Merge branch 'main' into lazy-config

.devcontainer/devcontainer.json

@@ -1,9 +1,16 @@
 {
     "dockerComposeFile": "docker-compose.yml",
-    "service": "aiida",
-    "workspaceFolder": "/home/aiida/aiida-core",
-    "postCreateCommand": "bash ./.devcontainer/post_create.sh",
-    "waitFor": "postCreateCommand",
+    "service": "daemon",
+    "workspaceFolder": "/workspaces/aiida-core",
+    "postCreateCommand": "/etc/init/aiida-prepare.sh",
+    "postStartCommand": "pip install -e /workspaces/aiida-core[tests,docs,rest,atomic_tools,pre-commit]",
+    "postAttachCommand": "verdi daemon start",
+    "waitFor": "postStartCommand",
+    "containerUser": "aiida",
+    "remoteUser": "aiida",
+    "remoteEnv": {
+        "HOME": "/home/aiida"
+    },
 	"customizations": {
         "vscode": {
             "extensions": ["ms-python.python", "eamodio.gitlens"]

.devcontainer/docker-compose.yml

@@ -1,54 +1,38 @@
+---
 version: '3.4'
 
 services:
 
-  rabbitmq:
-    image: rabbitmq:3.8.3-management
-    environment:
-        RABBITMQ_DEFAULT_USER: guest
-        RABBITMQ_DEFAULT_PASS: guest
-    ports:
-      - '5672:5672'
-      - '15672:15672'
+    database:
+        image: postgres:15
+        environment:
+            POSTGRES_USER: postgres
+            POSTGRES_PASSWORD: password
+            POSTGRES_HOST_AUTH_METHOD: trust
+        healthcheck:
+            test: [ "CMD-SHELL", "pg_isready"]
+            interval: 5s
+            timeout: 5s
+            retries: 10
 
-    healthcheck:
-      test: rabbitmq-diagnostics -q ping
-      interval: 30s
-      timeout: 30s
-      retries: 5
-    networks:
-      - aiida
+    messaging:
+        image: rabbitmq:3.8.14-management
+        environment:
+            RABBITMQ_DEFAULT_USER: guest
+            RABBITMQ_DEFAULT_PASS: guest
+        healthcheck:
+            test: rabbitmq-diagnostics check_port_connectivity
+            interval: 30s
+            timeout: 30s
+            retries: 10
 
-  postgres:
-    image: postgres:12
-    ports:
-      - '5432:5432'
-    networks:
-      - aiida
-    environment:
-      POSTGRES_HOST_AUTH_METHOD: trust
-
-  aiida:
-    #image: "aiidateam/aiida-core:main"
-    image: "aiida-core-dev"
-    build:
-      # need to add the parent directory to context to copy over new configure-aiida.sh
-      context: ..
-      dockerfile: .devcontainer/Dockerfile
-    user: aiida
-    environment:
-      DB_HOST: postgres
-      BROKER_HOST: rabbitmq
-
-    # no need for /sbin/my_init
-    entrypoint: tail -f /dev/null
-    volumes:
-      - ..:/home/aiida/aiida-core:cached
-    networks:
-      - aiida
-    depends_on:
-      - rabbitmq
-      - postgres
-
-networks:
-  aiida:
+    daemon:
+        image: ghcr.io/aiidateam/aiida-core-base:edge
+        user: aiida
+        entrypoint: tail -f /dev/null
+        environment:
+          SETUP_DEFAULT_AIIDA_PROFILE: 'true'
+          TZ: 'Europe/Zurich'
+        depends_on:
+            database:
+                condition: service_healthy

README.md

@@ -8,7 +8,7 @@ AiiDA (www.aiida.net) is a workflow manager for computational science with a str
 |Getting help| [![Docs status](https://readthedocs.org/projects/aiida-core/badge)](http://aiida-core.readthedocs.io/) [![Discourse status](https://img.shields.io/discourse/status?server=https%3A%2F%2Faiida.discourse.group%2F)](https://aiida.discourse.group/)
 |Build status| [![Build Status](https://github.com/aiidateam/aiida-core/actions/workflows/ci-code.yml/badge.svg)](https://github.com/aiidateam/aiida-core/actions) [![Coverage Status](https://codecov.io/gh/aiidateam/aiida-core/branch/main/graph/badge.svg)](https://codecov.io/gh/aiidateam/aiida-core) [Benchmarks](https://aiidateam.github.io/aiida-core/dev/bench/ubuntu-22.04/psql_dos/) |
 |Activity| [![PyPI-downloads](https://img.shields.io/pypi/dm/aiida-core.svg?style=flat)](https://pypistats.org/packages/aiida-core) [![Commit Activity](https://img.shields.io/github/commit-activity/m/aiidateam/aiida-core.svg)](https://github.com/aiidateam/aiida-core/pulse)
-|Community|  [![Affiliated with NumFOCUS](https://img.shields.io/badge/NumFOCUS-affiliated%20project-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org/sponsored-projects/affiliated-projects) [![Twitter](https://img.shields.io/twitter/follow/aiidateam.svg?style=social&label=Follow)](https://twitter.com/aiidateam)
+|Community|  [![Discourse](https://img.shields.io/discourse/topics?server=https%3A%2F%2Faiida.discourse.group%2F&logo=discourse)](https://aiida.discourse.group/) [![Affiliated with NumFOCUS](https://img.shields.io/badge/NumFOCUS-affiliated%20project-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org/sponsored-projects/affiliated-projects) [![Twitter](https://img.shields.io/twitter/follow/aiidateam.svg?style=social&label=Follow)](https://twitter.com/aiidateam)
 
 
 ## Features

aiida/manage/configuration/config.py

@@ -9,7 +9,7 @@
 ###########################################################################
 """Module that defines the configuration file of an AiiDA instance and functions to create and load it."""
 import codecs
-from functools import lru_cache
+from functools import cache
 from importlib.resources import files
 import json
 import os
@@ -28,7 +28,7 @@
 SCHEMA_FILE = 'config-v9.schema.json'
 
 
-@lru_cache(1)
+@cache
 def config_schema() -> Dict[str, Any]:
     """Return the configuration schema."""
     return json.loads(files(schema_module).joinpath(SCHEMA_FILE).read_text(encoding='utf8'))

aiida/manage/tests/pytest_fixtures.py

@@ -21,7 +21,6 @@
 
 import asyncio
 import contextlib
-import copy
 import inspect
 import io
 import os
@@ -33,6 +32,7 @@
 import uuid
 import warnings
 
+from importlib_metadata import EntryPoints
 import plumpy
 import pytest
 import wrapt
@@ -759,9 +759,16 @@ def suppress_deprecations(wrapped, _, args, kwargs):
 class EntryPointManager:
     """Manager to temporarily add or remove entry points."""
 
-    @staticmethod
-    def eps():
-        return plugins.entry_point.eps()
+    def __init__(self, entry_points: EntryPoints):
+        self.entry_points = entry_points
+
+    def eps(self) -> EntryPoints:
+        return self.entry_points
+
+    def eps_select(self, group, name=None) -> EntryPoints:
+        if name is None:
+            return self.eps().select(group=group)
+        return self.eps().select(group=group, name=name)
 
     @staticmethod
     def _validate_entry_point(entry_point_string: str | None, group: str | None, name: str | None) -> tuple[str, str]:
@@ -791,7 +798,6 @@ def _validate_entry_point(entry_point_string: str | None, group: str | None, nam
 
         return group, name
 
-    @suppress_deprecations
     def add(
         self,
         value: type | str,
@@ -817,9 +823,8 @@ def add(
 
         group, name = self._validate_entry_point(entry_point_string, group, name)
         entry_point = plugins.entry_point.EntryPoint(name, value, group)
-        self.eps()[group].append(entry_point)
+        self.entry_points = EntryPoints(self.entry_points + (entry_point,))
 
-    @suppress_deprecations
     def remove(
         self, entry_point_string: str | None = None, *, name: str | None = None, group: str | None = None
     ) -> None:
@@ -835,31 +840,23 @@ def remove(
         :raises ValueError: If `entry_point_string` is not a complete entry point string with group and name.
         """
         group, name = self._validate_entry_point(entry_point_string, group, name)
-
-        for entry_point in self.eps()[group]:
-            if entry_point.name == name:
-                self.eps()[group].remove(entry_point)
-                break
-        else:
+        try:
+            self.entry_points[name]
+        except KeyError:
             raise KeyError(f'entry point `{name}` does not exist in group `{group}`.')
+        self.entry_points = EntryPoints((ep for ep in self.entry_points if not (ep.name == name and ep.group == group)))
 
 
 @pytest.fixture
 def entry_points(monkeypatch) -> EntryPointManager:
     """Return an instance of the ``EntryPointManager`` which allows to temporarily add or remove entry points.
 
-    This fixture creates a deep copy of the entry point cache returned by the :func:`aiida.plugins.entry_point.eps`
-    method and then monkey patches that function to return the deepcopy. This ensures that the changes on the entry
-    point cache performed during the test through the manager are undone at the end of the function scope.
-
-    .. note:: This fixture does not use the ``suppress_deprecations`` decorator on purpose, but instead adds it manually
-        inside the fixture's body. The reason is that otherwise all deprecations would be suppressed for the entire
-        scope of the fixture, including those raised by the code run in the test using the fixture, which is not
-        desirable.
-
+    This fixture monkey patches the entry point caches returned by
+    the :func:`aiida.plugins.entry_point.eps` and :func:`aiida.plugins.entry_point.eps_select` functions
+    to class methods of the ``EntryPointManager`` so that we can dynamically add / remove entry points.
+    Note that we do not need a deepcopy here as ``eps()`` returns an immutable ``EntryPoints`` tuple type.
     """
-    with warnings.catch_warnings():
-        warnings.filterwarnings('ignore', category=DeprecationWarning)
-        eps_copy = copy.deepcopy(plugins.entry_point.eps())
-    monkeypatch.setattr(plugins.entry_point, 'eps', lambda: eps_copy)
-    yield EntryPointManager()
+    epm = EntryPointManager(plugins.entry_point.eps())
+    monkeypatch.setattr(plugins.entry_point, 'eps', epm.eps)
+    monkeypatch.setattr(plugins.entry_point, 'eps_select', epm.eps_select)
+    yield epm

aiida/orm/autogroup.py

@@ -86,7 +86,7 @@ def validate(strings: list[str] | None):
         """Validate the list of strings passed to set_include and set_exclude."""
         if strings is None:
             return
-        valid_prefixes = set(['aiida.node', 'aiida.calculations', 'aiida.workflows', 'aiida.data'])
+        valid_prefixes = {'aiida.node', 'aiida.calculations', 'aiida.workflows', 'aiida.data'}
         for string in strings:
             pieces = string.split(':')
             if len(pieces) != 2:

aiida/plugins/entry_point.py

@@ -8,6 +8,8 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Module to manage loading entrypoints."""
+from __future__ import annotations
+
 import enum
 import functools
 import traceback
@@ -30,9 +32,30 @@
 ENTRY_POINT_STRING_SEPARATOR = ':'
 
 
-@functools.lru_cache(maxsize=1)
-def eps():
-    return _eps()
+@functools.cache
+def eps() -> EntryPoints:
+    """Cache around entry_points()
+
+    This call takes around 50ms!
+    NOTE: For faster lookups, we sort the ``EntryPoints`` alphabetically
+    by the group name so that 'aiida.' groups come up first.
+    Unfortunately, this does not help with the entry_points.select() filter,
+    which will always iterate over all entry points since it looks for
+    possible duplicate entries.
+    """
+    entry_points = _eps()
+    return EntryPoints(sorted(entry_points, key=lambda x: x.group))
+
+
+@functools.lru_cache(maxsize=100)
+def eps_select(group: str, name: str | None = None) -> EntryPoints:
+    """
+    A thin wrapper around entry_points.select() calls, which are
+    expensive so we want to cache them.
+    """
+    if name is None:
+        return eps().select(group=group)
+    return eps().select(group=group, name=name)
 
 
 class EntryPointFormat(enum.Enum):
@@ -254,8 +277,7 @@ def get_entry_point_groups() -> Set[str]:
 
 def get_entry_point_names(group: str, sort: bool = True) -> List[str]:
     """Return the entry points within a group."""
-    all_eps = eps()
-    group_names = list(all_eps.select(group=group).names)
+    group_names = list(get_entry_points(group).names)
     if sort:
         return sorted(group_names)
     return group_names
@@ -268,7 +290,7 @@ def get_entry_points(group: str) -> EntryPoints:
     :param group: the entry point group
     :return: a list of entry points
     """
-    return eps().select(group=group)
+    return eps_select(group=group)
 
 
 def get_entry_point(group: str, name: str) -> EntryPoint:
@@ -283,7 +305,7 @@ def get_entry_point(group: str, name: str) -> EntryPoint:
     """
     # The next line should be removed for ``aiida-core==3.0`` when the old deprecated entry points are fully removed.
     name = convert_potentially_deprecated_entry_point(group, name)
-    found = eps().select(group=group, name=name)
+    found = eps_select(group=group, name=name)
     if name not in found.names:
         raise MissingEntryPointError(f"Entry point '{name}' not found in group '{group}'")
     # If multiple entry points are found and they have different values we raise, otherwise if they all
@@ -326,15 +348,9 @@ def get_entry_point_from_class(class_module: str, class_name: str) -> Tuple[Opti
     :param class_name: name of the class
     :return: a tuple of the corresponding group and entry point or None if not found
     """
-    for group in get_entry_point_groups():
-        for entry_point in get_entry_points(group):
-
-            if entry_point.module != class_module:
-                continue
-
-            if entry_point.attr == class_name:
-                return group, entry_point
-
+    for entry_point in eps():
+        if entry_point.module == class_module and entry_point.attr == class_name:
+            return entry_point.group, entry_point
     return None, None