes to current working directory.
+
+        :param handle: File handle to write config file to.
+        """
+        cwd = pathlib.Path(os.getcwd())
+        config_file_path = (cwd / CONFIG_FILE_NAME)
+
+        with open(config_file_path, 'w') as handle:
+            yaml.dump(self._dict, handle, Dumper=yaml.SafeDumper)
+
+    def __getitem__(self, item):
+        return self._dict.__getitem__(item)
+
+    def __setitem__(self, key, value):
+        return self._dict.__setitem__(key, value)
+
+    def __delitem__(self, key):
+        return self._dict.__delitem__(key)
+
+    def __iter__(self):
+        return self._dict.__iter__()
+
+    def __len__(self):
+        return self._dict.__len__()

aiida_testing/mock_code/__init__.py

@@ -4,8 +4,13 @@
 the executable.
 """
 
-import typing as ty
+from ._fixtures import *
 
-from ._fixtures import mock_code_factory
-
-__all__: ty.Tuple[str, ...] = ('mock_code_factory', )
+# Note: This is necessary for the sphinx doc - otherwise it does not find aiida_testing.mock_code.mock_code_factory
+__all__ = (
+    "pytest_addoption",
+    "testing_config_action",
+    "mock_regenerate_test_data",
+    "testing_config",
+    "mock_code_factory",
+)

aiida_testing/mock_code/_cli.py

@@ -31,10 +31,15 @@ def run() -> None:
     data_dir = os.environ[EnvKeys.DATA_DIR.value]
     executable_path = os.environ[EnvKeys.EXECUTABLE_PATH.value]
     ignore_files = os.environ[EnvKeys.IGNORE_FILES.value].split(':')
+    regenerate_data = os.environ[EnvKeys.REGENERATE_DATA.value] == 'True'
 
     hash_digest = get_hash().hexdigest()
+
     res_dir = pathlib.Path(data_dir) / f"mock-{label}-{hash_digest}"
 
+    if regenerate_data and res_dir.exists():
+        shutil.rmtree(res_dir)
+
     if not res_dir.exists():
         if not executable_path:
             sys.exit("No existing output, and no executable specified.")
@@ -116,7 +121,7 @@ def replace_submit_file(executable_path: str) -> None:
     for line in submit_file_content.splitlines():
         if 'export AIIDA_MOCK' in line:
             continue
-        elif 'aiida-mock-code' in line:
+        if 'aiida-mock-code' in line:
             submit_file_res_lines.append(
                 f"'{executable_path}' " + line.split("aiida-mock-code'")[1]
             )

aiida_testing/mock_code/_env_keys.py

@@ -15,3 +15,4 @@ class EnvKeys(Enum):
     DATA_DIR = 'AIIDA_MOCK_DATA_DIR'
     EXECUTABLE_PATH = 'AIIDA_MOCK_EXECUTABLE_PATH'
     IGNORE_FILES = 'AIIDA_MOCK_IGNORE_FILES'
+    REGENERATE_DATA = 'AIIDA_MOCK_REGENERATE_DATA'

aiida_testing/mock_code/_fixtures.py

@@ -8,33 +8,94 @@
 import inspect
 import pathlib
 import typing as ty
-
+import click
 import pytest
 
+from aiida.orm import Code
+
 from ._env_keys import EnvKeys
-from .._config import get_config
+from .._config import Config, CONFIG_FILE_NAME, ConfigActions
+
+__all__ = (
+    "pytest_addoption",
+    "testing_config_action",
+    "mock_regenerate_test_data",
+    "testing_config",
+    "mock_code_factory",
+)
+
+
+def pytest_addoption(parser):
+    """Add pytest command line options."""
+    parser.addoption(
+        "--testing-config-action",
+        type=click.Choice((c.value for c in ConfigActions)),
+        default=ConfigActions.READ.value,
+        help=f"Read {CONFIG_FILE_NAME} config file if present ('read'), require config file ('require') or " \
+             "generate new config file ('generate').",
+    )
+    parser.addoption(
+        "--mock-regenerate-test-data",
+        action="store_true",
+        default=False,
+        help="Regenerate test data."
+    )
+
+
+@pytest.fixture(scope='session')
+def testing_config_action(request):
+    return request.config.getoption("--testing-config-action")
+
+
+@pytest.fixture(scope='session')
+def mock_regenerate_test_data(request):
+    return request.config.getoption("--mock-regenerate-test-data")
+
+
+@pytest.fixture(scope='session')
+def testing_config(testing_config_action):  # pylint: disable=redefined-outer-name
+    """Get content of .aiida-testing-config.yml
+
+    testing_config_action :
+        Read config file if present ('read'), require config file ('require') or generate new config file ('generate').
+    """
+    config = Config.from_file()
 
-__all__ = ("mock_code_factory", )
+    if not config and testing_config_action == ConfigActions.REQUIRE.value:
+        raise ValueError(f"Unable to find {CONFIG_FILE_NAME}.")
+
+    yield config
+
+    if testing_config_action == ConfigActions.GENERATE.value:
+        config.to_file()
 
 
 @pytest.fixture(scope='function')
-def mock_code_factory(aiida_localhost):
+def mock_code_factory(
+    aiida_localhost, testing_config, testing_config_action, mock_regenerate_test_data
+):  # pylint: disable=redefined-outer-name
     """
     Fixture to create a mock AiiDA Code.
-    """
-    config = get_config().get('mock_code', {})
 
+    testing_config_action :
+        Read config file if present ('read'), require config file ('require') or generate new config file ('generate').
+
+
+    """
     def _get_mock_code(
         label: str,
         entry_point: str,
         data_dir_abspath: ty.Union[str, pathlib.Path],
-        ignore_files: ty.Iterable[str] = ('_aiidasubmit.sh', )
+        ignore_files: ty.Iterable[str] = ('_aiidasubmit.sh'),
+        executable_name: str = '',
+        _config: dict = testing_config,
+        _config_action: str = testing_config_action,
+        _regenerate_test_data: bool = mock_regenerate_test_data,
     ):
         """
         Creates a mock AiiDA code. If the same inputs have been run previously,
         the results are copied over from the corresponding sub-directory of
-        the ``data_dir_abspath``. Otherwise, the code is executed if an
-        executable is specified in the configuration, or fails if it is not.
+        the ``data_dir_abspath``. Otherwise, the code is executed.
 
         Parameters
         ----------
@@ -48,26 +109,59 @@ def _get_mock_code(
             stored.
         ignore_files :
             A list of files which are not copied to the results directory
-            when the code is executed.
+            after the code has been executed.
+        executable_name :
+            Name of code executable to search for in PATH, if configuration file does not specify location already.
+        _config :
+            Dict with contents of configuration file
+        _config_action :
+            If 'require', raise ValueError if config dictionary does not specify path of executable.
+            If 'generate', add new key (label) to config dictionary.
+        _regenerate_test_data :
+            If True, regenerate test data instead of reusing.
         """
-        from aiida.orm import Code
-
         # we want to set a custom prepend_text, which is why the code
         # can not be reused.
         code_label = f'mock-{label}-{uuid.uuid4()}'
 
-        executable_path = shutil.which('aiida-mock-code')
+        data_dir_pl = pathlib.Path(data_dir_abspath)
+        if not data_dir_pl.exists():
+            raise ValueError("Data directory '{}' does not exist".format(data_dir_abspath))
+        if not data_dir_pl.is_absolute():
+            raise ValueError("Please provide absolute path to data directory.")
+
+        mock_executable_path = shutil.which('aiida-mock-code')
+        if not mock_executable_path:
+            raise ValueError(
+                "'aiida-mock-code' executable not found in the PATH. " +
+                "Have you run `pip install aiida-testing` in this python environment?"
+            )
+
+        # try determine path to actual code executable
+        mock_code_config = _config.get('mock_code', {})
+        if _config_action == ConfigActions.REQUIRE.value and label not in mock_code_config:
+            raise ValueError(
+                f"Configuration file {CONFIG_FILE_NAME} does not specify path to executable for code label '{label}'."
+            )
+        code_executable_path = mock_code_config.get(label, 'TO_SPECIFY')
+        if (not code_executable_path) and executable_name:
+            code_executable_path = shutil.which(executable_name) or 'NOT_FOUND'
+        if _config_action == ConfigActions.GENERATE.value:
+            mock_code_config[label] = code_executable_path
+
         code = Code(
-            input_plugin_name=entry_point, remote_computer_exec=[aiida_localhost, executable_path]
+            input_plugin_name=entry_point,
+            remote_computer_exec=[aiida_localhost, mock_executable_path]
         )
         code.label = code_label
         code.set_prepend_text(
             inspect.cleandoc(
                 f"""
-                export {EnvKeys.LABEL.value}={label}
-                export {EnvKeys.DATA_DIR.value}={data_dir_abspath}
-                export {EnvKeys.EXECUTABLE_PATH.value}={config.get(label, '')}
-                export {EnvKeys.IGNORE_FILES.value}={':'.join(ignore_files)}
+                export {EnvKeys.LABEL.value}="{label}"
+                export {EnvKeys.DATA_DIR.value}="{data_dir_abspath}"
+                export {EnvKeys.EXECUTABLE_PATH.value}="{code_executable_path}"
+                export {EnvKeys.IGNORE_FILES.value}="{':'.join(ignore_files)}"
+                export {EnvKeys.REGENERATE_DATA.value}={'True' if _regenerate_test_data else 'False'}
                 """
             )
         )