PR 7: adopt CosmoSIS native SACC likelihood (sacc_like), validated against the converter path

.github/workflows/deploy-image.yml

@@ -44,6 +44,12 @@ jobs:
       - name: Import smoke test
         run: docker run --rm ${{ steps.meta.outputs.tags }} python -c "import sp_validation"
 
+      # The fast suite doesn't import the blinding stack, so a broken
+      # firecrown/smokescreen install would otherwise ship green. Prove the
+      # image can actually load it (sacc + patched firecrown + smokescreen).
+      - name: Blinding-stack import smoke test
+        run: docker run --rm ${{ steps.meta.outputs.tags }} python -c "import sacc; import firecrown.likelihood; import smokescreen"
+
       # Run the fast test suite against the freshly-built image *before*
       # pushing, so a failing suite blocks publication. The image carries the
       # full stack and the test files (COPY . + editable install), so this

Dockerfile

@@ -33,7 +33,28 @@ COPY pyproject.toml uv.lock /sp_validation/
 RUN uv sync --frozen --inexact --no-install-project \
     --extra test --extra glass --extra workflow
 
-# Install sp_validation itself (editable) into the same venv; deps are already
-# satisfied by the sync above.
+# Full source in place before the blinding-extra install below: it is an
+# editable install of the project itself and needs uv-overrides.txt and
+# scripts/patch_firecrown.py from the tree.
 COPY . /sp_validation
-RUN uv pip install --no-deps -e .
+
+# The [blinding] extra (SACC/Smokescreen blinding stack: firecrown + smokescreen)
+# is not in uv.lock — firecrown is not on PyPI and declares conda-forge-only /
+# unused sampler connectors as hard deps, so it needs the override file (see
+# uv-overrides.txt for the full story). Installed as a separate pass on top of
+# the locked sync.
+RUN uv pip install --no-cache-dir --overrides uv-overrides.txt -e '.[blinding]'
+
+# Same uv gotcha as the cs_util upgrade above (astral-sh/uv #8410): if the base
+# image / locked sync already carries a numpy that violates the [blinding]
+# extra's `numpy<2.5` cap (firecrown 1.15.1 breaks on numpy 2.5 at import), the
+# editable install won't move it. Request the bound explicitly so the image is
+# deterministic either way; numpy 2.4.x is ABI-compatible with the compiled
+# stack (verified: pyccl/camb/treecorr/healpy/pymaster + fast suite).
+RUN uv pip install --no-cache-dir 'numpy>=2.2,<2.5'
+
+# firecrown is distributed for conda-forge (where NumCosmo always exists) and
+# hits NumCosmo at import time in a pip env, on paths unrelated to our use.
+# This patches the installed tree (surgical, pinned-version-checked, loud on
+# mismatch) and verifies `import firecrown.likelihood; import smokescreen`.
+RUN python scripts/patch_firecrown.py

cosmo_inference/cosmosis_config/cosmosis_pipeline_A_ia.ini

@@ -0,0 +1,108 @@
+#parameters used elsewhere in this file
+[DEFAULT]
+COSMOSIS_DIR = /n23data1/n06data/lgoh/scratch/cosmosis-standard-library_lisa
+
+
+[pipeline]
+modules = consistency sample_S8 camb load_nz_fits photoz_bias linear_alignment projection add_intrinsic 2pt_shear shear_m_bias 2pt_like 
+likelihoods = 2pt_like 
+extra_output = cosmological_parameters/omega_lambda cosmological_parameters/S_8 cosmological_parameters/sigma_8 cosmological_parameters/omega_m
+timing = T
+debug = T
+
+[runtime]
+sampler = polychord
+verbosity = debug
+
+[polychord]
+live_points = 192
+feedback = 3
+resume = T
+base_dir = %(SCRATCH)s/polychord
+
+[test]
+
+[output]
+format = text
+lock = F
+
+[consistency]
+file = %(COSMOSIS_DIR)s/utility/consistency/consistency_interface.py
+verbose = F
+
+[sample_S8]
+file = %(COSMOSIS_DIR)s/utility/sample_sigma8/sample_S8.py
+
+[camb]
+file = %(COSMOSIS_DIR)s/boltzmann/camb/camb_interface.py
+mode=power
+lmax=2508
+feedback=0
+do_reionization=F
+kmin=1e-5
+kmax=20.0
+nk=200
+zmax=5.0
+zmax_background=5.0
+nz_background=500
+halofit_version=mead2020_feedback
+nonlinear=pk
+neutrino_hierarchy=normal
+kmax_extrapolate = 500.0
+
+[load_nz_fits]
+file = %(COSMOSIS_DIR)s/number_density/load_nz_fits/load_nz_fits.py
+nz_file =%(FITS_FILE)s
+data_sets = SOURCE
+
+[photoz_bias]
+file = %(COSMOSIS_DIR)s/number_density/photoz_bias/photoz_bias.py
+mode = additive
+sample = nz_source
+bias_section = nofz_shifts
+interpolation = cubic
+output_deltaz_section_name = delta_z_out
+
+[linear_alignment]
+file = %(COSMOSIS_DIR)s/intrinsic_alignments/la_model/linear_alignments_interface_znla.py
+method = bk_corrected
+
+[projection]
+file = %(COSMOSIS_DIR)s/structure/projection/project_2d.py
+ell_min_logspaced = 1.0
+ell_max_logspaced = 25000.0
+n_ell_logspaced = 400
+shear-shear = source-source
+shear-intrinsic = source-source
+intrinsic-intrinsic = source-source
+get_kernel_peaks = F
+verbose = F
+
+[add_intrinsic]
+file = %(COSMOSIS_DIR)s/shear/add_intrinsic/add_intrinsic.py
+shear-shear=T
+position-shear=F
+perbin=F
+
+[2pt_shear]
+file = %(COSMOSIS_DIR)s/shear/cl_to_xi_nicaea/nicaea_interface.so
+corr_type = 0  ; shear_cl -> shear_xi
+
+[shear_m_bias]
+file = %(COSMOSIS_DIR)s/shear/shear_bias/shear_m_bias.py
+m_per_bin = True
+; Despite the parameter name, this can operate on xi as well as C_ell.
+cl_section = shear_xi_plus shear_xi_minus
+verbose = F
+
+[2pt_like]
+file = %(COSMOSIS_DIR)s/likelihood/2pt/2pt_like.py
+data_file=%(FITS_FILE)s
+gaussian_covariance=F
+covmat_name=COVMAT
+cut_zeros=F
+data_sets=XI_PLUS XI_MINUS
+like_name=2pt_like
+
+angle_range_XI_PLUS_1_1= 10.0 200.0
+angle_range_XI_MINUS_1_1= 20.0 200.0

cosmo_inference/cosmosis_config/cosmosis_pipeline_A_ia_sacc.ini

@@ -0,0 +1,110 @@
+#parameters used elsewhere in this file
+[DEFAULT]
+COSMOSIS_DIR = /n23data1/n06data/lgoh/scratch/cosmosis-standard-library_lisa
+
+
+[pipeline]
+modules = consistency sample_S8 camb load_nz_sacc photoz_bias linear_alignment projection add_intrinsic 2pt_shear shear_m_bias sacc_like
+likelihoods = 2pt_like
+extra_output = cosmological_parameters/omega_lambda cosmological_parameters/S_8 cosmological_parameters/sigma_8 cosmological_parameters/omega_m
+timing = T
+debug = T
+
+[runtime]
+sampler = polychord
+verbosity = debug
+
+[polychord]
+live_points = 192
+feedback = 3
+resume = T
+base_dir = %(SCRATCH)s/polychord
+
+[test]
+
+[output]
+format = text
+lock = F
+
+[consistency]
+file = %(COSMOSIS_DIR)s/utility/consistency/consistency_interface.py
+verbose = F
+
+[sample_S8]
+file = %(COSMOSIS_DIR)s/utility/sample_sigma8/sample_S8.py
+
+[camb]
+file = %(COSMOSIS_DIR)s/boltzmann/camb/camb_interface.py
+mode=power
+lmax=2508
+feedback=0
+do_reionization=F
+kmin=1e-5
+kmax=20.0
+nk=200
+zmax=5.0
+zmax_background=5.0
+nz_background=500
+halofit_version=mead2020_feedback
+nonlinear=pk
+neutrino_hierarchy=normal
+kmax_extrapolate = 500.0
+
+[load_nz_sacc]
+file = %(COSMOSIS_DIR)s/number_density/load_nz_sacc/load_nz_sacc.py
+nz_file = %(SACC_FILE)s
+data_sets = source
+
+[photoz_bias]
+file = %(COSMOSIS_DIR)s/number_density/photoz_bias/photoz_bias.py
+mode = additive
+sample = nz_source
+bias_section = nofz_shifts
+interpolation = cubic
+output_deltaz_section_name = delta_z_out
+
+[linear_alignment]
+file = %(COSMOSIS_DIR)s/intrinsic_alignments/la_model/linear_alignments_interface_znla.py
+method = bk_corrected
+
+[projection]
+file = %(COSMOSIS_DIR)s/structure/projection/project_2d.py
+ell_min_logspaced = 1.0
+ell_max_logspaced = 25000.0
+n_ell_logspaced = 400
+shear-shear = source-source
+shear-intrinsic = source-source
+intrinsic-intrinsic = source-source
+get_kernel_peaks = F
+verbose = F
+
+[add_intrinsic]
+file = %(COSMOSIS_DIR)s/shear/add_intrinsic/add_intrinsic.py
+shear-shear=T
+position-shear=F
+perbin=F
+
+[2pt_shear]
+file = %(COSMOSIS_DIR)s/shear/cl_to_xi_nicaea/nicaea_interface.so
+corr_type = 0  ; shear_cl -> shear_xi
+
+[shear_m_bias]
+file = %(COSMOSIS_DIR)s/shear/shear_bias/shear_m_bias.py
+m_per_bin = True
+; Despite the parameter name, this can operate on xi as well as C_ell.
+cl_section = shear_xi_plus shear_xi_minus
+verbose = F
+
+; Native SACC likelihood via the sp_validation shim (arcmin->rad + ordering
+; guard over CosmoSIS's SaccClLikelihood). data_sets/angle ranges use the SACC
+; grammar (full data-type names + tracer pairs). like_name=2pt_like keeps the
+; block keys identical to the 2pt_like path so chain post-processing is unchanged.
+[sacc_like]
+file = %(SP_VALIDATION_MODULES)s/sacc_like_unions.py
+csl_dir = %(COSMOSIS_DIR)s
+data_file = %(SACC_FILE)s
+data_sets = galaxy_shear_xi_plus galaxy_shear_xi_minus
+like_name = 2pt_like
+
+angle_range_galaxy_shear_xi_plus_source_0_source_0 = 10.0 200.0
+angle_range_galaxy_shear_xi_minus_source_0_source_0 = 20.0 200.0

papers/cosmo_val/config/config.yaml

@@ -120,11 +120,14 @@ harmonic:
     binning: powspace
     nbins: 32
 
-# Cosmological inference data-product locations (dormant subsystem).
+# Cosmological inference data-product locations + tooling.
 inference:
   chains_dir: "/n09data/guerrini/output_chains"
   glass_mock_data_dir: "/n09data/guerrini/glass_mock_v1.4.6/results"
   glass_mock_chains_dir: "/n09data/guerrini/glass_mock_chains"
+  # CosmoSIS Standard Library checkout — fills COSMOSIS_DIR in the generated
+  # pipeline inis (the module `file =` paths and the sacc_like shim's csl_dir).
+  csl_dir: "/n23data1/n06data/lgoh/scratch/cosmosis-standard-library_lisa"
 
 cosebis:
   theta_min: 1.0

pyproject.toml

@@ -9,9 +9,10 @@ authors = [
 ]
 license = {text = "MIT"}
 readme = "README.md"
-# 3.12 floor: cosmo-numba (a hard dependency below) requires >=3.12, and the
-# production container is Python 3.12 (shapepipe base image). Keeping the floor
-# in sync with the container is what makes `uv lock` resolvable.
+# 3.12 floor: Smokescreen 1.5.6 (and firecrown v1.15) require it, as does
+# cosmo-numba (a hard dependency below); the container base (shapepipe:develop)
+# is already python:3.12-slim-bookworm, so this aligns pyproject with the
+# actual runtime and keeps `uv lock` resolvable.
 requires-python = ">=3.12"
 classifiers = [
     "License :: OSI Approved :: MIT License",
@@ -164,6 +165,40 @@ workflow = [
     # published or resolvable (no public repo found) — left undeclared pending
     # its source. Same for `unions_wl` (scripts/check_footprint.py).
 ]
+# Data-vector blinding (PRD #241 §3-§5): Smokescreen applies the Muir et al.
+# shift d → d + t(hidden) − t(fid), with firecrown + CCL as the theory engine
+# (only compute_theory_vector is used; sampling stays with CosmoSIS). The blind
+# must be exactly recomputable from the seed at unblinding time, so the whole
+# theory stack is pinned exactly, as a set. Smokescreen 1.5.6 + firecrown v1.15
+# both set the python floor (>=3.12).
+#
+# firecrown is not on PyPI and declares conda-forge-only / unused sampler
+# connectors as hard deps, so installing this extra requires the dependency
+# override file: `uv pip install --overrides uv-overrides.txt -e '.[blinding]'`
+# (see uv-overrides.txt; the Dockerfile does this for the container).
+# After installing this extra, run `python scripts/patch_firecrown.py` — it
+# makes pip-installed firecrown importable without NumCosmo (conda-forge-only);
+# see that script's docstring for the full story.
+blinding = [
+    "firecrown @ git+https://github.com/LSSTDESC/firecrown.git@v1.15.1",
+    "smokescreen==1.5.6",
+    "pyccl==3.3.4",
+    # firecrown 1.15.1 subclasses npt.NDArray (DataVector); numpy 2.5 turned
+    # npt.NDArray into a non-subclassable typing alias, breaking firecrown at
+    # import. firecrown's own env caps numpy<2.4; 2.4.3 is verified against
+    # the full compiled stack (pyccl/camb/treecorr/healpy/pymaster) + the
+    # sp_validation fast suite.
+    "numpy>=2.2,<2.5",
+]
+# Native SACC inference likelihood (PR 7, sp_validation.sacc_like_unions). The
+# shim subclasses CosmoSIS's SaccClLikelihood; this pins the engine. Both engine
+# module files are pure-python (no CAMB / compiled CSL), so the equality tests
+# (tests/test_sacc_like.py) run with just this extra + a CosmoSIS Standard
+# Library checkout, located via the CSL_DIR env var:
+#   git clone --depth 1 https://github.com/joezuntz/cosmosis-standard-library CSL
+#   CSL_DIR=/path/to/CSL  pytest ... test_sacc_like.py
+# Inert in CI (its Dockerfile installs only [test,glass,blinding]).
+cosmosis = ["cosmosis>=3.25"]
 develop = ["sp_validation[test,docs]"]
 
 [tool.pytest.ini_options]