🔀 MERGE: Release v2.0.0b1

aiida/__init__.py

@@ -28,7 +28,7 @@
     'For further information please visit http://www.aiida.net/. All rights reserved.'
 )
 __license__ = 'MIT license, see LICENSE.txt file.'
-__version__ = '2.0.0a1'
+__version__ = '2.0.0b1'
 __authors__ = 'The AiiDA team.'
 __paper__ = (
     'S. P. Huber et al., "AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and '

aiida/cmdline/__init__.py

@@ -44,6 +44,13 @@
     'UserParamType',
     'WorkflowParamType',
     'dbenv',
+    'echo_critical',
+    'echo_dictionary',
+    'echo_error',
+    'echo_info',
+    'echo_report',
+    'echo_success',
+    'echo_warning',
     'format_call_graph',
     'is_verbose',
     'only_if_daemon_running',

aiida/cmdline/utils/__init__.py

@@ -18,9 +18,17 @@
 from .ascii_vis import *
 from .common import *
 from .decorators import *
+from .echo import *
 
 __all__ = (
     'dbenv',
+    'echo_critical',
+    'echo_dictionary',
+    'echo_error',
+    'echo_info',
+    'echo_report',
+    'echo_success',
+    'echo_warning',
     'format_call_graph',
     'is_verbose',
     'only_if_daemon_running',

aiida/cmdline/utils/echo.py

@@ -20,7 +20,7 @@
 
 CMDLINE_LOGGER = AIIDA_LOGGER.getChild('cmdline')
 
-__all__ = ('echo', 'echo_info', 'echo_success', 'echo_warning', 'echo_error', 'echo_critical', 'echo_dictionary')
+__all__ = ('echo_report', 'echo_info', 'echo_success', 'echo_warning', 'echo_error', 'echo_critical', 'echo_dictionary')
 
 
 class ExitCode(enum.IntEnum):

aiida/engine/processes/calcjobs/importer.py

@@ -1,14 +1,20 @@
 # -*- coding: utf-8 -*-
 """Abstract utility class that helps to import calculation jobs completed outside of AiiDA."""
-from abc import abstractmethod
+from abc import ABC, abstractmethod
 from typing import Dict, Union
 
 from aiida.orm import Node, RemoteData
 
 __all__ = ('CalcJobImporter',)
 
 
-class CalcJobImporter:
+class CalcJobImporter(ABC):
+    """An abstract class, to define an importer for computations completed outside of AiiDA.
+
+    This class is used to import the results of a calculation that was completed outside of AiiDA.
+    The importer is responsible for parsing the output files of the calculation and creating the
+    corresponding AiiDA nodes.
+    """
 
     @staticmethod
     @abstractmethod

aiida/manage/configuration/__init__.py

@@ -172,7 +172,7 @@ def profile_context(profile: Optional[str] = None, allow_switch=False) -> 'Profi
     """
     from aiida.manage import get_manager
     get_manager().load_profile(profile, allow_switch)
-    yield
+    yield profile
     get_manager().unload_profile()
 
 
@@ -248,6 +248,20 @@ def load_documentation_profile():
     """
     import tempfile
 
+    # imports required for docs/source/reference/api/public.rst
+    from aiida import (  # pylint: disable=unused-import
+        cmdline,
+        common,
+        engine,
+        manage,
+        orm,
+        parsers,
+        plugins,
+        schedulers,
+        tools,
+        transports,
+    )
+    from aiida.cmdline.params import arguments, options  # pylint: disable=unused-import
     from aiida.storage.psql_dos.models.base import get_orm_metadata
 
     from .config import Config

aiida/orm/__init__.py

@@ -61,6 +61,7 @@
     'GroupEntityLoader',
     'ImportGroup',
     'Int',
+    'JsonableData',
     'Kind',
     'KpointsData',
     'LinkManager',

aiida/orm/nodes/__init__.py

@@ -35,6 +35,7 @@
     'Float',
     'FolderData',
     'Int',
+    'JsonableData',
     'Kind',
     'KpointsData',
     'List',

aiida/orm/nodes/data/__init__.py

@@ -25,6 +25,7 @@
 from .float import *
 from .folder import *
 from .int import *
+from .jsonable import *
 from .list import *
 from .numeric import *
 from .orbital import *
@@ -47,6 +48,7 @@
     'Float',
     'FolderData',
     'Int',
+    'JsonableData',
     'Kind',
     'KpointsData',
     'List',

aiida/orm/nodes/data/jsonable.py

@@ -4,7 +4,9 @@
 import json
 import typing
 
-from aiida.orm import Data
+from .data import Data
+
+__all__ = ('JsonableData',)
 
 
 class JsonSerializableProtocol(typing.Protocol):

aiida/py.typed

@@ -0,0 +1 @@
+# Marker file for PEP 561

aiida/transports/transport.py

@@ -37,7 +37,7 @@ def validate_positive_number(ctx, param, value):  # pylint: disable=unused-argum
 
 
 class Transport(abc.ABC):
-    """Abstract class for a generic transport (ssh, local, ...) ontains the set of minimal methods."""
+    """Abstract class for a generic transport (ssh, local, ...) contains the set of minimal methods."""
     # pylint: disable=too-many-public-methods
 
     # This is used as a global default in case subclasses don't redefine this,

docs/source/conf.py

@@ -67,6 +67,7 @@
 ]
 
 intersphinx_mapping = {
+    'aep': ('https://aep.readthedocs.io/en/latest/', None),
     'click': ('https://click.palletsprojects.com/', None),
     'flask': ('http://flask.pocoo.org/docs/latest/', None),
     'flask_restful': ('https://flask-restful.readthedocs.io/en/latest/', None),
@@ -80,7 +81,8 @@
 todo_include_todos = False
 ipython_mplbackend = ''
 
-myst_enable_extensions = []
+myst_enable_extensions = ['colon_fence', 'deflist']
+nb_merge_streams = True
 
 # -- Options for HTML output ---------------------------------------------------
 
@@ -187,6 +189,7 @@ def run_apidoc(_):
 
 
 # Warnings to ignore when using the -n (nitpicky) option
+nitpicky = True
 with open('nitpick-exceptions', 'r') as handle:
     nitpick_ignore = [
         tuple(line.strip().split(None, 1)) for line in handle.readlines() if line.strip() and not line.startswith('#')
@@ -265,7 +268,10 @@ def setup(app: Sphinx):
     'aiida.orm.AuthInfo': 'aiida.orm.authinfos.AuthInfo',
     'aiida.orm.Computer': 'aiida.orm.computers.Computer',
     'aiida.orm.Comment': 'aiida.orm.comments.Comment',
+    'aiida.orm.EnumData': 'aiida.orm.nodes.data.enum.EnumData',
     'aiida.orm.Group': 'aiida.orm.groups.Group',
+    'aiida.orm.JsonableData': 'aiida.orm.nodes.data.jsonable.JsonableData',
+    'aiida.orm.List': 'aiida.orm.nodes.data.list.List',
     'aiida.orm.Log': 'aiida.orm.logs.Log',
     'aiida.orm.Node': 'aiida.orm.nodes.node.Node',
     'aiida.orm.User': 'aiida.orm.users.User',

docs/source/howto/archive_profile.md

@@ -0,0 +1,88 @@
+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.4
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+(how-to:data:share:archive:profile)=
+
+# How to inspect an archive
+
+```{note}
+This tutorial can be downloaded and run as a Jupyter Notebook: {nb-download}`archive_profile.ipynb` {octicon}`download`, together with the archive {download}`include/process.aiida`.
+```
+
+The AiiDA archive is a file format for long term storage of data from a particular profile.
+
+See {ref}`how-to:share:archives` for information on how to create and migrate an archive.
+Once you have an archive at the latest version, you can inspect its contents in the same way you would with a standard AiiDA profile.
+
+We first create a profile instance from the archive path:
+
+```{code-cell} ipython3
+from aiida import manage, orm, profile_context
+from aiida.storage.sqlite_zip.backend import SqliteZipBackend
+
+archive_profile = SqliteZipBackend.create_profile('include/process.aiida')
+print(archive_profile)
+```
+
+The {py:func}`~aiida.manage.configuration.profile_context` function works similarly to the {py:func}`~aiida.manage.configuration.load_profile` function,
+but is used within a context manager, that insures that the storage is properly closed when the context is exited.
+With this, we can load our archive as a profile:
+
+```{code-cell} ipython3
+with profile_context(archive_profile):
+    print(manage.get_manager().get_profile())
+```
+
+To directly access the storage backend, and view information about it, we can use:
+
+```{code-cell} ipython3
+import json
+with profile_context(archive_profile):
+    storage = manage.get_manager().get_profile_storage()
+    print(storage)
+    print(json.dumps(storage.get_info(), indent=2))
+```
+
+This is directly equivalent to the command-line call:
+
+```{code-cell} ipython3
+!verdi archive info include/process.aiida
+```
+
+Note, that once the context manager is exited, the storage is closed, and will except on further calls.
+
+```{code-cell} ipython3
+print(storage)
+```
+
+As per a standard profile, we can now use the {py:class}`~aiida.orm.QueryBuilder`, to [find and query for data](how-to:query):
+
+```{code-cell} ipython3
+with profile_context(archive_profile):
+    process = orm.QueryBuilder().append(orm.ProcessNode).first(flat=True)
+    print(process)
+```
+
+and also use {py:class}`~aiida.tools.visualization.graph.Graph`, to [visualize data provenance](how-to:data:visualise-provenance):
+
+```{code-cell} ipython3
+from aiida.tools.visualization import Graph
+
+with profile_context(archive_profile):
+    process = orm.QueryBuilder().append(orm.ProcessNode).first(flat=True)
+    graph = Graph(graph_attr={"size": "8!,8!", "rankdir": "LR"})
+    graph.add_incoming(process, annotate_links="both")
+    graph.add_outgoing(process, annotate_links="both")
+
+graph.graphviz
+```

docs/source/howto/index.rst

@@ -16,7 +16,8 @@ How-To Guides
    data
    query
    share_data
-   visualising_graphs/visualising_graphs
+   archive_profile
+   visualising_graphs
    installation
    plugins_develop
    cookbook

docs/source/howto/installation.rst

@@ -484,6 +484,10 @@ Updating from 0.x.* to 1.*
 - `Additional instructions on how to migrate from versions 0.4 -- 0.11 <https://aiida.readthedocs.io/projects/aiida-core/en/v1.2.1/install/updating_installation.html#older-versions>`_.
 - For a list of breaking changes between the 0.x and the 1.x series of AiiDA, `see here <https://aiida.readthedocs.io/projects/aiida-core/en/v1.2.1/install/updating_installation.html#breaking-changes-from-0-12-to-1>`_.
 
+Updating from 1.* to 2.*
+------------------------
+
+See the :doc:`../reference/_changelog` for a list of breaking changes.
 
 .. _how-to:installation:backup:
 

docs/source/howto/interact.rst

@@ -61,6 +61,24 @@ If, for whatever reason, ``verdi run`` nor the special shebang can be used, a pr
 
 One can pass a particular profile name to :meth:`~aiida.manage.configuration.load_profile`, otherwise the default profile is loaded.
 
+Within a script or Python instance, you can also switch to a different profile, or use one within a context manager:
+
+.. code-block:: python
+
+    from aiida import load_profile, profile_context, orm
+
+    with profile_context('my_profile_1'):
+        # The profile will be loaded within the context
+        node_from_profile_1 = orm.load_node(1)
+        # then the profile will be unloaded automatically
+
+    # load a global profile
+    load_profile('my_profile_2')
+    node_from_profile_2 = orm.load_node(1)
+
+    # switch to a different global profile
+    load_profile('my_profile_3', allow_switch=True)
+    node_from_profile_3 = orm.load_node(1)
 
 .. _how-to:interact-shell: