Merge branch 'main' of https://github.com/joezuntz/cosmosis-standard-…

…library

.github/workflows/ci.yml

@@ -137,7 +137,7 @@ jobs:
       - name: Install likelihood python dependencies from pip
         shell: bash -l {0}
         run: |
-          pip install "act_dr6_lenslike>=1.0.2"
+          pip install "act_dr6_lenslike>=1.0.2" "git+https://github.com/carronj/planck_PR4_lensing"
 
       - name: Run Tests
         shell: bash -l {0}
@@ -232,7 +232,7 @@ jobs:
         python -m pip install --upgrade pip wheel setuptools
         pip install "cosmosis==3.9.2" "nautilus-sampler==1.0.1" "scipy<1.14"
         pip install -v --no-cache-dir --no-binary=mpi4py,camb mpi4py camb
-        pip install fitsio astropy fast-pt "Cython>=3.0" jupyter sacc
+        pip install fitsio astropy fast-pt "Cython>=3.0" jupyter sacc "git+https://github.com/carronj/planck_PR4_lensing"
 
     - name: Install likelihood python dependencies
       run: |

examples/npipe-priors.ini

@@ -0,0 +1,7 @@
+[cosmological_parameters]
+n_s = gaussian 0.96 0.02
+ombh2 = gaussian 0.0222 0.0005
+
+
+[planck]
+a_planck = gaussian 1.0 0.0025

examples/npipe-values.ini

@@ -0,0 +1,42 @@
+[planck]
+a_planck          = 0.9 1.0 1.1 ; Total Planck calibration (relative to 1) at map level, scales all channels
+
+
+[cosmological_parameters]
+ cosmomc_theta =  0.9   1.040909   1.2 ; this is actually 100 * theta_mc
+;h0 = 0.4  0.7  1.0
+omch2 = 0.05  0.12  0.2
+log1e10As = 2.9  3.0448  3.1     ; structure amplitude parameter
+
+ombh2 = 0.020 0.0222  0.025
+n_s = 0.9  0.96  1.02
+
+
+omega_k = 0.0     ;spatial curvature
+
+;reionization
+tau = 0.055      ;reionization optical depth
+
+
+;neutrinos
+mnu = 0.06
+nnu = 3.046
+num_massive_neutrinos = 1
+
+;helium 
+yhe = 0.245341  ;helium mass fraction
+
+
+k_s = 0.05      ;Power spectrum pivot scale 
+n_run = 0.0     ;running of scalar spectrum 
+r_t = 0.0       ;tensor to scalar ratio
+n_t = 0.0       ;tensor spectral index 
+
+;dark energy equation of state
+w = -1.0   ;equation of state of dark energy
+wa = 0.0   ;equation of state of dark energy (redshift dependency)
+
+
+[halo_model_parameters]
+A = 3.13
+eta = 0.603

examples/npipe.ini

@@ -0,0 +1,59 @@
+[runtime]
+sampler = test
+root = ${PWD}
+verbosity = standard
+
+[nautilus]
+n_live = 1000
+verbose = T
+
+
+
+[test]
+save_dir=output/npipe
+fatal_errors=T
+
+
+[output]
+filename = output/npipe.txt
+
+[DEFAULT]
+; This value is used below as %(planck_path)s
+planck_path = likelihood/planck2018/baseline/plc_3.0
+
+
+[pipeline]
+; these names refer to sections later in the file:
+modules = consistency camb planck_npipe
+values = examples/npipe-values.ini
+priors = examples/npipe-priors.ini
+debug=T
+timing=F
+extra_output = cosmological_parameters/sigma_8 cosmological_parameters/omega_m cosmological_parameters/h0
+
+[planck_npipe]
+;Planck 2018 high ell TT,TE and EE + low ell TT + low ell EE (in Planck notations = TT+lowE)
+;without CMB lensing
+file = likelihood/planck-npipe/npipe_interface.py
+use_marginalized = T
+
+; The consistency module translates between our chosen parameterization
+; and any other that modules in the pipeline may want (e.g. camb)
+[consistency]
+file = ./utility/consistency/consistency_interface.py
+cosmomc_theta = T
+
+
+[camb]
+file = boltzmann/camb/camb_interface.py
+mode = cmb
+lmax = 2800          ;max ell to use for cmb calculation
+feedback=0         ;amount of output to print
+AccuracyBoost=1.1 ;CAMB accuracy boost parameter
+do_tensors = True   ;include tensor modes
+do_lensing = true    ;lensing is required w/ Planck data
+NonLinear = lens
+accurate_massive_neutrino_transfers = T
+theta_H0_range = "40 100"
+halofit_version = mead
+

likelihood/planck-npipe/npipe_interface.py

@@ -0,0 +1,49 @@
+from cosmosis.datablock import option_section
+try:
+    from planckpr4lensing import PlanckPR4LensingMarged, PlanckPR4Lensing
+except ImportError:
+    raise ImportError("Please install the planckpr4lensing with: pip install git+https://github.com/carronj/planck_PR4_lensing")
+import numpy as np
+
+
+
+def setup(options):
+    marged = options.get_bool(option_section, "use_marginalized", default=True)
+    if marged:
+        calculator = PlanckPR4LensingMarged()
+        print("Using primary CMB-marginalized PR4 likelihood. TT, EE, TE, BB, will not be used")
+    else:
+        calculator = PlanckPR4Lensing()
+        print("NOT using primary CMB-marginalized PR4 likelihood. TT, EE, TE, BB, will be used")
+    return calculator, marged
+
+
+
+def execute(block, config):
+    calculator, marged = config
+    ell = block['cmb_cl', 'ell']
+    A = block['planck', 'a_planck']
+
+    # Convert from D_ell to the PP pre-factor, ell**2 (ell+1)**2 / 2pi
+    pp = block['cmb_cl', 'pp'] * ell * (ell + 1.)
+    cl = {"pp":pp}
+
+    # If we are not using the marginalized version, we need to provide the full set of Cls
+    # If we are using the marginalized version these are pre-marginalized over
+    if not marged:
+        cl["tt"] = block['cmb_cl', 'tt']
+        cl["te"] = block['cmb_cl', 'te']
+        cl["ee"] = block['cmb_cl', 'ee']
+        cl["bb"] = block['cmb_cl', 'bb']
+
+
+    # npipe wants to start at zero
+    if ell[0] == 2:
+        ell = np.concatenate([[0, 1], ell])
+        for key in cl:
+            cl[key] = np.concatenate([[0.0, 0.0], cl[key]])
+
+    block["likelihoods", "npipe_like"] = calculator.log_likelihood(cl, A_planck=A)
+
+
+    return 0

tests/test_cosmosis_standard_library.py

@@ -186,6 +186,14 @@ def test_hsc_real(capsys):
     run_cosmosis("examples/hsc-y3-shear-real.ini")
     check_likelihood(capsys, "-122.5")
 
+def test_npipe(capsys):
+    try:
+        import planckpr4lensing
+    except ImportError:
+        pytest.skip("Planck PR4 lensing likelihood not found")
+    run_cosmosis("examples/npipe.ini")
+    check_likelihood(capsys, "-4.22", "-4.23")
+
 def test_desi(capsys):
     run_cosmosis("examples/desi.ini")
     check_likelihood(capsys, "-11.25")