Merge branch 'main' into dependabot/pip/monty-2025.1.9

.ci_support/environment-docs.yml

@@ -7,23 +7,23 @@ dependencies:
 - myst-parser
 - conda =24.7.1
 - conda_subprocess =0.0.5
-- cloudpickle =3.1.0
+- cloudpickle =3.1.1
 - gitpython =3.1.44
-- h5io_browser =0.1.5
+- h5io_browser =0.1.6
 - h5py =3.12.1
 - jinja2 =3.1.5
 - monty =2025.1.9
-- numpy =2.2.1
+- numpy =2.2.2
 - pandas =2.2.3
 - pint =0.24.4
 - psutil =6.1.1
-- pyfileindex =0.0.32
+- pyfileindex =0.0.33
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.4
-- executorlib =0.0.7
+- executorlib =0.0.8
 - pysqa =0.2.3
-- pytables =3.10.1
-- sqlalchemy =2.0.36
+- pytables =3.10.2
+- sqlalchemy =2.0.37
 - tqdm =4.67.1
 - traitlets =5.14.3
 - jupyter-book =1.0.0

.ci_support/environment-mini.yml

@@ -1,20 +1,20 @@
 channels:
 - conda-forge
 dependencies:
-- cloudpickle =3.1.0
-- h5io_browser =0.1.5
+- cloudpickle =3.1.1
+- h5io_browser =0.1.6
 - h5py =3.12.1
 - monty =2025.1.9
-- numpy =2.2.1
+- numpy =2.2.2
 - pandas =2.2.3
 - psutil =6.1.1
-- pyfileindex =0.0.32
+- pyfileindex =0.0.33
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.3
-- executorlib =0.0.7
+- executorlib =0.0.8
 - pysqa =0.2.3
-- pytables =3.10.1
-- sqlalchemy =2.0.36
+- pytables =3.10.2
+- sqlalchemy =2.0.37
 - tqdm =4.67.1
 - traitlets =5.14.3
 - setuptools

.ci_support/environment.yml

@@ -5,22 +5,22 @@ dependencies:
 - codacy-coverage
 - conda =24.7.1
 - conda_subprocess =0.0.5
-- cloudpickle =3.1.0
+- cloudpickle =3.1.1
 - gitpython =3.1.44
-- h5io_browser =0.1.5
+- h5io_browser =0.1.6
 - h5py =3.12.1
 - jinja2 =3.1.5
 - monty =2025.1.9
-- numpy =2.2.1
+- numpy =2.2.2
 - pandas =2.2.3
 - pint =0.24.4
 - psutil =6.1.1
-- pyfileindex =0.0.32
+- pyfileindex =0.0.33
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.4
-- executorlib =0.0.7
+- executorlib =0.0.8
 - pysqa =0.2.3
-- pytables =3.10.1
-- sqlalchemy =2.0.36
+- pytables =3.10.2
+- sqlalchemy =2.0.37
 - tqdm =4.67.1
 - traitlets =5.14.3

.github/workflows/unittests.yml

@@ -28,10 +28,6 @@ jobs:
         - operating-system: ubuntu-latest
           python-version: '3.11'
           label: linux-64-py-3-11
-
-        - operating-system: ubuntu-latest
-          python-version: '3.10'
-          label: linux-64-py-3-10
 
     steps:
     - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.2
     hooks:
       - id: ruff
         name: ruff lint

.readthedocs.yml

@@ -6,9 +6,9 @@
 version: 2
 
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
   jobs:
     pre_build:
       # Generate the Sphinx configuration for this Jupyter Book so it builds.
@@ -21,10 +21,11 @@ build:
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
+  configuration: docs/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: []
 
 # Install pyiron from conda
 conda:
-  environment: .ci_support/environment-docs.yml
+  environment: .ci_support/environment-docs.yml

binder/environment.yml

@@ -4,22 +4,22 @@ dependencies:
 - python
 - conda =24.7.1
 - conda_subprocess =0.0.5
-- cloudpickle =3.1.0
+- cloudpickle =3.1.1
 - gitpython =3.1.44
-- h5io_browser =0.1.5
+- h5io_browser =0.1.6
 - h5py =3.12.1
 - jinja2 =3.1.5
 - monty =2025.1.9
-- numpy =2.2.1
+- numpy =2.2.2
 - pandas =2.2.3
 - pint =0.24.4
 - psutil =6.1.1
-- pyfileindex =0.0.32
+- pyfileindex =0.0.33
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.4
-- executorlib =0.0.7
+- executorlib =0.0.8
 - pysqa =0.2.3
-- pytables =3.10.1
-- sqlalchemy =2.0.36
+- pytables =3.10.2
+- sqlalchemy =2.0.37
 - tqdm =4.67.1
 - traitlets =5.14.3

pyiron_base/cli/control.py

@@ -54,7 +54,7 @@ def main() -> None:
             mod.register(sub_parser)
         except AttributeError:
             warnings.warn(
-                "module '{}' does not define main or register " "function, ignoring"
+                "module '{}' does not define main or register function, ignoring"
             )
 
     args = parser.parse_args()

pyiron_base/database/filetable.py

@@ -280,7 +280,7 @@ def get_items_dict(
             return_all_columns (bool): return all columns or only the 'id' - still the format stays the same.
 
         Returns:
-            list: the function returns a list of dicts like get_items_sql, but it does not format datetime:
+            list: the function returns a list of dicts, but it does not format datetime:
                  [{'chemicalformula': u'Ni108',
                   'computer': u'mapc157',
                   'hamilton': u'LAMMPS',

pyiron_base/database/generic.py

@@ -281,7 +281,7 @@ def _job_dict(
             element_lst (list): list of elements required in the chemical formular - by default None
 
         Returns:
-            list: the function returns a list of dicts like get_items_sql, but it does not format datetime:
+            list: the function returns a list of dicts, but it does not format datetime:
                  [{'chemicalformula': u'Ni108',
                   'computer': u'mapc157',
                   'hamilton': u'LAMMPS',
@@ -312,10 +312,30 @@ def _job_dict(
                   'username': u'test'},.......]
 
         """
+        if not self._sql_lite:
+
+            def escape(s, escape_char="\\", special_chars="_%"):
+                """Insert escape_char in front of special_chars, unless present.
+
+                Handles the cases where s already contains escaped characters,
+                including the escape character itself.
+
+                Defaults for LIKE in SQL statements."""
+                for c in special_chars:
+                    if c in s:
+                        s = s.replace(escape_char + c, c)
+                    s = s.replace(c, escape_char + c)
+                return s
+
+        else:
+
+            def escape(s, escape_char="\\", special_chars="_%"):
+                return s
+
         dict_clause = {}
         # FOR GET_ITEMS_SQL: clause = []
         if user is not None:
-            dict_clause["username"] = str(user)
+            dict_clause["username"] = escape(str(user))
             # FOR GET_ITEMS_SQL: clause.append("username = '" + self.user + "'")
         if sql_query is not None:
             # FOR GET_ITEMS_SQL: clause.append(self.sql_query)
@@ -329,18 +349,18 @@ def _job_dict(
                 {str(element.split()[0]): element.split()[2] for element in cl_split}
             )
         if job is not None:
-            dict_clause["job"] = str(job)
+            dict_clause["job"] = escape(str(job))
 
         if project_path == "./":
             project_path = ""
         if recursive:
-            dict_clause["project"] = str(project_path) + "%"
+            dict_clause["project"] = escape(str(project_path)) + "%"
         else:
-            dict_clause["project"] = str(project_path)
+            dict_clause["project"] = escape(str(project_path))
         if sub_job_name is None:
             dict_clause["subjob"] = None
         elif sub_job_name != "%":
-            dict_clause["subjob"] = str(sub_job_name)
+            dict_clause["subjob"] = escape(str(sub_job_name))
         if element_lst is not None:
             dict_clause["element_lst"] = element_lst
 
@@ -502,100 +522,6 @@ def change_column_type(
         else:
             raise PermissionError("Not avilable in viewer mode.")
 
-    def get_items_sql(
-        self, where_condition: Optional[str] = None, sql_statement: Optional[str] = None
-    ) -> List[dict]:
-        """
-        Submit an SQL query to the database
-
-        Args:
-            where_condition (str): SQL where query, query like: "project LIKE 'lammps.phonons.Ni_fcc%'"
-            sql_statement (str): general SQL query, normal SQL statement
-
-        Returns:
-            list: get a list of dictionaries, where each dictionary represents one item of the table like:
-                 [{u'chemicalformula': u'BO',
-                  u'computer': u'localhost',
-                  u'hamilton': u'VAMPS',
-                  u'hamversion': u'1.1',
-                  u'id': 1,
-                  u'job': u'testing',
-                  u'masterid': None,
-                  u'parentid': 0,
-                  u'project': u'database.testing',
-                  u'projectpath': u'/TESTING',
-                  u'status': u'KAAAA',
-                  u'subjob': u'testJob',
-                  u'timestart': u'2016-05-02 11:31:04.253377',
-                  u'timestop': u'2016-05-02 11:31:04.371165',
-                  u'totalcputime': 0.117788,
-                  u'username': u'User'},
-                 {u'chemicalformula': u'BO',
-                  u'computer': u'localhost',
-                  u'hamilton': u'VAMPS',
-                  u'hamversion': u'1.1',
-                  u'id': 2,
-                  u'job': u'testing',
-                  u'masterid': 0,
-                  u'parentid': 0,
-                  u'project': u'database.testing',
-                  u'projectpath': u'/TESTING',
-                  u'status': u'KAAAA',
-                  u'subjob': u'testJob',
-                  u'timestart': u'2016-05-02 11:31:04.253377',
-                  u'timestop': u'2016-05-02 11:31:04.371165',
-                  u'totalcputime': 0.117788,
-                  u'username': u'User'}.....]
-        """
-
-        if where_condition:
-            where_condition = (
-                where_condition.replace("like", "similar to")
-                if self._engine.dialect.name == "postgresql"
-                else where_condition
-            )
-            try:
-                query = "select * from " + self.table_name + " where " + where_condition
-                query.replace("%", "%%")
-                result = self.conn.execute(text(query))
-            except Exception as except_msg:
-                print("EXCEPTION in get_items_sql: ", except_msg)
-                raise ValueError("EXCEPTION in get_items_sql: ", except_msg)
-        elif sql_statement:
-            sql_statement = (
-                sql_statement.replace("like", "similar to")
-                if self._engine.dialect.name == "postgresql"
-                else sql_statement
-            )
-            # TODO: make it save against SQL injection
-            result = self.conn.execute(text(sql_statement))
-        else:
-            result = self.conn.execute(text("select * from " + self.table_name))
-        row = result.mappings().all()
-        if not self._keep_connection:
-            self.conn.close()
-
-        # change the date of str datatype back into datetime object
-        output_list = []
-        for col in row:
-            # ensures working with db entries, which are camel case
-            timestop_index = [item.lower() for item in col.keys()].index("timestop")
-            timestart_index = [item.lower() for item in col.keys()].index("timestart")
-            tmp_values = list(col.values())
-            if (tmp_values[timestop_index] and tmp_values[timestart_index]) is not None:
-                # changes values
-                try:
-                    tmp_values[timestop_index] = datetime.strptime(
-                        str(tmp_values[timestop_index]), "%Y-%m-%d %H:%M:%S.%f"
-                    )
-                    tmp_values[timestart_index] = datetime.strptime(
-                        str(tmp_values[timestart_index]), "%Y-%m-%d %H:%M:%S.%f"
-                    )
-                except ValueError:
-                    print("error in: ", str(col))
-            output_list += [dict(zip(col.keys(), tmp_values))]
-        return output_list
-
     def _check_chem_formula_length(self, par_dict: dict) -> dict:
         """
         performs a check whether the length of chemical formula exceeds the defined limit
@@ -900,7 +826,7 @@ def get_items_dict(
             return_all_columns (bool): return all columns or only the 'id' - still the format stays the same.
 
         Returns:
-            list: the function returns a list of dicts like get_items_sql, but it does not format datetime:
+            list: the function returns a list of dicts, but it does not format datetime:
                  [{'chemicalformula': u'Ni108',
                   'computer': u'mapc157',
                   'hamilton': u'LAMMPS',
@@ -974,10 +900,10 @@ def get_items_dict(
                 self.conn.connection.create_function("like", 2, self.regexp)
 
             result = self.conn.execute(query)
-        row = result.fetchall()
+        results = [row._asdict() for row in result.fetchall()]
         if not self._keep_connection:
             self.conn.close()
-        return [dict(zip(col._mapping.keys(), col._mapping.values())) for col in row]
+        return results
 
     def get_job_status(self, job_id: int) -> Union[str, None]:
         try:

pyiron_base/jobs/job/core.py

@@ -876,6 +876,7 @@ def _internal_copy_to(
                 _copy_database_entry(
                     new_job_core=new_job_core,
                     job_copied_id=self.job_id,
+                    username=state.settings.login_user,
                 )
             else:
                 new_job_core.reset_job_id(job_id=None)