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

README.md

@@ -87,6 +87,26 @@ docker run --rm -it ghcr.io/cosmostat/sp_validation:develop python -c "import sp
 
 We do not currently build images for Apple Silicon/arm64; however the amd64 images should work on these systems, albeit with reduced performance.
 
+## Local Installation
+
+Requires Python ≥ 3.12 (the floor is set by the blinding stack; the container
+already runs 3.12). With [uv](https://docs.astral.sh/uv/):
+
+```bash
+uv venv --python 3.12
+uv pip install -e '.[test]'
+```
+
+To also install the data-vector blinding stack (Smokescreen + firecrown, PRD
+[#241](https://github.com/CosmoStat/sp_validation/issues/241)), pass the
+dependency-override file — firecrown is not pip-resolvable without it (see
+`uv-overrides.txt` for why):
+
+```bash
+uv pip install --overrides uv-overrides.txt -e '.[test,blinding]'
+python scripts/patch_firecrown.py  # make pip-installed firecrown importable without NumCosmo
+```
+
 
 
 ## Flow chart

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/bmodes/scripts/run_xi_sweep.py

@@ -2,8 +2,8 @@
 
 Loops the [non-fiducial version list](sweep_versions.nonfiducial_versions) and
 runs the same ``run_2pcf.run_2pcf`` compute the fiducial two_point recipes call,
-once per version, writing every version's ξ± text dump (+ ξ+/ξ- FITS) into one
-lc ``{output}`` dir under run_2pcf's native, already-canonical name
+once per version, writing every version's ξ± text dump into one lc ``{output}``
+dir under run_2pcf's native, already-canonical name
 ``{ver}_xi_minsep={min}_maxsep={max}_nbins={nbins}_npatch={npatch}.txt`` — the
 exact pattern ``cosebis_version_comparison._xi_integration`` reconstructs.
 
@@ -72,11 +72,15 @@ def _from_cli(argv=None):
     versions = a.versions or nonfiducial_versions(config)
     for ver in versions:
         for grid in a.grids:
+            # The sweep consumes only the .txt dump (cosebis_version_comparison
+            # reconstructs it by binning). run_2pcf is born-as-SACC, so give its
+            # coarse part a grid-qualified name — the default {ver}_xi_coarse.sacc
+            # carries no binning, so the two grids per version would collide.
             run_2pcf(
                 ver=ver,
                 cat_config=a.cat_config,
                 output_dir=a.out,
-                save_fits=True,
+                sacc_out=os.path.join(a.out, f"{ver}_xi_coarse_{grid}.sacc"),
                 **GRIDS[grid],
             )
 

papers/cosmo_val/config/config.yaml

@@ -116,11 +116,14 @@ 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