Merge remote-tracking branch 'origin/clustercount_cov_validation' int…

…o clustercount_cov_validation

.github/workflows/ci.yaml

@@ -62,22 +62,21 @@ jobs:
           use-mamba: true
           activate-environment: tjpcov
           miniforge-version: latest
-          miniforge-variant: Mambaforge
 
-      - name: Cache Date
-        id: get-date
-        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
-
-      - name: Check for cached environment
-        uses: actions/cache@v3
-        id: cache
-        env:
-          # Increase this value to reset cache if etc/example-environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ${{env.CONDA}}/envs
-          key:
-            ${{runner.os}}.${{runner.arch}}.mamba-py.${{matrix.python-version}}.${{hashFiles('pyproject.toml')}}.${{hashFiles('environment.yml')}}.${{steps.get-date.outputs.today}}.${{env.CACHE_NUMBER}}
+      # - name: Cache Date
+      #   id: get-date
+      #   run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+      #   
+      # - name: Check for cached environment
+      #   uses: actions/cache@v3
+      #   id: cache
+      #   env:
+      #     # Increase this value to reset cache if etc/example-environment.yml has not changed
+      #     CACHE_NUMBER: 0
+      #   with:
+      #     path: ${{env.CONDA}}/envs
+      #     key:
+      #       ${{runner.os}}.${{runner.arch}}.mamba-py.${{matrix.python-version}}.${{hashFiles('pyproject.toml')}}.${{hashFiles('environment.yml')}}.${{steps.get-date.outputs.today}}.${{env.CACHE_NUMBER}}
 
       - name: Install environment packages
         if: steps.cache.outputs.cache-hit != 'true'
@@ -97,7 +96,7 @@ jobs:
           pip install -U mpi4py --no-cache-dir --no-deps
 
       - name: Run Tests
-        run: coverage run --source=tjpcov -m pytest -vv tests/ 
+        run: coverage run --source=tjpcov -m pytest -vv tests && coverage lcov
 
       - name: Run MPI Tests (OpenMPI)
         run: |
@@ -122,6 +121,7 @@ jobs:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           flag-name: run-${{ join(matrix.*, '-') }}
           parallel: true
+          path-to-lcov: coverage.lcov
 
   finish:
     needs: tests

environment.yml

@@ -11,11 +11,12 @@ dependencies:
   - pytest-rerunfailures
   - coveralls
   - numpy
-  - scipy
+    # - scipy
+  - scipy<1.12 # <1.12 to avoid bug in CCL<3.1 (not in pypy) with simpson integration
   - pyyaml
-  - pyccl>=3.0.0
+  - pyccl>=3.2
   - sacc>=0.12
-  - namaster
+  - namaster>2
   - camb
   - Jinja2
   - healpy

pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Physics"
 ]
 dependencies = [
-    "scipy",
+    "scipy<1.12", # <1.12 to avoid bug in CCL<3.1 (not in pypy) with simpson integration
     "numpy",
     "Jinja2",
     "pyyaml",
@@ -47,13 +47,13 @@ doc = [
     "sphinx-book-theme",
 ]
 nmt = [
-    "pymaster>=1.4.0"
+    "pymaster>=2"
 ]
 mpi = [
     "mpi4py"
 ]
 full = [
-    "pymaster>=1.4.0",
+    "pymaster>=2",
     "mpi4py",
     "sphinx",
     "sphinx-autoapi",

tests/data/conf_covariance_cNG.yaml

@@ -0,0 +1,65 @@
+tjpcov:
+  # sacc input file 
+  sacc_file: ./tests/benchmarks/32_DES_tjpcov_bm/cls_cov.fits
+
+  # 'set' from parameters OR pass CCL cosmology object OR yaml file
+  cosmo: 'set'
+
+  # Setting mask OR fsky approximation
+  mask_file:
+    DESgc__0: ./tests/benchmarks/32_DES_tjpcov_bm/catalogs/mask_DESgc__0.fits.gz
+    DESwl__0: ./tests/benchmarks/32_DES_tjpcov_bm/catalogs/DESwlMETACAL_mask_zbin0_ns32.fits.gz
+    DESwl__1: ./tests/benchmarks/32_DES_tjpcov_bm/catalogs/DESwlMETACAL_mask_zbin1_ns32.fits.gz
+
+  mask_names:
+    DESgc__0: mask_DESgc0
+    DESwl__0: mask_DESwl0
+    DESwl__1: mask_DESwl1
+
+  outdir: ./tests/tmp/
+
+  # Survey params:
+  # 5 lens bins
+  Ngal_DESgc__0: 26
+
+  Ngal_DESwl__0: 26
+  Ngal_DESwl__1: 26
+  # # constant bin sigma_e
+  sigma_e_DESwl__0: 0.26
+  sigma_e_DESwl__1: 0.26
+
+  # linear bias for lenses constant for redshift bin (example notebook)
+  bias_DESgc__0: 1.48
+
+  # IA: 0.5
+
+parameters:
+  # Not used for while (read by ccl.cosmo):
+  Omega_c: 0.2640
+  Omega_b: 0.0493
+  h: 0.6736
+  n_s: 0.9649
+  sigma8: 0.8111
+  w0: -1
+  wa: 0
+  transfer_function: 'boltzmann_camb'
+HOD:
+  # automatically creates massdef and concentration objects 
+  log10Mmin_0: 12.0
+  log10Mmin_p: 0.0
+  siglnM_0: 0.4
+  siglnM_p: 0.0
+  log10M0_0: 7.0
+  log10M0_p: 0.0
+  log10M1_0: 13.3
+  log10M1_p: 0.0
+  alpha_0: 1.0
+  alpha_p: 0.0
+  fc_0: 1.0
+  fc_p: 0.0
+  bg_0: 1.0
+  bg_p: 0.0
+  bmax_0: 1.0
+  bmax_p: 0.0
+  a_pivot: 1.0
+  ns_independent: False

tests/data/conf_covariance_cNG_fsky.yaml

@@ -0,0 +1,55 @@
+tjpcov:
+  # sacc input file 
+  sacc_file: ./tests/benchmarks/32_DES_tjpcov_bm/cls_cov.fits
+
+  # 'set' from parameters OR pass CCL cosmology object OR yaml file
+  cosmo: 'set'
+
+  outdir: ./tests/tmp/
+
+  # Survey params:
+  # 5 lens bins
+  Ngal_DESgc__0: 26
+
+  Ngal_DESwl__0: 26
+  Ngal_DESwl__1: 26
+  # # constant bin sigma_e
+  sigma_e_DESwl__0: 0.26
+  sigma_e_DESwl__1: 0.26
+
+  # linear bias for lenses constant for redshift bin (example notebook)
+  bias_DESgc__0: 1.48
+
+  # IA: 0.5
+  fsky: 0.05
+
+parameters:
+  # Not used for while (read by ccl.cosmo):
+  Omega_c: 0.2640
+  Omega_b: 0.0493
+  h: 0.6736
+  n_s: 0.9649
+  sigma8: 0.8111
+  w0: -1
+  wa: 0
+  transfer_function: 'boltzmann_camb'
+HOD:
+  # automatically creates massdef and concentration objects 
+  log10Mmin_0: 12.0
+  log10Mmin_p: 0.0
+  siglnM_0: 0.4
+  siglnM_p: 0.0
+  log10M0_0: 7.0
+  log10M0_p: 0.0
+  log10M1_0: 13.3
+  log10M1_p: 0.0
+  alpha_0: 1.0
+  alpha_p: 0.0
+  fc_0: 1.0
+  fc_p: 0.0
+  bg_0: 1.0
+  bg_p: 0.0
+  bmax_0: 1.0
+  bmax_p: 0.0
+  a_pivot: 1.0
+  ns_independent: False

tests/data/conf_covariance_calculator.yml

@@ -41,19 +41,17 @@ NaMaster:
   module: pymaster
   f:
     n_iter: 0
-    lmax_sht: -1
+    lmax: null
+    lmax_mask: null
   w:
-    lmax_mask: -1
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
   cw:
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
 
 cache:

tests/data/conf_covariance_calculator_mpi.yml

@@ -42,19 +42,17 @@ NaMaster:
   module: pymaster
   f:
     n_iter: 0
-    lmax_sht: -1
+    lmax: null
+    lmax_mask: null
   w:
-    lmax_mask: -1
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
   cw:
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
 
 cache:

tests/data/conf_covariance_gaussian_fourier_nmt.yaml

@@ -40,19 +40,17 @@ NaMaster:
   module: pymaster
   f:
     n_iter: 0
-    lmax_sht: -1
+    lmax: null
+    lmax_mask: null 
   w:
-    lmax_mask: -1
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
   cw:
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
 
 parameters:

tests/data/conf_covariance_gaussian_fourier_nmt_txpipe.yaml

@@ -26,19 +26,17 @@ NaMaster:
   module: pymaster
   f:
     n_iter: 0
-    lmax_sht: -1
+    lmax: null
+    lmax_mask: null
   w:
-    lmax_mask: -1
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
   cw:
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
 
 parameters:

tests/data/conf_covariance_gaussian_fourier_nmt_txpipe_mpi.yaml

@@ -26,19 +26,17 @@ NaMaster:
   module: pymaster
   f:
     n_iter: 0
-    lmax_sht: -1
+    lmax: null
+    lmax_mask: null
   w:
-    lmax_mask: -1
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
   cw:
     l_toeplitz: -1
     l_exact: -1
     dl_band: -1
-    n_iter: 3
     recompute: True
 
 parameters:

tests/data/conf_covariance_gaussian_fsky_fourier.yaml

@@ -27,6 +27,4 @@ tjpcov:
   {% endfor %}
 
   IA: 0.5
-
-GaussianFsky:
   fsky: 0.3

tests/data/conf_covariance_gaussian_fsky_real.yaml

@@ -26,8 +26,6 @@ tjpcov:
   {% endfor %}
 
   IA: 0.5
-
-GaussianFsky:
   fsky: 0.3
 
 ProjectedReal:

tests/data/conf_covariance_ssc_fsky.yaml

@@ -0,0 +1,35 @@
+tjpcov:
+  # sacc input file 
+  sacc_file: ./tests/benchmarks/32_DES_tjpcov_bm/cls_cov.fits
+
+  # 'set' from parameters OR pass CCL cosmology object OR yaml file
+  cosmo: 'set'
+
+  outdir: ./tests/tmp/
+
+  # Survey params:
+  # 5 lens bins
+  Ngal_DESgc__0: 26
+
+  Ngal_DESwl__0: 26
+  Ngal_DESwl__1: 26
+  # # constant bin sigma_e
+  sigma_e_DESwl__0: 0.26
+  sigma_e_DESwl__1: 0.26
+
+  # linear bias for lenses constant for redshift bin (example notebook)
+  bias_DESgc__0: 1.48
+
+  # IA: 0.5
+  fsky: 0.05
+
+parameters:
+  # Not used for while (read by ccl.cosmo):
+  Omega_c: 0.2640
+  Omega_b: 0.0493
+  h: 0.6736
+  n_s: 0.9649
+  sigma8: 0.8111
+  w0: -1
+  wa: 0
+  transfer_function: 'boltzmann_camb'