Merge branch 'main' into fix-windows-running

.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:
@@ -187,18 +193,6 @@ 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:

pyproject.toml

@@ -517,4 +517,8 @@ 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/transports/plugins/local.py

@@ -872,7 +872,7 @@ def rename(self, oldpath: TransportPath, newpath: TransportPath):
         :param str oldpath: existing name of the file or folder
         :param str newpath: new name for the file or folder
 
-        :raises OSError: if src/dst is not found
+        :raises OSError: if oldpath is not found or newpath already exists
         :raises ValueError: if src/dst is not a valid string
         """
         oldpath = str(oldpath)
@@ -883,8 +883,8 @@ def rename(self, oldpath: TransportPath, newpath: TransportPath):
             raise ValueError(f'Destination {newpath} is not a valid string')
         if not os.path.exists(oldpath):
             raise OSError(f'Source {oldpath} does not exist')
-        if not os.path.exists(newpath):
-            raise OSError(f'Destination {newpath} does not exist')
+        if os.path.exists(newpath):
+            raise OSError(f'Destination {newpath} already exists.')
 
         shutil.move(oldpath, newpath)
 

src/aiida/transports/plugins/ssh.py

@@ -1357,8 +1357,8 @@ def rename(self, oldpath: TransportPath, newpath: TransportPath):
         :param str oldpath: existing name of the file or folder
         :param str newpath: new name for the file or folder
 
-        :raises OSError: if oldpath/newpath is not found
-        :raises ValueError: if sroldpathc/newpath is not a valid path
+        :raises OSError: if oldpath is not found or newpath already exists
+        :raises ValueError: if oldpath/newpath is not a valid path
         """
         if not oldpath:
             raise ValueError(f'Source {oldpath} is not a valid path')
@@ -1371,13 +1371,9 @@ def rename(self, oldpath: TransportPath, newpath: TransportPath):
         if not self.isfile(oldpath):
             if not self.isdir(oldpath):
                 raise OSError(f'Source {oldpath} does not exist')
-        # TODO: this seems to be a bug (?)
-        # why to raise an OSError if the newpath does not exist?
-        # ofcourse newpath shouldn't exist, that's why we are renaming it!
-        # issue opened here: https://github.com/aiidateam/aiida-core/issues/6725
-        if not self.isfile(newpath):
-            if not self.isdir(newpath):
-                raise OSError(f'Destination {newpath} does not exist')
+
+        if self.path_exists(newpath):
+            raise OSError(f'Destination {newpath} already exist')
 
         return self.sftp.rename(oldpath, newpath)
 

tests/transports/test_all_plugins.py

@@ -1232,3 +1232,28 @@ def test_asynchronous_execution(custom_transport, tmp_path):
             except ProcessLookupError:
                 # If the process is already dead (or has never run), I just ignore the error
                 pass
+
+
+def test_rename(custom_transport, tmp_path_remote):
+    """Test the rename function of the transport plugin."""
+    with custom_transport as transport:
+        old_file = tmp_path_remote / 'oldfile.txt'
+        new_file = tmp_path_remote / 'newfile.txt'
+        another_file = tmp_path_remote / 'anotherfile.txt'
+
+        # Create a test file to rename
+        old_file.touch()
+        another_file.touch()
+        assert old_file.exists()
+        assert another_file.exists()
+
+        # Perform rename operation
+        transport.rename(old_file, new_file)
+
+        # Verify rename was successful
+        assert not old_file.exists()
+        assert new_file.exists()
+
+        # Perform rename operation if new file already exists
+        with pytest.raises(OSError, match='already exist|destination exists'):
+            transport.rename(new_file, another_file)