Merge remote-tracking branch 'origin/main' into server_remove_hdf

.ci_support/environment-docs.yml

@@ -22,4 +22,4 @@ dependencies:
 - pytables =3.9.2
 - sqlalchemy =2.0.28
 - tqdm =4.66.2
-- traitlets =5.14.1
+- traitlets =5.14.2

.ci_support/environment.yml

@@ -21,4 +21,4 @@ dependencies:
 - pytables =3.9.2
 - sqlalchemy =2.0.28
 - tqdm =4.66.2
-- traitlets =5.14.1
+- traitlets =5.14.2

pyiron_base/database/generic.py

@@ -739,7 +739,7 @@ def _item_update(self, par_dict, item_id):
         else:
             raise PermissionError("Not avilable in viewer mode.")
 
-    def delete_item(self, item_id):
+    def delete_item(self, item_id: int):
         """
         Delete Item from database
 
@@ -749,18 +749,21 @@ def delete_item(self, item_id):
         Returns:
 
         """
-        if not self._view_mode:
-            self.conn.execute(
-                self.simulation_table.delete().where(
-                    self.simulation_table.c["id"] == int(item_id)
-                )
-            )
-            self.conn.commit()
-            if not self._keep_connection:
-                self.conn.close()
-        else:
+        if self._view_mode:
             raise PermissionError("Not avilable in viewer mode.")
 
+        res = self.conn.execute(
+            self.simulation_table.delete().where(
+                self.simulation_table.c["id"] == int(item_id)
+            )
+        )
+        if res.rowcount == 0:
+            raise RuntimeError(f"Failed to delete job ({item_id}) from database!")
+        self.conn.commit()
+
+        if not self._keep_connection:
+            self.conn.close()
+
     # IsDatabase impl'
     def _get_jobs(self, sql_query, user, project_path, recursive=True, columns=None):
         df = self.job_table(

pyiron_base/jobs/datamining.py

@@ -792,12 +792,13 @@ def update_table(self, job_status_list=None):
             if self._executor_type is None and self.server.cores > 1:
                 self._executor_type = "pympipool.mpi.executor.PyMPIExecutor"
             if self._executor_type is not None:
-                self._pyiron_table.create_table(
-                    file=hdf5_input,
-                    job_status_list=job_status_list,
-                    enforce_update=self._enforce_update,
-                    executor=self._get_executor(max_workers=self.server.cores),
-                )
+                with self._get_executor(max_workers=self.server.cores) as exe:
+                    self._pyiron_table.create_table(
+                        file=hdf5_input,
+                        job_status_list=job_status_list,
+                        enforce_update=self._enforce_update,
+                        executor=exe,
+                    )
             else:
                 self._pyiron_table.create_table(
                     file=hdf5_input,

pyiron_base/jobs/flex/pythonfunctioncontainer.py

@@ -102,9 +102,8 @@ def run_static(self):
         ):
             input_dict = self.input.to_builtin()
             del input_dict["executor"]
-            output = self._function(
-                **input_dict, executor=self._get_executor(max_workers=self.server.cores)
-            )
+            with self._get_executor(max_workers=self.server.cores) as exe:
+                output = self._function(**input_dict, executor=exe)
         else:
             output = self._function(**self.input.to_builtin())
         self.output.update({"result": output})

pyiron_base/jobs/job/generic.py

@@ -9,6 +9,7 @@
 from datetime import datetime
 from inspect import isclass
 import os
+import platform
 import posixpath
 import warnings
 
@@ -1534,6 +1535,14 @@ def _get_executor(self, max_workers=None):
             raise ValueError(
                 "No executor type defined - Please set self.executor_type."
             )
+        elif (
+            self._executor_type == "pympipool.mpi.executor.PyMPIExecutor"
+            and platform.system() == "Darwin"
+        ):
+            # The Mac firewall might prevent connections based on the network address - especially Github CI
+            return import_class(self._executor_type)(
+                max_workers=max_workers, hostname_localhost=True
+            )
         elif isinstance(self._executor_type, str):
             return import_class(self._executor_type)(max_workers=max_workers)
         else:

pyiron_base/project/generic.py

@@ -1782,7 +1782,7 @@ def _remove_jobs_helper(self, recursive=False, progress=True):
                 self.remove_job(job_specifier=job_id)
                 state.logger.debug("Remove job with ID {0} ".format(job_id))
             except (IndexError, Exception):
-                state.logger.debug("Could not remove job with ID {0} ".format(job_id))
+                state.logger.warning("Could not remove job with ID {0} ".format(job_id))
 
     def _remove_files(self, pattern="*"):
         """

pyproject.toml

@@ -40,7 +40,7 @@ dependencies = [
     "sqlalchemy==2.0.28",
     "tables==3.9.2",
     "tqdm==4.66.2",
-    "traitlets==5.14.1",
+    "traitlets==5.14.2",
 ]
 dynamic = ["version"]
 

tests/database/test_database_access.py

@@ -191,7 +191,10 @@ def test_delete_item(self):
         self.database.delete_item(key)
         self.assertRaises(
             Exception, self.database.delete_item, [key]
-        )  # use only str or int
+        )  # call function with unsupported list as argument
+        self.assertRaises(
+            RuntimeError, self.database.delete_item, 123456789
+        )  # remove non existent job id
         # self.assertRaises(Exception, self.database.get_item_by_id, key)  # ensure item does not exist anymore
 
     def test_get_item_by_id(self):