Merge remote-tracking branch 'refs/remotes/origin/SSC_fsky' into SSC_…

…fsky
LSSTDESC · Nov 26, 2024 · 72a39e3 · 72a39e3
2 parents 4f0ec83 + ffe8f8b
commit 72a39e3
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Showing 14 changed files with 48 additions and 436 deletions.
diff --git a/.github/workflows/ci.yaml b/.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

diff --git a/Untitled.ipynb b/Untitled.ipynb
diff --git a/disk_fsky_04.fits b/disk_fsky_04.fits
diff --git a/environment.yml b/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
   - sacc>=0.12
-  - namaster
+  - namaster>2
   - camb
   - Jinja2
   - healpy

diff --git a/pyproject.toml b/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",

diff --git a/tests/data/conf_covariance_calculator.yml b/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:

diff --git a/tests/data/conf_covariance_calculator_mpi.yml b/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:

diff --git a/tests/data/conf_covariance_gaussian_fourier_nmt.yaml b/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:

diff --git a/tests/data/conf_covariance_gaussian_fourier_nmt_txpipe.yaml b/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:

diff --git a/tests/data/conf_covariance_gaussian_fourier_nmt_txpipe_mpi.yaml b/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:

diff --git a/tests/test_covariance_fourier_gaussian_nmt.py b/tests/test_covariance_fourier_gaussian_nmt.py
@@ -389,16 +389,18 @@ def test_get_cl_for_cov(cov_fg_nmt):
 
     with pytest.raises(ValueError):
         cov_fg_nmt.get_cl_for_cov(
-            cl_fid_Sh, cl["nl_cp"], m, m, w, nl_is_cp=True
+            cl_fid_Sh["cl"], cl["nl_cp"], m, m, w, nl_is_cp=True
         )
 
     with pytest.raises(ValueError):
         # Uncoupled binned noise
-        cov_fg_nmt.get_cl_for_cov(cl_fid, cl["nl"], m, m, w, nl_is_cp=True)
+        cov_fg_nmt.get_cl_for_cov(
+            cl_fid["cl"], cl["nl"], m, m, w, nl_is_cp=True
+        )
 
     with pytest.raises(ValueError):
         cov_fg_nmt.get_cl_for_cov(
-            cl_fid, cl["nl_cp"], m, m, wSh, nl_is_cp=True
+            cl_fid["cl"], cl["nl_cp"], m, m, wSh, nl_is_cp=True
         )
 
 
@@ -662,7 +664,7 @@ def test_get_covariance_block_cache(cov_fg_nmt, tracer_comb1, tracer_comb2):
 
 @pytest.mark.parametrize(
     "kwargs",
-    [{}, {"l_toeplitz": 10, "l_exact": 10, "dl_band": 10, "n_iter": 0}],
+    [{}, {"l_toeplitz": 10, "l_exact": 10, "dl_band": 10}],
 )
 def test_get_covariance_workspace(cov_fg_nmt, kwargs):
     m1 = get_mask_from_dtype("galaxy_clustering")
@@ -715,7 +717,7 @@ def test_get_covariance_workspace(cov_fg_nmt, kwargs):
     # Check only the first is written/computed created & that cw is correct
 
     for fields, masks_names in zip(combinations, combinations_names):
-        spins = [fi.fl.spin for fi in fields]
+        spins = [fi.spin for fi in fields]
         cw_code = cov_fg_nmt.get_covariance_workspace(
             *fields, *masks_names, **kwargs
         )
@@ -967,7 +969,7 @@ def get_data_types(self):
 
 @pytest.mark.parametrize(
     "kwargs",
-    [{}, {"l_toeplitz": 10, "l_exact": 10, "dl_band": 10, "n_iter": 0}],
+    [{}, {"l_toeplitz": 10, "l_exact": 10, "dl_band": 10}],
 )
 def test_get_workspace(cov_fg_nmt, kwargs):
     # Compute NmtBins
@@ -1030,7 +1032,7 @@ def test_get_workspace(cov_fg_nmt, kwargs):
 
 @pytest.mark.parametrize(
     "kwargs",
-    [{}, {"l_toeplitz": 10, "l_exact": 10, "dl_band": 10, "n_iter": 0}],
+    [{}, {"l_toeplitz": 10, "l_exact": 10, "dl_band": 10}],
 )
 def test_get_workspace_dict(cov_fg_nmt, kwargs):
     tracers = get_tracers_dict_for_cov()