Commit changes to continue.

src/aiida/cmdline/commands/cmd_profile.py

@@ -273,37 +273,57 @@ def profile_delete(force, delete_data, profiles):
 
 @verdi_profile.command('mirror')
 @options.PATH()
+@options.DRY_RUN()
 @options.OVERWRITE()
-# @options.INCREMENTAL()
 @options.DUMP_PROCESSES()
-@options.DEDUPLICATE()
+@options.GROUPS()
+@options.ORGANIZE_BY_GROUPS()
+# @options.DEDUPLICATE()
+# @click.option(
+#     '--check-dirs/--no-check-dirs',
+#     default=False,
+#     show_default=True,
+#     help='Check for existence of dump directories. Otherwise, incremental mirroring is only evaluated from the log.')
+@click.option(
+    '--symlink-duplicates/--no-symlink-duplicates',
+    default=True,
+    show_default=True,
+    help='Symlink data if the same node is contained in multiple groups.')
+@click.option(
+    '--delete-missing/--no-delete-missing',
+    default=False,
+    show_default=True,
+    help="If a previously dumped node is deleted from AiiDA's DB, also delete the corresponding dump directory.")
+@click.option(
+    '--extra-calc-dirs/--no-extra-calc-dirs',
+    default=False,
+    show_default=True,
+    help='If a top-level process calls sub-processes, create a designated directory only for the top-level process.')
 @options.INCLUDE_INPUTS()
 @options.INCLUDE_OUTPUTS()
 @options.INCLUDE_ATTRIBUTES()
 @options.INCLUDE_EXTRAS()
 @options.FLAT()
-@options.DUMP_CONFIG_FILE()
-@options.GROUPS()
-@options.ORGANIZE_BY_GROUPS()
-@options.DRY_RUN()
 @click.pass_context
 def profile_mirror(
     ctx,
     path,
-    overwrite,
-    organize_by_groups,
     dry_run,
+    overwrite,
     dump_processes,
-    deduplicate,
+    groups,
+    organize_by_groups,
+    symlink_duplicates,
+    delete_missing,
+    extra_calc_dirs,
+    # check_dirs,
     include_inputs,
     include_outputs,
     include_attributes,
     include_extras,
     flat,
-    dump_config_file,
-    groups,
 ):
-    """Dump all data in an AiiDA profile's storage to disk."""
+    """Dump all data in an AiiDA profile's storage to disk in a human-readable directory tree."""
 
     import json
     from datetime import datetime
@@ -313,6 +333,7 @@ def profile_mirror(
     from aiida.tools.dumping.base import BaseDumper
     from aiida.tools.dumping.logger import DumpLogger
     from aiida.tools.dumping.utils import prepare_dump_path
+    from aiida.tools.dumping.config import ProfileDumpConfig
 
     profile = ctx.obj['profile']
 
@@ -321,7 +342,7 @@ def profile_mirror(
     if path is None:
         path = Path.cwd() / f'{profile.name}-mirror'
 
-    echo.echo_report(f'Mirroring data of profile `{profile.name}`at path: `{path}`.')
+    echo.echo_report(f'Mirroring data of profile `{profile.name}` at path: `{path}`.')
 
     SAFEGUARD_FILE: str = '.verdi_profile_mirror'  # noqa: N806
     safeguard_file_path: Path = path / SAFEGUARD_FILE
@@ -336,8 +357,6 @@ def profile_mirror(
     except FileExistsError as exc:
         echo.echo_critical(str(exc))
 
-    breakpoint()
-
     try:
         with safeguard_file_path.open('r') as fhandle:
             last_dump_time = datetime.fromisoformat(fhandle.readlines()[-1].strip().split()[-1]).astimezone()
@@ -346,9 +365,10 @@ def profile_mirror(
 
     if dry_run:
         node_counts = ProfileDumper._get_number_of_nodes_to_dump(last_dump_time)
-        node_counts_str = ' & '.join(f'{count} {node_type}' for node_type, count in node_counts.items())
-        dry_run_message = f'Dry run for mirroring of profile `{profile.name}`: {node_counts_str} to dump.\n'
+        dry_run_message = f'Dry run for mirroring of profile `{profile.name}`. Would dump:'
         echo.echo_report(dry_run_message)
+        for count, node_type in node_counts.items():
+            echo.echo_report(f'{count}: {node_type}')
         return
 
     if incremental:
@@ -376,18 +396,25 @@ def profile_mirror(
         flat=flat,
     )
 
+    # breakpoint()
+    profile_dump_config = ProfileDumpConfig(
+        dump_processes=dump_processes,
+        symlink_duplicates=symlink_duplicates,
+        delete_missing=delete_missing,
+        extra_calc_dirs=extra_calc_dirs,
+        organize_by_groups=organize_by_groups,
+    )
+
     profile_dumper = ProfileDumper(
+        profile=profile,
+        profile_dump_config=profile_dump_config,
         base_dumper=base_dumper,
         process_dumper=process_dumper,
         dump_logger=dump_logger,
         groups=groups,
-        organize_by_groups=organize_by_groups,
-        deduplicate=deduplicate,
-        profile=profile,
-        dump_processes=dump_processes,
     )
 
-    profile_dumper.dump()
+    profile_dumper.dump_processes()
 
     # Append the current time to the file
     last_dump_time = datetime.now().astimezone()

src/aiida/cmdline/params/options/main.py

@@ -53,12 +53,10 @@
     'DB_PORT',
     'DB_USERNAME',
     'DEBUG',
-    'DEDUPLICATE',
     'DESCRIPTION',
     'DICT_FORMAT',
     'DICT_KEYS',
     'DRY_RUN',
-    'DUMP_CONFIG_FILE',
     'DUMP_PROCESSES',
     'EXIT_STATUS',
     'EXPORT_FORMAT',
@@ -792,13 +790,13 @@ def set_log_level(ctx, _param, value):
     show_default=True,
 )
 
-DEDUPLICATE = OverridableOption(
-    '--deduplicate/--no-deduplicate',
-    is_flag=True,
-    default=True,
-    show_default=True,
-    help='',
-)
+# DEDUPLICATE = OverridableOption(
+#     '--deduplicate/--no-deduplicate',
+#     is_flag=True,
+#     default=True,
+#     show_default=True,
+#     help='',
+# )
 
 DUMP_PROCESSES = OverridableOption(
     '--dump-processes/--no-dump-processes',
@@ -808,13 +806,6 @@ def set_log_level(ctx, _param, value):
     help='Dump process data.',
 )
 
-DUMP_CONFIG_FILE = OverridableOption(
-    '--dump-config-file',
-    default=None,
-    type=types.FileOrUrl(),
-    help='Provide dumping options via a config file in YAML format.',
-)
-
 ORGANIZE_BY_GROUPS = OverridableOption(
     '--organize-by-groups/--no-organize-by-groups',
     default=True,

src/aiida/common/utils.py

@@ -17,6 +17,8 @@
 from datetime import datetime
 from typing import Any, Dict
 from uuid import UUID
+from aiida.manage import get_manager, load_profile
+from aiida.manage.configuration.profile import Profile
 
 from .lang import classproperty
 

src/aiida/repository/repository.py

@@ -519,6 +519,7 @@ def copy_tree(self, target: Union[str, pathlib.Path], path: Optional[FilePath] =
                 dirpath.mkdir(parents=True, exist_ok=True)
 
                 with self.open(root / filename) as handle:
+                    # TODO: Possibly skip 
                     filepath.write_bytes(handle.read())
 
     # these methods are not actually used in aiida-core, but are here for completeness

src/aiida/tools/dumping/base.py

@@ -14,9 +14,13 @@
 
 @dataclass
 class BaseDumper:
+    """Container for shared arguments of all Dumper classes."""
+
     dump_parent_path: Path | None = None
     overwrite: bool = False
     incremental: bool = True
+    check_dirs: bool = False
+    # TODO: Make this a per-class attribute?
     last_dump_time: datetime | None = None
 
     def __post_init__(self):