Merge branch 'main' into fix/6448/s6-notification-polling-check

.github/workflows/docker-build-test.yml

@@ -41,7 +41,7 @@ jobs:
       uses: docker/setup-buildx-action@v3
 
     - name: Build images
-      uses: docker/bake-action@v4
+      uses: docker/bake-action@v5
       with:
         # Load to Docker engine for testing
         load: true

.github/workflows/docker-build.yml

@@ -54,7 +54,7 @@ jobs:
 
     - name: Build and upload to ghcr.io 📤
       id: build
-      uses: docker/bake-action@v4
+      uses: docker/bake-action@v5
       with:
         push: true
         workdir: .docker/

.github/workflows/docker-publish.yml

@@ -59,6 +59,12 @@ jobs:
         vars=$(cat build.json | jq -c '[.variable | to_entries[] | {"key": .key, "value": .value.default}] | from_entries')
         echo "vars=$vars" | tee -a "${GITHUB_OUTPUT}"
 
+    - id: get-version
+      if: ${{ github.ref_type == 'tag'  && startsWith(github.ref_name, 'v') }}
+      run: |
+        tag="${{ github.ref_name }}"
+        echo "AIIDA_VERSION=${tag#v}" >> $GITHUB_OUTPUT
+
     - name: Docker meta
       id: meta
       uses: docker/metadata-action@v5
@@ -69,7 +75,7 @@ jobs:
           type=ref,event=pr
           type=ref,event=branch,enable=${{ github.ref_name != 'main' }}
           type=edge,enable={{is_default_branch}}
-          type=raw,value=aiida-${{ env.AIIDA_VERSION }},enable=${{ github.ref_type == 'tag'  && startsWith(github.ref_name, 'v') }}
+          type=raw,value=aiida-${{ steps.get-version.outputs.AIIDA_VERSION }},enable=${{ github.ref_type == 'tag'  && startsWith(github.ref_name, 'v') }}
           type=raw,value=python-${{ env.PYTHON_VERSION }},enable=${{ github.ref_type == 'tag' && startsWith(github.ref_name, 'v') }}
           type=raw,value=postgresql-${{ env.PGSQL_VERSION }},enable=${{ github.ref_type == 'tag' && startsWith(github.ref_name, 'v') }}
           type=match,pattern=v(\d{4}\.\d{4}(-.+)?),group=1

.github/workflows/release.yml

@@ -40,8 +40,9 @@ jobs:
     - name: Install aiida-core and pre-commit
       uses: ./.github/actions/install-aiida-core
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         extras: '[pre-commit]'
+        from-requirements: 'false'
 
     - name: Run pre-commit
       run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/test-install.yml

@@ -229,7 +229,7 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      run: pytest --cov aiida --verbose tests -m 'not nightly'
+      run: pytest --verbose tests -m 'not nightly'
 
     - name: Freeze test environment
       run: pip freeze | sed '1d' | tee requirements-py-${{ matrix.python-version }}.txt

.pre-commit-config.yaml

@@ -26,7 +26,7 @@ repos:
     exclude: *exclude_pre_commit_hooks
 
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.28.2
+  rev: 0.28.6
   hooks:
   - id: check-github-workflows
 
@@ -37,7 +37,7 @@ repos:
     args: [--line-length=120, --fail-on-change]
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.1
+  rev: v0.5.0
   hooks:
   - id: ruff-format
     exclude: &exclude_ruff >

docs/source/_static/aiida-custom.css

@@ -1,3 +1,110 @@
+/* AiiDA colors in HTML format
+blue:   #0096d2
+orange: #fe7d17
+green:  #30b808
+*/
+
+html[data-theme="light"] {
+    --pst-color-primary: #0096d2;
+    --pst-color-secondary: #fe7d17;
+    --pst-color-surface: #f5f5f5;
+}
+
+html[data-theme="dark"] {
+    --pst-color-primary: #0096d2;
+    --pst-color-secondary: #fe7d17;
+}
+
+code {
+    --pst-color-inline-code: #0096d2;
+    font-weight: bold;
+}
+
+html[data-theme=light] .highlight .ch,
+html[data-theme=light] .highlight .sd {
+    color: #777777;
+    font-style: italic
+}
+
+html[data-theme=light] .highlight .s1,
+html[data-theme=light] .highlight .si {
+    color: #30b808;
+    font-weight: bold;
+}
+
+html[data-theme=light] .highlight .k,
+html[data-theme=light] .highlight .kc,
+html[data-theme=light] .highlight .kn,
+html[data-theme=light] .highlight .ow,
+html[data-theme=light] .highlight .mf,
+html[data-theme=light] .highlight .mi {
+    color: #0096d2;
+    font-weight: bold;
+}
+
+html[data-theme=dark] .highlight .ch,
+html[data-theme=dark] .highlight .sd {
+    color: #999999;
+    font-style: italic
+}
+
+html[data-theme=dark] .highlight .s1,
+html[data-theme=dark] .highlight .si {
+    color: #30b808;
+    font-weight: bold;
+}
+
+html[data-theme=dark] .highlight .k,
+html[data-theme=dark] .highlight .kc,
+html[data-theme=dark] .highlight .kn,
+html[data-theme=dark] .highlight .ow,
+html[data-theme=dark] .highlight .mf,
+html[data-theme=dark] .highlight .mi {
+    color: #0096d2;
+    font-weight: bold;
+}
+
+.sd-card-hover:hover {
+    border-color: var(--pst-color-primary);
+    transform: none;
+}
+
+.aiida-green {
+    color: #30b808;
+}
+
+.aiida-blue {
+    color: #0096d2;
+}
+
+.aiida-orange {
+    color: #fe7d17;
+}
+
+.aiida-red {
+    color: rgb(192, 11, 80);
+}
+
+img.logo-shell {
+    width: 20px;
+    padding-bottom: 3px;
+    margin-right: 3px;
+}
+
+.sd-card-footer {
+    padding-top: 0rem;
+    border-top: none !important;
+}
+
+.sd-card-footer table {
+    margin-bottom: 0rem;
+    border-color: transparent;
+}
+
+.sd-card-footer table td:last-child {
+    text-align: right;
+}
+
 /* Fix CSS of top bar link icons */
 a.nav-link.nav-external i {
     padding-left: 0.3em !important;

docs/source/conf.py

@@ -49,15 +49,9 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = [
-    'datatypes/**',
     'developer_guide/**',
-    'get_started/**',
-    'howto/installation_more/index.rst',
     'import_export/**',
     'internals/global_design.rst',
-    'internals/orm.rst',
-    'scheduler/index.rst',
-    'working_with_aiida/**',
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.
@@ -103,7 +97,7 @@
 ipython_mplbackend = ''
 
 myst_enable_extensions = ['colon_fence', 'deflist']
-myst_heading_anchors = 3
+myst_heading_anchors = 4
 nb_execution_show_tb = 'READTHEDOCS' in os.environ
 nb_merge_streams = True
 nb_mime_priority_overrides = [
@@ -177,6 +171,9 @@
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
 html_show_copyright = False
 
+# This is to tell search engines to index only stable and latest version
+html_extra_path = ['robots.txt']
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

docs/source/howto/archive_profile.md

@@ -25,7 +25,7 @@ See {ref}`how-to:share:archives` for information on how to create and migrate an
 The easiest way to inspect the contents of an archive is to create a profile that "mounts" the archive as its data storage:
 
 ```{code-cell} ipython3
-!verdi profile setup core.sqlite_zip -n --profile archive --filepath process.aiida
+!verdi profile setup core.sqlite_zip -n --profile-name archive --filepath process.aiida
 ```
 
 You can now inspect the contents of the `process.aiida` archive by using the `archive` profile in the same way you would a standard AiiDA profile.

docs/source/howto/daemon.rst

@@ -0,0 +1,13 @@
+
+.. _how-to:manage-daemon:
+
+How to manage the daemon
+------------------------
+
+The AiiDA daemon process runs in the background and takes care of processing your submitted calculations and workflows, checking their status, retrieving their results once they are finished and storing them in the AiiDA database.
+
+The AiiDA daemon is controlled using three simple commands:
+
+* ``verdi daemon start``: start the daemon
+* ``verdi daemon status``: check the status of the daemon
+* ``verdi daemon stop``: stop the daemon

docs/source/howto/index.rst

@@ -6,6 +6,7 @@ How-To Guides
    :maxdepth: 1
 
    interact
+   daemon
    plugins_install
    run_codes
    run_workflows

docs/source/howto/installation.rst

@@ -14,7 +14,7 @@ Creating profiles
 -----------------
 Each AiiDA installation can have multiple profiles, each of which can have its own individual database and file repository to store the contents of the :ref:`provenance graph<topics:provenance:concepts>`.
 Profiles allow you to run multiple projects completely independently from one another with just a single AiiDA installation and at least one profile is required to run AiiDA.
-A new profile can be created using :ref:`verdi quicksetup<reference:command-line:verdi-quicksetup>` or :ref:`verdi setup<reference:command-line:verdi-setup>`, which works similar to the former but gives more control to the user.
+A new profile can be created using :ref:`verdi presto<reference:command-line:verdi-presto>` or :ref:`verdi profile setup<reference:command-line:verdi-profile>`, which works similar to the former but gives more control to the user.
 
 Listing profiles
 ----------------
@@ -296,7 +296,7 @@ Isolating multiple instances
 An AiiDA instance is defined as the installed source code plus the configuration folder that stores the configuration files with all the configured profiles.
 It is possible to run multiple AiiDA instances on a single machine, simply by isolating the code and configuration in a virtual environment.
 
-To isolate the code, make sure to install AiiDA into a virtual environment, e.g., with conda or venv, as described :ref:`here <intro:get_started:setup>`.
+To isolate the code, make sure to install AiiDA into a virtual environment, e.g., with conda or venv.
 Whenever you activate this particular environment, you will be running the particular version of AiiDA (and all the plugins) that you installed specifically for it.
 
 This is separate from the configuration of AiiDA, which is stored in the configuration directory which is always named ``.aiida`` and by default is stored in the home directory.
@@ -619,12 +619,12 @@ Alternatively to the CLI command, one can also manually create a backup. This re
 .. _how-to:installation:backup:restore:
 
 Restoring data from a backup
-==================================
+============================
 
 Restoring a backed up AiiDA profile requires:
 
 * restoring the profile information in the AiiDA ``config.json`` file. Simply copy the`profiles` entry from
-  the backed up `config.json`to the one of the running AiiDA instance (see `verdi status` for exact location).
+  the backed up ``config.json`` to the one of the running AiiDA instance (see ``verdi status`` for exact location).
   Some information (e.g. the database parameters) might need to be updated.
 
 * restoring the data of of the backed up profile according to the ``config.json`` entry.
@@ -642,7 +642,7 @@ To test if the restoration worked, run ``verdi -p <profile-name> status`` to ver
 
         **PostgreSQL database**
 
-        To restore the PostgreSQL database from the ``db.psql`` file that was backed up, first you should create an empty database following the instructions described in :ref:`database <intro:install:database>` skipping the ``verdi setup`` phase.
+        To restore the PostgreSQL database from the ``db.psql`` file that was backed up, first you should create an empty database following the instructions described in :ref:`the installation guide <installation:guide-complete:create-profile:core-psql-dos>`.
         The backed up data can then be imported by calling:
 
         .. code-block:: console

docs/source/howto/interact.rst

@@ -125,6 +125,18 @@ Interactive notebooks
 =====================
 
 Similar to :ref:`interactive shells <how-to:interact-shell>`, AiiDA is also directly compatbile with interactive Python notebooks, such as `Jupyter <https://jupyter.org/>`_.
+To install the required Python packages, install ``aiida-core`` with the ``notebook`` extra, e.g. run:
+
+.. code-block:: console
+
+    pip install aiida-core[notebook]
+
+You should now be able to start a Jupyter notebook server:
+
+.. code-block:: console
+
+    jupyter notebook
+
 To use AiiDA's Python API in a notebook, first a profile has to be loaded:
 
 .. code-block:: ipython
@@ -142,8 +154,14 @@ The same can be accomplished using the following magic statement:
     %load_ext aiida
     %aiida
 
-This magic line will replicate the same environment as :ref:`the interactive shell <how-to:interact-shell>` provided by ``verdi shell``.
-However, it does require some one-time installation, as detailed in the section on how to :ref:`intro:install:jupyter`.
+This magic line replicates the same environment as :ref:`the interactive shell <how-to:interact-shell>` provided by ``verdi shell``.
+
+It is also possible to run ``verdi`` commands inside the notebook, for example:
+
+.. code-block:: ipython
+
+   %verdi status
+
 
 
 .. _how-to:interact-restapi:

docs/source/howto/ssh.rst

@@ -269,6 +269,6 @@ Using kerberos tokens
 If the remote machine requires authentication through a Kerberos token (that you need to obtain before using ssh), you typically need to
 
 * install ``libffi`` (``sudo apt-get install libffi-dev`` under Ubuntu)
-* install the ``ssh_kerberos`` extra during the installation of aiida-core (see :ref:`intro:install:setup`).
+* install the ``ssh_kerberos`` extra during the installation of aiida-core (see :ref:`installation:guide-complete:python-package:optional-requirements`).
 
 If you provide all necessary ``GSSAPI`` options in your ``~/.ssh/config`` file, ``verdi computer configure`` should already pick up the appropriate values for all the gss-related options.