DevOps: Add AIIDA_WARN_V3 environment variable to CI (#836)

This will enable deprecation warnings so that they can easily be
addressed in the code. All deprecated code has been replaced.

.github/workflows/ci.yml

@@ -66,4 +66,6 @@ jobs:
  run: pip install -e .[tests]
 
  - name: Run pytest
+ env:
+ AIIDA_WARN_v3: 1
  run: pytest -sv tests

.github/workflows/nightly.yml

@@ -54,6 +54,8 @@ jobs:
 
  - name: Run pytest
  id: tests
+ env:
+ AIIDA_WARN_v3: 1
  run: pytest -sv tests
 
  - name: Slack notification

src/aiida_quantumespresso/calculations/__init__.py

@@ -576,7 +576,7 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
  try:
  structure_parameters = get_parameters_from_cell(
  ibrav=ibrav,
- cell=structure.get_attribute('cell'),
+ cell=structure.base.attributes.get('cell'),
  tolerance=settings.pop('IBRAV_CELL_TOLERANCE', 1e-6)
  )
  except ValueError as exc:

src/aiida_quantumespresso/calculations/ph.py

@@ -103,7 +103,7 @@ def prepare_for_submission(self, folder):
  settings = {}
 
  parent_folder = self.inputs.parent_folder
- parent_calcs = parent_folder.get_incoming(node_class=orm.CalcJobNode).all()
+ parent_calcs = parent_folder.base.links.get_incoming(node_class=orm.CalcJobNode).all()
 
  if not parent_calcs:
  raise exceptions.NotExistent(f'parent_folder<{parent_folder.pk}> has no parent calculation')

src/aiida_quantumespresso/calculations/pwimmigrant.py

@@ -301,7 +301,7 @@ class or using the ``set_`` methods (e.g. ``set_remote_workdir``).
  if settings_dict:
  self.use_settings(Dict(settings_dict))
 
- self.set_attribute('input_nodes_created', True)
+ self.base.attributes.set('input_nodes_created', True)
 
  def _prepare_for_retrieval(self, open_transport):
  """Prepare the calculation for retrieval by daemon.
@@ -322,8 +322,8 @@ def _prepare_for_retrieval(self, open_transport):
  # Manually set the files that will be copied to the repository and that
  # the parser will extract the results from. This would normally be
  # performed in self._prepare_for_submission prior to submission.
- self.set_attribute('retrieve_list', [self._OUTPUT_FILE_NAME] + self.xml_filenames)
- self.set_attribute('retrieve_singlefile_list', [])
+ self.base.attributes.set('retrieve_list', [self._OUTPUT_FILE_NAME] + self.xml_filenames)
+ self.base.attributes.set('retrieve_singlefile_list', [])
 
  # Make sure the calculation and input links are stored.
  self.store_all()
@@ -403,7 +403,7 @@ def set_remote_workdir(self, remote_workdir):
  """
  # This is the functionality as self._set_remote_workir, but it bypasses
  # the need to have the calculation state set as SUBMITTING.
- self.set_attribute('remote_workdir', remote_workdir)
+ self.base.attributes.set('remote_workdir', remote_workdir)
 
  def set_output_subfolder(self, output_subfolder):
  """Manually set the job's ``outdir`` variable (e.g. ``'./out/'``).
@@ -469,28 +469,28 @@ def _OUTPUT_SUBFOLDER(self):
 
  @_OUTPUT_SUBFOLDER.setter
  def _OUTPUT_SUBFOLDER(self, value):
- self.set_attribute('output_subfolder', value)
+ self.base.attributes.set('output_subfolder', value)
 
  @property
  def _PREFIX(self):
  return self.get_attr('prefix', None)
 
  @_PREFIX.setter
  def _PREFIX(self, value):
- self.set_attribute('prefix', value)
+ self.base.attributes.set('prefix', value)
 
  @property
  def _INPUT_FILE_NAME(self):
  return self.get_attr('input_file_name', None)
 
  @_INPUT_FILE_NAME.setter
  def _INPUT_FILE_NAME(self, value):
- self.set_attribute('input_file_name', value)
+ self.base.attributes.set('input_file_name', value)
 
  @property
  def _OUTPUT_FILE_NAME(self):
  return self.get_attr('output_file_name', None)
 
  @_OUTPUT_FILE_NAME.setter
  def _OUTPUT_FILE_NAME(self, value):
- self.set_attribute('output_file_name', value)
+ self.base.attributes.set('output_file_name', value)

src/aiida_quantumespresso/calculations/xspectra.py

@@ -8,7 +8,7 @@
 
 from aiida_quantumespresso.calculations.namelists import NamelistsCalculation
 
-KpointsData = DataFactory('array.kpoints')
+KpointsData = DataFactory('core.array.kpoints')
 
 
 class XspectraCalculation(NamelistsCalculation):

src/aiida_quantumespresso/cli/calculations/dos.py

@@ -32,7 +32,8 @@ def launch_calculation(code, calculation, max_num_machines, max_wallclock_second
  raise click.BadParameter(
  f'input calculation node has process_type: {calculation.process_type}; should be {expected_process_type}'
  )
- parent_folder = calculation.get_outgoing(node_class=RemoteData, link_label_filter='remote_folder').one().node
+ parent_folder = calculation.base.links.get_outgoing(node_class=RemoteData,
+ link_label_filter='remote_folder').one().node
 
  inputs = {
  'code': code,

src/aiida_quantumespresso/cli/calculations/epw.py

@@ -41,16 +41,18 @@ def launch_calculation(
  f'--pw-nscf-parent node has process_type: {pw_nscf_parent.process_type}; should be {expected_process_type}'
  )
 
- pw_nscf_parent_folder = pw_nscf_parent.get_outgoing(node_class=orm.RemoteData,
- link_label_filter='remote_folder').one().node
+ pw_nscf_parent_folder = pw_nscf_parent.base.links.get_outgoing(
+ node_class=orm.RemoteData, link_label_filter='remote_folder'
+ ).one().node
 
  expected_process_type = 'aiida.calculations:quantumespresso.ph'
  if ph_parent.process_type != expected_process_type:
  raise click.BadParameter(
  f'--ph-parent has process_type: {ph_parent.process_type}; should be {expected_process_type}'
  )
 
- ph_parent_folder = ph_parent.get_outgoing(node_class=orm.RemoteData, link_label_filter='remote_folder').one().node
+ ph_parent_folder = ph_parent.base.links.get_outgoing(node_class=orm.RemoteData,
+ link_label_filter='remote_folder').one().node
 
  parameters = {
  'INPUTEPW': {

src/aiida_quantumespresso/cli/calculations/ph.py

@@ -34,7 +34,8 @@ def launch_calculation(code, kpoints_mesh, calculation, max_num_machines, max_wa
  f'input calculation node has process_type: {calculation.process_type}; should be {expected_process_type}'
  )
 
- parent_folder = calculation.get_outgoing(node_class=orm.RemoteData, link_label_filter='remote_folder').one().node
+ parent_folder = calculation.base.links.get_outgoing(node_class=orm.RemoteData,
+ link_label_filter='remote_folder').one().node
 
  inputs = {
  'code': code,

src/aiida_quantumespresso/cli/calculations/pp.py

@@ -33,7 +33,8 @@ def launch_calculation(code, calculation, max_num_machines, max_wallclock_second
  f'input calculation node has process_type: {calculation.process_type}; should be {expected_process_type}'
  )
 
- parent_folder = calculation.get_outgoing(node_class=orm.RemoteData, link_label_filter='remote_folder').one().node
+ parent_folder = calculation.base.links.get_outgoing(node_class=orm.RemoteData,
+ link_label_filter='remote_folder').one().node
 
  inputs = {
  'code': code,

src/aiida_quantumespresso/cli/calculations/projwfc.py

@@ -32,7 +32,8 @@ def launch_calculation(code, calculation, max_num_machines, max_wallclock_second
  raise click.BadParameter(
  f'input calculation node has process_type: {calculation.process_type}; should be {expected_process_type}'
  )
- parent_folder = calculation.get_outgoing(node_class=RemoteData, link_label_filter='remote_folder').one().node
+ parent_folder = calculation.base.links.get_outgoing(node_class=RemoteData,
+ link_label_filter='remote_folder').one().node
 
  inputs = {
  'code': code,

src/aiida_quantumespresso/cli/utils/display.py

@@ -13,7 +13,7 @@ def echo_process_results(node):
  from aiida.common.links import LinkType
 
  class_name = node.process_class.__name__
- outputs = node.get_outgoing(link_type=(LinkType.CREATE, LinkType.RETURN)).all()
+ outputs = node.base.links.get_outgoing(link_type=(LinkType.CREATE, LinkType.RETURN)).all()
 
  if hasattr(node, 'dry_run_info'):
  # It is a dry-run: get the information and print it

src/aiida_quantumespresso/data/force_constants.py

@@ -22,71 +22,71 @@ def set_file(self, file, filename=None, **kwargs):
 
  # Add all other attributes found in the parsed dictionary
  for key, value in dictionary.items():
- self.set_attribute(key, value)
+ self.base.attributes.set(key, value)
 
  @property
  def number_of_species(self):
  """Return the number of atom species.
 
  :return: a scalar
  """
- return self.get_attribute('number_of_species')
+ return self.base.attributes.get('number_of_species')
 
  @property
  def number_of_atoms(self):
  """Return the number of atoms.
 
  :return: a scalar
  """
- return self.get_attribute('number_of_atoms')
+ return self.base.attributes.get('number_of_atoms')
 
  @property
  def cell(self):
  """Return the crystal unit cell where rows are the crystal vectors.
 
  :return: a 3x3 numpy.array
  """
- return numpy.array(self.get_attribute('cell'))
+ return numpy.array(self.base.attributes.get('cell'))
 
  @property
  def atom_list(self):
  """Return the list of atoms.
 
  :return: a list of length-5 tuple (element name, element mass amu_ry, 3 coordinates in cartesian Angstrom)
  """
- return self.get_attribute('atom_list')
+ return self.base.attributes.get('atom_list')
 
  @property
  def has_done_electric_field(self):
  """Return flag to indicate if dielectric tensor and effective charges were computed.
 
  :return: a boolean
  """
- return self.get_attribute('has_done_electric_field')
+ return self.base.attributes.get('has_done_electric_field')
 
  @property
  def dielectric_tensor(self):
  """Return the dielectric tensor matrix.
 
  :return: a 3x3 tuple
  """
- return self.get_attribute('dielectric_tensor')
+ return self.base.attributes.get('dielectric_tensor')
 
  @property
  def effective_charges_eu(self):
  """Return the effective charges for each atom.
 
  :return: a list of number_of_atoms elements, each being a 3x3 tuple
  """
- return self.get_attribute('effective_charges_eu')
+ return self.base.attributes.get('effective_charges_eu')
 
  @property
  def qpoints_mesh(self):
  """Return the number of q-points in each direction.
 
  :return: a length-3 tuple
  """
- return tuple(self.get_attribute('qpoints_mesh'))
+ return tuple(self.base.attributes.get('qpoints_mesh'))
 
 
 def parse_q2r_force_constants_file(lines, also_force_constants=False):

src/aiida_quantumespresso/parsers/cp.py

@@ -19,10 +19,10 @@ def parse(self, **kwargs):
  retrieved = self.retrieved
 
  # check what is inside the folder
- list_of_files = retrieved.list_object_names()
+ list_of_files = retrieved.base.repository.list_object_names()
 
  # options.metadata become attributes like this:
- stdout_filename = self.node.get_attribute('output_filename')
+ stdout_filename = self.node.base.attributes.get('output_filename')
  # at least the stdout should exist
  if stdout_filename not in list_of_files:
  return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_READ)
@@ -63,9 +63,9 @@ def parse(self, **kwargs):
  self.logger.info('print counter in xml format')
  filename_counter = filename_counter_xml
 
- output_stdout = retrieved.get_object_content(stdout_filename)
- output_xml = retrieved.get_object_content(xml_files[0])
- output_xml_counter = None if no_trajectory_output else retrieved.get_object_content(filename_counter)
+ output_stdout = retrieved.base.repository.get_object_content(stdout_filename)
+ output_xml = retrieved.base.repository.get_object_content(xml_files[0])
+ output_xml_counter = None if no_trajectory_output else retrieved.base.repository.get_object_content(filename_counter)
  out_dict, _raw_successful = parse_cp_raw_output(
  output_stdout, output_xml, output_xml_counter, print_counter_xml
  )
@@ -115,7 +115,7 @@ def parse(self, **kwargs):
 
  for name, extension, scale, elements in trajectories:
  try:
- with retrieved.open(f'{self.node.process_class._PREFIX}.{extension}') as datafile:
+ with retrieved.base.repository.open(f'{self.node.process_class._PREFIX}.{extension}') as datafile:
  data = [l.split() for l in datafile]
  # POSITIONS stored in angstrom
  traj_data = parse_cp_traj_stanzas(
@@ -138,7 +138,7 @@ def parse(self, **kwargs):
 
  # =============== EVP trajectory ============================
  try:
- with retrieved.open(f'{self._node.process_class._PREFIX}.evp') as handle:
+ with retrieved.base.repository.open(f'{self._node.process_class._PREFIX}.evp') as handle:
  matrix = numpy.genfromtxt(handle)
  # there might be a different format if the matrix has one row only
  try:

src/aiida_quantumespresso/parsers/dos.py

@@ -21,7 +21,7 @@ def parse(self, **kwargs):
  # Read standard out
  try:
  filename_stdout = self.node.get_option('output_filename') # or get_attribute(), but this is clearer
- with retrieved.open(filename_stdout, 'r') as fil:
+ with retrieved.base.repository.open(filename_stdout, 'r') as fil:
  out_file = fil.readlines()
  except OSError:
  return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_READ)
@@ -37,7 +37,7 @@ def parse(self, **kwargs):
 
  # check that the dos file is present, if it is, read it
  try:
- with retrieved.open(self.node.process_class._DOS_FILENAME, 'r') as fil:
+ with retrieved.base.repository.open(self.node.process_class._DOS_FILENAME, 'r') as fil:
  dos_file = fil.readlines()
  except OSError:
  return self.exit(self.exit_codes.ERROR_READING_DOS_FILE)

src/aiida_quantumespresso/parsers/matdyn.py

@@ -16,13 +16,13 @@ def parse(self, **kwargs):
  filename_stdout = self.node.get_option('output_filename')
  filename_frequencies = MatdynCalculation._PHONON_FREQUENCIES_NAME
 
- if filename_stdout not in retrieved.list_object_names():
+ if filename_stdout not in retrieved.base.repository.list_object_names():
  return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_READ)
 
- if 'JOB DONE' not in retrieved.get_object_content(filename_stdout):
+ if 'JOB DONE' not in retrieved.base.repository.get_object_content(filename_stdout):
  return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE)
 
- if filename_frequencies not in retrieved.list_object_names():
+ if filename_frequencies not in retrieved.base.repository.list_object_names():
  return self.exit(self.exit_codes.ERROR_OUTPUT_STDOUT_READ)
 
  # Extract the kpoints from the input data and create the `KpointsData` for the `BandsData`
@@ -34,7 +34,7 @@ def parse(self, **kwargs):
  kpoints_for_bands = orm.KpointsData()
  kpoints_for_bands.set_kpoints(kpoints)
 
- parsed_data = parse_raw_matdyn_phonon_file(retrieved.get_object_content(filename_frequencies))
+ parsed_data = parse_raw_matdyn_phonon_file(retrieved.base.repository.get_object_content(filename_frequencies))
 
  try:
  num_kpoints = parsed_data.pop('num_kpoints')