Merge branch 'main' of github.com:rabbull/aiida-core into bulk-update…

…-json

docs/source/index.rst

@@ -114,39 +114,56 @@
 
          To the topics
 
-   .. grid-item-card:: :fa:`cogs;mr-1` API Reference
+   .. grid-item-card:: :fa:`sitemap;mr-1` Internal Architecture
       :text-align: center
       :shadow: md
 
-      Comprehensive documentation of CLI, Python API and REST API.
+      Detailed information on AiiDA's design and architecture.
 
       +++++++++++++++++++++++++++++++++++++++++++++
 
-      .. button-ref:: reference/index
+      .. button-ref:: internals/index
          :ref-type: doc
          :click-parent:
          :expand:
          :color: primary
          :outline:
 
-         To the reference guide
+         To the architecture guide
 
-   .. grid-item-card:: :fa:`sitemap;mr-1` Internal Architecture
+   .. grid-item-card:: :fa:`puzzle-piece;mr-1` Core plugins
       :text-align: center
       :shadow: md
 
-      Detailed information on AiiDA's design and architecture.
+      Commonly used AiiDA plugins to extend core functionality
 
       +++++++++++++++++++++++++++++++++++++++++++++
 
-      .. button-ref:: internals/index
+      .. button-ref:: reference/core_plugins
          :ref-type: doc
          :click-parent:
          :expand:
          :color: primary
          :outline:
 
-         To the architecture guide
+         To the plugin overview
+
+   .. grid-item-card:: :fa:`cogs;mr-1` API Reference
+      :text-align: center
+      :shadow: md
+
+      Comprehensive documentation of CLI, Python API and REST API.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-ref:: reference/index
+         :ref-type: doc
+         :click-parent:
+         :expand:
+         :color: primary
+         :outline:
+
+         To the reference guide
 
 ------------------------------
 
@@ -172,8 +189,9 @@
    tutorials/index
    howto/index
    topics/index
-   reference/index
    internals/index
+   reference/core_plugins
+   reference/index
 
 ===========
 How to cite

docs/source/reference/core_plugins.rst

@@ -0,0 +1,135 @@
+.. _reference:core_plugins:
+
+============
+Core plugins
+============
+
+This page lists common AiiDA plugins which are not specific to any research domain, but extend the core functionality:
+
+.. grid:: 1 2 2 4
+   :gutter: 3
+
+   .. grid-item-card:: AiiDA WorkGraph
+      :text-align: center
+      :shadow: md
+
+      Efficiently design and manage flexible workflows with AiiDA.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/aiidateam/aiida-workgraph
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+   .. grid-item-card:: AiiDA shell
+      :text-align: center
+      :shadow: md
+
+      Plugin that makes running shell commands easy.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/sphuber/aiida-shell
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+   .. grid-item-card:: AiiDA submission controller
+      :text-align: center
+      :shadow: md
+
+      Classes to help managing large numbers of submissions.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/aiidateam/aiida-submission-controller/
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+   .. grid-item-card:: AiiDA hyperqueue
+      :text-align: center
+      :shadow: md
+
+      Plugin for the HyperQueue metascheduler enabling sub-node jobs.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/aiidateam/aiida-hyperqueue
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+   .. grid-item-card:: AiiDA project
+      :text-align: center
+      :shadow: md
+
+      AiiDA project manager with custom Python environments and isolated project directories.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/aiidateam/aiida-project
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+   .. grid-item-card:: AiiDA code registry
+      :text-align: center
+      :shadow: md
+
+      Registry of simulation codes and computers for easy setup in AiiDA.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/aiidateam/aiida-code-registry
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+   .. grid-item-card:: AiiDA plugin cutter
+      :text-align: center
+      :shadow: md
+
+      Cookie cutter recipe for AiiDA plugins.
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/aiidateam/aiida-plugin-cutter
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+   .. grid-item-card:: AiiDA PythonJob
+      :text-align: center
+      :shadow: md
+
+      Run non-AiiDA Python functions on a remote computer (pre-alpha).
+
+      +++++++++++++++++++++++++++++++++++++++++++++
+
+      .. button-link:: https://github.com/aiidateam/aiida-pythonjob
+         :color: primary
+         :outline:
+
+         Go to GitHub
+
+
+Honorable mentions
+===================
+
+- `aiida-firecrest <https://github.com/aiidateam/aiida-firecrest>`_: Transport/Scheduler plugins for interfacing with
+  FirecREST (RESTful services gateway and interface for managing HPC resources).
+- `aiida-resource-registry <https://github.com/aiidateam/aiida-resource-registry>`_: Registry of simulation codes and computers for easy setup in AiiDAlab.
+- `aiida-restapi <https://github.com/aiidateam/aiida-restapi>`_: RESTful AiiDA Web API for data queries and workflow management.
+- `aiida-diff <https://github.com/aiidateam/aiida-diff>`_: AiiDA demo plugin that computes the difference between two
+  files.
+
+The full list of available plugins can be found on the `AiiDA plugin registry <https://aiidateam.github.io/aiida-registry/>`_.

docs/source/reference/index.rst

@@ -9,4 +9,5 @@ Reference
    api/index
    rest_api
    cheatsheet
+   core_plugins
    _changelog.md

environment.yml

@@ -33,5 +33,6 @@ dependencies:
 - sqlalchemy~=2.0
 - tabulate<0.10.0,>=0.8.0
 - tqdm~=4.45
+- typing-extensions~=4.0
 - upf_to_json~=0.9.2
 - wrapt~=1.11

pyproject.toml

@@ -45,6 +45,7 @@ dependencies = [
   'sqlalchemy~=2.0',
   'tabulate>=0.8.0,<0.10.0',
   'tqdm~=4.45',
+  'typing-extensions~=4.0;python_version<"3.10"',
   'upf_to_json~=0.9.2',
   'wrapt~=1.11'
 ]

src/aiida/orm/nodes/data/singlefile.py

@@ -39,6 +39,17 @@ def from_string(cls, content: str, filename: str | pathlib.Path | None = None, *
         """
         return cls(io.StringIO(content), filename, **kwargs)
 
+    @classmethod
+    def from_bytes(
+        cls, content: bytes, filename: str | pathlib.Path | None = None, **kwargs: t.Any
+    ) -> 'SinglefileData':
+        """Construct a new instance and set ``content`` as its contents.
+
+        :param content: The content as bytes.
+        :param filename: Specify filename to use (defaults to ``file.txt``).
+        """
+        return cls(io.BytesIO(content), filename, **kwargs)
+
     def __init__(
         self, file: str | pathlib.Path | t.IO, filename: str | pathlib.Path | None = None, **kwargs: t.Any
     ) -> None:

tests/orm/nodes/data/test_singlefile.py

@@ -189,18 +189,40 @@ def test_from_string():
     content = 'some\ncontent'
     node = SinglefileData.from_string(content).store()
     assert node.get_content() == content
+    assert node.get_content('rb') == content.encode()
     assert node.filename == SinglefileData.DEFAULT_FILENAME
 
     content = 'some\ncontent'
     filename = 'custom_filename.dat'
     node = SinglefileData.from_string(content, filename).store()
     assert node.get_content() == content
+    assert node.get_content('rb') == content.encode()
+    assert node.filename == filename
+
+
+def test_from_bytes():
+    """Test the :meth:`aiida.orm.nodes.data.singlefile.SinglefileData.from_bytes` classmethod."""
+    content = b'some\ncontent'
+    node = SinglefileData.from_bytes(content).store()
+    assert node.get_content(mode='rb') == content
+    assert node.get_content(mode='r') == content.decode('utf-8')
+    assert node.filename == SinglefileData.DEFAULT_FILENAME
+
+    content = b'some\ncontent'
+    filename = 'custom_filename.dat'
+    node = SinglefileData.from_bytes(content, filename).store()
+    assert node.get_content(mode='rb') == content
+    assert node.get_content(mode='r') == content.decode('utf-8')
     assert node.filename == filename
 
 
 def test_get_content():
     """Test the :meth:`aiida.orm.nodes.data.singlefile.SinglefileData.get_content` method."""
+    content = 'some\ncontent'
+    node = SinglefileData.from_string(content).store()
+    assert node.get_content() == content
+    assert node.get_content('rb') == content.encode()
     content = b'some\ncontent'
-    node = SinglefileData.from_string(content.decode('utf-8')).store()
+    node = SinglefileData.from_bytes(content).store()
     assert node.get_content() == content.decode('utf-8')
     assert node.get_content('rb') == content