Refactor: Add the _prepare_yaml method to AbstractCode (#6565)

As specified in the docs, the `Data` class implements an `export()` method. For actually exporting `Data` nodes, subclasses should implement a `_prepare_XXX` method, where `XXX` is the desired export file format. When running `verdi data <orm-data-type> export`, the available data formats for exporting are dynamically determined based on the implemented `_prepare_XXX` methods. The `Code` classes didn't follow this specification (likely because `Code` wasn't historically a subclass of `Data`), but instead a custom implementation was used for `verdi code export` in `cmd_code.py`.

With the goal of increasing consistency, this PR moves the code of this custom implementation to the new `_prepare_yaml` method of the `AbstractCode` class (`_prepare_yml` is also added, as the previous default file extension was `.yml`, but it basically just calls `prepare_yaml`). The `export` function in `cmd_code.py` now instead calls the `data_export` function, as is done when exporting other classes derived from `Data`. Thus, exporting a `Code` via the CLI through `verdi code export` remains unchanged.

Lastly, for the `PortableCode` class, the `prepare_yaml` method is overridden to temporarily attach the `filepath_files` attribute to the instance, as this field is defined via the `pydantic` model, but not actually saved as an attribute (instead, the contents of the given folder are added to the `NodeRepository` via `put_object_from_tree`). Without temporarily attaching the attribute, this would otherwise lead to an exception in `test_data.py` which tests the exporting of the derived `Data` nodes, as the `filepath_files` field is tried to be accessed from the instance via `getattr`. In addition, the files contained in the `NodeRepository` of the `PortableCode` are also dumped to disk, such that upon exporting the code configuration to a YAML, the `PortableCode` _can_ actually be fully re-created from this file and the additional directory.

src/aiida/cmdline/commands/cmd_code.py

@@ -14,12 +14,13 @@
 
 import click
 
+from aiida.cmdline.commands.cmd_data.cmd_export import data_export
 from aiida.cmdline.commands.cmd_verdi import verdi
 from aiida.cmdline.groups.dynamic import DynamicEntryPointCommandGroup
 from aiida.cmdline.params import arguments, options, types
 from aiida.cmdline.params.options.commands import code as options_code
 from aiida.cmdline.utils import echo, echo_tabulate
-from aiida.cmdline.utils.common import generate_validate_output_file
+from aiida.cmdline.utils.common import validate_output_filename
 from aiida.cmdline.utils.decorators import with_dbenv
 from aiida.common import exceptions
 
@@ -241,28 +242,37 @@ def show(code):
 @options.SORT()
 @with_dbenv()
 def export(code, output_file, overwrite, sort):
-    """Export code to a yaml file."""
+    """Export code to a yaml file. If no output file is given, default name is created based on the code label."""
 
-    import yaml
+    other_args = {'sort': sort}
 
-    code_data = {}
+    fileformat = 'yaml'
 
-    for key in code.Model.model_fields.keys():
-        value = getattr(code, key).label if key == 'computer' else getattr(code, key)
-
-        # If the attribute is not set, for example ``with_mpi`` do not export it, because the YAML won't be valid for
-        # use in ``verdi code create`` since ``None`` is not a valid value on the CLI.
-        if value is not None:
-            code_data[key] = str(value)
+    if output_file is None:
+        output_file = pathlib.Path(f'{code.full_label}.{fileformat}')
 
     try:
-        output_file = generate_validate_output_file(
-            output_file=output_file, entity_label=code.label, overwrite=overwrite, appendix=f'@{code_data["computer"]}'
+        # In principle, output file validation is also done in the `data_export` function. However, the
+        # `validate_output_filename` function is applied here, as well, as it is also used in the `Computer` export, and
+        # as `Computer` is not derived from `Data`, it cannot be exported by `data_export`, so
+        # `validate_output_filename` cannot be removed in favor of the validation done in `data_export`.
+        validate_output_filename(
+            output_file=output_file,
+            overwrite=overwrite,
         )
     except (FileExistsError, IsADirectoryError) as exception:
         raise click.BadParameter(str(exception), param_hint='OUTPUT_FILE') from exception
 
-    output_file.write_text(yaml.dump(code_data, sort_keys=sort))
+    try:
+        data_export(
+            node=code,
+            output_fname=output_file,
+            fileformat=fileformat,
+            other_args=other_args,
+            overwrite=overwrite,
+        )
+    except Exception as exception:
+        echo.echo_critical(f'Error in the `data_export` function: {exception}')
 
     echo.echo_success(f'Code<{code.pk}> {code.label} exported to file `{output_file}`.')
 

src/aiida/cmdline/commands/cmd_computer.py

@@ -20,7 +20,7 @@
 from aiida.cmdline.params import arguments, options
 from aiida.cmdline.params.options.commands import computer as options_computer
 from aiida.cmdline.utils import echo, echo_tabulate
-from aiida.cmdline.utils.common import generate_validate_output_file
+from aiida.cmdline.utils.common import validate_output_filename
 from aiida.cmdline.utils.decorators import with_dbenv
 from aiida.common.exceptions import EntryPointError, ValidationError
 from aiida.plugins.entry_point import get_entry_point_names
@@ -766,10 +766,10 @@ def computer_export_setup(computer, output_file, overwrite, sort):
         'append_text': computer.get_append_text(),
     }
 
+    if output_file is None:
+        output_file = pathlib.Path(f'{computer.label}-setup.yaml')
     try:
-        output_file = generate_validate_output_file(
-            output_file=output_file, entity_label=computer.label, overwrite=overwrite, appendix='-setup'
-        )
+        validate_output_filename(output_file=output_file, overwrite=overwrite)
     except (FileExistsError, IsADirectoryError) as exception:
         raise click.BadParameter(str(exception), param_hint='OUTPUT_FILE') from exception
 
@@ -804,10 +804,10 @@ def computer_export_config(computer, output_file, user, overwrite, sort):
             ' because computer has not been configured yet.'
         )
     else:
+        if output_file is None:
+            output_file = pathlib.Path(f'{computer.label}-config.yaml')
         try:
-            output_file = generate_validate_output_file(
-                output_file=output_file, entity_label=computer.label, overwrite=overwrite, appendix='-config'
-            )
+            validate_output_filename(output_file=output_file, overwrite=overwrite)
         except (FileExistsError, IsADirectoryError) as exception:
             raise click.BadParameter(str(exception), param_hint='OUTPUT_FILE') from exception
 

src/aiida/cmdline/utils/common.py

@@ -486,13 +486,17 @@ def build_entries(ports):
         echo.echo(style('\nExit codes that invalidate the cache are marked in bold red.\n', italic=True))
 
 
-def generate_validate_output_file(
-    output_file: Path | None, entity_label: str, appendix: str = '', overwrite: bool = False
+def validate_output_filename(
+    output_file: Path | str,
+    overwrite: bool = False,
 ):
-    """Generate default output filename for `Code`/`Computer` export and validate."""
+    """Validate output filename."""
 
     if output_file is None:
-        output_file = Path(f'{entity_label}{appendix}.yml')
+        raise TypeError('Output filename must be passed for validation.')
+
+    if isinstance(output_file, str):
+        output_file = Path(output_file)
 
     if output_file.is_dir():
         raise IsADirectoryError(
@@ -501,5 +505,3 @@ def generate_validate_output_file(
 
     if output_file.is_file() and not overwrite:
         raise FileExistsError(f'File `{output_file}` already exists, use `--overwrite` to overwrite.')
-
-    return output_file

src/aiida/orm/nodes/data/code/abstract.py

@@ -381,3 +381,24 @@ def get_builder(self) -> 'ProcessBuilder':
         builder.code = self
 
         return builder
+
+    def _prepare_yaml(self, *args, **kwargs):
+        """Export code to a YAML file."""
+        import yaml
+
+        code_data = {}
+        sort = kwargs.get('sort', False)
+
+        for key in self.Model.model_fields.keys():
+            value = getattr(self, key).label if key == 'computer' else getattr(self, key)
+
+            # If the attribute is not set, for example ``with_mpi`` do not export it
+            # so that there are no null-values in the resulting YAML file
+            if value is not None:
+                code_data[key] = str(value)
+
+        return yaml.dump(code_data, sort_keys=sort, encoding='utf-8'), {}
+
+    def _prepare_yml(self, *args, **kwargs):
+        """Also allow for export as .yml"""
+        return self._prepare_yaml(*args, **kwargs)

src/aiida/orm/nodes/data/code/portable.py

@@ -19,6 +19,8 @@
 
 from __future__ import annotations
 
+import contextlib
+import logging
 import pathlib
 import typing as t
 
@@ -34,6 +36,7 @@
 from .legacy import Code
 
 __all__ = ('PortableCode',)
+_LOGGER = logging.getLogger(__name__)
 
 
 class PortableCode(Code):
@@ -71,7 +74,7 @@ def validate_filepath_files(cls, value: str) -> pathlib.Path:
                 raise ValueError(f'The filepath `{value}` is not a directory.')
             return filepath
 
-    def __init__(self, filepath_executable: str, filepath_files: pathlib.Path, **kwargs):
+    def __init__(self, filepath_executable: str, filepath_files: pathlib.Path | str, **kwargs):
         """Construct a new instance.
 
         .. note:: If the files necessary for this code are not all located in a single directory or the directory
@@ -177,3 +180,33 @@ def filepath_executable(self, value: str) -> None:
             raise ValueError('The `filepath_executable` should not be absolute.')
 
         self.base.attributes.set(self._KEY_ATTRIBUTE_FILEPATH_EXECUTABLE, value)
+
+    def _prepare_yaml(self, *args, **kwargs):
+        """Export code to a YAML file."""
+        try:
+            target = pathlib.Path().cwd() / f'{self.label}'
+            setattr(self, 'filepath_files', str(target))
+            result = super()._prepare_yaml(*args, **kwargs)[0]
+
+            extra_files = {}
+            node_repository = self.base.repository
+
+            # Logic taken from `copy_tree` method of the `Repository` class and adapted to return
+            # the relative file paths and their utf-8 encoded content as `extra_files` dictionary
+            path = '.'
+            for root, dirnames, filenames in node_repository.walk():
+                for filename in filenames:
+                    rel_output_file_path = root.relative_to(path) / filename
+                    full_output_file_path = target / rel_output_file_path
+                    full_output_file_path.parent.mkdir(exist_ok=True, parents=True)
+
+                    extra_files[str(full_output_file_path)] = node_repository.get_object_content(
+                        str(rel_output_file_path), mode='rb'
+                    )
+            _LOGGER.warning(f'Repository files for PortableCode <{self.pk}> dumped to folder `{target}`.')
+
+        finally:
+            with contextlib.suppress(AttributeError):
+                delattr(self, 'filepath_files')
+
+        return result, extra_files

tests/cmdline/commands/test_code.py

@@ -345,7 +345,7 @@ def test_code_export_default_filename(run_cli_command, aiida_code_installed):
     options = [str(code.pk)]
     run_cli_command(cmd_code.export, options)
 
-    assert pathlib.Path('code@localhost.yml').is_file()
+    assert pathlib.Path('code@localhost.yaml').is_file()
 
 
 @pytest.mark.parametrize('non_interactive_editor', ('vim -cwq',), indirect=True)
@@ -461,10 +461,13 @@ def test_code_setup_local_duplicate_full_label_interactive(run_cli_command, non_
 
 
 @pytest.mark.usefixtures('aiida_profile_clean')
-def test_code_setup_local_duplicate_full_label_non_interactive(run_cli_command):
+def test_code_setup_local_duplicate_full_label_non_interactive(run_cli_command, tmp_path):
     """Test ``verdi code setup`` for a local code in non-interactive mode specifying an existing full label."""
     label = 'some-label'
-    code = PortableCode(filepath_executable='bash', filepath_files=pathlib.Path('/bin/bash'))
+    tmp_bin_dir = tmp_path / 'bin'
+    tmp_bin_dir.mkdir()
+    (tmp_bin_dir / 'bash').touch()
+    code = PortableCode(filepath_executable='bash', filepath_files=tmp_bin_dir)
     code.label = label
     code.base.repository.put_object_from_filelike(io.BytesIO(b''), 'bash')
     code.store()
@@ -477,7 +480,7 @@ def test_code_setup_local_duplicate_full_label_non_interactive(run_cli_command):
         '-P',
         'core.arithmetic.add',
         '--store-in-db',
-        '--code-folder=/bin',
+        f'--code-folder={tmp_bin_dir}',
         '--code-rel-path=bash',
         '--label',
         label,

tests/cmdline/commands/test_computer.py

@@ -525,7 +525,7 @@ def test_computer_export_setup(self, tmp_path, file_regression, sort_option):
         comp = self.comp_builder.new()
         comp.store()
 
-        exported_setup_filename = tmp_path / 'computer-setup.yml'
+        exported_setup_filename = tmp_path / 'computer-setup.yaml'
 
         # Successfull write behavior
         result = self.cli_runner(computer_export_setup, [comp.label, exported_setup_filename, sort_option])
@@ -534,9 +534,9 @@ def test_computer_export_setup(self, tmp_path, file_regression, sort_option):
 
         # file regresssion check
         content = exported_setup_filename.read_text()
-        file_regression.check(content, extension='.yml')
+        file_regression.check(content, extension='.yaml')
 
-        # verifying correctness by comparing internal and loaded yml object
+        # verifying correctness by comparing internal and loaded yaml object
         configure_setup_data = yaml.safe_load(exported_setup_filename.read_text())
         assert configure_setup_data == self.comp_builder.get_computer_spec(
             comp
@@ -550,7 +550,7 @@ def test_computer_export_setup_overwrite(self, tmp_path):
         comp = self.comp_builder.new()
         comp.store()
 
-        exported_setup_filename = tmp_path / 'computer-setup.yml'
+        exported_setup_filename = tmp_path / 'computer-setup.yaml'
         # Check that export fails if the file already exists
         exported_setup_filename.touch()
         result = self.cli_runner(computer_export_setup, [comp.label, exported_setup_filename], raises=True)
@@ -581,7 +581,7 @@ def test_computer_export_setup_default_filename(self):
         comp = self.comp_builder.new()
         comp.store()
 
-        exported_setup_filename = f'{comp_label}-setup.yml'
+        exported_setup_filename = f'{comp_label}-setup.yaml'
 
         self.cli_runner(computer_export_setup, [comp.label])
         assert pathlib.Path(exported_setup_filename).is_file()
@@ -593,7 +593,7 @@ def test_computer_export_config(self, tmp_path):
         comp = self.comp_builder.new()
         comp.store()
 
-        exported_config_filename = tmp_path / 'computer-configure.yml'
+        exported_config_filename = tmp_path / 'computer-configure.yaml'
 
         # We have not configured the computer yet so it should exit with an critical error
         result = self.cli_runner(computer_export_config, [comp.label, exported_config_filename], raises=True)
@@ -613,7 +613,7 @@ def test_computer_export_config(self, tmp_path):
         content = exported_config_filename.read_text()
         assert content.startswith('safe_interval: 0.0')
 
-        # verifying correctness by comparing internal and loaded yml object
+        # verifying correctness by comparing internal and loaded yaml object
         configure_config_data = yaml.safe_load(exported_config_filename.read_text())
         assert (
             configure_config_data == comp.get_configuration()
@@ -641,7 +641,7 @@ def test_computer_export_config_overwrite(self, tmp_path):
         comp.store()
         comp.configure(safe_interval=0.0)
 
-        exported_config_filename = tmp_path / 'computer-configure.yml'
+        exported_config_filename = tmp_path / 'computer-configure.yaml'
 
         # Create directory with the same name and check that command fails
         exported_config_filename.mkdir()
@@ -673,7 +673,7 @@ def test_computer_export_config_default_filename(self):
         comp.store()
         comp.configure(safe_interval=0.0)
 
-        exported_config_filename = f'{comp_label}-config.yml'
+        exported_config_filename = f'{comp_label}-config.yaml'
 
         self.cli_runner(computer_export_config, [comp.label])
         assert pathlib.Path(exported_config_filename).is_file()

tests/cmdline/utils/test_common.py

@@ -12,7 +12,7 @@
 
 import pytest
 from aiida.cmdline.utils import common
-from aiida.cmdline.utils.common import generate_validate_output_file
+from aiida.cmdline.utils.common import validate_output_filename
 from aiida.common import LinkType
 from aiida.engine import Process, calcfunction
 from aiida.orm import CalcFunctionNode, CalculationNode, WorkflowNode
@@ -95,35 +95,30 @@ def test_with_docstring():
 
 
 @pytest.mark.usefixtures('chdir_tmp_path')
-def test_generate_validate_output():
+def test_validate_output_filename():
     test_entity_label = 'test_code'
     test_appendix = '@test_computer'
+    fileformat = 'yaml'
 
-    expected_output_file = Path(f'{test_entity_label}{test_appendix}.yml')
+    expected_output_file = Path(f'{test_entity_label}{test_appendix}.{fileformat}')
 
-    # Test default label creation
-    obtained_output_file = generate_validate_output_file(
-        output_file=None, entity_label=test_entity_label, appendix=test_appendix
-    )
-    assert expected_output_file == obtained_output_file, 'Filenames differ'
+    # Test failure if no actual file to be validated is passed
+    with pytest.raises(TypeError, match='.*passed for validation.'):
+        validate_output_filename(output_file=None)
 
     # Test failure if file exists, but overwrite False
     expected_output_file.touch()
     with pytest.raises(FileExistsError, match='.*use `--overwrite` to overwrite.'):
-        generate_validate_output_file(
-            output_file=None, entity_label=test_entity_label, appendix=test_appendix, overwrite=False
-        )
+        validate_output_filename(output_file=expected_output_file, overwrite=False)
 
-    # Test that overwrite does the job
-    obtained_output_file = generate_validate_output_file(
-        output_file=None, entity_label=test_entity_label, appendix=test_appendix, overwrite=True
-    )
-    assert expected_output_file == obtained_output_file, 'Overwrite unsuccessful'
+    # Test that overwrite does the job -> No exception raised
+    validate_output_filename(output_file=expected_output_file, overwrite=True)
     expected_output_file.unlink()
 
     # Test failure if directory exists
     expected_output_file.mkdir()
     with pytest.raises(IsADirectoryError, match='A directory with the name.*'):
-        generate_validate_output_file(
-            output_file=None, entity_label=test_entity_label, appendix=test_appendix, overwrite=False
+        validate_output_filename(
+            output_file=expected_output_file,
+            overwrite=False,
         )