Devops: Address deprecation warnings from internal code and dependencies

docs/source/topics/processes/functions.rst

@@ -345,7 +345,7 @@ They can be accessed through the corresponding properties on the process node as
     :code: python
 
 The source code of the file in which the function is defined is also stored, but since it can be quite big, it is stored as a raw file in the repository of the process node.
-It can be retrieved through the :py:meth:`~aiida.orm.utils.mixins.FunctionCalculationMixin.get_function_source_code` method.
+It can be retrieved through the :py:meth:`~aiida.orm.utils.mixins.FunctionCalculationMixin.get_source_code_file` method.
 
 The attributes give some querability to the process functions stored in the provenance graph and by storing the source code of the function that was executed, there will be some reference in the future to track how the function created its output nodes.
 Note, however, that just storing the source file of the function does not guarantee that one can reproduce the exact result.

pyproject.toml

@@ -218,7 +218,7 @@ rest = [
   'flask-cors~=3.0',
   'flask-restful~=0.3.7',
   'flask~=2.2',
-  'pyparsing~=2.4',
+  'pyparsing~=3.0',
   'python-memcached~=1.59',
   'seekpath~=1.9,>=1.9.3'
 ]
@@ -233,12 +233,12 @@ tests = [
   'pytest~=7.0',
   'pytest-asyncio~=0.12,<0.17',
   'pytest-timeout~=2.0',
-  'pytest-cov~=2.7,<2.11',
+  'pytest-cov~=4.1',
   'pytest-rerunfailures~=12.0',
   'pytest-benchmark~=4.0',
   'pytest-regressions~=2.2',
-  'pympler~=0.9',
-  'coverage~=6.0',
+  'pympler~=1.0',
+  'coverage~=7.0',
   'sphinx~=7.2',
   'docutils~=0.20'
 ]
@@ -356,8 +356,11 @@ filterwarnings = [
   'ignore::DeprecationWarning:pymatgen:',
   'ignore::DeprecationWarning:jsonbackend:',
   'ignore::DeprecationWarning:pkg_resources:',
-  'ignore:Object of type .* not in session, .* operation along .* will not proceed:sqlalchemy.exc.SAWarning',
   'ignore::pytest.PytestCollectionWarning',
+  'ignore:Creating AiiDA configuration folder.*:UserWarning',
+  'ignore:Object of type .* not in session, .* operation along .* will not proceed:sqlalchemy.exc.SAWarning',
+  'ignore:The `aiida.orm.nodes.data.upf` module is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
+  'ignore:The `Code` class is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
   'default::ResourceWarning'
 ]
 markers = [

requirements/requirements-py-3.10.txt

@@ -34,7 +34,7 @@ click==8.1.3
 click-spinner==0.1.10
 comm==0.1.3
 contourpy==1.1.0
-coverage==6.5.0
+coverage==7.4.1
 cryptography==41.0.1
 cycler==0.11.0
 debugpy==1.6.7
@@ -136,15 +136,15 @@ pydantic==2.4.0
 pydata-sphinx-theme==0.13.3
 pygments==2.15.1
 pymatgen==2023.9.25
-pympler==0.9
+pympler==1.0.1
 pymysql==0.9.3
 pynacl==1.5.0
-pyparsing==2.4.7
+pyparsing==3.1.1
 pyrsistent==0.19.3
 pytest==7.3.2
 pytest-asyncio==0.16.0
 pytest-benchmark==4.0.0
-pytest-cov==2.10.1
+pytest-cov==4.1.0
 pytest-datadir==1.4.1
 pytest-regressions==2.4.2
 pytest-rerunfailures==12.0.0

requirements/requirements-py-3.11.txt

@@ -34,7 +34,7 @@ click==8.1.3
 click-spinner==0.1.10
 comm==0.1.3
 contourpy==1.1.0
-coverage==6.5.0
+coverage==7.4.1
 cryptography==41.0.1
 cycler==0.11.0
 debugpy==1.6.7
@@ -135,15 +135,15 @@ pydantic==2.4.0
 pydata-sphinx-theme==0.13.3
 pygments==2.15.1
 pymatgen==2023.9.25
-pympler==0.9
+pympler==1.0.1
 pymysql==0.9.3
 pynacl==1.5.0
-pyparsing==2.4.7
+pyparsing==3.1.1
 pyrsistent==0.19.3
 pytest==7.3.2
 pytest-asyncio==0.16.0
 pytest-benchmark==4.0.0
-pytest-cov==2.10.1
+pytest-cov==4.1.0
 pytest-datadir==1.4.1
 pytest-regressions==2.4.2
 pytest-rerunfailures==12.0.0

requirements/requirements-py-3.12.txt

@@ -34,7 +34,7 @@ click==8.1.7
 click-spinner==0.1.10
 comm==0.1.4
 contourpy==1.1.1
-coverage==6.5.0
+coverage==7.4.1
 cryptography==41.0.5
 cycler==0.12.1
 debugpy==1.8.0
@@ -133,15 +133,15 @@ pydantic==2.4.0
 pydata-sphinx-theme==0.13.3
 pygments==2.16.1
 pymatgen==2023.10.11
-pympler==0.9
+pympler==1.0.1
 pymysql==0.9.3
 pynacl==1.5.0
-pyparsing==2.4.7
+pyparsing==3.1.1
 pyrsistent==0.19.3
 pytest==7.4.2
 pytest-asyncio==0.16.0
 pytest-benchmark==4.0.0
-pytest-cov==2.10.1
+pytest-cov==4.1.0
 pytest-datadir==1.5.0
 pytest-regressions==2.5.0
 pytest-rerunfailures==12.0.0

requirements/requirements-py-3.9.txt

@@ -34,7 +34,7 @@ click==8.1.3
 click-spinner==0.1.10
 comm==0.1.3
 contourpy==1.1.0
-coverage==6.5.0
+coverage==7.4.1
 cryptography==41.0.1
 cycler==0.11.0
 debugpy==1.6.7
@@ -138,15 +138,15 @@ pydantic==2.4.0
 pydata-sphinx-theme==0.13.3
 pygments==2.15.1
 pymatgen==2023.9.25
-pympler==0.9
+pympler==1.0.1
 pymysql==0.9.3
 pynacl==1.5.0
-pyparsing==2.4.7
+pyparsing==3.1.1
 pyrsistent==0.19.3
 pytest==7.3.2
 pytest-asyncio==0.16.0
 pytest-benchmark==4.0.0
-pytest-cov==2.10.1
+pytest-cov==4.1.0
 pytest-datadir==1.4.1
 pytest-regressions==2.4.2
 pytest-rerunfailures==12.0.0

src/aiida/engine/processes/calcjobs/calcjob.py

@@ -548,7 +548,7 @@ def run(self) -> Union[plumpy.process_states.Stop, int, plumpy.process_states.Wa
             # this case, the parser will not be called. The outputs will already have been added to the process node
             # though, so all that needs to be done here is just also assign them to the process instance. This such that
             # when the process returns its results, it returns the actual outputs and not an empty dictionary.
-            self._outputs = self.node.get_outgoing(link_type=LinkType.CREATE).nested()
+            self._outputs = self.node.base.links.get_outgoing(link_type=LinkType.CREATE).nested()
             return self.node.exit_status
 
         # Launch the upload operation

src/aiida/engine/runners.py

@@ -162,6 +162,8 @@ def close(self) -> None:
         """Close the runner by stopping the loop."""
         assert not self._closed
         self.stop()
+        if not self._loop.is_running():
+            self._loop.close()
         reset_event_loop_policy()
         self._closed = True
 

src/aiida/orm/nodes/data/code/legacy.py

@@ -169,10 +169,7 @@ def get_description(self):
 
         :return: string description of this Code instance
         """
-        warn_deprecation(
-            '`Code.get_description` method is deprecated, use the `description` property instead.', version=3
-        )
-        return f'{self.description}'
+        return self.full_label
 
     @classmethod
     def get_code_helper(cls, label, machinename=None, backend=None):

src/aiida/storage/sqlite_zip/migrations/utils.py

@@ -143,13 +143,14 @@ def copy_tar_to_zip(
         temp_extracted = Path(tmpdirname) / 'extracted'
         with get_progress_reporter()(total=1) as progress:
             callback = create_callback(progress)
-            TarPath(inpath, mode='r:*').extract_tree(
-                temp_extracted,
-                allow_dev=False,
-                allow_symlink=False,
-                callback=callback,
-                cb_descript=f'{title} (extracting tar)',
-            )
+            with TarPath(inpath, mode='r:*') as path:
+                path.extract_tree(
+                    temp_extracted,
+                    allow_dev=False,
+                    allow_symlink=False,
+                    callback=callback,
+                    cb_descript=f'{title} (extracting tar)',
+                )
         temp_archive = Path(tmpdirname) / 'archive.zip'
         with ZipPath(temp_archive, mode='w', compresslevel=compression, info_order=info_order) as new_path:
             length = sum(1 for _ in temp_extracted.glob('**/*'))

src/aiida/transports/util.py

@@ -64,6 +64,14 @@ def close(self):
                     break
                 time.sleep(0.2)
 
+        for f in [self.process.stdout, self.process.stderr, self.process.stdin]:
+            if f is None:
+                continue
+            try:
+                f.close()
+            except ValueError:
+                pass
+
 
 def copy_from_remote_to_remote(transportsource, transportdestination, remotesource, remotedestination, **kwargs):
     """Copy files or folders from a remote computer to another remote computer.

tests/cmdline/commands/test_node.py

@@ -11,6 +11,7 @@
 import gzip
 import io
 import os
+import warnings
 
 import pytest
 from aiida import orm
@@ -401,11 +402,13 @@ def test_node_id_label_format(self, run_cli_command):
     @pytest.mark.parametrize('output_file', ('without_extension', 'without_extension.pdf'))
     def test_output_file(self, run_cli_command, output_file):
         """Test that the output file can be specified through an argument."""
-        try:
-            run_cli_command(cmd_node.graph_generate, [str(self.node.pk), output_file])
-            assert os.path.isfile(output_file)
-        finally:
-            delete_temporary_file(output_file)
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore')
+            try:
+                run_cli_command(cmd_node.graph_generate, [str(self.node.pk), output_file])
+                assert os.path.isfile(output_file)
+            finally:
+                delete_temporary_file(output_file)
 
 
 COMMENT = 'Well I never...'

tests/cmdline/params/options/test_config.py

@@ -8,7 +8,6 @@
 ###########################################################################
 """Unit tests for the :class:`aiida.cmdline.params.options.config.ConfigOption`."""
 import functools
-import tempfile
 import textwrap
 
 import click
@@ -32,37 +31,40 @@ def cmd(integer, boolean):
     click.echo(f'Boolean: {boolean}')
 
 
-def test_valid(run_cli_command):
+def test_valid(run_cli_command, tmp_path):
     """Test the option for a valid configuration file."""
-    with tempfile.NamedTemporaryFile('w+') as handle:
-        handle.write(
-            textwrap.dedent(
-                """
+    filepath = tmp_path / 'config.yml'
+    filepath.write_text(
+        textwrap.dedent(
+            """
             integer: 1
             boolean: false
-        """
-            )
+            """
         )
-        handle.flush()
+    )
 
-        result = run_cli_command(cmd, ['--config', handle.name])
-        assert 'Integer: 1' in result.output_lines[0]
-        assert 'Boolean: False' in result.output_lines[1]
+    result = run_cli_command(cmd, ['--config', str(filepath)])
+    assert 'Integer: 1' in result.output_lines[0]
+    assert 'Boolean: False' in result.output_lines[1]
 
 
-def test_invalid_unknown_keys(run_cli_command):
-    """Test the option for an invalid configuration file containing unknown keys."""
-    with tempfile.NamedTemporaryFile('w+') as handle:
-        handle.write(
-            textwrap.dedent(
-                """
+@pytest.mark.filterwarnings('ignore')
+def test_invalid_unknown_keys(run_cli_command, tmp_path):
+    """Test the option for an invalid configuration file containing unknown keys.
+
+    The test emits a ``ResourceWarning`` because the config file is not closed since the command errors, but this is
+    just a side-effect of how the test is run and doesn't apply to the real CLI command invocation.
+    """
+    filepath = tmp_path / 'config.yml'
+    filepath.write_text(
+        textwrap.dedent(
+            """
             integer: 1
             unknown: 2.0
-        """
-            )
+            """
         )
-        handle.flush()
+    )
 
-        result = run_cli_command(cmd, ['--config', handle.name], raises=True)
-        assert "Error: Invalid value for '--config': Invalid configuration file" in result.stderr
-        assert "the following keys are not supported: {'unknown'}" in result.stderr
+    result = run_cli_command(cmd, ['--config', str(filepath)], raises=True)
+    assert "Error: Invalid value for '--config': Invalid configuration file" in result.stderr
+    assert "the following keys are not supported: {'unknown'}" in result.stderr

tests/cmdline/params/options/test_interactive.py

@@ -295,7 +295,6 @@ def test_default_value_prompt(run_cli_command):
     returns.append(result)
     expected = 'Opt [default]: TEST\nTEST\n'
     assert expected in result.output
-    return returns
 
 
 def test_default_value_empty_opt(run_cli_command):

tests/engine/processes/calcjobs/test_calc_job.py

@@ -507,7 +507,7 @@ def test_get_hash(self, get_calcjob_builder):
         """Test that :meth:`aiida.orm.CalcJobNode.get_hash` returns the same hash as what is stored in the extras."""
         builder = get_calcjob_builder()
         _, node = launch.run_get_node(builder)
-        assert node.base.extras.get(node.base.caching._HASH_EXTRA_KEY) == node.get_hash()
+        assert node.base.extras.get(node.base.caching._HASH_EXTRA_KEY) == node.base.caching.get_hash()
 
     def test_process_status(self):
         """Test that the process status is properly reset if calculation ends successfully."""

tests/engine/processes/workchains/test_restart.py

@@ -7,6 +7,8 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Tests for `aiida.engine.processes.workchains.restart` module."""
+import warnings
+
 import pytest
 from aiida import engine, orm
 from aiida.engine.processes.workchains.awaitable import Awaitable
@@ -66,7 +68,9 @@ def test_get_process_handlers():
 )
 def test_get_process_handlers_by_priority(generate_work_chain, inputs, priorities):
     """Test the `BaseRestartWorkChain.get_process_handlers_by_priority` method."""
-    process = generate_work_chain(SomeWorkChain, inputs)
+    with warnings.catch_warnings():
+        warnings.simplefilter('ignore')
+        process = generate_work_chain(SomeWorkChain, inputs)
     process.setup()
     assert sorted([priority for priority, handler in process.get_process_handlers_by_priority()]) == priorities
 

tests/engine/test_calcfunctions.py

@@ -109,7 +109,7 @@ def test_calcfunction_caching_change_code(self):
             result_cached, cached = add_calcfunction.run_get_node(self.default_int)
             assert result_original != result_cached
             assert not cached.base.caching.is_created_from_cache
-            assert cached.is_valid_cache
+            assert cached.base.caching.is_valid_cache
 
             # Test that the locally-created calcfunction can be cached in principle
             result2_cached, cached2 = add_calcfunction.run_get_node(self.default_int)

tests/engine/test_process.py

@@ -477,7 +477,7 @@ def define(cls, spec):
         spec.input('any_type', required=False)
 
 
-@pytest.mark.usefixtures('clear_database_before_test')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_not_required_accepts_none():
     """Test that a port that is not required, accepts ``None``."""
     from aiida.engine.utils import instantiate_process