Fold packages #610

marcpaterno · 2026-01-27T19:02:58Z

Description

This PR consolidates the ccl_factory module into modeling_tools and moves the parameters module into updatable to improve code organization and better reflect the architectural relationships between these components.

The CCL factory functionality is closely related to modeling tools and now resides within the same module. Similarly, parameter-related classes are now part of the updatable module, reflecting their tight coupling with updatable objects.

Both old modules (firecrown.ccl_factory and firecrown.parameters) remain as deprecated compatibility layers that re-export from their new locations with deprecation warnings, ensuring backward compatibility for existing code.

All imports throughout the codebase (examples, tests, connectors, and tutorials) have been updated to use the new module paths.

Type of Change

Refactoring, with backward compatibility support

Checklist:

The following checklist will make sure that you are following the code style and
guidelines of the project as described in the
contributing page.

[x] I have run bash pre-commit-check and fixed any issues
[x] I have added tests that prove my fix is effective or that my feature works
[x] I have made corresponding changes to the documentation
[ ] I have 100% test coverage for my changes (please check this after the CI system has verified the coverage)

* Introduce BinPairSelector class system for bin combinations. * Reorganize all tutorials. * New tutorial for Selectors. --------- Co-authored-by: Marc Paterno <[email protected]>

Consolidate the ccl_factory module into modeling_tools to improve code organization. The CCL factory functionality is closely related to the modeling tools and belongs in the same module. Changes: - Move ccl_factory submodules into modeling_tools as _ccl_* files - Update modeling_tools __init__ to export CCL factory classes - Replace ccl_factory with deprecation wrapper that re-exports - Update all imports across examples, tests, and connectors - Add deprecation warning when ccl_factory is imported - Add tests for deprecated module backward compatibility - Rename test_ccl_factory.py to test_modeling_tools_ccl_factory.py

Correct the module path reference in the two-point integration tutorial from `firecrown.generators.inferred_galaxy_zdist` to `firecrown.generators`, which is the accurate import location for the lens and source redshift bin collections.

The firecrown.parameters module has been moved into firecrown.updatable to better reflect the architectural relationship between parameters and updatable objects. All parameter-related classes (DerivedParameter, DerivedParameterCollection, InternalParameter, ParamsMap, RequiredParameters, SamplerParameter) and functions (handle_unused_params, parameter_get_full_name, register_new_updatable_parameter) are now exported from firecrown.updatable. The old firecrown.parameters module remains as a deprecated compatibility layer that re-exports from firecrown.updatable with deprecation warnings. All imports throughout the codebase have been updated to use firecrown.updatable instead of firecrown.parameters. Tests have been added to verify the deprecated module continues to work correctly with appropriate warnings, and existing parameter tests have been renamed to reflect their new location.

Copilot

Pull request overview

This is a significant refactoring pull request titled "Fold packages" that reorganizes Firecrown's module structure and adds extensive tutorial documentation. The PR includes:

Changes:

Module reorganization: Moves parameter-related classes from firecrown.parameters to firecrown.updatable, and CCL factory classes from firecrown.ccl_factory to firecrown.modeling_tools
Deprecation wrappers: Maintains backward compatibility through deprecated modules with proper warnings
New tutorial structure: Adds 6 new comprehensive tutorial files for two-point statistics workflows
Bin pair selectors: Introduces a powerful new filtering system for tomographic bin pair selection
Generator naming: Updates LSST bin naming convention to be more systematic

Reviewed changes

Copilot reviewed 114 out of 118 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
tutorial/*.qmd	New comprehensive tutorial documentation
firecrown/parameters/init.py	Deprecation wrapper maintaining backward compatibility
firecrown/ccl_factory/init.py	Deprecation wrapper maintaining backward compatibility
firecrown/updatable/*	Reorganized parameter-related functionality
firecrown/modeling_tools/*	Reorganized CCL factory functionality
firecrown/metadata_types/_pair_selector.py	New bin pair selector system (780 lines)
tests/*	Updated imports throughout test suite
examples/*	Updated imports in example scripts

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Copilot · 2026-01-27T19:06:28Z

tests/test_ccl_factory_deprecated.py

+        match="firecrown.ccl_factory is deprecated and will be removed",
+    ):
+        # pylint: disable=import-outside-toplevel,unused-import
+        import firecrown.ccl_factory  # noqa: F401


Module 'firecrown.ccl_factory' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:28Z

tests/test_ccl_factory_deprecated.py

+    We just verify the module is importable.
+    """
+    # pylint: disable=import-outside-toplevel,unused-import
+    import firecrown.ccl_factory  # noqa: F401


Module 'firecrown.ccl_factory' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:28Z

tests/test_ccl_factory_deprecated.py

+def test_module_import_as_alias():
+    """Test importing the module with an alias."""
+    # pylint: disable=import-outside-toplevel
+    import firecrown.ccl_factory as fac


Module 'firecrown.ccl_factory' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:29Z

tests/test_ccl_factory_deprecated.py

+def test_ccl_factory_all_list():
+    """Test that __all__ is preserved in deprecated module."""
+    # pylint: disable=import-outside-toplevel
+    import firecrown.ccl_factory


Module 'firecrown.ccl_factory' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:29Z

tests/likelihood/gauss_family/test_const_gaussian.py

 import sacc

-import firecrown.parameters
+import firecrown.updatable


Module 'firecrown.updatable' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:30Z

tests/test_parameters_deprecated.py

+        warnings.simplefilter("always")
+        # Import should trigger warning
+        # pylint: disable=unused-import,import-outside-toplevel
+        import firecrown.parameters  # noqa: F401


Module 'firecrown.parameters' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:30Z

tests/test_parameters_deprecated.py

+def test_parameters_exports_all_names():
+    """All expected names should be available from firecrown.parameters."""
+    # pylint: disable=import-outside-toplevel
+    import firecrown.parameters as params


Module 'firecrown.parameters' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:30Z

tests/test_parameters_deprecated.py

+def test_parameters_exports_are_same_as_updatable():
+    """Exported names should be the same objects as in firecrown.updatable."""
+    # pylint: disable=import-outside-toplevel
+    import firecrown.parameters as params


Module 'firecrown.parameters' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:31Z

tests/test_pt_systematics.py

-from firecrown.ccl_factory import CCLFactory, PoweSpecAmplitudeParameter
-import firecrown.parameters as fcp
+from firecrown.modeling_tools import CCLFactory, PoweSpecAmplitudeParameter
+import firecrown.updatable as fcp


Module 'firecrown.updatable' is imported with both 'import' and 'import from'.

Copilot · 2026-01-27T19:06:31Z

tests/likelihood/gauss_family/test_student_t.py

 import sacc

-import firecrown.parameters
+import firecrown.updatable


Module 'firecrown.updatable' is imported with both 'import' and 'import from'.

codecov · 2026-01-27T19:22:20Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.0%. Comparing base (de854f0) to head (f55f3c2).
⚠️ Report is 2 commits behind head on devel.

Additional details and impacted files

@@           Coverage Diff            @@
##            devel     #610    +/-   ##
========================================
  Coverage   100.0%   100.0%            
========================================
  Files         150      151     +1     
  Lines        8787     9044   +257     
  Branches     1012     1033    +21     
========================================
+ Hits         8787     9044   +257

Files with missing lines	Coverage Δ
firecrown/app/analysis/_types.py	`100.0% <100.0%> (ø)`
firecrown/app/cosmology.py	`100.0% <100.0%> (ø)`
firecrown/app/examples/_cosmic_shear_template.py	`100.0% <100.0%> (ø)`
...irecrown/app/examples/_des_y1_3x2pt_pt_template.py	`100.0% <100.0%> (ø)`
firecrown/app/examples/_des_y1_3x2pt_template.py	`100.0% <100.0%> (ø)`
...app/examples/_des_y1_cosmic_shear_hmia_template.py	`100.0% <100.0%> (ø)`
...mples/_des_y1_cosmic_shear_pk_modifier_template.py	`100.0% <100.0%> (ø)`
...app/examples/_des_y1_cosmic_shear_tatt_template.py	`100.0% <100.0%> (ø)`
firecrown/app/examples/_sn_srd_template.py	`100.0% <100.0%> (ø)`
firecrown/ccl_factory/__init__.py	`100.0% <100.0%> (ø)`
... and 44 more

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marcpaterno · 2026-01-27T19:24:00Z

Close because of confusion with earlier commits. Will create a new PR.

marcpaterno and others added 6 commits January 12, 2026 15:20

Temporarily pin numpy to less than version 2.4 (#604)

855ac88

Introducing BinPairSelector class system for bin pair selection. (#552)

a92b250

* Introduce BinPairSelector class system for bin combinations. * Reorganize all tutorials. * New tutorial for Selectors. --------- Co-authored-by: Marc Paterno <[email protected]>

Fix Module Path In Tutorial

ea32a02

Correct the module path reference in the two-point integration tutorial from `firecrown.generators.inferred_galaxy_zdist` to `firecrown.generators`, which is the accurate import location for the lens and source redshift bin collections.

Pin black version for formatting stability

f55f3c2

marcpaterno requested review from Copilot and vitenti January 27, 2026 19:02

Copilot started reviewing on behalf of marcpaterno January 27, 2026 19:03 View session

Copilot AI reviewed Jan 27, 2026

View reviewed changes

marcpaterno closed this Jan 27, 2026

marcpaterno deleted the fold_packages branch January 27, 2026 19:26

marcpaterno restored the fold_packages branch January 27, 2026 19:26

marcpaterno deleted the fold_packages branch January 27, 2026 23:03

Fold packages #610

Fold packages #610

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