Merge pull request #1 from SBU-COSMOLIKE/main

v3.1

Cocoa/.gitignore

@@ -11,6 +11,8 @@ core.*
 *.egg-info/
 *.out
 *.egg
+*.vfproj
+*.sln
 
 Cocoa/external_modules/code/planck/code/spt_clik/svnversion
 Cocoa/external_modules/code/PolyChordLite/dist/

Cocoa/cobaya/cobaya/collection.py

@@ -99,9 +99,11 @@ def compute_temperature(logpost, logprior, loglike, check=True):
     of the sample temperature, and raises ``AssertionError`` if inconsistent.
     """
     temp = (logprior + loglike) / logpost
+    #VM BEGINS
     if check and isinstance(temp, Iterable) and len(temp) > 1:
         assert np.allclose(temp, temp[0]), "Inconsistent temperature in sample."
         temp = temp[0]
+    #VM ENDS
     return temp
 
 

Cocoa/external_modules/code/CAMB/.gitattributes

@@ -0,0 +1,7 @@
+*.txt           text
+*.f90           text
+*.F90           text
+Makefile*	text
+*.m             text
+*.dat           text
+*.ini           text

Cocoa/external_modules/code/CAMB/.readthedocs.yml

@@ -0,0 +1,21 @@
+version: 2
+
+python:
+  version: 3.8
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+
+sphinx:
+  configuration: docs/source/conf.py
+
+formats: all
+
+build:
+  apt_packages:
+    - gfortran
+
+
+submodules:
+  include: all

Cocoa/external_modules/code/CAMB/.travis.yml

@@ -0,0 +1,105 @@
+os: linux
+language: python
+
+git:
+  depth: false
+
+dist: bionic
+
+branches:
+  except:
+    - CAMB_sources
+    - rayleigh
+
+jobs:
+  include:
+    - name: "Ubuntu 20.04 + Python 3.7"
+      dist: focal
+      addons:
+        apt:
+          packages:
+            - gfortran
+      python: "3.7"
+      env:
+        - PYPI_DIST="true"
+    - name: "GCC10 + Python 3.10 anaconda"
+      dist: focal
+      addons:
+        apt:
+          packages:
+            - gfortran-10
+      env:
+        - GCC_VERSION="10"
+        - CHANNEL="defaults"
+        - PYDIST="ANACONDA"
+        - FORTRAN="test"
+      python: "3.10"
+    - name: "Ubuntu 22.04 + Python 3.11"
+      dist: jammy
+      addons:
+        apt:
+          packages:
+            - gfortran
+      env:
+        - CHANNEL="defaults"
+      python: "3.11"
+    - name: "GCC trunk cosmobox"
+      language: shell
+      services:
+        - docker
+      before_install:
+        - if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then
+            echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin;
+          fi
+        - docker pull cmbant/cosmobox:devel
+      install:
+        - chmod +x fortran/tests/run_tests.sh
+      script:
+        - docker run -v $(pwd):/camb  -t cmbant/cosmobox:devel /bin/bash -c "cd /camb; fortran/tests/run_tests.sh"
+      after_failure:
+        - echo "docker fail"
+
+install:
+  - if [[ "$PYDIST" == "ANACONDA" ]]; then
+      wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+      bash miniconda.sh -b -p $HOME/miniconda;
+      export PATH="$HOME/miniconda/bin:$PATH";
+      hash -r;
+      conda config --set always_yes yes --set changeps1 no;
+      conda info -a;
+      conda create -q -n test-environment -c $CHANNEL python=$TRAVIS_PYTHON_VERSION numpy scipy sympy;
+      source activate test-environment;
+    fi
+  - if [[ "$FORTRAN" == "test" ]]; then
+      mkdir -p gfortran-symlinks;
+      ln -s /usr/bin/gfortran-$GCC_VERSION gfortran-symlinks/gfortran;
+      export PATH=$PWD/gfortran-symlinks:$PATH;
+    fi
+  - if [[ "$GCC_VERSION" == "10" ]]; then
+      export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgfortran.so.5;
+    fi
+  - gfortran --version
+  - chmod +x fortran/tests/run_tests.sh
+  - pip install flake8
+
+script:
+  - flake8 camb --select=E713,E704,E703,E714,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,E741,F405,F406,F5,F6,F7,F8,W1,W2,W3,W6 --show-source --statistics
+  - fortran/tests/run_tests.sh
+
+after_failure:
+  - test $TRAVIS_PULL_REQUEST == "false" && test $PYPI_DIST == "true" && test $TRAVIS_REPO_SLUG == "cmbant/CAMB" && [ -d fortran/testfiles ] && bash fortran/tests/upload_tests.sh
+
+before_deploy:
+  - pushd fortran; make clean delete; popd
+
+deploy:
+  - provider: pypi
+    distributions: sdist
+    username: "cmbant"
+    password:
+      secure: "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"
+    on:
+      branch: master
+      repo: cmbant/CAMB
+      tags: true
+      condition: $PYPI_DIST = true

Cocoa/external_modules/code/CAMB/camb/__init__.py

@@ -7,7 +7,7 @@
 __author__ = "Antony Lewis"
 __contact__ = "antony at cosmologist dot info"
 __url__ = "https://camb.readthedocs.io"
-__version__ = "1.4.2.1"
+__version__ = "1.5.0"
 
 from . import baseconfig
 

Cocoa/external_modules/code/CAMB/camb/_compilers.py

@@ -25,18 +25,16 @@ def call_command(cmd):
 def get_ifort_version():
     return call_command("ifort -v")
 
-
 #VM BEGINS
 #COCOA BEGINS
-def get_gfortran_version():
+def get_gfortran_version(command='gfortran'):
     ver = call_command("$FORTRAN_COMPILER -dumpversion")
     if ver and '.' not in ver:
         ver = call_command("$FORTRAN_COMPILER -dumpfullversion")
     return ver
 #COCOA ENDS
 #VM ENDS
 
-
 def check_ifort():
     return get_ifort_version() or False
 

Cocoa/external_modules/code/CAMB/docs/CAMBdemo.ipynb

@@ -2825,7 +2825,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

Cocoa/external_modules/code/CAMB/fortran/Makefile

@@ -98,7 +98,6 @@ gfortErr = 0
 #VM ENDS
 ifeq "$(gfortErr)" "0"
 #Gfortran compiler (version 6+):
-compiler_ver = $(shell gfortran -dumpversion 2>&1)
 #VM BEGINS
 #COCOA BEGINS
 #COMPILER = gfortran

Cocoa/external_modules/code/CAMB/fortran/camb.f90

@@ -32,7 +32,7 @@ subroutine CAMB_TransfersToPowers(CData)
             Cdata%OnlyTransfer = .true. !prevent ClTransferToCl
             Cdata%CP%WantTensors = .false.
             CData%CP%WantVectors = .false.
-            call TimeSourcesToCl
+            call TimeSourcesToCl(CData%ClData%CTransScal)
             Cdata%CP%WantTensors = want_tensors
             CData%CP%WantVectors = want_vectors
             Cdata%OnlyTransfer = .false.

Cocoa/external_modules/code/CAMB/fortran/cmbmain.f90

@@ -105,7 +105,6 @@ module CAMBmain
     integer :: max_bessels_l_index  = 1000000
     real(dl) :: max_bessels_etak = 1000000*2
 
-    Type(ClTransferData), pointer :: ThisCT => null()
     Type(TTimeSources) , pointer :: ThisSources => null()
     Type(TTimeSources), allocatable, target :: TempSources
 
@@ -126,6 +125,7 @@ subroutine cmbmain
     type(EvolutionVars) EV
     Type(TTimer) :: Timer
     real(dl) starttime
+    Type(ClTransferData), pointer :: ThisCT 
 
     WantLateTime =  CP%DoLensing .or. State%num_redshiftwindows > 0 .or. CP%CustomSources%num_custom_sources>0
 
@@ -216,7 +216,7 @@ subroutine cmbmain
     !     integrating the sources over time and over k.
 
     if (CP%WantCls .and. (.not. CP%WantScalars .or. .not. State%HasScalarTimeSources)) then
-        call TimeSourcesToCl
+        call TimeSourcesToCl(ThisCT)
 
         if (CP%WantScalars) then
             deallocate(State%ScalarTimeSources)
@@ -231,9 +231,10 @@ subroutine cmbmain
 
     end subroutine cmbmain
 
-    subroutine TimeSourcesToCl
-    Type(TTimer) :: Timer
+    subroutine TimeSourcesToCl(ThisCT)
+    Type(ClTransferData) :: ThisCT 
     integer q_ix
+    Type(TTimer) :: Timer
 
     if (CP%WantScalars) ThisSources => State%ScalarTimeSources
 
@@ -255,21 +256,21 @@ subroutine TimeSourcesToCl
         max_bessels_l_index = ThisCT%ls%nl
         max_bessels_etak  = maximum_qeta
 
-        if (CP%WantScalars) call GetLimberTransfers
+        if (CP%WantScalars) call GetLimberTransfers(ThisCT)
         ThisCT%max_index_nonlimber = max_bessels_l_index
 
         if (State%flat) call InitSpherBessels(ThisCT%ls, CP, max_bessels_l_index,max_bessels_etak )
         !This is only slow if not called before with same (or higher) Max_l, Max_eta_k
         !Preferably stick to Max_l being a multiple of 50
 
-        call SetkValuesForInt
+        call SetkValuesForInt(ThisCT)
 
         if (DebugMsgs .and. Feedbacklevel > 0) call WriteFormat('Set %d integration k values',ThisCT%q%npoints)
 
         !Begin k-loop and integrate Sources*Bessels over time
         !$OMP PARALLEL DO DEFAULT(SHARED), SCHEDULE(STATIC,4)
         do q_ix=1,ThisCT%q%npoints
-            call SourceToTransfers(q_ix)
+            call SourceToTransfers(ThisCT, q_ix)
         end do !q loop
         !$OMP END PARALLEL DO
 
@@ -398,7 +399,8 @@ subroutine CalcLimberScalCls(CTrans)
 
     end subroutine CalcLimberScalCls
 
-    subroutine GetLimberTransfers
+    subroutine GetLimberTransfers(ThisCT)
+    Type(ClTransferData), target :: ThisCT 
     integer ell, ell_needed
     integer i, s_ix, s_ix_lens
     type(TRedWin), pointer :: W
@@ -517,7 +519,8 @@ subroutine GetLimberTransfers
 
     end subroutine GetLimberTransfers
 
-    subroutine SourceToTransfers(q_ix)
+    subroutine SourceToTransfers(ThisCT, q_ix)
+    type(ClTransferData), target :: ThisCT 
     integer q_ix
     type(IntegrationVars) :: IV
 
@@ -532,7 +535,7 @@ subroutine SourceToTransfers(q_ix)
 
     call InterpolateSources(IV)
 
-    call DoSourceIntegration(IV)
+    call DoSourceIntegration(IV, ThisCT)
 
     if (.not.State%flat) deallocate(IV%ddSource_q)
     deallocate(IV%Source_q)
@@ -1106,7 +1109,7 @@ subroutine TransferOut
 
 
     if (DebugMsgs .and. Feedbacklevel > 0) &
-        call WriteFormat('Transfer k values: %f',State%MT%num_q_trans-n_source_points)
+        call WriteFormat('Transfer k values: %d',State%MT%num_q_trans-n_source_points)
 
     !     loop over wavenumbers.
     !$OMP PARALLEL DO DEFAULT(SHARED),SCHEDULE(DYNAMIC), PRIVATE(EV, tau, q_ix)
@@ -1231,7 +1234,8 @@ subroutine InitSourceInterpolation
     end subroutine InitSourceInterpolation
 
 
-    subroutine SetkValuesForInt
+    subroutine SetkValuesForInt(ThisCT)
+    Type(ClTransferData) :: ThisCT 
     integer no
     real(dl) dk,dk0,dlnk1, dk2, max_k_dk, k_max_log, k_max_0
     integer lognum
@@ -1392,10 +1396,11 @@ subroutine IntegrationVars_Init(IV)
     end  subroutine IntegrationVars_Init
 
 
-    subroutine DoSourceIntegration(IV) !for particular wave number q
+    subroutine DoSourceIntegration(IV, ThisCT) !for particular wave number q
+    type(IntegrationVars) IV
+    Type(ClTransferData) :: ThisCT    
     integer j,ll,llmax
     real(dl) nu
-    type(IntegrationVars) IV
     real(dl) :: sixpibynu
 
     nu=IV%q*State%curvature_radius
@@ -1418,12 +1423,12 @@ subroutine DoSourceIntegration(IV) !for particular wave number q
     end if
 
     if (State%flat) then
-        call DoFlatIntegration(IV,llmax)
+        call DoFlatIntegration(IV,ThisCT, llmax)
     else
         do j=1,ThisCT%ls%nl
             ll=ThisCT%ls%l(j)
             if (ll>llmax) exit
-            call IntegrateSourcesBessels(IV,j,ll,nu)
+            call IntegrateSourcesBessels(IV,ThisCT,j,ll,nu)
         end do !j loop
     end if
 
@@ -1449,9 +1454,10 @@ function UseLimber(l)
     end function UseLimber
 
     !flat source integration
-    subroutine DoFlatIntegration(IV, llmax)
+    subroutine DoFlatIntegration(IV, ThisCT, llmax)
     implicit none
     type(IntegrationVars) IV
+    Type(ClTransferData) :: ThisCT 
     integer llmax
     integer j
     logical DoInt
@@ -1641,9 +1647,10 @@ end subroutine DoFlatIntegration
 
     !non-flat source integration
 
-    subroutine IntegrateSourcesBessels(IV,j,l,nu)
+    subroutine IntegrateSourcesBessels(IV,ThisCT,j,l,nu)
     use SpherBessels
     type(IntegrationVars) IV
+    Type(ClTransferData) :: ThisCT 
     logical DoInt
     integer l,j, nstart,nDissipative,ntop,nbot,nrange,nnow
     real(dl) nu,ChiDissipative,ChiStart,tDissipative,y1,y2,y1dis,y2dis

Cocoa/external_modules/code/CAMB/fortran/config.f90

@@ -3,7 +3,7 @@ module config
     use constants, only: const_twopi
     implicit none
 
-    character(LEN=*), parameter :: version = '1.4.2.1'
+    character(LEN=*), parameter :: version = '1.5.0'
 
     integer :: FeedbackLevel = 0 !if >0 print out useful information about the model
 

Cocoa/external_modules/code/CAMB/forutils/Makefile_compiler

@@ -56,8 +56,6 @@ endif
 endif
 
 else
-
-#VM BEGINS
 #COCOA BEGINS
 #major_version = $(shell gfortran -dumpversion 2>&1 | cut -d " " -f 3 | cut -d. -f 1)
 #ifneq ($(shell test $(major_version) -gt 5; echo $$?),0)