Merge pull request #88 from joezuntz/cosmosis3-changes

CosmoSIS 3 changes

.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
 
       - name: Install dependencies with conda
         shell: bash -l {0}
-        run: mamba install -c conda-forge cosmosis "numpy<1.24" cosmosis-build-standard-library
+        run: mamba install -c conda-forge "cosmosis>=3.0.1" cosmosis-build-standard-library
 
       - name: Build standard library
         shell: bash -l {0}
@@ -215,7 +215,6 @@ jobs:
 
 
 
-
   apt-get-test:
     runs-on: ubuntu-20.04
     strategy:
@@ -258,9 +257,9 @@ jobs:
     - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip wheel setuptools
-        pip install cosmosis
+        pip install "cosmosis>=3.0.1"
         pip install -v --no-cache-dir --no-binary=mpi4py,camb mpi4py camb
-        pip install fitsio astropy fast-pt Cython
+        pip install fitsio astropy fast-pt "Cython<3.0" jupyter
 
     - name: Build
       run: |
@@ -279,6 +278,17 @@ jobs:
         source .github/ci-setup.sh
         python -c "import camb"
 
+    - name: Test campaign commands
+      shell: bash -l {0}
+      run: |
+        source .github/ci-setup.sh
+        cosmosis-campaign -l examples/des-campaign.yml | tee output/campaign.log
+        grep -e "mira-titan" campaign.log
+        grep -e "fiducial" campaign.log
+        cosmosis-campaign --run fiducial-test-only examples/des-campaign.yml
+        cosmosis-campaign  examples/des-campaign.yml --status fiducial-test-only > output/campaign.log
+        grep -e "🟢 fiducial-test-only" output/campaign.log
+        cosmosis-campaign  examples/des-campaign.yml --status
 
     - name: Demo 2 Planck 2018 Likelihood
       run: |
@@ -287,10 +297,16 @@ jobs:
         cosmosis-postprocess demos/demo2.ini -o output/demo2
         test -f output/demo2/comoving_distance.png
 
-
     - name: Demo 9 Low-Resolution Multinest
       run: |
         source .github/ci-setup.sh
         cosmosis demos/demo9.ini -p multinest.live_points=100
         cosmosis-postprocess output/demo9.txt -o output/demo9
         test -f output/demo9/2D_supernova_params--deltam_cosmological_parameters--omega_m.png
+
+    - name: ExampleNotebook
+      shell: bash -l {0}
+      run: |
+        source cosmosis-configure
+        rm -f output/pantheon.txt
+        jupyter nbconvert --to notebook --execute "examples/example.ipynb"

demos/chaining.ini

@@ -2,6 +2,7 @@
 ; The emcee sampler, which uses the Goodman & Weare algorithm
 sampler = emcee
 ;  metropolis
+verbosity = quiet
 
 
 [emcee]
@@ -30,7 +31,6 @@ nsteps = 50
 [output]
 filename = demo5.txt
 format = text
-verbosity= debug
 
 [pipeline]
 ; We use two likelihoods, the JLA (for high redshift) and
@@ -40,7 +40,6 @@ modules = consistency camb jla riess11
 values = demos/values5.ini
 extra_output =
 likelihoods = jla riess
-quiet=T
 debug=F
 timing=F
 

demos/demo1.ini

@@ -2,6 +2,7 @@
 ; The test sampler just runs a single parameter set
 sampler = test
 root = ${PWD}
+verbosity = standard
 
 [test]
 ; These are the parameters for this sampler.
@@ -24,7 +25,6 @@ values = demos/values1.ini
 ; Not used here, becuase we are not sampling
 likelihoods = 
 extra_output = 
-quiet=F
 debug=T
 timing=F
 

demos/demo10.ini

@@ -1,6 +1,7 @@
 [runtime]
 ; changed sampler from test to grid
 sampler = grid
+verbosity = standard
 
 [grid]
 ;parameters for grid are here
@@ -19,8 +20,6 @@ values = demos/values10.ini
 likelihoods = cfhtlens
 extra_output = 
 
-; We can get a little more output during the run by setting some values
-quiet=F
 timing=F
 debug=F
 

demos/demo12.ini

@@ -1,6 +1,6 @@
 [runtime]
 sampler = test
-
+verbosity = standard
 
 [test]
 save_dir=output/demo12
@@ -13,7 +13,6 @@ values = demos/values12.ini
 likelihoods = evs
 priors = demos/priors12.ini
 extra_output = 
-quiet=T
 debug=T
 timing=F
 

demos/demo13.ini

@@ -9,7 +9,7 @@
 ;it's still useful
 
 sampler = snake
-
+verbosity = quiet
 
 [snake]
 ; Snake tries to explore at most 5 log-like points away from the peak
@@ -25,7 +25,6 @@ nsample_dimension = 20
 [output]
 filename = output/demo13.txt
 format = text
-verbosity= debug
 
 [pipeline]
 ; We use two likelihoods, the JLA (for high redshift) and
@@ -35,7 +34,6 @@ modules = consistency camb jla riess11
 values = demos/values13.ini
 extra_output = likelihoods/jla_like
 likelihoods = jla riess
-quiet=T
 debug=F
 timing=F
 

demos/demo15.ini

@@ -1,6 +1,7 @@
 ; Demonstrate the different angular two-point functions in the standard library
 [runtime]
 sampler = test
+verbosity = standard
 
 [test]
 save_dir=output/demo15
@@ -12,7 +13,6 @@ values = demos/values15.ini
 ; Not used here, becuase we are not sampling
 likelihoods =
 extra_output =
-quiet=F
 debug=T
 timing=F
 

demos/demo19.ini

@@ -2,6 +2,7 @@
 ; The test sampler just runs a single parameter set
 sampler = grid
 root = .
+verbosity = standard
 
 [grid]
 nsample_dimension=50
@@ -32,7 +33,6 @@ values = demos/values19.ini
 ; Not used here, becuase we are not sampling
 likelihoods = he0435
 extra_output = 
-quiet=T
 debug=F
 timing=F
 

demos/demo3.ini

@@ -1,5 +1,6 @@
 [runtime]
 sampler = grid
+verbosity = standard
 
 [grid]
 ; The number of samples to take in each
@@ -9,7 +10,6 @@ nsample_dimension = 25
 [pipeline]
 modules = consistency camb bicep2
 values = demos/values3.ini
-quiet = F
 
 
 [output]

demos/demo5.ini

@@ -2,6 +2,7 @@
 ; The emcee sampler, which uses the Goodman & Weare algorithm
 sampler = emcee
 root = ${PWD}
+verbosity = quiet
 
 [emcee]
 ; The emcee sampler uses the concept of walkers, a collection
@@ -22,7 +23,6 @@ nsteps = 100
 [output]
 filename = output/demo5.txt
 format = text
-verbosity= debug
 
 [pipeline]
 ; We use two likelihoods, the JLA (for high redshift) and
@@ -31,7 +31,6 @@ verbosity= debug
 modules = consistency camb jla riess11
 values = demos/values5.ini
 extra_output =
-quiet=T
 debug=F
 timing=F
 

demos/demo6.ini

@@ -1,6 +1,7 @@
 [runtime]
 ; The test sampler just runs a single parameter set
 sampler = test
+verbosity = standard
 
 [test]
 save_dir=output/demo6
@@ -25,7 +26,6 @@ likelihoods = cfhtlens
 extra_output = 
 
 ; We can get a little more output during the run by setting some values
-quiet=F
 timing=T
 debug=T
 

demos/demo7.ini

@@ -1,7 +1,7 @@
 [runtime]
 ; We use the grid sampler, as in demo 3.  But this time we go over 2 dimensions.
 sampler = grid
-
+verbosity = quiet
 
 [grid]
 ; We do a 20 x 20 grid for a total of 400 points
@@ -14,7 +14,6 @@ nstep = 100
 [output]
 filename = output/demo7.txt
 format = text
-verbosity= debug
 
 [pipeline]
 ; We use one likelihood, the boss likelihood which uses growth parameters
@@ -23,7 +22,6 @@ modules = growthfunction boss
 values = demos/values7.ini
 likelihoods = boss
 extra_output =
-quiet=T
 debug=F
 timing=F
 

demos/demo8.ini

@@ -1,6 +1,7 @@
 [runtime]
 ; The test sampler just runs a single parameter set
 sampler = test
+verbosity = standard
 
 [test]
 save_dir=output/demo8
@@ -15,7 +16,6 @@ values = demos/values8.ini
 ; Not used here, becuase we are not sampling
 likelihoods = 
 extra_output = 
-quiet=F
 debug=T
 timing=F
 

demos/demo_abc.ini

@@ -2,6 +2,7 @@
 ; The test sampler just runs a single parameter set
 sampler = abc
 root = .
+verbosity = quiet
 
 [abc]
 ;For a given set of parameters the ABC
@@ -26,7 +27,6 @@ ngauss = 4
 [output]
 filename = demo_abc.txt
 format = text
-verbosity= debug
 
 [test]
 ; These are the parameters for this sampler.
@@ -49,9 +49,6 @@ values = demos/values_abc.ini
 ; Not used here, becuase we are not sampling
 likelihoods = abc_multigauss
 extra_output = 
-;ABC sampler runs the pipeline many times over before parameters 
-;are accepted, best to set quiet = T 
-quiet=T
 debug=F
 timing=F
 

demos/metropolis.ini

@@ -1,6 +1,7 @@
 [runtime]
 ; The emcee sampler, which uses the Goodman & Weare algorithm
 sampler = metropolis
+verbosity = quiet
 
 [metropolis]
 samples = 20000
@@ -11,7 +12,6 @@ random_start = F
 [output]
 filename = demo_mcmc.txt
 format = text
-verbosity= debug
 
 [pipeline]
 ; We use two likelihoods, the JLA (for high redshift) and
@@ -21,7 +21,6 @@ modules = consistency camb jla riess11
 values = demos/values5.ini
 extra_output =
 likelihoods = jla riess
-quiet=T
 debug=F
 timing=F
 

demos/mocks.ini

@@ -2,6 +2,7 @@
 ; The test sampler just runs a single parameter set
 sampler = test
 root = .
+verbosity = standard
 
 [test]
 ; These are the parameters for this sampler.
@@ -24,7 +25,6 @@ values = demos/values1.ini
 ; Not used here, becuase we are not sampling
 likelihoods = 
 extra_output = 
-quiet=F
 debug=T
 timing=F
 

examples/act-dr6-lens.ini

@@ -2,6 +2,7 @@
 sampler = test
 root = ${PWD}
 resume = T
+verbosity = noisy
 
 [test]
 save_dir=output/act_dr6_lens
@@ -22,7 +23,6 @@ nsteps = 5
 modules = consistency camb act_dr6_lens
 values = examples/act-dr6-lens-values.ini
 priors = examples/act-dr6-lens-priors.ini
-quiet=F
 debug=F
 timing=F
 extra_output=cosmological_parameters/sigma_8 cosmological_parameters/omega_m

examples/bao.ini

@@ -1,13 +1,12 @@
 [runtime]
 sampler = test
-
+verbosity = quiet
 
 
 ; WARNING: Some of these likelihoods have data in common.
 ; You shouldn't use them all in a real pipeline - this is just for testing
 [pipeline]
 modules =  consistency  camb  6dfgs_1 6dfgs_2 6dfgs_3 6dfgs_4 boss_0 boss_1 boss_dr12_0 boss_dr12_1 eboss_lrg eboss_lya des_y3_bao_1 des_y3_bao_2 des_y3_bao_3 des_y3_bao_4 eboss16_boss_0 eboss16_boss_1 eboss16_elg_0 eboss16_elg_1 eboss16_lrg_0 eboss16_lrg_1 eboss16_lya eboss16_mgs eboss16_qso_0 eboss16_qso_1 mgs wigglez 
-quiet=T
 timing=F
 debug=F
 values = examples/bao-values.ini