Nexus: replace obj and DevBase classes by jtkrogel · Pull Request #6037 · QMCPACK/qmcpack

jtkrogel · 2026-07-11T20:57:16Z

This PR replaces the old obj and DevBase with new streamlined versions. This was done because:

The old classes introduced an inordinate amount of functions and baggage.
The old classes included functions that masked other standard Python classes like list, making it very hard to reason about the code.
The new classes provide a cleaner, minimal base for future Nexus development that is also friendlier to incoming/new developers.
The new classes mirror classes developed by me outside of Nexus. With these updates, I will be able to integrate functionality developed externally into Nexus proper (e.g. multideterminant file handling, SHDMC functionality, etc).

A main change it to make the widely used obj class dict-conformant. It now operates as a standard container class and enables design choices based on use case or preference between obj and dict. A natural consequence is that users can now use dict as Nexus inputs wherever obj was used (and sometimes required) previously. This insulates users from having to be aware of any Nexus-specific container semantics.

The DevBase class also no longer inherits directly from obj. In this sense, it is no longer a generic container (this is too broad for a generic base class), but instead only introduces simpler conveniences like iterability.

Extensive efforts have been made to complete the rollover without introducing errors due to the significant change in the obj and DevBase interfaces. Defensive measures have been taken to minimize the impact of any uncaptured errors to the Nexus userbase. Intermediate classes have been introduced that inherit a defensive interface: any interaction with the new obj and DevBase classes that uses a deprecated part of the old interface will raise an error that

Instructs the user to report the error to the developers.
Provides instructions on how to restore the original functionality by uncommenting two lines in the source.

It is envisioned that the original classes (now obj_deprecated and DevBaseDeprecated) will be removed along with the intermediary classes in an upcoming release. This will give the user base some time to report issues before the final rollover occurs. At that point, only the obj and DevBase classes will remain - so please tolerate the temporary (but ugly) intermediate class hierarchy. Future refactoring will simplify the current generic.py, developer.py, and developer_tools.py (pure obj and DevBase classes) modules in the codebase.

This PR was developed with assistance from ChatGPT 5.6 Sol.

prckent · 2026-07-12T15:39:44Z

Excellent. I assume we'll be merging on Tuesday or later once our self-hosted CI is back and people have had time to provide feedback. Q. Does this need sequencing around any of the existing PRs?

brockdyer03

Got through all of the changes in bin, examples, and tests. Lots of leftover comment lines, some prints, some unused functions spotted.

So far I haven't noticed any really critical flaws in the changes, though I haven't seen much of the library code yet.

brockdyer03 · 2026-07-12T15:09:43Z

@@ -713,7 +713,8 @@ if __name__=='__main__':
    fit_type = args.fit_type
    if fit_type in fit_types:
        fit_functions.clear()
-        fit_functions.transfer_from(all_fit_functions[fit_type])
+        #fit_functions.transfer_from(all_fit_functions[fit_type])


Leftover comment?

brockdyer03 · 2026-07-12T15:13:55Z

+
+
+
+


Slightly excessive whitespace.

brockdyer03 · 2026-07-12T18:08:57Z

@@ -60,7 +59,8 @@ def test_xsffile(tmp_path):

    # populate reference object
    ref = XsfFile()
-    ref.set(
+    #ref.set(


Leftover comment

brockdyer03 · 2026-07-12T18:09:06Z

@@ -178,7 +178,8 @@ def test_poscar_file(tmp_path):

    # populate reference object
    ref = PoscarFile()
-    ref.set(
+    #ref.set(


brockdyer03 · 2026-07-12T18:09:57Z

@@ -247,6 +247,8 @@ def test_analyze():
            ),
        )

-    assert(object_eq(ga.to_obj(),ga_ref))
+    print_diff(to_obj(ga),ga_ref)


Leftover from testing?

brockdyer03 · 2026-07-12T18:50:47Z

@@ -151,7 +151,8 @@ def check_generated_files(
        #end if
        if failed:
            # report on failures
-            from nexus.generic import obj
+            #from nexus.generic import obj


brockdyer03 · 2026-07-12T18:51:44Z

@@ -40,7 +40,9 @@ def format_value(v):


 def make_serial_reference(gi):


This function is unused

brockdyer03 · 2026-07-12T18:52:34Z

@@ -141,7 +143,8 @@ def get_serial_references():
 def check_vs_serial_reference(gi,name):
    from ..developer import obj
    sr = obj(get_serial_references()[name])
-    sg = gi.serial()
+    #sg = gi.serial()


brockdyer03 · 2026-07-12T18:52:54Z

@@ -17,7 +17,8 @@


 def test_read():
-    from ..developer import obj
+    #from ..developer import obj


brockdyer03 · 2026-07-12T18:53:01Z

@@ -241,7 +242,8 @@ def test_read():
    x = readxml(TEST_FILES['vmc.in.xml'])
    assert(isinstance(x,XMLelement))
    x.remove_hidden()
-    o = x.to_obj()
+    #o = x.to_obj()


brockdyer03 · 2026-07-12T19:01:58Z

Q. Does this need sequencing around any of the existing PRs?

I think this PR should wait until #6030 is merged, but that is already set to happen on Tuesday once the self-hosted CI comes back online.

@jtkrogel will need to resolve any merge conflicts too, though I doubt there will be that many truly challenging merge conflicts.

jtkrogel · 2026-07-14T01:37:31Z

Thanks for the review. Out at the beach. Will address Friday.

jtkrogel added 19 commits June 23, 2026 01:32

nexus: partial, no physical system

2752caf

nexus: through NexusCore

827797d

nexus: all tests pass

33ca92b

nexus: small change

75e429e

nexus: add

bc14813

nexus: fix more old obj usage

0cfde92

nexus: more fixes

e15e334

nexus: partial fix for disabling DevBase.copy

3bf677b

nexus: more fixes for disabling DevBase.copy

fff6fd6

nexus: fixes

634be52

nexus: migrate hidden to new obj

da91b2e

nexus: restore imports

5523bd8

nexus: add deeper dict-like tests

528bfd2

nexus: remove not_implemented

12d1244

nexus: move functions

4d5401e

nexus: start dev refactor

d3747ff

nexus: partial refactor

1d726b8

nexus: add defenses

3084a4c

nexus: add final tests

514cb55

jtkrogel requested a review from brockdyer03 July 11, 2026 20:57

nexus: missing *

28564db

brockdyer03 requested changes Jul 12, 2026

View reviewed changes

		@@ -40,7 +40,9 @@ def format_value(v):


		def make_serial_reference(gi):

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brockdyer03 commented Jul 12, 2026

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jtkrogel commented Jul 11, 2026 •

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