Refactor #796

jan-janssen · 2022-07-22T01:18:42Z

The new structure consists of:

cli - command line interface
database - database interface
interfaces - abstract definition of interfaces
jobs - all job classes defined in pyiron_base
project - the project class
state - the configuration object
storage - the HDF5 interface
utils - general utilities which do not belong to one of the above

For more details:
pyiron/pyiron_developer_tutorial#6

jan-janssen · 2022-07-22T02:08:05Z

One error remaining:

======================================================================
[279](https://github.com/pyiron/pyiron_base/runs/7460806627?check_suite_focus=true#step:5:280)
FAIL: test_copy_to_job (job.test_copyto.TestCopyTo)
[280](https://github.com/pyiron/pyiron_base/runs/7460806627?check_suite_focus=true#step:5:281)
----------------------------------------------------------------------
[281](https://github.com/pyiron/pyiron_base/runs/7460806627?check_suite_focus=true#step:5:282)
Traceback (most recent call last):
[282](https://github.com/pyiron/pyiron_base/runs/7460806627?check_suite_focus=true#step:5:283)
  File "/home/runner/work/pyiron_base/pyiron_base/tests/job/test_copyto.py", line 15, in test_copy_to_job
[283](https://github.com/pyiron/pyiron_base/runs/7460806627?check_suite_focus=true#step:5:284)
    self.assertTrue(job_ser['job_single/input/custom_dict'] is not None)
[284](https://github.com/pyiron/pyiron_base/runs/7460806627?check_suite_focus=true#step:5:285)
AssertionError: False is not true

jan-janssen · 2022-07-22T02:38:13Z

The integration tests fail until pyiron/pyiron_atomistics#687 is merged.

# Conflicts: # pyiron_base/__init__.py

jan-janssen · 2022-07-22T04:34:54Z

======================================================================
[871](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:872)
ERROR: sphinx.test_structure (unittest.loader._FailedTest)
[872](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:873)
----------------------------------------------------------------------
[873](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:874)
ImportError: Failed to import test module: sphinx.test_structure
[874](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:875)
Traceback (most recent call last):
[875](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:876)
  File "/usr/share/miniconda/envs/test/lib/python3.10/unittest/loader.py", line 436, in _find_test_path
[876](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:877)
    module = self._get_module_from_name(name)
[877](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:878)
  File "/usr/share/miniconda/envs/test/lib/python3.10/unittest/loader.py", line 377, in _get_module_from_name
[878](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:879)
    __import__(name)
[879](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:880)
  File "/home/runner/work/pyiron_base/pyiron_atomistics/tests/sphinx/test_structure.py", line 10, in <module>
[880](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:881)
    from pyiron_atomistics.atomistics.structure.atoms import Atoms
[881](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:882)
  File "/home/runner/work/pyiron_base/pyiron_atomistics/pyiron_atomistics/atomistics/structure/atoms.py", line 18, in <module>
[882](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:883)
    from pyiron_atomistics.atomistics.structure.pyscal import pyiron_to_pyscal_system
[883](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:884)
  File "/home/runner/work/pyiron_base/pyiron_atomistics/pyiron_atomistics/atomistics/structure/pyscal.py", line 7, in <module>
[884](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:885)
    import pyiron_atomistics.atomistics.structure.atoms
[885](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:886)
  File "/home/runner/work/pyiron_base/pyiron_atomistics/pyiron_atomistics/__init__.py", line 4, in <module>
[886](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:887)
    from pyiron_atomistics.project import Project
[887](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:888)
  File "/home/runner/work/pyiron_base/pyiron_atomistics/pyiron_atomistics/project.py", line 32, in <module>
[888](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:889)
    from pyiron_atomistics.atomistics.structure.atoms import Atoms
[889](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:890)
ImportError: cannot import name 'Atoms' from partially initialized module 'pyiron_atomistics.atomistics.structure.atoms' (most likely due to a circular import) (/home/runner/work/pyiron_base/pyiron_atomistics/pyiron_atomistics/atomistics/structure/atoms.py)
[890](https://github.com/pyiron/pyiron_base/runs/7461310675?check_suite_focus=true#step:8:891)

jan-janssen · 2022-07-22T04:50:26Z

Waiting for pyiron/pyiron_contrib#459

jan-janssen · 2022-07-22T14:49:56Z

Ready for review

liamhuber · 2022-07-23T05:14:19Z

Won't be able to look at it in depth until Monday, but I like the principle and the top level folder names look pretty reasonable!

jan-janssen · 2022-07-25T13:19:15Z

pyiron_base/storage/hdfio.py

@@ -1366,7 +1366,14 @@ def to_object(self, class_name=None, **qwargs):
            )
        class_name = class_name or self.get("TYPE")
        class_path = class_name.split("<class '")[-1].split("'>")[0]
-        if not class_path.startswith("abc."):
+        class_convert_dict = {  # Fix backwards compatibility


Add comment up to which version this backwards fix is required 0.5.19

jan-janssen · 2022-07-25T13:21:36Z

Move object to interfaces

jan-janssen · 2022-07-25T13:22:46Z

Split pyiron_base.utils.util into separate modules.

jan-janssen · 2022-07-25T13:23:52Z

Add description

pmrv · 2022-09-02T09:50:23Z

It would be nice to have a little spec file that details what code goes into which module for new devs.

jan-janssen added 6 commits July 21, 2022 19:18

Refactoring

0be71b8

Refactoring

ab77bba

black formating

9066985

bug fixes

a0cc357

more bug fixes

b153bfa

and more

0fb2b43

jan-janssen added 2 commits July 21, 2022 20:10

another round of fixes

befab20

fixes for static_isinstance()

34d622b

jan-janssen added the integration Start the integration tests with pyiron_atomistics/contrib for this PR label Jul 22, 2022

Add more imports to __init__.py

ff571ed

jan-janssen added 4 commits July 21, 2022 20:39

Merge remote-tracking branch 'origin/init' into refactor

9acd39d

# Conflicts: # pyiron_base/__init__.py

Merge remote-tracking branch 'origin/master' into refactor

90ca3d2

fix file data

6f5bc11

Merge remote-tracking branch 'origin/master' into refactor

aa9db5c

# Conflicts: # pyiron_base/__init__.py

jan-janssen added 2 commits July 21, 2022 22:40

Merge remote-tracking branch 'origin/master' into refactor

28e0cd4

Fix import loop

8676713

jan-janssen added 4 commits July 22, 2022 07:08

backwards compatiblity for old classes

fc095a2

add more classes

566faf0

only required for inputlist and datacontainer

39c570f

minor bugfix

b570576

jan-janssen mentioned this pull request Jul 22, 2022

Introduction to pyiron_base pyiron/pyiron_developer_tutorial#6

Open

jan-janssen commented Jul 25, 2022

View reviewed changes

liamhuber approved these changes Jul 25, 2022

View reviewed changes

jan-janssen added 3 commits July 25, 2022 20:49

Corrections as discussed in the pyiron meeting

efd3451

black formatting

f5d16e4

fix Docstrings

c09d890

jan-janssen merged commit 9827ff4 into master Jul 26, 2022

delete-merged-branch bot deleted the refactor branch July 26, 2022 03:49

pmrv mentioned this pull request Sep 2, 2022

Import breaks with newer pyiron_base version pyiron/pyiron_gui#168

Closed

pmrv mentioned this pull request Nov 25, 2022

Add flattenedstorage to backwards compat list of class loading paths #909

Merged

pmrv mentioned this pull request Jul 11, 2023

Pyiron tables: Backwards compatibility broken again by #796 #1163

Closed

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Refactor #796

Refactor #796

jan-janssen commented Jul 22, 2022 •

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pmrv commented Sep 2, 2022

Refactor #796

Refactor #796

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