More deprecated APIs

aiidalab · Nov 20, 2022 · b8c50d8 · b8c50d8
1 parent 4e6df77
commit b8c50d8
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Showing 6 changed files with 49 additions and 37 deletions.
diff --git a/aiidalab_qe/process.py b/aiidalab_qe/process.py
@@ -4,8 +4,8 @@
 
 import ipywidgets as ipw
 import traitlets
-from aiida.cmdline.utils.query.calculation import CalculationQueryBuilder
 from aiida.orm import load_node
+from aiida.tools.query.calculation import CalculationQueryBuilder
 
 
 class WorkChainSelector(ipw.HBox):

diff --git a/aiidalab_qe/report.py b/aiidalab_qe/report.py
@@ -1,3 +1,4 @@
+from aiida.orm import WorkChainNode
 from aiida.plugins import WorkflowFactory
 
 PwBaseWorkChain = WorkflowFactory("quantumespresso.pw.base")
@@ -25,8 +26,8 @@
 }
 
 
-def _generate_report_dict(qeapp_wc):
-    builder_parameters = qeapp_wc.get_extra("builder_parameters", {})
+def _generate_report_dict(qeapp_wc: WorkChainNode):
+    builder_parameters = qeapp_wc.base.extras.get("builder_parameters", {})
 
     # Properties
     run_relax = builder_parameters.get("relax_type") != "none"

diff --git a/aiidalab_qe/setup_codes.py b/aiidalab_qe/setup_codes.py
@@ -7,7 +7,7 @@
 import ipywidgets as ipw
 import traitlets
 from aiida.common.exceptions import NotExistent
-from aiida.orm import InstalledCode, load_code, load_computer
+from aiida.orm import load_code
 from filelock import FileLock, Timeout
 
 from aiidalab_qe.widgets import ProgressBar
@@ -67,18 +67,29 @@ def _setup_code(code_name, computer_name="localhost"):
     try:
         load_code(f"{code_name}-{QE_VERSION}@localhost")
     except NotExistent:
-        localhost = load_computer(computer_name)
-        code = InstalledCode(
-            computer=localhost,
-            filepath_executable=CONDA_ENV_PREFIX.joinpath(
-                "bin", f"{code_name}.x"
-            ).as_posix(),
-            default_calc_job_plugin=f"quantumespresso.{code_name}",
-            prepend_text=f'eval "$(conda shell.posix hook)"\nconda activate {CONDA_ENV_PREFIX}\nexport OMP_NUM_THREADS=1',
+        run(
+            [
+                "verdi",
+                "code",
+                "create",
+                "core.code.installed",
+                "--non-interactive",
+                "--label",
+                f"{code_name}-{QE_VERSION}",
+                "--description",
+                f"{code_name}.x ({QE_VERSION}) setup by AiiDAlab.",
+                "--default-calc-job-plugin",
+                f"quantumespresso.{code_name}",
+                "--computer",
+                computer_name,
+                "--prepend-text",
+                f'eval "$(conda shell.posix hook)"\nconda activate {CONDA_ENV_PREFIX}\nexport OMP_NUM_THREADS=1',
+                "--filepath-executable",
+                CONDA_ENV_PREFIX.joinpath("bin", f"{code_name}.x"),
+            ],
+            check=True,
+            capture_output=True,
         )
-        code.label = f"{code_name}-{QE_VERSION}"
-        code.description = f"{code_name}.x ({QE_VERSION} setup by AiiDAlab)"
-        code.store()
     else:
         raise RuntimeError(f"Code {code_name} (v{QE_VERSION}) is already setup!")
 

diff --git a/aiidalab_qe/steps.py b/aiidalab_qe/steps.py
@@ -34,10 +34,10 @@
 )
 from aiidalab_qe_workchain import QeAppWorkChain
 
-StructureData = DataFactory("structure")
-Float = DataFactory("float")
-Dict = DataFactory("dict")
-Str = DataFactory("str")
+StructureData = DataFactory("core.structure")
+Float = DataFactory("core.float")
+Dict = DataFactory("core.dict")
+Str = DataFactory("core.str")
 
 
 class WorkChainSettings(ipw.VBox):
@@ -768,7 +768,9 @@ def _observe_process(self, change):
             process_node = change["new"]
             if process_node is not None:
                 self.input_structure = process_node.inputs.structure
-                builder_parameters = process_node.get_extra("builder_parameters", None)
+                builder_parameters = process_node.base.extras.get(
+                    "builder_parameters", None
+                )
                 if builder_parameters is not None:
                     self.set_selected_codes(builder_parameters)
             self._update_state()
@@ -895,7 +897,7 @@ def update_builder(buildy, resources, npools):
         with self.hold_trait_notifications():
             self.process = submit(builder)
             # Set the builder parameters on the work chain
-            self.process.set_extra("builder_parameters", parameters)
+            self.process.base.extras.set("builder_parameters", parameters)
 
     def reset(self):
         with self.hold_trait_notifications():

diff --git a/aiidalab_qe/widgets.py b/aiidalab_qe/widgets.py
@@ -295,15 +295,15 @@ def _fetch_output(self, calcjob):
         assert isinstance(calcjob, CalcJobNode)
         if "retrieved" in calcjob.outputs:
             try:
-                self.filename = calcjob.attributes["output_filename"]
+                self.filename = calcjob.base.attributes.get("output_filename")
                 with calcjob.outputs.retrieved.open(self.filename) as f:
                     return f.read().splitlines()
             except OSError:
                 return list()
 
         elif "remote_folder" in calcjob.outputs:
             try:
-                fn_out = calcjob.attributes["output_filename"]
+                fn_out = calcjob.base.attributes.get("output_filename")
                 self.filename = fn_out
                 with NamedTemporaryFile() as tmpfile:
                     calcjob.outputs.remote_folder.getfile(fn_out, tmpfile.name)

diff --git a/qe.ipynb b/qe.ipynb
@@ -73,7 +73,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f17c6bb582de487ea6f9196a1b315165",
+       "model_id": "3dd5155dd0b74226be9eeddecf4621ed",
        "version_major": 2,
        "version_minor": 0
       },
@@ -86,24 +86,22 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/opt/conda/lib/python3.9/site-packages/aiida/cmdline/utils/query/calculation.py:15: AiidaDeprecationWarning: This module is deprecated, use `aiida.tools.query.calculation` instead. (this will be removed in v3)\n",
-      "  warn_deprecation('This module is deprecated, use `aiida.tools.query.calculation` instead.', version=3)\n",
-      "/opt/conda/lib/python3.9/site-packages/aiida/cmdline/utils/query/formatting.py:15: AiidaDeprecationWarning: This module is deprecated, use `aiida.tools.query.formatting` instead. (this will be removed in v3)\n",
-      "  warn_deprecation('This module is deprecated, use `aiida.tools.query.formatting` instead.', version=3)\n",
-      "/opt/conda/lib/python3.9/site-packages/aiida/plugins/entry_point.py:310: AiidaDeprecationWarning: The entry point `structure` is deprecated. Please replace it with `core.structure`. (this will be removed in v3)\n",
-      "  warn_deprecation(\n",
-      "/opt/conda/lib/python3.9/site-packages/aiida/plugins/entry_point.py:310: AiidaDeprecationWarning: The entry point `float` is deprecated. Please replace it with `core.float`. (this will be removed in v3)\n",
-      "  warn_deprecation(\n",
-      "/opt/conda/lib/python3.9/site-packages/aiida/plugins/entry_point.py:310: AiidaDeprecationWarning: The entry point `dict` is deprecated. Please replace it with `core.dict`. (this will be removed in v3)\n",
-      "  warn_deprecation(\n",
-      "/opt/conda/lib/python3.9/site-packages/aiida/plugins/entry_point.py:310: AiidaDeprecationWarning: The entry point `str` is deprecated. Please replace it with `core.str`. (this will be removed in v3)\n",
-      "  warn_deprecation(\n"
+      "/opt/conda/lib/python3.9/site-packages/aiida/orm/nodes/data/code/legacy.py:121: AiidaDeprecationWarning: This property is deprecated, use the `Code.is_hidden` property instead. (this will be removed in v3)\n",
+      "  warn_deprecation('This property is deprecated, use the `Code.is_hidden` property instead.', version=3)\n",
+      "/opt/conda/lib/python3.9/site-packages/aiida/orm/nodes/data/code/legacy.py:121: AiidaDeprecationWarning: This property is deprecated, use the `Code.is_hidden` property instead. (this will be removed in v3)\n",
+      "  warn_deprecation('This property is deprecated, use the `Code.is_hidden` property instead.', version=3)\n",
+      "/opt/conda/lib/python3.9/site-packages/aiida/orm/nodes/data/code/legacy.py:121: AiidaDeprecationWarning: This property is deprecated, use the `Code.is_hidden` property instead. (this will be removed in v3)\n",
+      "  warn_deprecation('This property is deprecated, use the `Code.is_hidden` property instead.', version=3)\n",
+      "/opt/conda/lib/python3.9/site-packages/aiida/orm/nodes/data/code/legacy.py:121: AiidaDeprecationWarning: This property is deprecated, use the `Code.is_hidden` property instead. (this will be removed in v3)\n",
+      "  warn_deprecation('This property is deprecated, use the `Code.is_hidden` property instead.', version=3)\n",
+      "/opt/conda/lib/python3.9/site-packages/aiida/orm/nodes/data/code/legacy.py:121: AiidaDeprecationWarning: This property is deprecated, use the `Code.is_hidden` property instead. (this will be removed in v3)\n",
+      "  warn_deprecation('This property is deprecated, use the `Code.is_hidden` property instead.', version=3)\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ce3c3a2503cb4e359ff3e3b255a1db7b",
+       "model_id": "02aea8ac0d0f47e6b997d54f41a9ecf6",
        "version_major": 2,
        "version_minor": 0
       },