Tranport/core.openssh

.github/workflows/ci-code.yml

@@ -70,6 +70,9 @@ jobs:
     - name: Setup environment
       run: .github/workflows/setup.sh
 
+    - name: Setup upterm session
+      uses: lhotari/action-upterm@v1
+
     - name: Run test suite
       env:
         AIIDA_TEST_PROFILE: test_aiida
@@ -107,6 +110,9 @@ jobs:
     - name: Setup SSH on localhost
       run: .github/workflows/setup_ssh.sh
 
+    - name: Setup upterm session
+      uses: lhotari/action-upterm@v1
+
     - name: Run test suite
       env:
         AIIDA_WARN_v3: 0
@@ -133,3 +139,55 @@ jobs:
         verdi devel check-load-time
         verdi devel check-undesired-imports
         .github/workflows/verdi.sh
+
+
+  test-pytest-fixtures:
+    # Who watches the watchmen?
+    # Here we test the pytest fixtures in isolation from the rest of aiida-core test suite,
+    # since they can be used outside of aiida core context, e.g. in plugins.
+    # Unlike in other workflows in this file, we purposefully don't setup a test profile.
+
+    runs-on: ubuntu-24.04
+    timeout-minutes: 10
+
+    services:
+      postgres:
+        image: postgres:10
+        env:
+          POSTGRES_DB: test_aiida
+          POSTGRES_PASSWORD: ''
+          POSTGRES_HOST_AUTH_METHOD: trust
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+        - 5432:5432
+      rabbitmq:
+        image: rabbitmq:3.8.14-management
+        ports:
+        - 5672:5672
+        - 15672:15672
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install aiida-core
+      uses: ./.github/actions/install-aiida-core
+      with:
+        python-version: '3.9'
+        from-lock: 'true'
+        extras: tests
+
+    - name: Test legacy pytest fixtures
+      run: pytest --cov aiida --noconftest src/aiida/manage/tests/test_pytest_fixtures.py
+
+    - name: Upload coverage report
+      if: github.repository == 'aiidateam/aiida-core'
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        name: test-pytest-fixtures
+        files: ./coverage.xml
+        fail_ci_if_error: false  # don't fail job, if coverage upload fails

src/aiida/cmdline/commands/cmd_process.py

@@ -25,6 +25,16 @@
     verdi daemon start
 """
 
+ACTION_TIMEOUT = OverridableOption(
+    '-t',
+    '--timeout',
+    type=click.FloatRange(0, float('inf')),
+    default=float('inf'),
+    show_default=True,
+    help='Time in seconds to wait for a response before timing out. '
+    'If timeout is 0 the command does not wait for response.',
+)
+
 
 def valid_projections():
     """Return list of valid projections for the ``--project`` option of ``verdi process list``.
@@ -320,15 +330,7 @@ def process_status(call_link_label, most_recent_node, max_depth, processes):
 @verdi_process.command('kill')
 @arguments.PROCESSES()
 @options.ALL(help='Kill all processes if no specific processes are specified.')
-@OverridableOption(
-    '-t',
-    '--timeout',
-    type=click.FLOAT,
-    default=5.0,
-    show_default=True,
-    help='Time in seconds to wait for a response of the kill task before timing out.',
-)()
-@options.WAIT()
+@ACTION_TIMEOUT()
 @OverridableOption(
     '-F',
     '--force',
@@ -338,7 +340,7 @@ def process_status(call_link_label, most_recent_node, max_depth, processes):
     'Note: This may lead to orphaned jobs on your HPC and should be used with caution.',
 )()
 @decorators.with_dbenv()
-def process_kill(processes, all_entries, timeout, wait, force):
+def process_kill(processes, all_entries, timeout, force):
     """Kill running processes.
 
     Kill one or multiple running processes."""
@@ -368,7 +370,6 @@ def process_kill(processes, all_entries, timeout, wait, force):
                 force=force,
                 all_entries=all_entries,
                 timeout=timeout,
-                wait=wait,
             )
         except control.ProcessTimeoutException as exception:
             echo.echo_critical(f'{exception}\n{REPAIR_INSTRUCTIONS}')
@@ -380,10 +381,9 @@ def process_kill(processes, all_entries, timeout, wait, force):
 @verdi_process.command('pause')
 @arguments.PROCESSES()
 @options.ALL(help='Pause all active processes if no specific processes are specified.')
-@options.TIMEOUT()
-@options.WAIT()
+@ACTION_TIMEOUT()
 @decorators.with_dbenv()
-def process_pause(processes, all_entries, timeout, wait):
+def process_pause(processes, all_entries, timeout):
     """Pause running processes.
 
     Pause one or multiple running processes."""
@@ -404,7 +404,6 @@ def process_pause(processes, all_entries, timeout, wait):
                 msg_text='Paused through `verdi process pause`',
                 all_entries=all_entries,
                 timeout=timeout,
-                wait=wait,
             )
         except control.ProcessTimeoutException as exception:
             echo.echo_critical(f'{exception}\n{REPAIR_INSTRUCTIONS}')
@@ -416,10 +415,9 @@ def process_pause(processes, all_entries, timeout, wait):
 @verdi_process.command('play')
 @arguments.PROCESSES()
 @options.ALL(help='Play all paused processes if no specific processes are specified.')
-@options.TIMEOUT()
-@options.WAIT()
+@ACTION_TIMEOUT()
 @decorators.with_dbenv()
-def process_play(processes, all_entries, timeout, wait):
+def process_play(processes, all_entries, timeout):
     """Play (unpause) paused processes.
 
     Play (unpause) one or multiple paused processes."""
@@ -435,7 +433,7 @@ def process_play(processes, all_entries, timeout, wait):
 
     with capture_logging() as stream:
         try:
-            control.play_processes(processes, all_entries=all_entries, timeout=timeout, wait=wait)
+            control.play_processes(processes, all_entries=all_entries, timeout=timeout)
         except control.ProcessTimeoutException as exception:
             echo.echo_critical(f'{exception}\n{REPAIR_INSTRUCTIONS}')
 

src/aiida/cmdline/params/options/main.py

@@ -125,7 +125,6 @@
     'USER_LAST_NAME',
     'VERBOSITY',
     'VISUALIZATION_FORMAT',
-    'WAIT',
     'WITH_ELEMENTS',
     'WITH_ELEMENTS_EXCLUSIVE',
     'active_process_states',
@@ -690,12 +689,6 @@ def set_log_level(ctx, _param, value):
     help='Time in seconds to wait for a response before timing out.',
 )
 
-WAIT = OverridableOption(
-    '--wait/--no-wait',
-    default=False,
-    help='Wait for the action to be completed otherwise return as soon as it is scheduled.',
-)
-
 FORMULA_MODE = OverridableOption(
     '-f',
     '--formula-mode',

src/aiida/engine/daemon/execmanager.py

@@ -34,6 +34,7 @@
 from aiida.orm.utils.log import get_dblogger_extra
 from aiida.repository.common import FileType
 from aiida.schedulers.datastructures import JobState
+from aiida.transports import has_magic
 
 if TYPE_CHECKING:
     from aiida.transports import Transport
@@ -465,7 +466,7 @@ async def stash_calculation(calculation: CalcJobNode, transport: Transport) -> N
         target_basepath = target_base / uuid[:2] / uuid[2:4] / uuid[4:]
 
         for source_filename in source_list:
-            if transport.has_magic(source_filename):
+            if has_magic(source_filename):
                 copy_instructions = []
                 for globbed_filename in await transport.glob_async(source_basepath / source_filename):
                     target_filepath = target_basepath / Path(globbed_filename).relative_to(source_basepath)
@@ -679,7 +680,7 @@ async def retrieve_files_from_list(
         if isinstance(item, (list, tuple)):
             tmp_rname, tmp_lname, depth = item
             # if there are more than one file I do something differently
-            if transport.has_magic(tmp_rname):
+            if has_magic(tmp_rname):
                 remote_names = await transport.glob_async(workdir.joinpath(tmp_rname))
                 local_names = []
                 for rem in remote_names:
@@ -702,7 +703,7 @@ async def retrieve_files_from_list(
         else:
             abs_item = item if item.startswith('/') else str(workdir.joinpath(item))
 
-            if transport.has_magic(abs_item):
+            if has_magic(abs_item):
                 remote_names = await transport.glob_async(abs_item)
                 local_names = [os.path.split(rem)[1] for rem in remote_names]
             else: