Dependencies: update requirement aiida-core~=2.0

Adds compatibility with AiiDA v2.0. Notable changes:

* Entry points are now loaded through built-in modules instead of the
  custom `reentry`, so `reentry scan` no longer needs to be called.
* Tab-completion now ships with `click` itself, so `click_completion`
  and its manual activiation is removed.
* Update entry points from `aiida-core` by prefixing with `core.`

Also enable the `AIIDA_WARN_v3` environment variable in the `tests` job
of the CI workflow. This will print deprecation warnings from
`aiida-core`. These are also addressed in this commit:

* `Entity.objects` -> `Entity.collection`
* `Node.get_attribute` -> `Node.base.attributes.get`
* `Node.set_attribute` -> `Node.base.attributes.set`
* `Node.get_extra` -> `Node.base.extras.get`
* `Node.set_extra` -> `Node.base.extras.set`
* `Node.get_object_content` -> `Node.base.repository.get_object_content`
* `Node.add_incoming` -> `Node.base.links.add_incoming`

Due to the updated requirements of `click`, the `sphinx-click`
dependency of the `docs` extra also had to be upgraded because the lower
versions had an upper limit on `click`.

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: continuous-integration
+name: ci
 
 on: [push, pull_request]
 
@@ -11,8 +11,7 @@ jobs:
         steps:
         -   uses: actions/checkout@v2
 
-        -   name: Cache python dependencies
-            id: cache-pip
+        -   name: Cache Python dependencies
             uses: actions/cache@v1
             with:
                 path: ~/.cache/pip
@@ -25,13 +24,11 @@ jobs:
             with:
                 python-version: '3.9'
 
-        -   name: Install python dependencies
-            run:
-                pip install -e .[pre-commit,tests]
+        -   name: Install Python dependencies
+            run: pip install -e .[pre-commit,tests]
 
         -   name: Run pre-commit
-            run:
-                pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+            run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
     tests:
 
@@ -43,6 +40,8 @@ jobs:
                 python-version: ['3.8', '3.9', '3.10']
 
         services:
+            postgres:
+                image: postgres:12
             rabbitmq:
                 image: rabbitmq:latest
                 ports:
@@ -51,8 +50,7 @@ jobs:
         steps:
         -   uses: actions/checkout@v2
 
-        -   name: Cache python dependencies
-            id: cache-pip
+        -   name: Cache Python dependencies
             uses: actions/cache@v1
             with:
                 path: ~/.cache/pip
@@ -65,17 +63,10 @@ jobs:
             with:
                 python-version: ${{ matrix.python-version }}
 
-        -   name: Install system dependencies
-            run: |
-                sudo apt update
-                sudo apt install postgresql
-
-        -   name: Install python dependencies
-            run: |
-                pip install --upgrade setuptools
-                pip install -e .[tests]
-                reentry scan
+        -   name: Install Python dependencies
+            run: pip install -e .[tests]
 
         -   name: Run pytest
-            run:
-                pytest -sv tests
+            env:
+                AIIDA_WARN_v3: True
+            run: pytest -sv tests

aiida_pseudo/cli/__init__.py

@@ -1,11 +1,5 @@
 # -*- coding: utf-8 -*-
-# pylint: disable=wrong-import-position,wildcard-import
 """Module for the command line interface."""
-import click_completion
-
-# Activate the completion of parameter types provided by the click_completion package
-click_completion.init()
-
 from .family import cmd_family
 from .install import cmd_install, cmd_install_family, cmd_install_pseudo_dojo, cmd_install_sssp
 from .list import cmd_list

aiida_pseudo/cli/install.py

@@ -244,7 +244,7 @@ def cmd_install_sssp(version, functional, protocol, download_only, traceback):
 
         for element, values in metadata.items():
             if family.get_pseudo(element).md5 != values['md5']:
-                Group.objects.delete(family.pk)
+                Group.collection.delete(family.pk)
                 msg = f"md5 of pseudo for element {element} does not match that of the metadata {values['md5']}"
                 echo.echo_critical(msg)
 
@@ -345,7 +345,7 @@ def cmd_install_pseudo_dojo(
 
         for element, md5 in md5s.items():
             if family.get_pseudo(element).md5 != md5:
-                Group.objects.delete(family.pk)
+                Group.collection.delete(family.pk)
                 msg = f'md5 of pseudo for element {element} does not match that of the metadata {md5}'
                 echo.echo_critical(msg)
 

aiida_pseudo/cli/list.py

@@ -39,7 +39,7 @@ def cmd_list(project, raw, family_type):
     }
 
     if get_families_builder().count() == 0:
-        echo.echo_info('no pseudo potential families have been installed yet: use `aiida-pseudo install`.')
+        echo.echo_report('no pseudo potential families have been installed yet: use `aiida-pseudo install`.')
         return
 
     rows = []
@@ -61,7 +61,7 @@ def cmd_list(project, raw, family_type):
         rows.append(row)
 
     if not rows:
-        echo.echo_info('no pseudo potential families found that match the filtering criteria.')
+        echo.echo_report('no pseudo potential families found that match the filtering criteria.')
         return
 
     if raw:

aiida_pseudo/cli/params/arguments.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 """Reusable arguments for CLI commands."""
-from aiida.cmdline.params.arguments import OverridableArgument
+from aiida.cmdline.params.arguments.overridable import OverridableArgument
 
 from .types import PseudoPotentialFamilyParam
 

aiida_pseudo/cli/root.py

@@ -4,7 +4,43 @@
 import click
 
 
+class VerbosityGroup(click.Group):
+    """Custom command group that automatically adds the ``VERBOSITY`` option to all subcommands."""
+
+    @staticmethod
+    def add_verbosity_option(cmd):
+        """Apply the ``verbosity`` option to the command, which is common to all ``verdi`` commands."""
+        if 'verbosity' not in [param.name for param in cmd.params]:
+            cmd = options.VERBOSITY()(cmd)
+
+        return cmd
+
+    def group(self, *args, **kwargs):
+        """Ensure that sub command groups use the same class but do not override an explicitly set value."""
+        kwargs.setdefault('cls', self.__class__)
+        return super().group(*args, **kwargs)
+
+    def get_command(self, ctx, cmd_name):
+        """Return the command that corresponds to the requested ``cmd_name``.
+
+        This method is overridden from the base class in order to automatically add the verbosity option.
+
+        Note that if the command is not found and ``resilient_parsing`` is set to True on the context, then the latter
+        feature is disabled because most likely we are operating in tab-completion mode.
+        """
+        cmd = super().get_command(ctx, cmd_name)
+
+        if cmd is not None:
+            return self.add_verbosity_option(cmd)
+
+        if ctx.resilient_parsing:
+            return None
+
+        return ctx.fail(f'`{cmd_name}` is not a {self.name} command.')
+
+
 @click.group('aiida-pseudo', context_settings={'help_option_names': ['-h', '--help']})
-@options.PROFILE(type=types.ProfileParamType(load_profile=True))
-def cmd_root(profile):  # pylint: disable=unused-argument
+@options.PROFILE(type=types.ProfileParamType(load_profile=True), expose_value=False)
+@options.VERBOSITY()
+def cmd_root():
     """CLI for the ``aiida-pseudo`` plugin."""

aiida_pseudo/cli/utils.py

@@ -18,18 +18,18 @@ def attempt(message, exception_types=Exception, include_traceback=False):
     import sys
     import traceback
 
-    echo.echo_info(message, nl=False)
+    echo.echo_report(message, nl=False)
 
     try:
         yield
     except exception_types as exception:  # pylint: disable=broad-except
-        echo.echo_highlight(' [FAILED]', color='error', bold=True)
+        echo.echo(' [FAILED]', fg='red', bold=True)
         message = str(exception)
         if include_traceback:
             message += f"\n{''.join(traceback.format_exception(*sys.exc_info()))}"
         echo.echo_critical(message)
     else:
-        echo.echo_highlight(' [OK]', color='success', bold=True)
+        echo.echo(' [OK]', fg='green', bold=True)
 
 
 def create_family_from_archive(cls, label, filepath_archive: Path, fmt=None, pseudo_type=None):

aiida_pseudo/data/pseudo/pseudo.py

@@ -12,7 +12,7 @@
 __all__ = ('PseudoPotentialData',)
 
 
-class PseudoPotentialData(plugins.DataFactory('singlefile')):
+class PseudoPotentialData(plugins.DataFactory('core.singlefile')):
     """Base class for data types representing pseudo potentials."""
 
     _key_element = 'element'
@@ -34,11 +34,9 @@ def get_or_create(cls, source: typing.Union[str, pathlib.Path, typing.BinaryIO],
         query = orm.QueryBuilder()
         query.append(cls, subclassing=False, filters={f'attributes.{cls._key_md5}': md5_from_filelike(source)})
 
-        existing = query.first()
+        pseudo = query.first(flat=True)
 
-        if existing:
-            pseudo = existing[0]  # pylint: disable=unsubscriptable-object
-        else:
+        if not pseudo:
             source.seek(0)
             pseudo = cls(source, filename)
 
@@ -155,7 +153,7 @@ def element(self) -> typing.Optional[int]:
 
         :return: the symbol of the element following the IUPAC naming standard or None if not defined.
         """
-        return self.get_attribute(self._key_element, None)
+        return self.base.attributes.get(self._key_element, None)
 
     @element.setter
     def element(self, value: str):
@@ -165,15 +163,15 @@ def element(self, value: str):
         :raises ValueError: if the element symbol is invalid.
         """
         self.validate_element(value)
-        self.set_attribute(self._key_element, value)
+        self.base.attributes.set(self._key_element, value)
 
     @property
     def md5(self) -> typing.Optional[int]:
         """Return the md5.
 
         :return: the md5 of the stored file.
         """
-        return self.get_attribute(self._key_md5, None)
+        return self.base.attributes.get(self._key_md5, None)
 
     @md5.setter
     def md5(self, value: str):
@@ -183,4 +181,4 @@ def md5(self, value: str):
         :raises ValueError: if the md5 does not match that of the currently stored file.
         """
         self.validate_md5(value)
-        self.set_attribute(self._key_md5, value)
+        self.base.attributes.set(self._key_md5, value)

aiida_pseudo/data/pseudo/upf.py

@@ -95,7 +95,7 @@ def z_valence(self) -> typing.Optional[int]:
 
         :return: the Z valence.
         """
-        return self.get_attribute(self._key_z_valence, None)
+        return self.base.attributes.get(self._key_z_valence, None)
 
     @z_valence.setter
     def z_valence(self, value: int):
@@ -107,4 +107,4 @@ def z_valence(self, value: int):
         if not isinstance(value, int) or value < 0:
             raise ValueError(f'`{value}` is not a positive integer')
 
-        self.set_attribute(self._key_z_valence, value)
+        self.base.attributes.set(self._key_z_valence, value)

aiida_pseudo/data/pseudo/vps.py

@@ -135,7 +135,7 @@ def z_valence(self) -> typing.Optional[int]:
 
         :return: the Z valence.
         """
-        return self.get_attribute(self._key_z_valence, None)
+        return self.base.attributes.get(self._key_z_valence, None)
 
     @z_valence.setter
     def z_valence(self, value: int):
@@ -147,15 +147,15 @@ def z_valence(self, value: int):
         if not isinstance(value, int) or value < 0:
             raise ValueError(f'`{value}` is not a positive integer.')
 
-        self.set_attribute(self._key_z_valence, value)
+        self.base.attributes.set(self._key_z_valence, value)
 
     @property
     def xc_type(self) -> typing.Optional[int]:
         """Return the exchange-correlation type.
 
         :return: the exchange-correlation type.
         """
-        return self.get_attribute(self._key_xc_type, None)
+        return self.base.attributes.get(self._key_xc_type, None)
 
     @xc_type.setter
     def xc_type(self, value: str):
@@ -167,4 +167,4 @@ def xc_type(self, value: str):
         if not isinstance(value, str) or value not in VALID_XC_TYPES:
             raise ValueError(f'`{value}` is not a valid OpenMX XcType string.')
 
-        self.set_attribute(self._key_xc_type, value)
+        self.base.attributes.set(self._key_xc_type, value)

aiida_pseudo/groups/family/pseudo.py

@@ -13,7 +13,7 @@
 
 __all__ = ('PseudoPotentialFamily',)
 
-StructureData = DataFactory('structure')
+StructureData = DataFactory('core.structure')
 
 
 class PseudoPotentialFamily(Group):
@@ -172,7 +172,7 @@ def create_from_folder(cls, dirpath, label, *, description='', pseudo_type=None,
         """
         type_check(description, str, allow_none=True)
 
-        if cls.objects.count(filters={'label': label}):
+        if cls.collection.count(filters={'label': label}):
             raise ValueError(f'the {cls.__name__} `{label}` already exists')
 
         family = cls(label=label, description=description)
@@ -191,7 +191,7 @@ def pseudo_type(self):
 
         :return: the pseudopotential type or ``None`` if none has been set yet.
         """
-        return self.get_extra(self._key_pseudo_type, None)
+        return self.base.extras.get(self._key_pseudo_type, None)
 
     def update_pseudo_type(self):
         """Update the pseudo type, stored as an extra, based on the current nodes in the family."""
@@ -203,7 +203,7 @@ def update_pseudo_type(self):
         else:
             entry_point_name = None
 
-        self.set_extra(self._key_pseudo_type, entry_point_name)
+        self.base.extras.set(self._key_pseudo_type, entry_point_name)
 
     def add_nodes(self, nodes):
         """Add a node or a set of nodes to the family.