Merge branch 'main' into dependabot/pip/tables-3.10.2

.ci_support/environment-docs.yml

@@ -5,25 +5,25 @@ dependencies:
 - sphinx
 - sphinx_rtd_theme
 - myst-parser
-- conda =24.5.0
+- conda =24.7.1
 - conda_subprocess =0.0.5
 - cloudpickle =3.1.0
 - gitpython =3.1.44
-- h5io_browser =0.1.4
+- h5io_browser =0.1.5
 - h5py =3.12.1
-- jinja2 =3.1.4
+- jinja2 =3.1.5
 - monty =2024.12.10
-- numpy =1.26.4
+- numpy =2.2.1
 - pandas =2.2.3
 - pint =0.24.4
 - psutil =6.1.1
-- pyfileindex =0.0.31
+- pyfileindex =0.0.32
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.4
 - executorlib =0.0.7
 - pysqa =0.2.3
 - pytables =3.10.2
-- sqlalchemy =2.0.36
+- sqlalchemy =2.0.37
 - tqdm =4.67.1
 - traitlets =5.14.3
 - jupyter-book =1.0.0

.ci_support/environment-mini.yml

@@ -2,19 +2,19 @@ channels:
 - conda-forge
 dependencies:
 - cloudpickle =3.1.0
-- h5io_browser =0.1.4
+- h5io_browser =0.1.5
 - h5py =3.12.1
 - monty =2024.12.10
-- numpy =1.26.4
+- numpy =2.2.1
 - pandas =2.2.3
 - psutil =6.1.1
-- pyfileindex =0.0.31
+- pyfileindex =0.0.32
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.3
 - executorlib =0.0.7
 - pysqa =0.2.3
 - pytables =3.10.2
-- sqlalchemy =2.0.36
+- sqlalchemy =2.0.37
 - tqdm =4.67.1
 - traitlets =5.14.3
 - setuptools

.ci_support/environment.yml

@@ -3,24 +3,24 @@ channels:
 dependencies:
 - coverage
 - codacy-coverage
-- conda =24.5.0
+- conda =24.7.1
 - conda_subprocess =0.0.5
 - cloudpickle =3.1.0
 - gitpython =3.1.44
-- h5io_browser =0.1.4
+- h5io_browser =0.1.5
 - h5py =3.12.1
-- jinja2 =3.1.4
+- jinja2 =3.1.5
 - monty =2024.12.10
-- numpy =1.26.4
+- numpy =2.2.1
 - pandas =2.2.3
 - pint =0.24.4
 - psutil =6.1.1
-- pyfileindex =0.0.31
+- pyfileindex =0.0.32
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.4
 - executorlib =0.0.7
 - pysqa =0.2.3
 - pytables =3.10.2
-- sqlalchemy =2.0.36
+- sqlalchemy =2.0.37
 - tqdm =4.67.1
 - traitlets =5.14.3

.github/workflows/unittests.yml

@@ -16,12 +16,10 @@ jobs:
         - operating-system: macos-latest
           python-version: '3.12'
           label: osx-64-py-3-12
-          prefix: /Users/runner/miniconda3/envs/my-env
 
         - operating-system: windows-latest
           python-version: '3.12'
           label: win-64-py-3-12
-          prefix: C:\Miniconda3\envs\my-env
 
         - operating-system: ubuntu-latest
           python-version: '3.12'

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.9.1
     hooks:
       - id: ruff
         name: ruff lint

binder/environment.yml

@@ -2,24 +2,24 @@ channels:
 - conda-forge
 dependencies:
 - python
-- conda =24.5.0
+- conda =24.7.1
 - conda_subprocess =0.0.5
 - cloudpickle =3.1.0
 - gitpython =3.1.44
-- h5io_browser =0.1.4
+- h5io_browser =0.1.5
 - h5py =3.12.1
-- jinja2 =3.1.4
+- jinja2 =3.1.5
 - monty =2024.12.10
-- numpy =1.26.4
+- numpy =2.2.1
 - pandas =2.2.3
 - pint =0.24.4
 - psutil =6.1.1
-- pyfileindex =0.0.31
+- pyfileindex =0.0.32
 - pyiron_dataclasses =0.0.1
 - pyiron_snippets =0.1.4
 - executorlib =0.0.7
 - pysqa =0.2.3
 - pytables =3.10.2
-- sqlalchemy =2.0.36
+- 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/jobs/master/list.py

@@ -218,7 +218,7 @@ def run_if_refresh(self):
         Internal helper function the run if refresh function is called when the job status is 'refresh'. If the job was
         suspended previously, the job is going to be started again, to be continued.
         """
-        log_str = "{}, status: {}, finished: {} parallel master " "refresh".format(
+        log_str = "{}, status: {}, finished: {} parallel master refresh".format(
             self.job_info_str, self.status, self.is_finished()
         )
         self._logger.info(log_str)

pyiron_base/jobs/master/parallel.py

@@ -308,7 +308,7 @@ def run_if_refresh(self):
         Internal helper function the run if refresh function is called when the job status is 'refresh'. If the job was
         suspended previously, the job is going to be started again, to be continued.
         """
-        log_str = "{}, status: {}, finished: {} parallel master " "refresh".format(
+        log_str = "{}, status: {}, finished: {} parallel master refresh".format(
             self.job_info_str, self.status, self.is_finished()
         )
         self._logger.info(log_str)

pyiron_base/storage/flattenedstorage.py

@@ -1040,7 +1040,7 @@ def read_array(name, hdf):
                     # itemsize of original a is four bytes per character, so divide by four to get
                     # length of the orignal stored unicode string; np.dtype('U1').itemsize is just a
                     # platform agnostic way of knowing how wide a unicode charater is for numpy
-                    dtype=f"U{a.dtype.itemsize//np.dtype('U1').itemsize}",
+                    dtype=f"U{a.dtype.itemsize // np.dtype('U1').itemsize}",
                 )
             return a
 

pyproject.toml

@@ -25,17 +25,17 @@ classifiers = [
 dependencies = [
     "cloudpickle==3.1.0",
     "executorlib==0.0.7",
-    "h5io_browser==0.1.4",
+    "h5io_browser==0.1.5",
     "h5py==3.12.1",
-    "numpy==1.26.4",
+    "numpy==2.2.1",
     "monty==2024.12.10",
     "pandas==2.2.3",
     "psutil==6.1.1",
-    "pyfileindex==0.0.31",
+    "pyfileindex==0.0.32",
     "pyiron_dataclasses==0.0.1",
     "pyiron_snippets==0.1.4",
     "pysqa==0.2.3",
-    "sqlalchemy==2.0.36",
+    "sqlalchemy==2.0.37",
     "tables==3.10.2",
     "tqdm==4.67.1",
     "traitlets==5.14.3",
@@ -49,14 +49,14 @@ Repository = "https://github.com/pyiron/pyiron_base"
 
 [project.optional-dependencies]
 conda = [
-    "conda==24.5.0",
+    "conda==24.7.1",
     "conda_subprocess==0.0.5",
 ]
 devel = [
     "gitpython==3.1.44",
 ]
 flux = [
-    "jinja2==3.1.4",
+    "jinja2==3.1.5",
 ]
 stats = [
     "pint==0.24.4",

tests/unit/database/test_database_access.py

@@ -107,7 +107,7 @@ def test_get_items_sql(self):
         # be sure that get_items_sql returns right result with right statement
         result = self.database.get_items_sql(
             where_condition="",
-            sql_statement="select * from simulation " "where id=%s" % key,
+            sql_statement="select * from simulation where id=%s" % key,
         )[-1]
         self.assertTrue(par_dict.items() <= result.items())
 

tests/unit/job/test_jobtypechoice.py

@@ -33,7 +33,7 @@ def test_attr(self):
                 getattr(self.jobtypechoice, k)
         except AttributeError:
             self.fail(
-                "job class {} in JOB_CLASS_DICT, but not on " "JobTypeChoice".format(k)
+                "job class {} in JOB_CLASS_DICT, but not on JobTypeChoice".format(k)
             )
 
     def test_extend_job_class_dict(self):
@@ -44,14 +44,13 @@ def test_extend_job_class_dict(self):
         JOB_CLASS_DICT["TestClass"] = "my.own.test.module"
         self.assertTrue(
             "TestClass" in dir(self.jobtypechoice),
-            "new job class added to JOB_CLASS_DICT, but not " "returned in dir()",
+            "new job class added to JOB_CLASS_DICT, but not returned in dir()",
         )
         try:
             getattr(self.jobtypechoice, "TestClass")
         except AttributeError:
             self.fail(
-                "new job class added to JOB_CLASS_DICT, but not defined "
-                "JobTypeChoice"
+                "new job class added to JOB_CLASS_DICT, but not defined JobTypeChoice"
             )
 
 
@@ -81,5 +80,5 @@ def test_attr(self):
                 getattr(self.job_factory, k)
         except AttributeError:
             self.fail(
-                "job class {} in JOB_CLASS_DICT, but not on " "JobTypeChoice".format(k)
+                "job class {} in JOB_CLASS_DICT, but not on JobTypeChoice".format(k)
             )

tests/unit/project/test_jobloader.py

@@ -22,8 +22,7 @@ def test_load(self):
         self.assertEqual(
             len(self.project.job_table()),
             len(self.project.load.__dir__()),
-            msg="Tab completion (`__dir__`) should see both jobs at this project "
-            "level",
+            msg="Tab completion (`__dir__`) should see both jobs at this project level",
             # Note: When job names are duplicated at different sub-project levels, the
             # job name occurs in the __dir__ multiple times, even though it will only
             # show up in the tab-completion menu once (where it accesses the top-most