Merge branch 'main' into rmq-out-small-step-try

.github/actions/install-aiida-core/action.yml

@@ -7,16 +7,18 @@ inputs:
     default: '3.9'              # Lowest supported version
     required: false
   extras:
-    description: aiida-core extras (including brackets)
-    default: ''
+    description: list of optional dependencies
+    # NOTE: The default 'pre-commit' extra recursively contains
+    # other extras needed to run the tests.
+    default: pre-commit
     required: false
   # NOTE: Hard-learned lesson: we cannot use type=boolean here, apparently :-(
   # https://stackoverflow.com/a/76294014
   # NOTE2: When installing from lockfile, aiida-core and its dependencies
   # are installed in a virtual environment located in .venv directory.
   # Subsuquent jobs steps must either activate the environment or use `uv run`
   from-lock:
-    description: Install aiida-core dependencies from a uv lock file
+    description: Install aiida-core dependencies from uv lock file
     default: 'true'
     required: false
 
@@ -29,19 +31,18 @@ runs:
       python-version: ${{ inputs.python-version }}
 
   - name: Set up uv
-    uses: astral-sh/setup-uv@v4
+    uses: astral-sh/setup-uv@v5
     with:
-      version: 0.5.6
+      version: 0.5.x
+      python-version: ${{ inputs.python-version }}
 
   - name: Install dependencies from uv lock
     if: ${{ inputs.from-lock == 'true' }}
     # NOTE: We're asserting that the lockfile is up to date
-    # NOTE2: 'pre-commit' extra recursively contains other extras
-    # needed to run the tests.
-    run: uv sync --locked --extra pre-commit
+    run: uv sync --locked ${{ inputs.extras && format('--extra {0}', inputs.extras) || '' }}
     shell: bash
 
   - name: Install aiida-core
     if: ${{ inputs.from-lock != 'true' }}
-    run: uv pip install --system -e .${{ inputs.extras }}
+    run: uv pip install -e .${{ inputs.extras }}
     shell: bash

.github/workflows/ci-code.yml

@@ -27,6 +27,10 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ['3.9', '3.12']
+        database-backend: [psql]
+        include:
+        - python-version: '3.9'
+          database-backend: sqlite
 
     services:
       postgres:
@@ -64,16 +68,22 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Setup environment
-      # Note: The virtual environment in .venv was created by uv in previous step
-      run: source .venv/bin/activate && .github/workflows/setup.sh
+      run: .github/workflows/setup.sh
 
     - name: Run test suite
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      # Python 3.12 has a performance regression when running with code coverage
+      # NOTE1: Python 3.12 has a performance regression when running with code coverage
       # so run code coverage only for python 3.9.
-      run: uv run pytest -n auto --db-backend psql -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
+      # NOTE2: Unset CI envvar to workaround a pymatgen issue for Python 3.9
+      # https://github.com/materialsproject/pymatgen/issues/4243
+      # TODO: Remove a workaround for VIRTUAL_ENV once the setup-uv action is updated
+      # https://github.com/astral-sh/setup-uv/issues/219
+      run: |
+        ${{ matrix.python-version == '3.9' && 'unset CI' || '' }}
+        ${{ matrix.python-version == '3.9' && 'VIRTUAL_ENV=$PWD/.venv' || '' }}
+        pytest -n auto --db-backend ${{ matrix.database-backend }} -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
 
     - name: Upload coverage report
       if: matrix.python-version == 3.9 && github.repository == 'aiidateam/aiida-core'
@@ -84,7 +94,6 @@ jobs:
         file: ./coverage.xml
         fail_ci_if_error: false  # don't fail job, if coverage upload fails
 
-
   tests-presto:
 
     runs-on: ubuntu-latest
@@ -122,7 +131,10 @@ jobs:
       uses: ./.github/actions/install-aiida-core
       with:
         python-version: '3.12'
-        from-lock: 'false'
+        from-lock: 'true'
+        # NOTE: The `verdi devel check-undesired-imports` fails if
+        # the 'tui' extra is installed.
+        extras: ''
 
     - name: Run verdi tests
       run: |

.github/workflows/test-install.yml

@@ -11,6 +11,9 @@ on:
   schedule:
   - cron: 30 02 * * *      # nightly build
 
+env:
+  FORCE_COLOR: 1
+
 # 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
@@ -32,18 +35,18 @@ jobs:
     - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
 
     - name: Set up uv
-      uses: astral-sh/setup-uv@v4
+      uses: astral-sh/setup-uv@v5
       with:
-        version: 0.5.6
+        version: 0.5.x
 
     - name: Install utils/ dependencies
       run: uv pip install --system -r utils/requirements.txt
 
     - name: Validate uv lockfile
-      run: uv lock --locked
+      run: uv lock --check
 
     - name: Validate conda environment file
       run: python ./utils/dependency_management.py validate-environment-yml
@@ -208,4 +211,11 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      run: pytest -n auto --db-backend psql tests -m 'not nightly' tests/
+      # Unset CI envvar to workaround a pymatgen issue for Python 3.9
+      # https://github.com/materialsproject/pymatgen/issues/4243
+      # TODO: Remove a workaround for VIRTUAL_ENV once the setup-uv action is updated
+      # https://github.com/astral-sh/setup-uv/issues/219
+      run: |
+        ${{ matrix.python-version == '3.9' && 'unset CI' || '' }}
+        ${{ matrix.python-version == '3.9' && 'VIRTUAL_ENV=$PWD/.venv' || '' }}
+        pytest -n auto --db-backend psql -m 'not nightly' tests/

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-merge-conflict
   - id: check-yaml
@@ -26,7 +26,7 @@ repos:
     exclude: *exclude_pre_commit_hooks
 
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.28.6
+  rev: 0.30.0
   hooks:
   - id: check-github-workflows
 
@@ -37,14 +37,14 @@ repos:
     args: [--line-length=120, --fail-on-change]
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.0
+  rev: v0.8.6
   hooks:
   - id: ruff-format
   - id: ruff
     args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.13.0
+  rev: v2.14.0
   hooks:
   - id: pretty-format-toml
     args: [--autofix]
@@ -191,12 +191,13 @@ repos:
   - id: check-uv-lock
     name: Check uv lockfile up to date
     # NOTE: This will not automatically update the lockfile
-    entry: uv lock --locked
+    entry: uv lock --check
     language: system
     pass_filenames: false
     files: >-
       (?x)^(
         pyproject.toml|
+        uv.lock|
       )$
 
   - id: generate-conda-environment

docs/source/reference/command_line.rst

@@ -451,7 +451,7 @@ Below is a list with all available subcommands.
       --broker-host HOSTNAME          Hostname for the message broker.  [default: 127.0.0.1]
       --broker-port INTEGER           Port for the message broker.  [default: 5672]
       --broker-virtual-host TEXT      Name of the virtual host for the message broker without
-                                      leading forward slash.
+                                      leading forward slash.  [default: ""]
       --repository DIRECTORY          Absolute path to the file repository.
       --test-profile                  Designate the profile to be used for running the test
                                       suite only.

pyproject.toml

@@ -388,7 +388,7 @@ minversion = '7.0'
 testpaths = [
   'tests'
 ]
-timeout = 30
+timeout = 240
 xfail_strict = true
 
 [tool.ruff]

src/aiida/cmdline/commands/cmd_data/cmd_remote.py

@@ -9,6 +9,7 @@
 """`verdi data core.remote` command."""
 
 import stat
+from pathlib import Path
 
 import click
 
@@ -87,3 +88,43 @@ def remote_show(datum):
     """Show information for a RemoteData object."""
     echo.echo(f'- Remote computer name: {datum.computer.label}')
     echo.echo(f'- Remote folder full path: {datum.get_remote_path()}')
+
+
+@remote.command('size')
+@arguments.NODE()
+@click.option(
+    '-m',
+    '--method',
+    type=click.STRING,
+    default='du',
+    help='The method that should be used to evaluate the size (either ``du`` or ``stat``.)',
+)
+@click.option(
+    '-p',
+    '--path',
+    type=click.Path(),
+    default=None,
+    help='Relative path of the object of the ``RemoteData`` node for which the size should be evaluated.',
+)
+@click.option(
+    '-b',
+    '--bytes',
+    'return_bytes',
+    type=bool,
+    is_flag=True,
+    default=False,
+    help='Return the size in bytes or human-readable format?',
+)
+def remote_size(node, method, path, return_bytes):
+    """Obtain the total size of a file or directory at a given path that is stored via a ``RemoteData`` object."""
+    try:
+        # `method` might change, if `du` fails, so assigning to new variable here
+        total_size, used_method = node.get_size_on_disk(relpath=path, method=method, return_bytes=return_bytes)
+        remote_path = Path(node.get_remote_path())
+        full_path = remote_path / path if path is not None else remote_path
+        echo.echo_success(
+            f'Estimated total size of path `{full_path}` on the Computer '
+            f'<{node.computer.label}> obtained via `{used_method}`: {total_size}'
+        )
+    except (OSError, FileNotFoundError, NotImplementedError) as exc:
+        echo.echo_critical(str(exc))

src/aiida/common/utils.py

@@ -572,3 +572,34 @@ def __init__(self, dtobj, precision):
 
         self.dtobj = dtobj
         self.precision = precision
+
+
+def format_directory_size(size_in_bytes: int) -> str:
+    """Converts a size in bytes to a human-readable string with the appropriate prefix.
+
+    :param size_in_bytes: Size in bytes.
+    :raises ValueError: If the size is negative.
+    :return: Human-readable size string with a prefix (e.g., "1.23 KB", "5.67 MB").
+
+    The function converts a given size in bytes to a more readable format by
+    adding the appropriate unit suffix (e.g., KB, MB, GB). It uses the binary
+    system (base-1024) for unit conversions.
+
+    Example:
+        >>> format_directory_size(123456789)
+        '117.74 MB'
+    """
+    if size_in_bytes < 0:
+        raise ValueError('Size cannot be negative.')
+
+    # Define size prefixes
+    prefixes = ['B', 'KB', 'MB', 'GB', 'TB', 'PB']
+    factor = 1024  # 1 KB = 1024 B
+    index = 0
+
+    while size_in_bytes >= factor and index < len(prefixes) - 1:
+        size_in_bytes /= factor
+        index += 1
+
+    # Format the size to two decimal places
+    return f'{size_in_bytes:.2f} {prefixes[index]}'