Fold packages #611

marcpaterno · 2026-01-27T19:28:41Z

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.

I have run bash pre-commit-check and fixed any issues
I have added tests that prove my fix is effective or that my feature works
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)

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 PR reorganizes Firecrown’s public API by moving ccl_factory into modeling_tools and moving parameter-related classes into updatable, while keeping firecrown.ccl_factory and firecrown.parameters as deprecated re-export shims for backward compatibility.

Changes:

Move/rehydrate CCL factory types/enums/models under firecrown.modeling_tools and update all imports accordingly.
Move/re-export parameter APIs under firecrown.updatable and update imports across code, tests, examples, and tutorials.
Add deprecation-layer tests for firecrown.parameters and firecrown.ccl_factory.

Reviewed changes

Copilot reviewed 93 out of 97 changed files in this pull request and generated 15 comments.

Show a summary per file

File	Description
tutorial/two_point_scale_cuts.qmd	Update tutorial imports to use `firecrown.modeling_tools.CCLFactory`.
tutorial/two_point_integration.qmd	Update docs to reference constants from `firecrown.generators`.
tutorial/two_point_factory_basics.qmd	Update tutorial imports to `firecrown.modeling_tools`/`firecrown.updatable`.
tutorial/systematics.qmd	Update tutorial parameter import to `firecrown.updatable`.
tutorial/inferred_zdist.qmd	Update tutorial imports to `firecrown.modeling_tools`/`firecrown.updatable`.
tests/test_updatable_parameters.py	Consolidate parameter/updatable imports under `firecrown.updatable`.
tests/test_updatable.py	Adjust imports for moved parameter symbols; still imports deprecated module.
tests/test_scale_cuts_with_window.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/test_pt_systematics.py	Update CCLFactory/parameter imports to new modules.
tests/test_parameters_deprecated.py	New tests validating `firecrown.parameters` deprecation shim behavior.
tests/test_number_counts_magnification_bias_systematic.py	Update parameter import to `firecrown.updatable`.
tests/test_modeling_tools_ccl_factory.py	Update imports to use `firecrown.modeling_tools` CCL factory API.
tests/test_modeling_tools.py	Update imports to use `firecrown.modeling_tools` types.
tests/test_hm_systematics.py	Update CCLFactory import to `firecrown.modeling_tools`.
tests/test_cmb_factories.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/test_ccl_factory_deprecated.py	New tests validating `firecrown.ccl_factory` deprecation shim behavior.
tests/test_bug_398.py	Update CCLFactory imports to `firecrown.modeling_tools`.
tests/models/two_point/test_theory.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/metadata/test_metadata_two_point_sacc.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/likelihood/test_weak_lensing.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/likelihood/test_likelihood.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/likelihood/test_factories.py	Update in-test import to `firecrown.modeling_tools.CCLFactory`.
tests/likelihood/lkdir/lkscript_pure_ccl.py	Update CCL factory imports to `firecrown.modeling_tools`.
tests/likelihood/lkdir/lkscript.py	Update CCLFactory imports to `firecrown.modeling_tools`.
tests/likelihood/lkdir/lkmodule.py	Update derived parameter imports to `firecrown.updatable`.
tests/likelihood/lkdir/lk_sampler_parameter.py	Update CCLFactory imports to `firecrown.modeling_tools`.
tests/likelihood/lkdir/lk_needing_param.py	Update CCLFactory imports to `firecrown.modeling_tools`.
tests/likelihood/lkdir/lk_derived_parameter.py	Update CCLFactory imports to `firecrown.modeling_tools`.
tests/likelihood/gauss_family/test_student_t.py	Update parameter module usage to `firecrown.updatable`.
tests/likelihood/gauss_family/test_const_gaussianPM.py	Update parameter module usage to `firecrown.updatable`.
tests/likelihood/gauss_family/test_const_gaussian.py	Update parameter module usage to `firecrown.updatable`.
tests/likelihood/gauss_family/statistic/test_two_point.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/likelihood/gauss_family/statistic/test_statistic.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/likelihood/gauss_family/statistic/source/test_source.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/likelihood/gauss_family/lkscript_two_point_pure_ccl.py	Update CCL factory imports to `firecrown.modeling_tools`.
tests/likelihood/gauss_family/lkscript_two_point.py	Update CCLFactory imports to `firecrown.modeling_tools`.
tests/likelihood/gauss_family/lkscript_const_gaussian.py	Update CCLFactory imports to `firecrown.modeling_tools`.
tests/integration/models/two_point/test_theory.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/fctools/test_generate_symbol_map.py	Update symbol scanning tests to target `firecrown.updatable`.
tests/connector/test_mapping.py	Update CCL/ParamsMap imports to new modules.
tests/connector/numcosmo/test_numcosmo_mapping.py	Update amplitude parameter import to `firecrown.modeling_tools`.
tests/connector/numcosmo/test_numcosmo_connector.py	Update `ParamsMap`/CCLCreationMode imports to new modules.
tests/connector/cobaya/test_model_likelihood.py	Update `ccl_factory` alias to import `firecrown.modeling_tools`.
tests/conftest.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/app/examples/test_des_y1_3x2pt.py	Update `ParamsMap` import to `firecrown.updatable`.
tests/app/analysis/test_types.py	Update CAMBExtraParams import to `firecrown.modeling_tools`.
firecrown/updatable/_utils.py	Replace deprecated `firecrown.parameters` import with internal `_parameters_map`.
firecrown/updatable/_types.py	Switch to internal parameter submodules to avoid deprecated layer.
firecrown/updatable/_parameters_types.py	Update internal import to renamed `_parameters_names`.
firecrown/updatable/_parameters_required.py	Update internal import to `_parameters_types`.
firecrown/updatable/_parameters_names.py	New module for parameter-name utilities/validation.
firecrown/updatable/_parameters_map.py	Update internal import to `_parameters_names`.
firecrown/updatable/_parameters_derived.py	New module housing derived-parameter classes.
firecrown/updatable/_collection.py	Switch to internal parameter submodules.
firecrown/updatable/_base.py	Switch to internal parameter submodules.
firecrown/updatable/init.py	Re-export parameter APIs from `firecrown.updatable`.
firecrown/parameters/init.py	Convert to deprecated shim re-exporting from `firecrown.updatable`.
firecrown/models/two_point/_theory.py	Update `ParamsMap` import to `firecrown.updatable`.
firecrown/models/cluster/_mass_proxy.py	Switch to direct `register_new_updatable_parameter` import.
firecrown/models/cluster/_kernel.py	Switch to direct `register_new_updatable_parameter` import.
firecrown/models/cluster/_deltasigma.py	Switch to direct `register_new_updatable_parameter` import.
firecrown/modeling_tools/_modeling_tools.py	Update internal imports to new CCL factory submodules.
firecrown/modeling_tools/_ccl_types.py	New typed definitions for CCL factory calculator args.
firecrown/modeling_tools/_ccl_models.py	Update parameter imports to `firecrown.updatable`.
firecrown/modeling_tools/_ccl_factory.py	Move CCL factory implementation under `modeling_tools` and update imports.
firecrown/modeling_tools/_ccl_enums.py	New enum types for CCL factory (creation mode, amplitude parameter, etc.).
firecrown/modeling_tools/init.py	Re-export CCL factory APIs/types/enums from `firecrown.modeling_tools`.
firecrown/likelihood/supernova/_supernova.py	Switch to direct `register_new_updatable_parameter` import.
firecrown/likelihood/number_counts/_systematics.py	Switch to direct `register_new_updatable_parameter` import.
firecrown/likelihood/number_counts/_source.py	Switch parameter-related imports to `firecrown.updatable`.
firecrown/likelihood/factories/_models.py	Update CCLFactory import to `firecrown.modeling_tools`.
firecrown/likelihood/_weak_lensing.py	Switch parameter-related imports to `firecrown.updatable`.
firecrown/likelihood/_student_t.py	Switch to direct `register_new_updatable_parameter` import.
firecrown/likelihood/_gaussfamily.py	Update `ParamsMap` import to `firecrown.updatable`.
firecrown/likelihood/_base.py	Switch parameter/updatable imports to `firecrown.updatable`.
firecrown/connector/numcosmo/numcosmo.py	Update CCL/ParamsMap imports to new modules.
firecrown/connector/numcosmo/helpers.py	Update `ccl_factory` alias to import `firecrown.modeling_tools`.
firecrown/connector/mapping.py	Update CCL types import source and ParamsMap type annotation.
firecrown/connector/cosmosis/likelihood.py	Update CCLCreationMode/ParamsMap imports to new modules.
firecrown/connector/cobaya/likelihood.py	Update CCL/ParamsMap imports to new modules.
firecrown/ccl_factory/init.py	Convert to deprecated shim re-exporting from `firecrown.modeling_tools`.
firecrown/app/examples/_sn_srd_template.py	Update CCLFactory import to `firecrown.modeling_tools`.
firecrown/app/examples/_des_y1_cosmic_shear_tatt_template.py	Update CCLFactory import to `firecrown.modeling_tools`.
firecrown/app/examples/_des_y1_cosmic_shear_pk_modifier_template.py	Update CCLFactory/parameter imports to new modules.
firecrown/app/examples/_des_y1_cosmic_shear_hmia_template.py	Update CCLFactory import to `firecrown.modeling_tools`.
firecrown/app/examples/_des_y1_3x2pt_template.py	Update CCLFactory import to `firecrown.modeling_tools`.
firecrown/app/examples/_des_y1_3x2pt_pt_template.py	Update CCLFactory import to `firecrown.modeling_tools`.
firecrown/app/examples/_cosmic_shear_template.py	Update CCLFactory import to `firecrown.modeling_tools`.
firecrown/app/cosmology.py	Update CAMBExtraParams import to `firecrown.modeling_tools`.
firecrown/app/analysis/_types.py	Update CAMBExtraParams/PoweSpecAmplitudeParameter import to `firecrown.modeling_tools`.
examples/des_y1_3x2pt/factory_PT.py	Update example imports to new modules.
examples/des_y1_3x2pt/factory_PM.py	Update CCLFactory import to `firecrown.modeling_tools`.
examples/des_y1_3x2pt/factory.py	Update CCLFactory import to `firecrown.modeling_tools`.
examples/des_y1_3x2pt/des_y1_cosmic_shear_pk_modifier.py	Update ParamsMap/register function/CCLFactory imports to new modules.
examples/des_y1_3x2pt/des_y1_cosmic_shear_TATT.py	Update ParamsMap/CCLFactory imports to new modules.
examples/des_y1_3x2pt/des_y1_cosmic_shear_HMIA.py	Update ParamsMap/CCLFactory imports to new modules.
environment.yml	Pin black version (with formatting that differs from other deps).

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Copilot · 2026-01-27T19:33:36Z

tests/test_parameters_deprecated.py

+    with warnings.catch_warnings(record=True) as w:
+        warnings.simplefilter("always")
+        # Import should trigger warning
+        # pylint: disable=unused-import,import-outside-toplevel
+        import firecrown.parameters  # noqa: F401
+
+        # Should have at least one warning (there might be multiple due to
+        # imports within the module)
+        assert len(w) >= 1
+        # First warning should be a DeprecationWarning
+        assert issubclass(w[0].category, DeprecationWarning)
+        # Check message content
+        assert "firecrown.parameters module is deprecated" in str(w[0].message)
+        assert "firecrown.updatable" in str(w[0].message)
+


The deprecation-warning assertion is order-dependent: w[0] may not be the firecrown.parameters DeprecationWarning if other warnings are emitted during import (your comment notes there may be multiple). Consider asserting that any captured warning is a DeprecationWarning whose message matches the expected substrings (or use pytest.warns(..., match=...)) to avoid flaky failures.

Copilot · 2026-01-27T19:33:37Z

tests/test_updatable.py

 )
+from firecrown import parameters



This test file imports the deprecated firecrown.parameters module, which will emit a DeprecationWarning (and pytest.ini does not filter it). Unless this file is intended to test the deprecated compatibility layer, prefer importing register_new_updatable_parameter from firecrown.updatable and drop the deprecated module import; otherwise, explicitly filter/silence the warning within the tests.

Copilot · 2026-01-27T19:33:37Z

environment.yml

  - alabaster
  - babel
-  - black
+  - black = 25.12.0


Conda dependency pins are usually written without spaces (e.g., black=25.12.0). black = 25.12.0 is inconsistent with the rest of this file and may not be parsed as intended by conda.

Copilot · 2026-01-27T19:33:37Z

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 · 2026-01-27T19:33:38Z

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 · 2026-01-27T19:33:39Z

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 · 2026-01-27T19:33:39Z

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 · 2026-01-27T19:33:40Z

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 · 2026-01-27T19:33:40Z

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 · 2026-01-27T19:33:40Z

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'.

marcpaterno added 4 commits January 16, 2026 09:01

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 19:28

Copilot started reviewing on behalf of marcpaterno January 27, 2026 19:29 View session

Copilot AI reviewed Jan 27, 2026

View reviewed changes

vitenti approved these changes Jan 27, 2026

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marcpaterno merged commit 286804f into devel Jan 27, 2026
37 checks passed

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

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marcpaterno commented Jan 27, 2026 •

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