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feat: Copy over the code from diffpy.srfit.structure to here - #1

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sbillinge merged 18 commits into
diffpy:mainfrom
cadenmyers13:cp-source
Oct 16, 2026
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feat: Copy over the code from diffpy.srfit.structure to here#1
sbillinge merged 18 commits into
diffpy:mainfrom
cadenmyers13:cp-source

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@cadenmyers13 cadenmyers13 commented Oct 7, 2026 •
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I took some liberty to

  1. update the docstrings so they are better
  2. rename some functions, variables, and attributes to be more descriptive
  3. reformat the tests so they follow actual_* == expected_* with case names

Also had to revert the max python version to 3.13 because of srreal

cadenmyers13 and others added 11 commits October 7, 2026 11:13
@cadenmyers13 @claude
chore: copy structure subpackage and tests from diffpy.srfit
c2686b4 
Copy src/diffpy/srfit/structure/ and its tests (test_diffpyparset,
test_objcrystparset, test_sgconstraints, plus LaMnO3.stru) verbatim
from diffpy.srfit upstream/main (8d8931a). No edits, so imports still
point at diffpy.srfit.structure and are fixed in the next commit.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
fix: repoint structure imports at diffpy.cmistructure
c4c83e7 
Replace diffpy.srfit.structure imports and references with
diffpy.cmistructure in the copied modules and tests, and make the
package importable and testable:

- __init__.py: restore the package header and __version__ import.
- src/diffpy/__init__.py: add extend_path so diffpy.cmistructure does
  not shadow the rest of the diffpy namespace.
- pyproject.toml: point the entry point at cmistructure_app:main.
- requirements: declare diffpy.srfit, diffpy.structure, diffpy.srreal,
  and pyobjcryst for tests.
- tests: add datafile and availability fixtures and tests/__init__.py;
  remove the template functions.py and its test.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
refactor: remove deprecation shims carried over from srfit
ca2a52f 
diffpy.cmistructure has never been released, so it has no users to
migrate. Drop constrainAsSpaceGroup, the three StretchModeParameter
setConst forwarders in objcrystparset, their deprecation messages and
diffpy.utils._deprecator imports, and the test for the
constrainAsSpaceGroup warning.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
refactor: rename camelCase API to snake_case with NumPy docstrings
4a847fe 
Rename every camelCase function and method in the package to snake_case
(e.g. canAdapt -> can_adapt, getScatterers -> get_scatterers,
restrainBondLength -> restrain_bond_length, struToParameterSet ->
stru_to_parameter_set), along with their call sites and tests. No
deprecation aliases are kept since the package has not been released.

Rewrite the public docstrings to the NumPy style: imperative one-line
summary, typed Parameters/Returns/Raises sections with descriptions
starting with "The", and the nonstandard "Managed Parameters" and
"Inherited Attributes" sections folded into Attributes.

Also replace ObjCrystMoleculeParSet.get_lattice's calls to newPar, which
no longer exists on srfit's ParameterSet, with new_parameter.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13
news fix
82807b1
@cadenmyers13
precommit fixes
547af59
@cadenmyers13 @claude
refactor: spell out abbreviated parameter, function, and attribute names
50a3c7b 
Replace abbreviations in the public API with full words, e.g.
stru_to_parameter_set -> structure_to_parameter_set, stru -> structure,
scat -> scatterer, res -> restraint, par -> parameter, cryst -> crystal,
idx -> index, sg -> space_group, matoms -> mutated_atoms,
angunits -> angle_units, sgpars -> space_group_parameters, and
latpars/xyzpars/adppars -> lattice/xyz/adp_parameters.

Parameters that have default values (sig, w, sgoffset, constrainlat,
adpsymbols, isosymbol, ...) and the default container name "sgpars"
are unchanged so keyword-argument callers keep working. Class and
module names are unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
test: remove package-availability skips
7b730f8 
pyobjcryst and diffpy.structure are declared test and runtime
dependencies, so the tests should fail rather than silently skip when
they are missing. Remove the pyobjcryst_available and
diffpy_structure_available fixtures, their skip checks, and the cctbx
import guard in the already-disabled xtestCreateSpaceGroup.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
test: use actual/expected assertions with case comments
b179b90 
Rewrite the assertions in test_diffpyparset, test_objcrystparset and
test_sgconstraints as `assert actual_* == expected_*`, with the code
under test on the actual side, and add C#/Expected comments for each
logical stage. Related checks (e.g. which coordinates are fixed, which
atoms moved) are compared as one dict or list so a failure reports
every mismatch at once. What each test checks, including tolerances,
is unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
chore: add diffpy.cmistructure headers to moved modules and tests
c6a87c0 
Merge the diffpy.cmistructure header into the original diffpy.srfit
header of each module and test moved from diffpy.srfit.structure. The
Columbia University copyright and original author are kept, as the BSD
license requires, and the header points to both LICENSE.rst and
LICENSE_DANSE.rst.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
chore: add LICENSE_DANSE.rst from diffpy.srfit
07c16ef 
The modules moved from diffpy.srfit.structure are covered by the DANSE
license from Columbia University, which must be distributed with them.
Copy it verbatim from diffpy.srfit; MANIFEST.in already includes
LICENSE*.rst in the sdist.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13

cadenmyers13 commented Oct 7, 2026

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@sbillinge ready for review. Please check that the headers in the source and tests files have the copyright correctly formated.

cadenmyers13 and others added 2 commits October 7, 2026 12:17
@cadenmyers13
change python version to 3.11-3.13
18c02f7
@cadenmyers13 @claude
fix: use non-deprecated diffpy.structure APIs
d774950 
Replace calls that diffpy.structure has deprecated for removal in 4.0.0
with their snake_case equivalents: GetSpaceGroup -> get_space_group,
positionFormulas -> position_formulas, UFormulas -> u_formulas,
IsSpaceGroupIdentifier -> is_space_group_identifier and, in the tests,
Lattice.setLatPar -> set_latt_parms. All of these exist in
diffpy.structure 3.4.0 and later.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13

cadenmyers13 commented Oct 7, 2026

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Some problems with testing... investigating

@sbillinge

sbillinge commented Oct 7, 2026

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is it that we haven't published to CF one of the dependencies with the deprecated variable names?

@cadenmyers13

cadenmyers13 commented Oct 8, 2026

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@sbillinge Yeah, something along those lines. In concept this migration is straightforward but in practice I need to think about it carefully. Im working with claude to come up with a good plan

@sbillinge

sbillinge commented Oct 8, 2026

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we don't need tests passing in principle to get this started. So don't stress oo much. As long as we don't break what is in produciton.

@cadenmyers13

cadenmyers13 commented Oct 8, 2026

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@sbillinge Yeah you're right. I'm working on some srfit cleanup today to ensure we're good over there before proceeding here which I think is necessary to some extent. I think we are going to need a small release of srfit before much work can be done here. Otherwise, we'll make additions here, fixes in srfit, then will have to make changes here again which adds extra unnecessary work

cadenmyers13 and others added 2 commits October 16, 2026 10:15
@cadenmyers13 @claude
fix: sync structure code with diffpy.srfit 3.4.0
ff73788 
Port the srfit changes to structure/ made after 8d8931a (#217, #220,
#226, #227) that d774950 did not already cover:

- objcrystparset.py: add molecule restraints through
  register_soft_bounds so the recipe is notified, and call add_observer
  instead of the deprecated addObserver.
- BVSRestraint and ObjCrystMoleculeRestraint: add __str__ so show()
  lists the restraint settings.
- Docstrings: point at remove_soft_bounds instead of the deprecated
  unrestrain.
- Tests: port srfit's three show() restraint tests and the
  capturestdout fixture.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
ci: install diffpy.srfit 3.4.0rc0 in CI
2cc4b01 
cmistructure needs srfit 3.4.0 names (add_parameter, register_soft_bounds,
add_observer), but conda-forge only has 3.3.1. Install the rc from PyPI
in the workflows' run step until 3.4.0 is on conda-forge.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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cadenmyers13 and others added 3 commits October 16, 2026 13:05
@cadenmyers13 @claude
fix: restore srfit's space group container names
865a211 
Revert the 50a3c7b renames of .sgpars, .latpars, .xyzpars and .adppars
(and their container names) per decision 8 of the split plan. diffpy.cmi
examples use these names 45 times, and as container names they appear in
parameter paths and fit results, so srfit cannot deprecate them cleanly.
The other attribute renames (stru, scat, res, matoms, angunits, ...) stay,
since srfit can forward those through properties.

Also add tests that pin the four names and drop the unittest.main()
leftovers from the structure test files.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
build: set Python 3.12-3.13, add pyobjcryst, check internal deprecations
685ad92 
- pyproject.toml, cookiecutter.json: support Python 3.12-3.13 only,
  since diffpy.srreal has no Python 3.14 build and 3.11 is below
  srfit's minimum.
- conda.txt, pip.txt: add pyobjcryst, a runtime dependency of
  objcrystparset.py.
- pyproject.toml: fail tests when cmistructure calls its own deprecated
  names, matching srfit.
- docs: replace the template API page with the cmistructure modules.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@cadenmyers13 @claude
build: support Python 3.11-3.13 for now
9902807 
Set requires-python, the classifiers and cookiecutter.json to
3.11-3.13, matching the other diffpy.cmi* packages.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@sbillinge
sbillinge merged commit 7066dd2 into diffpy:main Oct 16, 2026
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@cadenmyers13 @sbillinge