Fix GitHub Actions

.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
   - 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_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/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()

tjpcov/covariance_fourier_gaussian_nmt.py

@@ -319,7 +319,7 @@ def get_covariance_block(
                     mn[2],
                     mn[3],
                     mn[4],
-                    lmax=int(ell[-1]),
+                    # lmax=int(ell[-1]),  # Not available in NaMaster v2
                     **self.nmt_conf["cw"],
                 )
 
@@ -385,10 +385,10 @@ def get_covariance_workspace(
         """
         outdir = self.io.outdir
         spins = {
-            m1: f1.fl.spin,
-            m2: f2.fl.spin,
-            m3: f3.fl.spin,
-            m4: f4.fl.spin,
+            m1: f1.spin,
+            m2: f2.spin,
+            m3: f3.spin,
+            m4: f4.spin,
         }
 
         # Any other symmetry?
@@ -481,6 +481,7 @@ def get_fields_dict(self, tracer_names, cache=None, masks=None, **kwargs):
                 # We add the spin to make sure we distinguish fields of
                 # different types even though they share the same mask
                 k = mask_names[i] + str(spins[i])
+                print(nmt_conf)
                 if k not in f_by_mask_name:
                     f_by_mask_name[k] = nmt.NmtField(
                         masks[i], None, spin=spins[i], **nmt_conf
@@ -673,7 +674,7 @@ def get_workspace(self, f1, f2, m1, m2, bins, **kwargs):
             )
 
         outdir = self.io.outdir
-        s1, s2 = f1.fl.spin, f2.fl.spin
+        s1, s2 = f1.spin, f2.spin
 
         # Currently, outdir will be always not None. If not specified, it
         # will be the current directory. I leave this for now since we might
@@ -763,7 +764,7 @@ def get_workspaces_dict(
             if key in cache:
                 w[i] = cache[key]
             else:
-                s1, s2 = fields[i1].fl.spin, fields[i2].fl.spin
+                s1, s2 = fields[i1].spin, fields[i2].spin
                 # In this case you have to check for m1 x m2 and m2 x m1
                 k = (mask_names[i1], mask_names[i2])
                 sk = "".join(sorted(f"{s1}{s2}"))

tjpcov/covariance_gaussian_fsky.py

@@ -43,7 +43,7 @@ def get_binning_info(self, binning="linear"):
         # TODO: This should be obtained from the sacc file or the input
         # configuration. Check how it is done in TXPipe:
         # https://github.com/LSSTDESC/TXPipe/blob/a9dfdb7809ac7ed6c162fd3930c643a67a
-        out = self.get_binning_info()
+        out = super().get_binning_info()
         if out is not None:
             ell = out[0]
             ell_eff = out[1]