Merge branch 'main' into issue-6687-v2

Author: adityagh006

.github/system_tests/test_daemon.py

@@ -437,14 +437,20 @@ def launch_all():
     run_multiply_add_workchain()
 
     # Testing the stashing functionality
+    # To speedup, here we only check with StashMode.COPY.
+    # All stash_modes are tested individually in `test_execmanager.py`
     print('Testing the stashing functionality')
     process, inputs, expected_result = create_calculation_process(code=code_doubler, inputval=1)
     with tempfile.TemporaryDirectory() as tmpdir:
         # Delete the temporary directory to test that the stashing functionality will create it if necessary
         shutil.rmtree(tmpdir, ignore_errors=True)
 
         source_list = ['output.txt', 'triple_value.*']
-        inputs['metadata']['options']['stash'] = {'target_base': tmpdir, 'source_list': source_list}
+        inputs['metadata']['options']['stash'] = {
+            'stash_mode': StashMode.COPY.value,
+            'target_base': tmpdir,
+            'source_list': source_list,
+        }
         _, node = run.get_node(process, **inputs)
         assert node.is_finished_ok
         assert 'remote_stash' in node.outputs

.github/workflows/ci-code.yml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.12']
+        python-version: ['3.9', '3.13']
         database-backend: [psql]
         include:
         - python-version: '3.9'
@@ -102,7 +102,7 @@ jobs:
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
       with:
-        python-version: '3.11'
+        python-version: '3.13'
 
     - name: Setup SSH on localhost
       run: .github/workflows/setup_ssh.sh
@@ -124,7 +124,7 @@ jobs:
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
       with:
-        python-version: '3.12'
+        python-version: '3.13'
         from-lock: 'true'
         extras: ''
 

.github/workflows/nightly.yml

@@ -2,7 +2,7 @@ name: nightly
 
 on:
   schedule:
-  - cron: 0 0 * * *        # Run every day at midnight
+  - cron: 0 0 * * *   # Run every day at midnight
   pull_request:
     paths:
     - .github/workflows/nightly.yml
@@ -15,7 +15,7 @@ on:
 
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
-    # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags
+  # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
@@ -26,7 +26,7 @@ jobs:
 
   nightly-tests:
 
-    if: github.repository == 'aiidateam/aiida-core'      # Prevent running the builds on forks as well
+    if: github.repository == 'aiidateam/aiida-core'  # Prevent running the builds on forks as well
     runs-on: ubuntu-24.04
 
     services:

.github/workflows/pre-commit.yml

@@ -0,0 +1,32 @@
+name: pre-commit
+# NOTE: This job is not duplicating pre-commit.ci job,
+# since that once skips running mypy type-checking\
+# due to technical limitations of pre-commit.ci runners.
+
+on:
+  push:
+    branches-ignore: [gh-pages]
+  pull_request:
+    branches-ignore: [gh-pages]
+
+env:
+  FORCE_COLOR: 1
+
+jobs:
+
+  pre-commit:
+
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install python dependencies
+      uses: ./.github/actions/install-aiida-core
+      with:
+        python-version: '3.11'
+        from-lock: 'true'
+
+    - name: Run pre-commit
+      run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/test-install.yml

@@ -111,7 +111,7 @@ jobs:
       fail-fast: false
       matrix:
 
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
         # 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.
@@ -162,7 +162,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     services:
       postgres:

.pre-commit-config.yaml

@@ -201,7 +201,8 @@ repos:
     files: >-
       (?x)^(
         pyproject.toml|
-        utils/dependency_management.py
+        utils/dependency_management.py|
+        environment.yml|
       )$
 
   - id: validate-conda-environment

docs/source/index.rst

@@ -1,5 +1,9 @@
 :sd_hide_title:
 
+.. HTML meta tag to verify aiida.readthedocs.io in Google Search Console (aiidateam account)
+.. meta::
+   :google-site-verification: wLcoklPmiTRQs5TXRD6At5hNXGYSwexWnx0wygU4Uxk
+
 .. grid::
    :reverse:
    :gutter: 2 3 3 3

docs/source/installation/docker.rst

@@ -77,7 +77,7 @@ Any data that was created in a previous session is still available.
 
 .. caution::
 
-    When the container is not just stopped but *deleted*, any data stored in the container, including the data stored in the profile's storage, is permanently localhost
+    When the container is not just stopped but *deleted*, any data stored in the container, including the data stored in the profile's storage, is permanently deleted.
     To ensure the data is not lost, it should be persisted on a volume that is mounted to the container.
     Refer to the section on :ref:`persisting data <installation:docker:persisting-data>` for more details.
 

docs/source/installation/guide_complete.rst

@@ -157,7 +157,7 @@ Although it is possible to run AiiDA without a daemon it does provide significan
 
     .. tab-item:: MacOS X
 
-        #. Install `Homebrew <https://docs.brew.sh/Installation>`.
+        #. Install `Homebrew <https://docs.brew.sh/Installation>`__.
 
         #. Install RabbitMQ:
 
@@ -315,7 +315,7 @@ The options specific to the ``core.sqlite_dos`` storage plugin are:
 This storage plugin uses `PostgreSQL <https://www.postgresql.org/>`_ and the `disk-objectstore <https://disk-objectstore.readthedocs.io/en/latest/>`_ to store data.
 The ``disk-objectstore`` is a Python package that is automatically installed as a dependency when installing ``aiida-core``, which was covered in the :ref:`Python package installation section <installation:guide-complete:python-package>`.
 The storage plugin can connect to a PostgreSQL instance running on the localhost or on a server that can be reached over the internet.
-Instructions for installing PostgreSQL is beyond the scope of this guide.
+Instructions for installing PostgreSQL is beyond the scope of this guide. You can find the installation instructions for your system on the `PostgreSQL website <https://www.postgresql.org/docs/current/tutorial-install.html>`__.
 
 Before creating a profile, a database (and optionally a custom database user) has to be created.
 First, connect to PostgreSQL using ``psql``, the `native command line client for PostgreSQL <https://www.postgresql.org/docs/current/app-psql.html>`_:

docs/source/intro/index.rst

@@ -10,14 +10,14 @@ Introduction
 
 AiiDA is an open-source Python infrastructure to help researchers with automating, managing, persisting, sharing and reproducing the complex workflows associated with modern computational science and all associated data.
 
-AiiDA is built to support and streamline the four core pillars of the ADES model: Automation, Data, Environment, and Sharing (described `here <https://arxiv.org/abs/1504.01163>`__). Some of the key features of AiiDA include:
+AiiDA is built to support and streamline the four core pillars of the ADES model: Automation, Data, Environment, and Sharing (described `here <https://arxiv.org/abs/1504.01163>`__, `doi <https://doi.org/10.1016/j.commatsci.2015.09.013>`__). Some of the key features of AiiDA include:
 
 *  **Workflows:** AiiDA allows to build and execute complex, auto-documenting workflows linked to multiple codes on local and remote computers.
 *  **High-throughput:** AiiDA's event-based workflow engine supports tens of thousands of processes per hour with full check-pointing.
 *  **Data provenance:** AiiDA automatically tracks and records inputs, outputs and metadata of all calculations and workflows in extensive provenance graphs that preserve the full lineage of all data.
 *  **Advanced queries:** AiiDA's query language enables fast graph queries on millions of nodes.
 *  **Plugin interface:** AiiDA can support via plugins any computational code and data analytics tool, data type, scheduler, connection mode, etc. (see `public plugin repository <https://aiidateam.github.io/aiida-registry/>`__).
-*  **HPC interface:** AiiDA can seamlessly deal with heterogeneous and remote computing resources; it works with many schedulers out of the box (`SLURM <https://slurm.schedmd.com>`__, `PBS Pro <https://www.pbspro.org/>`__, `torque <http://www.adaptivecomputing.com/products/torque/>`__, `SGE <http://gridscheduler.sourceforge.net/>`__ or `LSF <https://www.ibm.com/docs/en/spectrum-lsf>`__).
+*  **HPC interface:** AiiDA can seamlessly deal with heterogeneous and remote computing resources; it works with many schedulers out of the box (`SLURM <https://slurm.schedmd.com>`__, `PBS Pro <https://www.pbspro.org/>`__, `torque <https://docs.adaptivecomputing.com/torque/5-0-0/help.htm>`__, `SGE <http://gridscheduler.sourceforge.net/>`__ or `LSF <https://www.ibm.com/docs/en/spectrum-lsf>`__).
 *  **Open science:** AiiDA allows to export both full databases and selected subsets, to be shared with collaborators or made available and browsable online on the `Archive <https://archive.materialscloud.org/>`__ and `Explore <https://www.materialscloud.org/explore>`__ sections of `Materials Cloud <https://www.materialscloud.org>`__.
 *  **Open source:** AiiDA is released under the `MIT open-source license <https://github.com/aiidateam/aiida-core/blob/main/LICENSE.txt>`__.