Merge branch 'develop' into 'master'

Current state of `develop` is `v2.0.0b1` that is about to be released.
The `master` branch has been `v1.6.x` up to this point, which will now
become a support branch and `master` will become `v2.x`.

.docker/opt/configure-aiida.sh

@@ -8,9 +8,6 @@ set -x
 # Environment.
 export SHELL=/bin/bash
 
-# Update the list of installed aiida plugins.
-reentry scan
-
 # Setup AiiDA autocompletion.
 grep _VERDI_COMPLETE /home/${SYSTEM_USER}/.bashrc &> /dev/null || echo 'eval "$(_VERDI_COMPLETE=source verdi)"' >> /home/${SYSTEM_USER}/.bashrc
 
@@ -36,17 +33,35 @@ if [[ ${NEED_SETUP_PROFILE} == true ]]; then
 
     # Setup and configure local computer.
     computer_name=localhost
+
+    # Determine the number of physical cores as a default for the number of
+    # available MPI ranks on the localhost. We do not count "logical" cores,
+    # since MPI parallelization over hyper-threaded cores is typically
+    # associated with a significant performance penalty. We use the
+    # `psutil.cpu_count(logical=False)` function as opposed to simply
+    # `os.cpu_count()` since the latter would include hyperthreaded (logical
+    # cores).
+    NUM_PHYSICAL_CORES=$(python -c 'import psutil; print(int(psutil.cpu_count(logical=False)))' 2>/dev/null)
+    LOCALHOST_MPI_PROCS_PER_MACHINE=${LOCALHOST_MPI_PROCS_PER_MACHINE:-${NUM_PHYSICAL_CORES}}
+
+    if [ -z $LOCALHOST_MPI_PROCS_PER_MACHINE ]; then
+      echo "Unable to automatically determine the number of logical CPUs on this "
+      echo "machine. Please set the LOCALHOST_MPI_PROCS_PER_MACHINE variable to "
+      echo "explicitly set the number of available MPI ranks."
+      exit 1
+    fi
+
     verdi computer show ${computer_name} || verdi computer setup   \
         --non-interactive                                          \
         --label "${computer_name}"                                 \
         --description "this computer"                              \
         --hostname "${computer_name}"                              \
-        --transport local                                          \
-        --scheduler direct                                         \
+        --transport core.local                                          \
+        --scheduler core.direct                                    \
         --work-dir /home/aiida/aiida_run/                          \
         --mpirun-command "mpirun -np {tot_num_mpiprocs}"           \
-        --mpiprocs-per-machine 1 &&                                \
-    verdi computer configure local "${computer_name}"              \
+        --mpiprocs-per-machine ${LOCALHOST_MPI_PROCS_PER_MACHINE} && \
+    verdi computer configure core.local "${computer_name}"              \
         --non-interactive                                          \
         --safe-interval 0.0
 fi
@@ -59,7 +74,7 @@ verdi profile show || echo "The default profile is not set."
 verdi daemon stop
 
 # Migration will run for the default profile.
-verdi database migrate --force || echo "Database migration failed."
+verdi storage migrate --force || echo "Database migration failed."
 
 # Daemon will start only if the database exists and is migrated to the latest version.
 verdi daemon start || echo "AiiDA daemon is not running."

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,7 @@
 contact_links:
+  - name: AiiDA Discussions
+    url: https://github.com/aiidateam/aiida-core/discussions
+    about: For aiida-core questions and discussion
   - name: AiiDA Users Forum
     url: http://www.aiida.net/mailing-list/
     about: For general questions and discussion

.github/config/add.yaml

@@ -1,7 +1,7 @@
 ---
 label: add
 description: add
-input_plugin: arithmetic.add
+input_plugin: core.arithmetic.add
 on_computer: true
 computer: localhost
 remote_abs_path: /bin/bash

.github/config/doubler.yaml

@@ -1,7 +1,7 @@
 ---
 label: doubler
 description: doubler
-input_plugin: templatereplacer
+input_plugin: core.templatereplacer
 on_computer: true
 computer: localhost
 remote_abs_path: PLACEHOLDER_REMOTE_ABS_PATH_DOUBLER

.github/config/localhost.yaml

@@ -2,8 +2,8 @@
 label: localhost
 description: localhost
 hostname: localhost
-transport: local
-scheduler: direct
+transport: core.local
+scheduler: core.direct
 shebang: '#!/usr/bin/env bash'
 work_dir: PLACEHOLDER_WORK_DIR
 mpirun_command: ' '

.github/config/profile.yaml

@@ -1,14 +1,14 @@
 ---
-profile: PLACEHOLDER_PROFILE
+profile: test_aiida
 email: aiida@localhost
 first_name: Giuseppe
 last_name: Verdi
 institution: Khedivial
-db_backend: PLACEHOLDER_BACKEND
+db_backend: psql_dos
 db_engine: postgresql_psycopg2
 db_host: localhost
 db_port: 5432
-db_name: PLACEHOLDER_DATABASE_NAME
+db_name: test_aiida
 db_username: postgres
 db_password: ''
 broker_protocol: amqp
@@ -17,4 +17,5 @@ broker_password: guest
 broker_host: 127.0.0.1
 broker_port: 5672
 broker_virtual_host: ''
-repository: PLACEHOLDER_REPOSITORY
+repository: /tmp/test_repository_test_aiida/
+test_profile: true

.github/config/slurm-ssh.yaml

@@ -2,8 +2,8 @@
 label: slurm-ssh
 description: slurm container
 hostname: localhost
-transport: ssh
-scheduler: slurm
+transport: core.ssh
+scheduler: core.slurm
 shebang: "#!/bin/bash"
 work_dir: /home/{username}/workdir
 mpirun_command: "mpirun -np {tot_num_mpiprocs}"

.github/system_tests/pytest/test_memory_leaks.py

@@ -8,13 +8,13 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Utilities for testing memory leakage."""
-from tests.utils import processes as test_processes  # pylint: disable=no-name-in-module,import-error
-from tests.utils.memory import get_instances  # pylint: disable=no-name-in-module,import-error
+from aiida import orm
 from aiida.engine import processes, run_get_node
 from aiida.plugins import CalculationFactory
-from aiida import orm
+from tests.utils import processes as test_processes  # pylint: disable=no-name-in-module,import-error
+from tests.utils.memory import get_instances  # pylint: disable=no-name-in-module,import-error
 
-ArithmeticAddCalculation = CalculationFactory('arithmetic.add')
+ArithmeticAddCalculation = CalculationFactory('core.arithmetic.add')
 
 
 def run_finished_ok(*args, **kwargs):
@@ -36,7 +36,7 @@ def test_leak_run_process():
 
 def test_leak_local_calcjob(aiida_local_code_factory):
     """Test whether running a local CalcJob leaks memory."""
-    inputs = {'x': orm.Int(1), 'y': orm.Int(2), 'code': aiida_local_code_factory('arithmetic.add', '/bin/bash')}
+    inputs = {'x': orm.Int(1), 'y': orm.Int(2), 'code': aiida_local_code_factory('core.arithmetic.add', '/bin/bash')}
     run_finished_ok(ArithmeticAddCalculation, **inputs)
 
     # check that no reference to the process is left in memory
@@ -51,7 +51,7 @@ def test_leak_ssh_calcjob():
     Note: This relies on the 'slurm-ssh' computer being set up.
     """
     code = orm.Code(
-        input_plugin_name='arithmetic.add', remote_computer_exec=[orm.load_computer('slurm-ssh'), '/bin/bash']
+        input_plugin_name='core.arithmetic.add', remote_computer_exec=[orm.load_computer('slurm-ssh'), '/bin/bash']
     )
     inputs = {'x': orm.Int(1), 'y': orm.Int(2), 'code': code}
     run_finished_ok(ArithmeticAddCalculation, **inputs)

.github/system_tests/pytest/test_pytest_fixtures.py

@@ -23,5 +23,5 @@ def test_aiida_localhost(aiida_localhost):
 def test_aiida_local_code(aiida_local_code_factory):
     """Test aiida_local_code_factory fixture.
     """
-    code = aiida_local_code_factory(entry_point='templatereplacer', executable='diff')
+    code = aiida_local_code_factory(entry_point='core.templatereplacer', executable='diff')
     assert code.computer.label == 'localhost-test'

.github/system_tests/test_daemon.py

@@ -16,20 +16,28 @@
 import tempfile
 import time
 
-from aiida.common import exceptions, StashMode
+from workchains import (
+    ArithmeticAddBaseWorkChain,
+    CalcFunctionRunnerWorkChain,
+    DynamicDbInput,
+    DynamicMixedInput,
+    DynamicNonDbInput,
+    ListEcho,
+    NestedInputNamespace,
+    NestedWorkChain,
+    SerializeWorkChain,
+    WorkFunctionRunnerWorkChain,
+)
+
+from aiida.common import StashMode, exceptions
 from aiida.engine import run, submit
 from aiida.engine.daemon.client import get_daemon_client
 from aiida.engine.persistence import ObjectLoader
-from aiida.manage.caching import enable_caching
 from aiida.engine.processes import Process
-from aiida.orm import CalcJobNode, load_node, Int, Str, List, Dict, load_code
+from aiida.manage.caching import enable_caching
+from aiida.orm import CalcJobNode, Dict, Int, List, Str, load_code, load_node
 from aiida.plugins import CalculationFactory, WorkflowFactory
-from aiida.workflows.arithmetic.add_multiply import add_multiply, add
-from workchains import (
-    NestedWorkChain, DynamicNonDbInput, DynamicDbInput, DynamicMixedInput, ListEcho, CalcFunctionRunnerWorkChain,
-    WorkFunctionRunnerWorkChain, NestedInputNamespace, SerializeWorkChain, ArithmeticAddBaseWorkChain
-)
-
+from aiida.workflows.arithmetic.add_multiply import add, add_multiply
 from tests.utils.memory import get_instances  # pylint: disable=import-error
 
 CODENAME_ADD = 'add@localhost'
@@ -276,7 +284,7 @@ def create_calculation_process(code, inputval):
     """
     Create the process and inputs for a submitting / running a calculation.
     """
-    TemplatereplacerCalculation = CalculationFactory('templatereplacer')
+    TemplatereplacerCalculation = CalculationFactory('core.templatereplacer')
     parameters = Dict(dict={'value': inputval})
     template = Dict(
         dict={
@@ -299,7 +307,7 @@ def create_calculation_process(code, inputval):
         },
         'max_wallclock_seconds': 5 * 60,
         'withmpi': False,
-        'parser_name': 'templatereplacer.doubler',
+        'parser_name': 'core.templatereplacer.doubler',
     }
 
     expected_result = {'value': 2 * inputval, 'retrieved_temporary_files': {'triple_value.tmp': str(inputval * 3)}}
@@ -317,7 +325,7 @@ def create_calculation_process(code, inputval):
 
 def run_arithmetic_add():
     """Run the `ArithmeticAddCalculation`."""
-    ArithmeticAddCalculation = CalculationFactory('arithmetic.add')
+    ArithmeticAddCalculation = CalculationFactory('core.arithmetic.add')
 
     code = load_code(CODENAME_ADD)
     inputs = {
@@ -377,7 +385,7 @@ def run_base_restart_workchain():
 
 def run_multiply_add_workchain():
     """Run the `MultiplyAddWorkChain`."""
-    MultiplyAddWorkChain = WorkflowFactory('arithmetic.multiply_add')
+    MultiplyAddWorkChain = WorkflowFactory('core.arithmetic.multiply_add')
 
     code = load_code(CODENAME_ADD)
     inputs = {
@@ -523,7 +531,7 @@ def relaunch_cached(results):
     """Launch the same calculations but with caching enabled -- these should be FINISHED immediately."""
     code_doubler = load_code(CODENAME_DOUBLER)
     cached_calcs = []
-    with enable_caching(identifier='aiida.calculations:templatereplacer'):
+    with enable_caching(identifier='aiida.calculations:core.templatereplacer'):
         for counter in range(1, NUMBER_CALCULATIONS + 1):
             inputval = counter
             calc, expected_result = run_calculation(code=code_doubler, counter=counter, inputval=inputval)

.github/system_tests/test_ipython_magics.py

@@ -9,6 +9,7 @@
 ###########################################################################
 """Test the AiiDA iPython magics."""
 from IPython.testing.globalipapp import get_ipython
+
 from aiida.tools.ipython.ipython_magics import register_ipython_extension