Merge branch 'main' into comments-typing

.docker/requirements.txt

@@ -1,4 +1,4 @@
 docker~=7.0.0
 pytest~=8.2.0
 requests~=2.32.0
-pytest-docker~=3.1.0
+pytest-docker~=3.2.0

.docker/tests/test_aiida.py

@@ -6,7 +6,7 @@
 
 
 def test_correct_python_version_installed(aiida_exec, python_version):
-    info = json.loads(aiida_exec('mamba list --json --full-name python').decode())[0]
+    info = json.loads(aiida_exec('mamba list --json --full-name python', ignore_stderr=True).decode())[0]
     assert info['name'] == 'python'
     assert parse(info['version']) == parse(python_version)
 
@@ -15,7 +15,7 @@ def test_correct_pgsql_version_installed(aiida_exec, pgsql_version, variant):
     if variant == 'aiida-core-base':
         pytest.skip('PostgreSQL is not installed in the base image')
 
-    info = json.loads(aiida_exec('mamba list --json --full-name postgresql').decode())[0]
+    info = json.loads(aiida_exec('mamba list --json --full-name postgresql', ignore_stderr=True).decode())[0]
     assert info['name'] == 'postgresql'
     assert parse(info['version']).major == parse(pgsql_version).major
 

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

@@ -31,9 +31,9 @@ runs:
       python-version: ${{ inputs.python-version }}
 
   - name: Set up uv
-    uses: astral-sh/[email protected].0
+    uses: astral-sh/[email protected].1
     with:
-      version: 0.5.x
+      version: 0.5.22
       python-version: ${{ inputs.python-version }}
 
   - name: Install dependencies from uv lock

.github/workflows/ci-code.yml

@@ -85,7 +85,7 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         name: aiida-pytests-py3.9
-        file: ./coverage.xml
+        files: ./coverage.xml
         fail_ci_if_error: false  # don't fail job, if coverage upload fails
 
   tests-presto:
@@ -126,8 +126,6 @@ jobs:
       with:
         python-version: '3.12'
         from-lock: 'true'
-        # NOTE: The `verdi devel check-undesired-imports` fails if
-        # the 'tui' extra is installed.
         extras: ''
 
     - name: Run verdi tests

.github/workflows/docker.yml

@@ -62,17 +62,11 @@ jobs:
       images: ${{ needs.build.outputs.images }}
       registry: ghcr.io
 
-  # IMPORTANT: To save arm64 runners resources,
-  # we run the test only when pushing to main.
-  # We also only test the aiida-core-dev image.
   test-arm64:
     needs: build
-    if: >-
-      github.repository == 'aiidateam/aiida-core'
-      && (github.ref_type == 'tag' || github.ref_name == 'main')
     uses: ./.github/workflows/docker-test.yml
     with:
-      runsOn: buildjet-4vcpu-ubuntu-2204-arm
+      runsOn: ubuntu-22.04-arm
       images: ${{ needs.build.outputs.images }}
       target: aiida-core-dev
 

.github/workflows/test-install.yml

@@ -38,16 +38,13 @@ jobs:
         python-version: '3.11'
 
     - name: Set up uv
-      uses: astral-sh/[email protected].0
+      uses: astral-sh/[email protected].1
       with:
-        version: 0.5.x
+        version: latest
 
     - name: Install utils/ dependencies
       run: uv pip install --system -r utils/requirements.txt
 
-    - name: Validate uv lockfile
-      run: uv lock --check
-
     - name: Validate conda environment file
       run: python ./utils/dependency_management.py validate-environment-yml
 

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ ci:
   autofix_prs: true
   autoupdate_commit_msg: 'Devops: Update pre-commit dependencies'
   autoupdate_schedule: quarterly
-  skip: [mypy, check-uv-lock, generate-conda-environment, validate-conda-environment, verdi-autodocs]
+  skip: [mypy, generate-conda-environment, validate-conda-environment, verdi-autodocs]
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -56,6 +56,12 @@ repos:
         environment.yml|
       )$
 
+- repo: https://github.com/astral-sh/uv-pre-commit
+  rev: 0.5.22
+  hooks:
+    # Check and update the uv lockfile
+  - id: uv-lock
+
 - repo: local
 
   hooks:
@@ -183,18 +189,6 @@ repos:
         src/aiida/workflows/arithmetic/multiply_add.py|
       )$
 
-  - id: check-uv-lock
-    name: Check uv lockfile up to date
-    # NOTE: This will not automatically update the lockfile
-    entry: uv lock --check
-    language: system
-    pass_filenames: false
-    files: >-
-      (?x)^(
-        pyproject.toml|
-        uv.lock|
-      )$
-
   - id: generate-conda-environment
     name: Update conda environment file
     entry: python ./utils/dependency_management.py generate-environment-yml

.readthedocs.yml

@@ -17,8 +17,8 @@ build:
     # https://docs.readthedocs.io/en/stable/build-customization.html#install-dependencies-with-uv
     pre_create_environment:
     - asdf plugin add uv
-    - asdf install uv 0.5.20
-    - asdf global uv 0.5.20
+    - asdf install uv 0.5.22
+    - asdf global uv 0.5.22
     create_environment:
     - uv venv
     install:

environment.yml

@@ -8,6 +8,7 @@ dependencies:
 - python~=3.9
 - alembic~=1.2
 - archive-path~=0.4.2
+- asyncssh~=2.19.0
 - circus~=0.18.0
 - click-spinner~=0.1.8
 - click~=8.1

pyproject.toml

@@ -20,6 +20,7 @@ classifiers = [
 dependencies = [
   'alembic~=1.2',
   'archive-path~=0.4.2',
+  "asyncssh~=2.19.0",
   'circus~=0.18.0',
   'click-spinner~=0.1.8',
   'click~=8.1',
@@ -175,6 +176,7 @@ requires-python = '>=3.9'
 [project.entry-points.'aiida.transports']
 'core.local' = 'aiida.transports.plugins.local:LocalTransport'
 'core.ssh' = 'aiida.transports.plugins.ssh:SshTransport'
+'core.ssh_async' = 'aiida.transports.plugins.ssh_async:AsyncSshTransport'
 'core.ssh_auto' = 'aiida.transports.plugins.ssh_auto:SshAutoTransport'
 
 [project.entry-points.'aiida.workflows']
@@ -308,6 +310,7 @@ module = 'tests.*'
 ignore_missing_imports = true
 module = [
   'ase.*',
+  'asyncssh.*',
   'bpython.*',
   'bs4.*',
   'CifFile.*',
@@ -388,6 +391,7 @@ testpaths = [
   'tests'
 ]
 timeout = 240
+timeout_method = "thread"
 xfail_strict = true
 
 [tool.ruff]
@@ -512,4 +516,8 @@ commands = molecule {posargs:test}
 """
 
 [tool.uv]
-required-version = ">=0.5.20"
+# NOTE: When you bump the minimum uv version, you also need to change it in:
+# .pre-commit-config.yaml
+# .github/actions/install-aiida-core/action.yml
+# .readthedocs.yml
+required-version = ">=0.5.21"

src/aiida/cmdline/commands/cmd_devel.py

@@ -61,12 +61,11 @@ def devel_check_load_time():
 def devel_check_undesired_imports():
     """Check that verdi does not import python modules it shouldn't.
 
-    Note: The blacklist was taken from the list of packages in the 'atomic_tools' extra but can be extended.
+    This is to keep the verdi CLI snappy, especially for tab-completion.
     """
     loaded_modules = 0
 
-    for modulename in [
-        'asyncio',
+    unwanted_modules = [
         'requests',
         'plumpy',
         'disk_objectstore',
@@ -78,7 +77,12 @@ def devel_check_undesired_imports():
         'spglib',
         'pymysql',
         'yaml',
-    ]:
+    ]
+    # trogon powers the optional TUI and uses asyncio.
+    # Check for asyncio only when the optional tui extras are not installed.
+    if 'trogon' not in sys.modules:
+        unwanted_modules += 'asyncio'
+    for modulename in unwanted_modules:
         if modulename in sys.modules:
             echo.echo_warning(f'Detected loaded module "{modulename}"')
             loaded_modules += 1

src/aiida/common/exceptions.py

@@ -200,6 +200,13 @@ class IncompatibleDatabaseSchema(ConfigurationError):  # noqa: N818
     """
 
 
+class IncompatibleExternalDependencies(ConfigurationError):  # noqa: N818
+    """Raised when incomptabale external depencies are found.
+
+    This could happen, when the dependency is not a python package and therefore not checked during installation.
+    """
+
+
 class IncompatibleStorageSchema(IncompatibleDatabaseSchema):
     """Raised when the storage schema is incompatible with that of the code."""