Dependencies: Add support for Python 3.12

.github/system_tests/pytest/test_memory_leaks.py

@@ -8,6 +8,10 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Utilities for testing memory leakage."""
+import sys
+
+import pytest
+
 from aiida import orm
 from aiida.engine import processes, run_get_node
 from aiida.plugins import CalculationFactory
@@ -23,6 +27,7 @@ def run_finished_ok(*args, **kwargs):
     assert node.is_finished_ok, (node.exit_status, node.exit_message)
 
 
+@pytest.mark.skipif(sys.version_info >= (3, 12), reason='Garbage collecting hangs on Python 3.12')
 def test_leak_run_process():
     """Test whether running a dummy process leaks memory."""
     inputs = {'a': orm.Int(2), 'b': orm.Str('test')}
@@ -34,6 +39,7 @@ def test_leak_run_process():
     assert not process_instances, f'Memory leak: process instances remain in memory: {process_instances}'
 
 
+@pytest.mark.skipif(sys.version_info >= (3, 12), reason='Garbage collecting hangs on Python 3.12')
 def test_leak_local_calcjob(aiida_local_code_factory):
     """Test whether running a local CalcJob leaks memory."""
     inputs = {'x': orm.Int(1), 'y': orm.Int(2), 'code': aiida_local_code_factory('core.arithmetic.add', '/bin/bash')}
@@ -45,6 +51,7 @@ def test_leak_local_calcjob(aiida_local_code_factory):
     assert not process_instances, f'Memory leak: process instances remain in memory: {process_instances}'
 
 
+@pytest.mark.skipif(sys.version_info >= (3, 12), reason='Garbage collecting hangs on Python 3.12')
 def test_leak_ssh_calcjob():
     """Test whether running a CalcJob over SSH leaks memory.
 

.github/workflows/ci-code.yml

@@ -23,10 +23,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.9
+    - name: Set up Python 3.12
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.12'
 
     - name: Install utils/ dependencies
       run: pip install -r utils/requirements.txt
@@ -55,7 +55,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.9', '3.12']
 
     services:
       postgres:
@@ -131,7 +131,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.9', '3.12']
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/test-install.yml

@@ -58,7 +58,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2
@@ -144,7 +144,7 @@ jobs:
       fail-fast: false
       matrix:
 
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
         # Not being able to install with conda on a specific Python version is
         # not sufficient to fail the run, but something we want to be aware of.
@@ -195,7 +195,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     services:
       postgres:

aiida/sphinxext/__init__.py

@@ -16,7 +16,6 @@ def setup(app):
 
     from . import calcjob, process, workchain
 
-    app.setup_extension('sphinxcontrib.details.directive')
     process.setup_extension(app)
     workchain.setup_extension(app)
     calcjob.setup_extension(app)

aiida/sphinxext/process.py

@@ -20,7 +20,6 @@
 from sphinx import addnodes
 from sphinx.ext.autodoc import ClassDocumenter
 from sphinx.util.docutils import SphinxDirective
-from sphinxcontrib.details.directive import details, summary
 
 from aiida.common.utils import get_object_from_string
 from aiida.engine import Process
@@ -156,12 +155,7 @@ def build_portnamespace_doctree(self, port_namespace):
                 if port.help is not None:
                     item += nodes.Text(' -- ')
                     item.extend(publish_doctree(port.help)[0].children)
-                sub_doctree = self.build_portnamespace_doctree(port)
-                if sub_doctree:
-                    sub_item = details(opened=self.EXPAND_NAMESPACES_FLAG in self.options)
-                    sub_item += summary(text='Namespace Ports')
-                    sub_item += sub_doctree
-                    item += sub_item
+                item += self.build_portnamespace_doctree(port)
             else:
                 raise NotImplementedError
             result += item

docs/source/internals/storage/psql_dos.rst

@@ -36,17 +36,17 @@ This is a 32-position hexadecimal sequence that is stored as a string with some
   - ``→`` indicate foreign keys
   - ``?`` indicate value types that are nullable.
 
-..
-    .. sqla-model:: ~aiida.storage.psql_dos.models.user.DbUser
-    .. sqla-model:: ~aiida.storage.psql_dos.models.node.DbNode
-    .. sqla-model:: ~aiida.storage.psql_dos.models.node.DbLink
-    .. sqla-model:: ~aiida.storage.psql_dos.models.group.DbGroup
-    .. sqla-model:: ~aiida.storage.psql_dos.models.group.DbGroupNode
-    .. sqla-model:: ~aiida.storage.psql_dos.models.computer.DbComputer
-    .. sqla-model:: ~aiida.storage.psql_dos.models.authinfo.DbAuthInfo
-    .. sqla-model:: ~aiida.storage.psql_dos.models.comment.DbComment
-    .. sqla-model:: ~aiida.storage.psql_dos.models.log.DbLog
-    .. sqla-model:: ~aiida.storage.psql_dos.models.settings.DbSetting
+
+    sqla-model:: ~aiida.storage.psql_dos.models.user.DbUser
+    sqla-model:: ~aiida.storage.psql_dos.models.node.DbNode
+    sqla-model:: ~aiida.storage.psql_dos.models.node.DbLink
+    sqla-model:: ~aiida.storage.psql_dos.models.group.DbGroup
+    sqla-model:: ~aiida.storage.psql_dos.models.group.DbGroupNode
+    sqla-model:: ~aiida.storage.psql_dos.models.computer.DbComputer
+    sqla-model:: ~aiida.storage.psql_dos.models.authinfo.DbAuthInfo
+    sqla-model:: ~aiida.storage.psql_dos.models.comment.DbComment
+    sqla-model:: ~aiida.storage.psql_dos.models.log.DbLog
+    sqla-model:: ~aiida.storage.psql_dos.models.settings.DbSetting
 
 The many-to-one relationship
 ----------------------------

docs/source/internals/storage/sqlite_zip.rst

@@ -83,15 +83,15 @@ The only differences are in the handling of certain data types by SQLite versus
 
 Also, `varchar_pattern_ops` indexes are not possible in SQLite.
 
-..
-    Tables
-    ......
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbUser
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbNode
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbLink
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbGroup
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbGroupNodes
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbComputer
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbAuthInfo
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbComment
-    .. sqla-model:: ~aiida.storage.sqlite_zip.models.DbLog
+
+Tables
+......
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbUser
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbNode
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbLink
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbGroup
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbGroupNodes
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbComputer
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbAuthInfo
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbComment
+sqla-model:: ~aiida.storage.sqlite_zip.models.DbLog

pyproject.toml

@@ -19,6 +19,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering"
 ]
 keywords = ["aiida", "workflows"]
@@ -78,15 +79,14 @@ rest = [
 ]
 docs = [
     "pydata-sphinx-theme~=0.13.3",
-    "sphinx~=4.1",
-    "sphinxcontrib-details-directive~=0.1.0",
+    "sphinx~=7.2",
     "sphinx-copybutton~=0.5.0",
-    "sphinx-design~=0.0.13",
-    "sphinx-notfound-page~=0.5",
+    "sphinx-design~=0.5.0",
+    "sphinx-notfound-page~=1.0",
     "sphinxext-rediraffe~=0.2.4",
-  #  "sphinx-sqlalchemy~=0.1.1",
+    "sphinx-sqlalchemy~=0.2.0",
     "sphinx-intl~=2.1.0",
-    "myst-nb~=0.17.0",
+    "myst-nb~=1.0.0",
 ]
 atomic_tools = [
     "PyCifRW~=4.4",
@@ -104,7 +104,7 @@ notebook = [
 ]
 pre-commit = [
     "mypy==0.991",
-    "packaging~=20.9",
+    "packaging~=23.0",
     "pre-commit~=2.2",
     "pylint~=2.17.4",
     "pylint-aiida~=0.1.1",
@@ -118,15 +118,15 @@ tests = [
     "pgtest~=1.3,>=1.3.1",
     "pytest~=7.0",
     "pytest-asyncio~=0.12,<0.17",
-    "pytest-timeout~=1.3",
+    "pytest-timeout~=2.0",
     "pytest-cov~=2.7,<2.11",
-    "pytest-rerunfailures~=9.1,>=9.1.1",
+    "pytest-rerunfailures~=12.0",
     "pytest-benchmark~=4.0",
     "pytest-regressions~=2.2",
     "pympler~=0.9",
     "coverage~=6.0",
-    "sphinx~=4.0",
-    "docutils==0.16",
+    "sphinx~=7.2",
+    "docutils~=0.20",
 ]
 bpython = [
     "bpython~=0.18.0"

requirements/requirements-py-3.10.txt

@@ -43,7 +43,8 @@ defusedxml==0.7.1
 deprecation==2.1.0
 disk-objectstore==1.0.0
 docstring-parser==0.15
-docutils==0.16
+docutils==0.20.1
+emmet-core==0.57.1
 exceptiongroup==1.1.1
 executing==1.2.0
 fastjsonschema==2.17.1
@@ -81,19 +82,19 @@ kiwisolver==1.4.4
 latexcodec==2.0.1
 linkify-it-py==2.0.2
 mako==1.2.4
-markdown-it-py[linkify,plugins]==2.2.0
+markdown-it-py[linkify,plugins]==3.0.0
 markupsafe==2.1.3
 matplotlib==3.7.1
 matplotlib-inline==0.1.6
-mdit-py-plugins==0.3.5
+mdit-py-plugins==0.4.0
 mdurl==0.1.2
 mistune==3.0.1
 monty==2023.9.25
 mpmath==1.3.0
 msgpack==1.0.5
 multidict==6.0.4
-myst-nb==0.17.2
-myst-parser==0.18.1
+myst-nb==1.0.0
+myst-parser==2.0.0
 nbclassic==1.0.0
 nbclient==0.7.4
 nbconvert==7.6.0
@@ -146,8 +147,8 @@ pytest-benchmark==4.0.0
 pytest-cov==2.10.1
 pytest-datadir==1.4.1
 pytest-regressions==2.4.2
-pytest-rerunfailures==9.1.1
-pytest-timeout==1.4.2
+pytest-rerunfailures==12.0.0
+pytest-timeout==2.2.0
 python-dateutil==2.8.2
 python-json-logger==2.0.7
 python-memcached==1.59
@@ -173,18 +174,18 @@ sniffio==1.3.0
 snowballstemmer==2.2.0
 soupsieve==2.4.1
 spglib==2.0.2
-sphinx==4.5.0
+sphinx==7.2.6
 sphinx-copybutton==0.5.2
-sphinx-design==0.0.13
+sphinx-design==0.5.0
 sphinx-intl==2.1.0
-sphinx-notfound-page==0.8.3
+sphinx-notfound-page==1.0.0
+sphinx-sqlalchemy==0.2.0
 sphinxcontrib-applehelp==1.0.4
-sphinxcontrib-details-directive==0.1.0
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.1
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-serializinghtml==1.1.9
 sphinxext-rediraffe==0.2.7
 sqlalchemy==2.0.23
 stack-data==0.6.2

requirements/requirements-py-3.11.txt

@@ -43,7 +43,8 @@ defusedxml==0.7.1
 deprecation==2.1.0
 disk-objectstore==1.0.0
 docstring-parser==0.15
-docutils==0.16
+docutils==0.20.1
+emmet-core==0.57.1
 executing==1.2.0
 fastjsonschema==2.17.1
 flask==2.3.2
@@ -80,19 +81,19 @@ kiwisolver==1.4.4
 latexcodec==2.0.1
 linkify-it-py==2.0.2
 mako==1.2.4
-markdown-it-py[linkify,plugins]==2.2.0
+markdown-it-py[linkify,plugins]==3.0.0
 markupsafe==2.1.3
 matplotlib==3.7.1
 matplotlib-inline==0.1.6
-mdit-py-plugins==0.3.5
+mdit-py-plugins==0.4.0
 mdurl==0.1.2
 mistune==3.0.1
 monty==2023.9.25
 mpmath==1.3.0
 msgpack==1.0.5
 multidict==6.0.4
-myst-nb==0.17.2
-myst-parser==0.18.1
+myst-nb==1.0.0
+myst-parser==2.0.0
 nbclassic==1.0.0
 nbclient==0.7.4
 nbconvert==7.6.0
@@ -145,8 +146,8 @@ pytest-benchmark==4.0.0
 pytest-cov==2.10.1
 pytest-datadir==1.4.1
 pytest-regressions==2.4.2
-pytest-rerunfailures==9.1.1
-pytest-timeout==1.4.2
+pytest-rerunfailures==12.0.0
+pytest-timeout==2.2.0
 python-dateutil==2.8.2
 python-json-logger==2.0.7
 python-memcached==1.59
@@ -172,18 +173,18 @@ sniffio==1.3.0
 snowballstemmer==2.2.0
 soupsieve==2.4.1
 spglib==2.0.2
-sphinx==4.5.0
+sphinx==7.2.6
 sphinx-copybutton==0.5.2
-sphinx-design==0.0.13
+sphinx-design==0.5.0
 sphinx-intl==2.1.0
-sphinx-notfound-page==0.8.3
+sphinx-notfound-page==1.0.0
+sphinx-sqlalchemy==0.2.0
 sphinxcontrib-applehelp==1.0.4
-sphinxcontrib-details-directive==0.1.0
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.1
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-serializinghtml==1.1.9
 sphinxext-rediraffe==0.2.7
 sqlalchemy==2.0.23
 stack-data==0.6.2