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OSX 12 tests are sometime timing out #1357

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liamhuber opened this issue Feb 23, 2024 · 3 comments · Fixed by #1390
Closed

OSX 12 tests are sometime timing out #1357

liamhuber opened this issue Feb 23, 2024 · 3 comments · Fixed by #1390

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@liamhuber
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E.g. in #1356 and #1349, although not in #1352.

Here's a dump of the tests section of the log from #1356:

2024-02-23T20:32:33.9496360Z ...../Users/runner/work/pyiron_base/pyiron_base/tests/archiving/test_export.py:49: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
2024-02-23T20:32:33.9542170Z   df_read["hamversion"] = float(df_read["hamversion"])
2024-02-23T20:32:33.9560290Z /Users/runner/work/pyiron_base/pyiron_base/tests/archiving/test_export.py:53: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
2024-02-23T20:32:33.9729270Z The job toy was saved and received the ID: 1
2024-02-23T20:32:33.9740370Z   df_exp["hamversion"] = float(df_exp["hamversion"])
2024-02-23T20:32:33.9802610Z .
2024-02-23T20:32:33.9919490Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:33.9951480Z 100%|██████████| 1/1 [00:00<00:00, 49.88it/s]
2024-02-23T20:32:33.9964460Z 
2024-02-23T20:32:34.0000380Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.0013220Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.0034450Z s
2024-02-23T20:32:34.0035640Z remove directory: /Users/runner/work/pyiron_base/pyiron_base/archive_folder/
2024-02-23T20:32:34.0037770Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.0041990Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.2560760Z 
2024-02-23T20:32:34.2561310Z The job toy was saved and received the ID: 1
2024-02-23T20:32:34.2562510Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.2563060Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.2639370Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.2642270Z   warnings.warn(
2024-02-23T20:32:34.2857390Z 
2024-02-23T20:32:34.2974240Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.2975270Z 100%|██████████| 1/1 [00:00<00:00, 87.70it/s]
2024-02-23T20:32:34.3154260Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.3157190Z   warnings.warn(
2024-02-23T20:32:34.4780130Z 
2024-02-23T20:32:34.4959390Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.4961310Z 100%|██████████| 1/1 [00:00<00:00, 56.58it/s]
2024-02-23T20:32:34.4994160Z .
2024-02-23T20:32:34.4994940Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.4996220Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.5039840Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.5044770Z   warnings.warn(
2024-02-23T20:32:34.5202750Z 
2024-02-23T20:32:34.5367390Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.5368650Z 100%|██████████| 1/1 [00:00<00:00, 61.96it/s]
2024-02-23T20:32:34.5397760Z .
2024-02-23T20:32:34.5398450Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.5399090Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.5440000Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.5442920Z   warnings.warn(
2024-02-23T20:32:34.5598640Z 
2024-02-23T20:32:34.5716770Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.5718200Z 100%|██████████| 1/1 [00:00<00:00, 86.24it/s]
2024-02-23T20:32:34.5749290Z .
2024-02-23T20:32:34.5749790Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.5750480Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.5797860Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.5800640Z   warnings.warn(
2024-02-23T20:32:34.6042180Z /Users/runner/work/pyiron_base/pyiron_base/tests/archiving/test_import.py:58: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
2024-02-23T20:32:34.6047050Z   df_import["hamversion"] = float(df_import["hamversion"])
2024-02-23T20:32:34.6051860Z /Users/runner/work/pyiron_base/pyiron_base/tests/archiving/test_import.py:59: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
2024-02-23T20:32:34.6055720Z   df_original["hamversion"] = float(df_original["hamversion"])
2024-02-23T20:32:34.6103430Z 
2024-02-23T20:32:34.6219530Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.6220620Z 100%|██████████| 1/1 [00:00<00:00, 87.87it/s]
2024-02-23T20:32:34.6249850Z .
2024-02-23T20:32:34.6250260Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.6250780Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.6290730Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.6293520Z   warnings.warn(
2024-02-23T20:32:34.6527780Z 
2024-02-23T20:32:34.6649290Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.6650390Z 100%|██████████| 1/1 [00:00<00:00, 84.49it/s]
2024-02-23T20:32:34.6813680Z 
2024-02-23T20:32:34.6933750Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.6935470Z 100%|██████████| 1/1 [00:00<00:00, 85.93it/s]
2024-02-23T20:32:34.6965170Z .
2024-02-23T20:32:34.6965910Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.6966410Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.7008320Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.7011090Z   warnings.warn(
2024-02-23T20:32:34.7251830Z 
2024-02-23T20:32:34.7391550Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.7393380Z 100%|██████████| 1/1 [00:00<00:00, 73.45it/s]
2024-02-23T20:32:34.7542610Z 
2024-02-23T20:32:34.7665900Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.7667200Z 100%|██████████| 1/1 [00:00<00:00, 83.15it/s]
2024-02-23T20:32:34.7697540Z .
2024-02-23T20:32:34.7698860Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.7699880Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.7741520Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.7745980Z   warnings.warn(
2024-02-23T20:32:34.8077450Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.8080280Z   warnings.warn(
2024-02-23T20:32:34.8200660Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.8203420Z   warnings.warn(
2024-02-23T20:32:34.8257980Z 
2024-02-23T20:32:34.8381860Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.8383020Z 100%|██████████| 1/1 [00:00<00:00, 82.61it/s]
2024-02-23T20:32:34.8419880Z 
2024-02-23T20:32:34.8475650Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.8476720Z 100%|██████████| 1/1 [00:00<00:00, 188.64it/s]
2024-02-23T20:32:34.8507080Z .
2024-02-23T20:32:34.8507570Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.8508010Z 0it [00:00, ?it/s]
2024-02-23T20:32:34.8554320Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.8557550Z   warnings.warn(
2024-02-23T20:32:34.8711480Z 
2024-02-23T20:32:34.8796160Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:34.8797700Z 100%|██████████| 1/1 [00:00<00:00, 124.05it/s]
2024-02-23T20:32:34.9049480Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:34.9053540Z   warnings.warn(
2024-02-23T20:32:35.1110230Z 
2024-02-23T20:32:35.1417430Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:35.1427320Z 100%|██████████| 1/1 [00:00<00:00, 61.67it/s]
2024-02-23T20:32:35.1442000Z .
2024-02-23T20:32:35.1454280Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.1472890Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.1485630Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:35.1494440Z   warnings.warn(
2024-02-23T20:32:35.1501570Z 
2024-02-23T20:32:35.1669770Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:35.1706660Z 100%|██████████| 1/1 [00:00<00:00, 62.17it/s]
2024-02-23T20:32:35.1713280Z .
2024-02-23T20:32:35.1747760Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.1798580Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.1833270Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:35.1906050Z   warnings.warn(
2024-02-23T20:32:35.1964600Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:32:35.1983100Z   warnings.warn(
2024-02-23T20:32:35.2919020Z 
2024-02-23T20:32:35.3382450Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:32:35.3384210Z remove directory: /Users/runner/work/pyiron_base/pyiron_base/archive_folder/
2024-02-23T20:32:35.3418240Z 100%|██████████| 2/2 [00:00<00:00, 293.43it/s]
2024-02-23T20:32:35.3453620Z 
2024-02-23T20:32:35.3513660Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:32:35.3557670Z 100%|██████████| 1/1 [00:00<00:00, 57.13it/s]
2024-02-23T20:32:35.3563350Z .
2024-02-23T20:32:35.3592050Z   0%|          | 0/3 [00:00<?, ?it/s]
2024-02-23T20:32:35.3628020Z 100%|██████████| 3/3 [00:00<00:00, 120.67it/s]
2024-02-23T20:32:35.3669520Z 
2024-02-23T20:32:35.3684340Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.3707760Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.3741970Z 
2024-02-23T20:32:35.3779200Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.3808320Z 0it [00:00, ?it/s]
2024-02-23T20:32:35.7763350Z s...............s/Users/runner/work/pyiron_base/pyiron_base/pyiron_base/database/filetable.py:138: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
2024-02-23T20:32:35.7809730Z   self._job_table = pandas.concat(
2024-02-23T20:32:36.3524060Z ........s.......
2024-02-23T20:32:36.3525580Z EXCEPTION in get_items_sql:  (sqlite3.OperationalError) near "Wrong": syntax error
2024-02-23T20:32:36.3556320Z 0it [00:00, ?it/s]
2024-02-23T20:32:36.3557150Z [SQL: select * from simulation where A Wrong where Clause]
2024-02-23T20:32:36.3606880Z 0it [00:00, ?it/s]
2024-02-23T20:32:36.3608090Z (Background on this error at: https://sqlalche.me/e/20/e3q8)
2024-02-23T20:32:36.3640530Z The job toy_1 was saved and received the ID: 6
2024-02-23T20:32:36.3676310Z ['2.82e-02', '2.31e-05']
2024-02-23T20:32:36.3989880Z TestWithProject: Setting up test project
2024-02-23T20:32:36.5434800Z TestWithProject: Setting up test project
2024-02-23T20:32:36.5436500Z s...
2024-02-23T20:32:36.5439700Z The job test was saved and received the ID: test
2024-02-23T20:32:36.5442370Z 0it [00:00, ?it/s]
2024-02-23T20:32:36.5450450Z You have selected to start the job manually. To run it, go into the working directory /Users/runner/work/pyiron_base/pyiron_base/tests/database/test_no_database_project/test_hdf5/test and call 'python -m pyiron_base.cli wrapper -p /Users/runner/work/pyiron_base/pyiron_base/tests/database/test_no_database_project/test_hdf5/test -f /Users/runner/work/pyiron_base/pyiron_base/tests/database/test_no_database_project/test.h5/test ' 
2024-02-23T20:32:36.5461230Z 0it [00:00, ?it/s]
2024-02-23T20:32:37.6688500Z s...2024-02-23 20:32:37,579 - pyiron_log - WARNING - The job job_test is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
2024-02-23T20:32:38.2134880Z .2024-02-23 20:32:38,213 - pyiron_log - WARNING - The job job_test is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
2024-02-23T20:32:45.3532440Z .../Users/runner/miniconda3/envs/my-env/lib/python3.12/subprocess.py:1127: ResourceWarning: subprocess 6830 is still running
2024-02-23T20:32:45.3534640Z   _warn("subprocess %s is still running" % self.pid,
2024-02-23T20:32:45.3545850Z ResourceWarning: Enable tracemalloc to get the object allocation traceback
2024-02-23T20:32:45.3551780Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/unittest/case.py:589: ResourceWarning: unclosed file <_io.BufferedReader name=22>
2024-02-23T20:32:45.3554400Z   if method() is not None:
2024-02-23T20:32:45.3556280Z ResourceWarning: Enable tracemalloc to get the object allocation traceback
2024-02-23T20:32:45.3559330Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/unittest/case.py:589: ResourceWarning: unclosed file <_io.BufferedReader name=24>
2024-02-23T20:32:45.3561890Z   if method() is not None:
2024-02-23T20:32:45.3563700Z ResourceWarning: Enable tracemalloc to get the object allocation traceback
2024-02-23T20:32:45.3849180Z TestWithProject: Setting up test project
2024-02-23T20:32:45.3980800Z .
2024-02-23T20:32:45.3981330Z The job job_test was saved and received the ID: 6
2024-02-23T20:32:45.3988770Z The job job_no was saved and received the ID: 7
2024-02-23T20:32:45.3990480Z The job job_output_files was saved and received the ID: 8
2024-02-23T20:32:45.3994770Z The job job_sleep was saved and received the ID: 9
2024-02-23T20:32:45.3998840Z You have selected to start the job manually. To run it, go into the working directory /Users/runner/work/pyiron_base/pyiron_base/tests/flex/test_executablecontainer/job_sleep_hdf5/job_sleep and call 'python -m pyiron_base.cli wrapper -p /Users/runner/work/pyiron_base/pyiron_base/tests/flex/test_executablecontainer/job_sleep_hdf5/job_sleep -j 9 ' 
2024-02-23T20:32:45.4362790Z   0%|          | 0/4 [00:00<?, ?it/s]
2024-02-23T20:32:45.4363720Z 100%|██████████| 4/4 [00:00<00:00, 78.60it/s]
2024-02-23T20:32:45.6667960Z s/Users/runner/miniconda3/envs/my-env/lib/python3.12/site-packages/boltons/timeutils.py:441: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC).
2024-02-23T20:32:45.6671620Z   EPOCH_NAIVE = datetime.utcfromtimestamp(0)
2024-02-23T20:33:03.5493380Z /Users/runner/work/pyiron_base/pyiron_base/pyiron_base/jobs/job/core.py:957: DeprecationWarning: Using __getitem__ on a job to access files in deprecated: use job.files instead!
2024-02-23T20:33:03.5511460Z   warnings.warn(
2024-02-23T20:33:03.5709730Z TestWithProject: Setting up test project
2024-02-23T20:33:03.5711340Z ..
2024-02-23T20:33:03.5711830Z The job job_conda_path was saved and received the ID: 6
2024-02-23T20:33:03.5871200Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:33:03.5875320Z 100%|██████████| 1/1 [00:00<00:00, 64.13it/s]
2024-02-23T20:33:03.7955760Z s2024-02-23 20:33:03,795 - pyiron_log - WARNING - The job my_function59f2ee8a4bfc7e75ebe938669f6a0c96 is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'
2024-02-23T20:33:05.0397180Z TestWithProject: Setting up test project
2024-02-23T20:33:05.0398550Z The job my_function59f2ee8a4bfc7e75ebe938669f6a0c96 was saved and received the ID: 6
2024-02-23T20:33:05.0411960Z The job my_functiona55e17d1c7f6aba6df9475974051f26f was saved and received the ID: 7
2024-02-23T20:33:05.0413280Z The job my_functiona11fb2d5fe5c0352fcb600288ff480f3 was saved and received the ID: 8
2024-02-23T20:33:05.0414270Z The job my_function was saved and received the ID: 8
2024-02-23T20:33:05.0415240Z The job my_sleep_funct8348d547c48d0ed908e8d0116020d7ff was saved and received the ID: 8
2024-02-23T20:33:10.1880690Z ....2024-02-23 20:33:10,187 - pyiron_log - INFO - Job 8 intercept signal 15, job is shutting down
2024-02-23T20:33:11.4388460Z The job my_sleep_funct013175f3677ded5964e4a1f7249faaa9 was saved and received the ID: 9
2024-02-23T20:33:12.8063180Z The job my_sleep_funct0acba0b907be8f65b86f8b468cb39699 was saved and received the ID: 10
2024-02-23T20:33:14.5980950Z The job my_function_exe5b57f4c80ac3723d65f4c7936b92e38b was saved and received the ID: 11
2024-02-23T20:33:15.7732930Z ....
2024-02-23T20:33:15.8607420Z   0%|          | 0/6 [00:00<?, ?it/s]
2024-02-23T20:33:15.8612270Z 100%|██████████| 6/6 [00:00<00:00, 68.90it/s]
2024-02-23T20:33:23.4591180Z ss........................................................
2024-02-23T20:33:23.4592160Z TestWithProject: Setting up test project
2024-02-23T20:33:23.5309230Z 0it [00:00, ?it/s]
2024-02-23T20:33:23.5315820Z 0it [00:00, ?it/s]
2024-02-23T20:33:23.5344510Z ..ss..s./Users/runner/work/pyiron_base/pyiron_base/pyiron_base/utils/error.py:89: ImportWarning: Reduced functionality, since ['PIL', 'nbformat'] could not be imported.
2024-02-23T20:33:23.5346480Z   warnings.warn(self.message, category=ImportWarning)
2024-02-23T20:33:23.5347580Z ....
2024-02-23T20:33:23.5348660Z 0it [00:00, ?it/s]
2024-02-23T20:33:23.5349860Z 0it [00:00, ?it/s]
2024-02-23T20:33:23.5352580Z ./Users/runner/work/pyiron_base/pyiron_base/pyiron_base/utils/error.py:89: ImportWarning: Reduced functionality, since ['PIL', 'nbformat'] could not be imported.
2024-02-23T20:33:23.5354420Z   warnings.warn(self.message, category=ImportWarning)
2024-02-23T20:33:23.5357500Z ./Users/runner/work/pyiron_base/pyiron_base/pyiron_base/utils/error.py:89: ImportWarning: Reduced functionality, since ['PIL', 'nbformat'] could not be imported.
2024-02-23T20:33:23.5359330Z   warnings.warn(self.message, category=ImportWarning)
2024-02-23T20:33:23.8575100Z TestWithProject: Setting up test project
2024-02-23T20:33:23.8576050Z .....s.............................
2024-02-23T20:33:23.8577560Z 0it [00:00, ?it/s]
2024-02-23T20:33:23.8578080Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.0467310Z TestWithProject: Setting up test project
2024-02-23T20:33:24.0467980Z ss.........
2024-02-23T20:33:24.0468550Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.0468960Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.0765320Z s..
2024-02-23T20:33:24.0765790Z TestWithProject: Setting up test project
2024-02-23T20:33:24.0766390Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.0766770Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.1424750Z ...
2024-02-23T20:33:24.1425230Z TestWithProject: Setting up test project
2024-02-23T20:33:24.1427180Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.1428310Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.2196200Z TestWithProject: Setting up test project
2024-02-23T20:33:24.2196820Z ...
2024-02-23T20:33:24.3198080Z 0it [00:00, ?it/s]
2024-02-23T20:33:24.4051640Z 0it [00:00, ?it/s]
2024-02-23T20:33:26.5183350Z s.s..s...........s
2024-02-23T20:33:26.5222300Z 0it [00:00, ?it/s]
2024-02-23T20:33:26.5333590Z 0it [00:00, ?it/s]
2024-02-23T20:33:28.2101230Z The job master was saved and received the ID: 6
2024-02-23T20:33:28.2102090Z .s..
2024-02-23T20:33:28.2105450Z The job child_1_1 was saved and received the ID: 7
2024-02-23T20:33:28.2107490Z The job child_1_2 was saved and received the ID: 8
2024-02-23T20:33:28.2110510Z The job child_1_3 was saved and received the ID: 9
2024-02-23T20:33:28.2112580Z The job child_1_4 was saved and received the ID: 10
2024-02-23T20:33:28.2114760Z The job child_1_5 was saved and received the ID: 11
2024-02-23T20:33:28.2118320Z The job child_1_6 was saved and received the ID: 12
2024-02-23T20:33:28.2120430Z The job child_1_7 was saved and received the ID: 13
2024-02-23T20:33:28.2122930Z The job child_1_8 was saved and received the ID: 14
2024-02-23T20:33:28.2125540Z The job child_1_9 was saved and received the ID: 15
2024-02-23T20:33:28.2127670Z The job master_2 was saved and received the ID: 16
2024-02-23T20:33:28.2129610Z The job child_2_1 was saved and received the ID: 17
2024-02-23T20:33:28.4654170Z   0%|          | 0/12 [00:00<?, ?it/s]
2024-02-23T20:33:28.4954850Z   8%|▊         | 1/12 [00:00<00:02,  3.93it/s]
2024-02-23T20:33:28.4956850Z 100%|██████████| 12/12 [00:00<00:00, 42.14it/s]
2024-02-23T20:33:28.4985470Z 
2024-02-23T20:33:28.4986960Z 0it [00:00, ?it/s]
2024-02-23T20:33:28.4988840Z 0it [00:00, ?it/s]
2024-02-23T20:33:30.6102160Z TestWithProject: Setting up test project
2024-02-23T20:33:30.6103310Z .....
2024-02-23T20:33:30.6104280Z The job job_script was saved and received the ID: 6
2024-02-23T20:33:30.6106010Z The job copy_test was saved and received the ID: 9
2024-02-23T20:33:30.7127320Z   0%|          | 0/3 [00:00<?, ?it/s]
2024-02-23T20:33:30.8038090Z 100%|██████████| 3/3 [00:00<00:00, 30.12it/s]
2024-02-23T20:33:30.8914010Z s...
2024-02-23T20:33:30.8915120Z The job job_test_run was saved and received the ID: 6
2024-02-23T20:33:30.8916580Z 0it [00:00, ?it/s]
2024-02-23T20:33:30.8917380Z 0it [00:00, ?it/s]
2024-02-23T20:33:32.5804460Z TestWithProject: Setting up test project
2024-02-23T20:33:32.5805940Z The job test was saved and received the ID: 6
2024-02-23T20:33:32.5807170Z s......
2024-02-23T20:33:32.5886050Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:33:32.5887260Z 100%|██████████| 1/1 [00:00<00:00, 134.17it/s]
2024-02-23T20:33:32.7438560Z .
2024-02-23T20:33:32.7439260Z 0it [00:00, ?it/s]
2024-02-23T20:33:32.7440000Z 0it [00:00, ?it/s]
2024-02-23T20:33:33.6283900Z s.....
2024-02-23T20:33:33.6285880Z TestWithProject: Setting up test project
2024-02-23T20:33:33.6333750Z 0it [00:00, ?it/s]
2024-02-23T20:33:33.6337520Z The job custom was saved and received the ID: 6
2024-02-23T20:33:33.6349720Z 0it [00:00, ?it/s]
2024-02-23T20:33:37.1758540Z TestWithProject: Setting up test project
2024-02-23T20:33:37.2121750Z The job toy_1 was saved and received the ID: 6
2024-02-23T20:33:37.2156890Z The job toy_2 was saved and received the ID: 7
2024-02-23T20:33:37.2541750Z The job toy_1 was saved and received the ID: 8
2024-02-23T20:33:37.2662740Z The job toy_2 was saved and received the ID: 9
2024-02-23T20:33:37.2715900Z The job toy_3 was saved and received the ID: 10
2024-02-23T20:33:37.2929760Z The job template was saved and received the ID: 11
2024-02-23T20:33:37.2967390Z The job template_copy was saved and received the ID: 12
2024-02-23T20:33:37.3055310Z The job job_single_debug was saved and received the ID: 12
2024-02-23T20:33:37.3209500Z The job job_with_executor_copy was saved and received the ID: 12
2024-02-23T20:33:38.9702490Z s..................................2024-02-23 20:33:38,969 - pyiron_log - INFO - job: job_with_executor_copy id: 12, status: submitted, run job (modal)
2024-02-23T20:33:38.9866770Z 2024-02-23 20:33:38,985 - pyiron_log - INFO - job: job_with_executor_copy id: 12, status: running, output: 
2024-02-23T20:33:38.9903110Z 2024-02-23 20:33:38,989 - pyiron_log - INFO - run job: job_with_executor_copy id: 12, status: collect
2024-02-23T20:33:39.0036220Z 2024-02-23 20:33:39,003 - pyiron_log - INFO - update master: None 12 executor
2024-02-23T20:33:39.4701350Z The job job_with_executor_run was saved and received the ID: 13
2024-02-23T20:33:41.1213810Z .2024-02-23 20:33:41,120 - pyiron_log - INFO - job: job_with_executor_run id: 13, status: submitted, run job (modal)
2024-02-23T20:33:41.1415810Z 2024-02-23 20:33:41,139 - pyiron_log - INFO - job: job_with_executor_run id: 13, status: running, output: 
2024-02-23T20:33:41.1455480Z 2024-02-23 20:33:41,142 - pyiron_log - INFO - run job: job_with_executor_run id: 13, status: collect
2024-02-23T20:33:41.2402050Z 2024-02-23 20:33:41,154 - pyiron_log - INFO - update master: None 13 executor
2024-02-23T20:33:41.2670610Z The job job_with_executor_wait was saved and received the ID: 14
2024-02-23T20:33:43.1442620Z .2024-02-23 20:33:43,141 - pyiron_log - INFO - job: job_with_executor_wait id: 14, status: submitted, run job (modal)
2024-02-23T20:33:43.1641280Z 2024-02-23 20:33:43,163 - pyiron_log - INFO - job: job_with_executor_wait id: 14, status: running, output: 
2024-02-23T20:33:43.1691860Z 2024-02-23 20:33:43,167 - pyiron_log - INFO - run job: job_with_executor_wait id: 14, status: collect
2024-02-23T20:33:43.1826020Z 2024-02-23 20:33:43,181 - pyiron_log - INFO - update master: None 14 executor
2024-02-23T20:33:43.2994250Z .../Users/runner/work/pyiron_base/pyiron_base/tests/job/test_genericJob.py:157: DeprecationWarning: pyiron_base.jobs.job.core.list_files is deprecated: use job.files.list().
2024-02-23T20:33:43.3172300Z   ham.list_files(), ["test_file"]
2024-02-23T20:33:43.3245700Z /Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:33:43.3374280Z   warnings.warn(
2024-02-23T20:33:44.1215740Z ...
2024-02-23T20:33:44.1216290Z 0it [00:00, ?it/s]
2024-02-23T20:33:44.1216910Z 0it [00:00, ?it/s]
2024-02-23T20:33:44.1296170Z 
2024-02-23T20:33:44.1297840Z 0it [00:00, ?it/s]
2024-02-23T20:33:44.1298720Z 0it [00:00, ?it/s]
2024-02-23T20:33:44.2989790Z .......2024-02-23 20:33:44,298 - pyiron_log - WARNING - Job 'job_without_hdf5' does not exist and cannot be loaded
2024-02-23T20:33:45.5197550Z .../Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:33:45.5206380Z   warnings.warn(
2024-02-23T20:33:45.5239060Z /Users/runner/work/pyiron_base/pyiron_base/tests/job/test_genericJob.py:512: DeprecationWarning: pyiron_base.jobs.job.core.list_files is deprecated: use job.files.list().
2024-02-23T20:33:45.5276580Z   wd_files = job_restart.list_files()
2024-02-23T20:33:45.7532180Z .2024-02-23 20:33:45,752 - pyiron_log - WARNING - Job aborted
2024-02-23T20:33:45.7534270Z 2024-02-23 20:33:45,753 - pyiron_log - WARNING - 
2024-02-23T20:33:46.0195730Z 2024-02-23 20:33:46,018 - pyiron_log - WARNING - Job aborted
2024-02-23T20:33:46.0197560Z 2024-02-23 20:33:46,019 - pyiron_log - WARNING - 
2024-02-23T20:33:46.6886830Z ....................../Users/runner/miniconda3/envs/my-env/lib/python3.12/tarfile.py:2221: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior.
2024-02-23T20:33:46.7883630Z   warnings.warn(
2024-02-23T20:33:46.7884320Z The job job_without_hdf5 was saved and received the ID: 16
2024-02-23T20:33:46.8788020Z The job toy_1_restart was saved and received the ID: 16
2024-02-23T20:33:46.8884510Z .......
2024-02-23T20:33:46.9791100Z The job success_0 was saved and received the ID: 17
2024-02-23T20:33:46.9886540Z   0%|          | 0/16 [00:00<?, ?it/s]
2024-02-23T20:33:47.0793370Z The job aborted_1 was saved and received the ID: 18
2024-02-23T20:33:47.1795330Z The job success_1 was saved and received the ID: 19
2024-02-23T20:33:47.2718430Z  44%|████▍     | 7/16 [00:00<00:00, 69.49it/s]
2024-02-23T20:33:47.2719250Z The job aborted_2 was saved and received the ID: 20
2024-02-23T20:33:47.2776740Z  88%|████████▊ | 14/16 [00:00<00:00, 28.78it/s]
2024-02-23T20:33:47.2778850Z The job rerun_aborted was saved and received the ID: 21
2024-02-23T20:33:47.2787440Z 100%|██████████| 16/16 [00:00<00:00, 34.20it/s]
2024-02-23T20:33:47.2788260Z The job rerun_aborted was saved and received the ID: 21
2024-02-23T20:33:47.4720110Z s...
2024-02-23T20:33:47.4721000Z The job job_test_run was saved and received the ID: 6
2024-02-23T20:33:47.4722210Z 0it [00:00, ?it/s]
2024-02-23T20:33:47.4723140Z 0it [00:00, ?it/s]
2024-02-23T20:33:47.6838290Z The job job_test_run was saved and received the ID: 6
2024-02-23T20:33:47.6855950Z s....
2024-02-23T20:33:47.6907830Z 0it [00:00, ?it/s]
2024-02-23T20:33:47.6947550Z 0it [00:00, ?it/s]
2024-02-23T20:33:47.8557360Z TestWithProject: Setting up test project
2024-02-23T20:33:47.8558500Z s.................
2024-02-23T20:33:47.8738040Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:33:47.8739440Z 100%|██████████| 1/1 [00:00<00:00, 57.14it/s]
2024-02-23T20:33:47.9619880Z ss.....s.......2024-02-23 20:33:47,961 - pyiron_log - WARNING - Job 'script' does not exist and cannot be loaded
2024-02-23T20:33:47.9623700Z 2024-02-23 20:33:47,961 - pyiron_log - WARNING - Job 'script' does not exist and could not be removed
2024-02-23T20:33:48.0577000Z .2024-02-23 20:33:48,057 - pyiron_log - WARNING - Job 'script' does not exist and cannot be loaded
2024-02-23T20:33:48.0581230Z 2024-02-23 20:33:48,057 - pyiron_log - WARNING - Job 'script' does not exist and could not be removed
2024-02-23T20:33:49.5064650Z TestWithProject: Setting up test project
2024-02-23T20:33:49.5135270Z .
2024-02-23T20:33:49.5135880Z The job script was saved and received the ID: 6
2024-02-23T20:33:49.5138120Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:33:49.5138800Z The job script was saved and received the ID: 6
2024-02-23T20:33:49.5141290Z 100%|██████████| 1/1 [00:00<00:00, 208.11it/s]
2024-02-23T20:33:49.5689440Z 2024-02-23 20:33:49,568 - pyiron_log - WARNING - Job 'script' does not exist and cannot be loaded
2024-02-23T20:33:49.5693560Z 2024-02-23 20:33:49,568 - pyiron_log - WARNING - Job 'script' does not exist and could not be removed
2024-02-23T20:33:51.0177100Z The job script was saved and received the ID: 6
2024-02-23T20:33:51.0180360Z .
2024-02-23T20:33:51.0231330Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:33:51.0233060Z 100%|██████████| 1/1 [00:00<00:00, 209.65it/s]
2024-02-23T20:33:51.2178560Z 2024-02-23 20:33:51,217 - pyiron_log - WARNING - Job 'script' does not exist and cannot be loaded
2024-02-23T20:33:51.2180390Z 2024-02-23 20:33:51,217 - pyiron_log - WARNING - Job 'script' does not exist and could not be removed
2024-02-23T20:33:51.4015860Z The job script was saved and received the ID: 6
2024-02-23T20:33:51.4016680Z .
2024-02-23T20:33:51.4060680Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:33:51.4061670Z 100%|██████████| 1/1 [00:00<00:00, 244.18it/s]
2024-02-23T20:33:51.4348360Z 2024-02-23 20:33:51,434 - pyiron_log - WARNING - Job 'script' does not exist and cannot be loaded
2024-02-23T20:33:51.4350100Z 2024-02-23 20:33:51,434 - pyiron_log - WARNING - Job 'script' does not exist and could not be removed
2024-02-23T20:33:51.4577700Z .
2024-02-23T20:33:51.4578760Z 0it [00:00, ?it/s]
2024-02-23T20:33:51.4579750Z 0it [00:00, ?it/s]
2024-02-23T20:33:51.4652520Z s
2024-02-23T20:33:51.4653010Z TestWithProject: Setting up test project
2024-02-23T20:33:51.4653860Z 0it [00:00, ?it/s]
2024-02-23T20:33:51.4655200Z 0it [00:00, ?it/s]
2024-02-23T20:33:51.5933600Z The job runner was saved and received the ID: 6
2024-02-23T20:34:06.8844710Z The job script was saved and received the ID: 7
2024-02-23T20:34:06.8845360Z ..
2024-02-23T20:34:06.8848770Z You have selected to start the job manually. To run it, go into the working directory /Users/runner/work/pyiron_base/pyiron_base/tests/job/test_worker/sub/script_hdf5/script and call 'python -m pyiron_base.cli wrapper -p /Users/runner/work/pyiron_base/pyiron_base/tests/job/test_worker/sub/script_hdf5/script -j 7 ' 
2024-02-23T20:34:06.8851890Z 0it [00:00, ?it/s]
2024-02-23T20:34:06.8852390Z 0it [00:00, ?it/s]
2024-02-23T20:34:07.0968490Z s..
2024-02-23T20:34:07.0970520Z 0it [00:00, ?it/s]
2024-02-23T20:34:07.0970890Z 0it [00:00, ?it/s]
2024-02-23T20:34:13.6842040Z remove directory: /Users/runner/work/pyiron_base/pyiron_base/tests/master/master_copy/
2024-02-23T20:34:13.6843620Z ....
2024-02-23T20:34:13.6853090Z TestWithProject: Setting up test project
2024-02-23T20:34:13.6854650Z The job master_toy was saved and received the ID: 6
2024-02-23T20:34:13.6855440Z The job test_0 was saved and received the ID: 7
2024-02-23T20:34:13.6856220Z The job test_1 was saved and received the ID: 8
2024-02-23T20:34:13.6856970Z The job test_2 was saved and received the ID: 9
2024-02-23T20:34:13.6857740Z The job test_3 was saved and received the ID: 10
2024-02-23T20:34:13.6858490Z The job test_4 was saved and received the ID: 11
2024-02-23T20:34:13.6859250Z The job test_5 was saved and received the ID: 12
2024-02-23T20:34:13.6860520Z The job test_6 was saved and received the ID: 13
2024-02-23T20:34:13.6861400Z The job test_7 was saved and received the ID: 14
2024-02-23T20:34:13.6862210Z The job test_8 was saved and received the ID: 15
2024-02-23T20:34:13.6863740Z The job test_9 was saved and received the ID: 16
2024-02-23T20:34:13.9052300Z   0%|          | 0/11 [00:00<?, ?it/s]
2024-02-23T20:34:13.9108010Z   9%|▉         | 1/11 [00:00<00:02,  4.54it/s]
2024-02-23T20:34:13.9109500Z 100%|██████████| 11/11 [00:00<00:00, 48.65it/s]
2024-02-23T20:34:13.9172140Z ss
2024-02-23T20:34:13.9173560Z 0it [00:00, ?it/s]
2024-02-23T20:34:13.9174800Z 0it [00:00, ?it/s]
2024-02-23T20:34:13.9484200Z .
2024-02-23T20:34:13.9485130Z 0it [00:00, ?it/s]
2024-02-23T20:34:13.9486740Z 0it [00:00, ?it/s]
2024-02-23T20:34:13.9883710Z .
2024-02-23T20:34:13.9887840Z 0it [00:00, ?it/s]
2024-02-23T20:34:13.9889720Z 0it [00:00, ?it/s]
2024-02-23T20:34:14.1035000Z .
2024-02-23T20:34:14.1036450Z 0it [00:00, ?it/s]
2024-02-23T20:34:14.1037110Z 0it [00:00, ?it/s]
2024-02-23T20:34:14.1384380Z .s......
2024-02-23T20:34:14.1386260Z 0it [00:00, ?it/s]
2024-02-23T20:34:14.1400160Z 0it [00:00, ?it/s]
2024-02-23T20:34:16.2140260Z TestWithProject: Setting up test project
2024-02-23T20:34:16.2141210Z ....
2024-02-23T20:34:16.2141780Z The job toy_1 was saved and received the ID: 6
2024-02-23T20:34:16.2142500Z The job toy_2 was saved and received the ID: 7
2024-02-23T20:34:16.2143190Z The job toy_1 was saved and received the ID: 8
2024-02-23T20:34:16.2143860Z The job toy_2 was saved and received the ID: 9
2024-02-23T20:34:16.2144550Z The job toy_3 was saved and received the ID: 10
2024-02-23T20:34:16.2649370Z   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:16.2650230Z 100%|██████████| 5/5 [00:00<00:00, 99.03it/s]
2024-02-23T20:34:17.8144540Z s./Users/runner/work/pyiron_base/pyiron_base/pyiron_base/project/maintenance.py:291: UserWarning: 
2024-02-23T20:34:17.8146260Z                 The database statistics is only available for a Postgresql database
2024-02-23T20:34:17.8147170Z                 
2024-02-23T20:34:17.8147570Z   warnings.warn(
2024-02-23T20:34:17.8202150Z TestWithProject: Setting up test project
2024-02-23T20:34:17.8203010Z 
2024-02-23T20:34:17.8203440Z The job toy_1 was saved and received the ID: 6
2024-02-23T20:34:17.8204260Z The job toy_2 was saved and received the ID: 7
2024-02-23T20:34:17.8204980Z The job toy_1 was saved and received the ID: 8
2024-02-23T20:34:17.8205700Z The job toy_2 was saved and received the ID: 9
2024-02-23T20:34:17.8206440Z The job toy_3 was saved and received the ID: 10
2024-02-23T20:34:17.8217400Z   0%|          | 0/5 [00:00<?, ?it/s]2024-02-23 20:34:17,821 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:18.0422210Z 
2024-02-23T20:34:18.0440000Z  20%|██        | 1/5 [00:00<00:00,  4.51it/s]2024-02-23 20:34:18,043 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:18.3220780Z 
2024-02-23T20:34:18.3255130Z  40%|████      | 2/5 [00:00<00:00,  4.20it/s]2024-02-23 20:34:18,293 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:18.5075420Z 
2024-02-23T20:34:18.5090150Z  60%|██████    | 3/5 [00:00<00:00,  4.39it/s]2024-02-23 20:34:18,508 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:18.6969980Z 
2024-02-23T20:34:18.6985200Z  80%|████████  | 4/5 [00:00<00:00,  4.70it/s]2024-02-23 20:34:18,698 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:19.0151520Z 
2024-02-23T20:34:19.0817530Z 100%|██████████| 5/5 [00:01<00:00,  4.51it/s]
2024-02-23T20:34:19.0823100Z 100%|██████████| 5/5 [00:01<00:00,  4.49it/s]
2024-02-23T20:34:19.8483780Z ..
2024-02-23T20:34:19.8967590Z   0%|          | 0.00/204k [00:00<?, ?B/s]2024-02-23 20:34:19,861 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:20.1268090Z 
2024-02-23T20:34:20.1598890Z  29%|██▉       | 59.7k/204k [00:00<00:00, 215kB/s]
2024-02-23T20:34:20.1599900Z 100%|██████████| 204k/204k [00:00<00:00, 657kB/s] 
2024-02-23T20:34:20.5198310Z Total Jobs: 5	Errors: 0	Skipped (no bug detected): 4
2024-02-23T20:34:20.5201530Z .
2024-02-23T20:34:20.5319910Z   0%|          | 0.00/196k [00:00<?, ?B/s]2024-02-23 20:34:20,531 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:20.7218870Z 
2024-02-23T20:34:20.7544980Z  26%|██▌       | 51.5k/196k [00:00<00:00, 256kB/s]
2024-02-23T20:34:20.7545980Z 100%|██████████| 196k/196k [00:00<00:00, 838kB/s] 
2024-02-23T20:34:21.1096770Z Total Jobs: 5	Errors: 0	Skipped (no bug detected): 4
2024-02-23T20:34:21.1097550Z .
2024-02-23T20:34:21.1204910Z   0%|          | 0.00/196k [00:00<?, ?B/s]2024-02-23 20:34:21,120 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:21.2979280Z 
2024-02-23T20:34:21.3420930Z  26%|██▌       | 51.5k/196k [00:00<00:00, 274kB/s]
2024-02-23T20:34:21.3423120Z 100%|██████████| 196k/196k [00:00<00:00, 846kB/s] 
2024-02-23T20:34:21.7497930Z Total Jobs: 5	Errors: 0	Skipped (no bug detected): 4
2024-02-23T20:34:21.7498900Z .
2024-02-23T20:34:21.7620980Z   0%|          | 0.00/196k [00:00<?, ?B/s]2024-02-23 20:34:21,761 - pyiron_log - WARNING - Specifying job_name is deprecated and ignored! Future versions will change signature.
2024-02-23T20:34:21.9510320Z 
2024-02-23T20:34:21.9835340Z  26%|██▌       | 51.5k/196k [00:00<00:00, 257kB/s]
2024-02-23T20:34:21.9836610Z 100%|██████████| 196k/196k [00:00<00:00, 842kB/s] 
2024-02-23T20:34:22.1346670Z Total Jobs: 5	Errors: 0	Skipped (no bug detected): 4
2024-02-23T20:34:22.1347700Z .
2024-02-23T20:34:22.2188730Z   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:22.3191810Z 100%|██████████| 5/5 [00:00<00:00, 59.71it/s]
2024-02-23T20:34:22.3475690Z ss
2024-02-23T20:34:22.3584930Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3633540Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3635120Z .
2024-02-23T20:34:22.3638140Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3641380Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3644600Z .
2024-02-23T20:34:22.3647750Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3650960Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3654170Z .
2024-02-23T20:34:22.3657500Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3660700Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3663100Z 
2024-02-23T20:34:22.3667010Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3672140Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3684920Z 
2024-02-23T20:34:22.3687270Z 0it [00:00, ?it/s]
2024-02-23T20:34:22.3692930Z 0it [00:00, ?it/s]
2024-02-23T20:34:24.0015820Z TestWithProject: Setting up test project
2024-02-23T20:34:24.0585510Z ....
2024-02-23T20:34:24.0586090Z The job toy_1 was saved and received the ID: 6
2024-02-23T20:34:24.0633960Z The job toy_2 was saved and received the ID: 7
2024-02-23T20:34:24.0718660Z The job toy_1 was saved and received the ID: 8
2024-02-23T20:34:24.0755930Z The job toy_2 was saved and received the ID: 9
2024-02-23T20:34:24.0783680Z The job toy_3 was saved and received the ID: 10
2024-02-23T20:34:24.1656070Z   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:24.3393110Z  20%|██        | 1/5 [00:00<00:00,  6.79it/s]
2024-02-23T20:34:24.4537510Z  40%|████      | 2/5 [00:00<00:00,  5.80it/s]
2024-02-23T20:34:24.5646300Z  60%|██████    | 3/5 [00:00<00:00,  6.86it/s]
2024-02-23T20:34:24.6743300Z  80%|████████  | 4/5 [00:00<00:00,  7.57it/s]
2024-02-23T20:34:24.6746930Z 100%|██████████| 5/5 [00:00<00:00,  8.06it/s]
2024-02-23T20:34:24.6748370Z 100%|██████████| 5/5 [00:00<00:00,  7.44it/s]
2024-02-23T20:34:24.6791010Z 
2024-02-23T20:34:24.6792400Z 0it [00:00, ?it/s]
2024-02-23T20:34:24.6793170Z 0it [00:00, ?it/s]
2024-02-23T20:34:24.6830990Z 
2024-02-23T20:34:24.8046830Z   0%|          | 0/1 [00:00<?, ?it/s]
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2024-02-23T20:34:25.2099350Z The job toy1 was saved and received the ID: toy1
2024-02-23T20:34:25.2100250Z .
2024-02-23T20:34:25.2100670Z The job toy2 was saved and received the ID: toy2
2024-02-23T20:34:25.3241110Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:34:25.4756590Z  50%|█████     | 1/2 [00:00<00:00,  8.80it/s]
2024-02-23T20:34:25.4758230Z 100%|██████████| 2/2 [00:00<00:00,  7.36it/s]
2024-02-23T20:34:25.4759470Z 100%|██████████| 2/2 [00:00<00:00,  7.53it/s]
2024-02-23T20:34:25.4945840Z 
2024-02-23T20:34:25.6871760Z   0%|          | 0/2 [00:00<?, ?it/s]
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2024-02-23T20:34:25.6994050Z 100%|██████████| 2/2 [00:00<00:00, 15.98it/s]
2024-02-23T20:34:25.7061230Z 
2024-02-23T20:34:25.7080960Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:34:25.7205180Z 100%|██████████| 2/2 [00:00<00:00, 39.36it/s]
2024-02-23T20:34:25.7619530Z ../Users/runner/work/pyiron_base/pyiron_base/pyiron_base/project/maintenance.py:291: UserWarning: 
2024-02-23T20:34:25.7626940Z                 The database statistics is only available for a Postgresql database
2024-02-23T20:34:25.7630090Z                 
2024-02-23T20:34:25.7636940Z   warnings.warn(
2024-02-23T20:34:26.5647010Z ...
2024-02-23T20:34:26.6453570Z   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:26.6455470Z 100%|██████████| 5/5 [00:00<00:00, 62.10it/s]
2024-02-23T20:34:29.4985290Z ..
2024-02-23T20:34:29.4986550Z TestWithProject: Setting up test project
2024-02-23T20:34:29.5189330Z The job toy_1 was saved and received the ID: 6
2024-02-23T20:34:29.5190190Z The job toy_2 was saved and received the ID: 7
2024-02-23T20:34:29.5191550Z The job toy_1 was saved and received the ID: 8
2024-02-23T20:34:29.5193340Z The job toy_2 was saved and received the ID: 9
2024-02-23T20:34:29.5195480Z The job toy_3 was saved and received the ID: 10
2024-02-23T20:34:29.6554310Z   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:29.7395720Z  80%|████████  | 4/5 [00:00<00:00, 25.57it/s]
2024-02-23T20:34:29.7399350Z 100%|██████████| 5/5 [00:00<00:00, 21.00it/s]
2024-02-23T20:34:29.8304200Z ..
2024-02-23T20:34:29.8304940Z TestWithProject: Setting up test project
2024-02-23T20:34:29.8306180Z 0it [00:00, ?it/s]
2024-02-23T20:34:29.8306730Z 0it [00:00, ?it/s]
2024-02-23T20:34:29.9172900Z sss.........s.......s..........s...s..2024-02-23 20:34:29,916 - pyiron_log - WARNING - Here is a warning
2024-02-23T20:34:30.0215110Z .................2024-02-23 20:34:30,021 - pyiron_log - WARNING - Credentials file can be read by other users - check permissions.
2024-02-23T20:34:31.9432530Z TestWithProject: Setting up test project
2024-02-23T20:34:31.9436210Z ....s......................................
2024-02-23T20:34:31.9452790Z 0it [00:00, ?it/s]
2024-02-23T20:34:31.9454420Z 0it [00:00, ?it/s]
2024-02-23T20:34:32.7675630Z s.........
2024-02-23T20:34:32.7676400Z TestWithProject: Setting up test project
2024-02-23T20:34:32.7681800Z 0it [00:00, ?it/s]
2024-02-23T20:34:32.7682570Z 0it [00:00, ?it/s]
2024-02-23T20:34:33.4253140Z s.........../Users/runner/work/pyiron_base/pyiron_base/pyiron_base/project/maintenance.py:291: UserWarning: 
2024-02-23T20:34:33.4254920Z                 The database statistics is only available for a Postgresql database
2024-02-23T20:34:33.4255990Z                 
2024-02-23T20:34:33.4256440Z   warnings.warn(
2024-02-23T20:34:33.4336360Z TestWithProject: Setting up test project
2024-02-23T20:34:33.4337160Z 
2024-02-23T20:34:33.4337460Z The job test_job was saved and received the ID: 6
2024-02-23T20:34:33.4847760Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:34:33.4848790Z 100%|██████████| 1/1 [00:00<00:00, 19.78it/s]
2024-02-23T20:34:33.5170780Z 
2024-02-23T20:34:33.5171560Z 0it [00:00, ?it/s]
2024-02-23T20:34:33.5172190Z 0it [00:00, ?it/s]
2024-02-23T20:34:33.5230690Z 
2024-02-23T20:34:33.5231650Z 0it [00:00, ?it/s]
2024-02-23T20:34:33.5232830Z 0it [00:00, ?it/s]
2024-02-23T20:34:33.8190810Z .
2024-02-23T20:34:33.8350580Z   0%|          | 0/1 [00:00<?, ?it/s]
2024-02-23T20:34:33.8353030Z 100%|██████████| 1/1 [00:00<00:00, 63.82it/s]
2024-02-23T20:34:35.0785790Z TestWithProject: Setting up test project
2024-02-23T20:34:35.0787520Z s
2024-02-23T20:34:35.0788300Z The job test_a was saved and received the ID: 6
2024-02-23T20:34:35.0789870Z The job test_b was saved and received the ID: 7
2024-02-23T20:34:35.0791530Z The job test_c was saved and received the ID: 8
2024-02-23T20:34:35.0793160Z The job test_d was saved and received the ID: 9
2024-02-23T20:34:35.0794860Z The job test_table was saved and received the ID: 10
2024-02-23T20:34:35.0854620Z Loading and filtering jobs:   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:35.0857160Z Loading and filtering jobs: 100%|██████████| 5/5 [00:00<00:00, 787.90it/s]
2024-02-23T20:34:35.0868370Z 
2024-02-23T20:34:35.0882410Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:34:35.0883980Z 100%|██████████| 2/2 [00:00<00:00, 1764.91it/s]
2024-02-23T20:34:35.2535520Z /Users/runner/work/pyiron_base/pyiron_base/pyiron_base/jobs/datamining.py:651: PerformanceWarning: 
2024-02-23T20:34:35.3540660Z your performance may suffer as PyTables will pickle object types that it cannot
2024-02-23T20:34:35.3619240Z map directly to c-types [inferred_type->mixed,key->block1_values] [items->Index(['name', 'array'], dtype='object')]
2024-02-23T20:34:35.4618940Z 
2024-02-23T20:34:35.4619670Z The job test_table was saved and received the ID: 10
2024-02-23T20:34:35.5508500Z   self.pyiron_table._df.to_hdf(
2024-02-23T20:34:35.5551940Z .
2024-02-23T20:34:35.5556800Z Loading and filtering jobs:   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:35.5561170Z Loading and filtering jobs: 100%|██████████| 5/5 [00:00<00:00, 528.94it/s]
2024-02-23T20:34:35.5565100Z 
2024-02-23T20:34:35.5569740Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:34:35.5575330Z 100%|██████████| 2/2 [00:00<00:00, 1378.35it/s]
2024-02-23T20:34:35.6041540Z /Users/runner/work/pyiron_base/pyiron_base/pyiron_base/jobs/datamining.py:651: PerformanceWarning: 
2024-02-23T20:34:35.6045020Z your performance may suffer as PyTables will pickle object types that it cannot
2024-02-23T20:34:35.6050450Z map directly to c-types [inferred_type->mixed,key->block1_values] [items->Index(['name', 'array'], dtype='object')]
2024-02-23T20:34:35.6053790Z 
2024-02-23T20:34:35.6055760Z   self.pyiron_table._df.to_hdf(
2024-02-23T20:34:35.9996420Z .
2024-02-23T20:34:35.9997270Z The job test_table was saved and received the ID: 10
2024-02-23T20:34:35.9999410Z Loading and filtering jobs:   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:36.0005520Z Loading and filtering jobs: 100%|██████████| 5/5 [00:00<00:00, 533.04it/s]
2024-02-23T20:34:36.0007720Z 
2024-02-23T20:34:36.0009280Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:34:36.0012870Z 100%|██████████| 2/2 [00:00<00:00, 1100.00it/s]
2024-02-23T20:34:36.1793440Z The job test_table was saved and received the ID: 10
2024-02-23T20:34:36.1794640Z .
2024-02-23T20:34:36.1848710Z Loading and filtering jobs:   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:36.1851000Z Loading and filtering jobs: 100%|██████████| 5/5 [00:00<00:00, 995.42it/s]
2024-02-23T20:34:36.1860680Z 
2024-02-23T20:34:36.1872370Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:34:36.1874020Z 100%|██████████| 2/2 [00:00<00:00, 2190.81it/s]
2024-02-23T20:34:36.5068690Z .
2024-02-23T20:34:36.5069560Z The job test_table was saved and received the ID: 10
2024-02-23T20:34:36.5122160Z Loading and filtering jobs:   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:36.5124120Z Loading and filtering jobs: 100%|██████████| 5/5 [00:00<00:00, 972.57it/s]
2024-02-23T20:34:36.5135480Z 
2024-02-23T20:34:36.5146340Z   0%|          | 0/2 [00:00<?, ?it/s]
2024-02-23T20:34:36.5147350Z 100%|██████████| 2/2 [00:00<00:00, 2167.04it/s]
2024-02-23T20:34:36.5643450Z /Users/runner/work/pyiron_base/pyiron_base/pyiron_base/jobs/datamining.py:651: PerformanceWarning: 
2024-02-23T20:34:36.5646680Z your performance may suffer as PyTables will pickle object types that it cannot
2024-02-23T20:34:36.5650520Z map directly to c-types [inferred_type->mixed,key->block1_values] [items->Index(['name', 'array'], dtype='object')]
2024-02-23T20:34:36.5652750Z 
2024-02-23T20:34:36.5653120Z   self.pyiron_table._df.to_hdf(
2024-02-23T20:34:36.7624110Z .
2024-02-23T20:34:36.8236880Z   0%|          | 0/4 [00:00<?, ?it/s]
2024-02-23T20:34:36.8238530Z 100%|██████████| 4/4 [00:00<00:00, 65.52it/s]
2024-02-23T20:34:38.0881480Z TestWithProject: Setting up test project
2024-02-23T20:34:38.1923620Z .
2024-02-23T20:34:38.1924200Z The job test_a was saved and received the ID: 6
2024-02-23T20:34:38.1986260Z Loading and filtering jobs:   0%|          | 0/5 [00:00<?, ?it/s]
2024-02-23T20:34:38.2571030Z The job test_b was saved and received the ID: 7
2024-02-23T20:34:38.2572470Z Loading and filtering jobs: 100%|██████████| 5/5 [00:00<00:00, 714.39it/s]
2024-02-23T20:34:38.2573330Z 
2024-02-23T20:34:38.2573650Z The job test_c was saved and received the ID: 8
2024-02-23T20:34:38.2576000Z The job test_d was saved and received the ID: 9
2024-02-23T20:34:38.2577220Z The job test_table was saved and received the ID: 10
2024-02-23T20:37:30.7053850Z ##[error]The action has timed out.
2024-02-23T20:37:30.7381440Z Post job cleanup.
2024-02-23T20:37:30.9676170Z [command]/usr/local/bin/git version
2024-02-23T20:37:30.9815000Z git version 2.43.0
2024-02-23T20:37:31.1645960Z Copying '/Users/runner/.gitconfig' to '/Users/runner/work/_temp/abc94698-4efd-4a12-9c86-fc8991bb9d2b/.gitconfig'
2024-02-23T20:37:31.2653050Z Temporarily overriding HOME='/Users/runner/work/_temp/abc94698-4efd-4a12-9c86-fc8991bb9d2b' before making global git config changes
2024-02-23T20:37:31.3549000Z Adding repository directory to the temporary git global config as a safe directory
2024-02-23T20:37:31.3630790Z [command]/usr/local/bin/git config --global --add safe.directory /Users/runner/work/pyiron_base/pyiron_base
2024-02-23T20:37:31.3787240Z [command]/usr/local/bin/git config --local --name-only --get-regexp core\.sshCommand
2024-02-23T20:37:31.4287210Z [command]/usr/local/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :"
2024-02-23T20:37:31.5352650Z [command]/usr/local/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2024-02-23T20:37:31.5358390Z http.https://github.com/.extraheader
2024-02-23T20:37:31.5375810Z [command]/usr/local/bin/git config --local --unset-all http.https://github.com/.extraheader
2024-02-23T20:37:31.5388130Z [command]/usr/local/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :"
2024-02-23T20:37:31.6138710Z Cleaning up orphan processes
2024-02-23T20:37:32.6681650Z Terminate orphan process: pid (8769) (python3.12)
2024-02-23T20:37:32.7164470Z Terminate orphan process: pid (8766) (python3.12)
2024-02-23T20:37:32.7591070Z Terminate orphan process: pid (6738) (python3.12)
2024-02-23T20:37:32.7788160Z Terminate orphan process: pid (6697) (python3.12)
@liamhuber
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@pmrv could this be related to #1350 or #1355 somehow?

@pmrv
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pmrv commented Feb 28, 2024

Did we agree on what to do in the mean time with open PRs? My gut feeling is that as long as other tests pass it's probably fine-ish.

@liamhuber
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Did we agree on what to do in the mean time with open PRs? My gut feeling is that as long as other tests pass it's probably fine-ish.

We didn't agree. The default position should be "don't merge things that don't pass tests". Your proposal for an exception in this case is not unreasonable, but I have a deep discomfort with the idea 😝

@jan-janssen jan-janssen linked a pull request Feb 29, 2024 that will close this issue
Increase timeout from 5min to 10min #1363
Closed
This was linked to pull requests Mar 17, 2024
Disable multi-core pyiron table test for mac os x #1383
Closed
pyiron table: Use with-statement for executor #1384
Merged
@jan-janssen jan-janssen removed a link to a pull request Mar 18, 2024
pyiron table: Use with-statement for executor #1384
Merged
@jan-janssen jan-janssen linked a pull request Mar 19, 2024 that will close this issue
Mac Os - pympipool: Use localhost for connection rather than the network address #1390
Merged
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@pmrv @liamhuber