Merge branch 'master' into cmb_parametrization

NumCosmo · Apr 23, 2024 · ab7445c · ab7445c
2 parents 4dfaf0d + fc63c39
commit ab7445c
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diff --git a/.flake8 b/.flake8
@@ -1,5 +1,3 @@
 [flake8]
 max-line-length = 88
-select = C,E,F,W,B,B950
 extend-ignore = E203, E501
-
diff --git a/.github/workflows/build_check.yml b/.github/workflows/build_check.yml
@@ -43,15 +43,15 @@ jobs:
     - name: Check NumCosmo
       run: meson test -C build || (cat build/meson-logs/testlog.txt && exit 1)
     - name: Create a NumCosmo tarball
-      run: meson dist -C build --no-tests 
+      run: meson dist -C build --no-tests
     - name: Upload a Build Artifact
       uses: actions/upload-artifact@v2
       with:
         name: release
         path: build/meson-dist/numcosmo-*.tar.xz
     - name: Test example compilation using installed library
       run: |
-        sudo meson install -C build 
+        sudo meson install -C build
         cd examples
         gcc -D_GNU_SOURCE -Wall example_simple.c -o example_simple $(pkg-config numcosmo --libs --cflags)
         gcc -D_GNU_SOURCE -Wall example_ca.c -o example_ca $(pkg-config numcosmo --libs --cflags)
@@ -73,9 +73,9 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4 
+    - uses: actions/setup-python@v4
       with:
-        python-version: '3.x' 
+        python-version: '3.x'
     - name: Brew install pre-requisites
       run: |
         brew install gobject-introspection gsl gmp mpfr fftw cfitsio libfyaml nlopt gfortran gtk-doc glib openblas
@@ -85,8 +85,8 @@ jobs:
     - name: Ensure clear Jupyter Notebooks
       uses: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1
     - name: Configure NumCosmo
-      run: | 
-        meson setup build -Dbuildtype=release -Dnumcosmo_py=true --prefix=/usr || (cat build/meson-logs/meson-log.txt && exit 1)
+      run: |
+        meson setup build -Dbuildtype=release -Dnumcosmo_py=true -Dmpi=disabled --prefix=/usr || (cat build/meson-logs/meson-log.txt && exit 1)
     - name: Building NumCosmo
       run: |
         meson compile -C build
@@ -98,15 +98,18 @@ jobs:
         python example_cbe.py
     - name: Check NumCosmo
       run: meson test -C build || (cat build/meson-logs/testlog.txt && exit 1)
-  
+
   build-miniforge:
     name: (${{ matrix.os }}, py${{ matrix.python-version }}, ${{ matrix.mpi }}, Miniforge)
     runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
         os: ["ubuntu", "macos"]
-        python-version: ["3.9"]
+        python-version: ["3.10"]
         mpi: ["openmpi", "mpich"]
+        exclude:
+          - os: "macos"
+            mpi: "openmpi"
     defaults:
       run:
         shell: bash -el {0}
@@ -175,7 +178,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu"]
-        python-version: ["3.9"]
+        python-version: ["3.10"]
     defaults:
       run:
         shell: bash -el {0}
@@ -224,12 +227,15 @@ jobs:
           meson test -C build --timeout-multiplier 0 || (cat build/meson-logs/testlog.txt && exit 1)
           lcov --config-file .lcovrc --no-external --capture --directory build --directory numcosmo --directory tests --base-directory $(pwd)/build --output-file numcosmo-coverage-tests.info
           lcov --config-file .lcovrc --add-tracefile numcosmo-coverage-base.info --add-tracefile numcosmo-coverage-tests.info --output-file numcosmo-coverage-full.info
-          lcov --config-file .lcovrc --remove numcosmo-coverage-full.info '*/class/*' '*/levmar/*' '*/libcuba/*' '*/plc/*' '*/sundials/*' '*/toeplitz/*' '*/tools/*' --output-file numcosmo-coverage.info 
+          lcov --config-file .lcovrc --remove numcosmo-coverage-full.info '*/class/*' '*/levmar/*' '*/libcuba/*' '*/plc/*' '*/sundials/*' '*/toeplitz/*' '*/tools/*' --output-file numcosmo-coverage.info
       - name: CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          disable_search: true
+          fail_ci_if_error: true
           files: ./numcosmo-coverage.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
       #- name: Generate coverage
       #    # For some reason, gcovr is ignoring the configured gcovr.cfg file
       #    # ninja coverage -C build -v -d stats -d explain

diff --git a/devel_environment.yml b/devel_environment.yml
@@ -3,20 +3,21 @@ channels:
   - conda-forge
 dependencies: 
   - astropy
-  - black<24
+  - black
   - c-compiler
   - cfitsio
   - fftw
   - flake8
   - fortran-compiler
   - gcovr
   - getdist
-  - glib
-  - glib-tools
+  - glib <=2.78.4
+  - glib-tools <=2.78.4
   - gmp
-  - gobject-introspection
+  - gobject-introspection <=1.78
   - gsl
   - hdf5
+  - healpy
   - lcov
   - libflint
   - libfyaml
@@ -26,7 +27,7 @@ dependencies:
   - mypy
   - ninja
   - nlopt
-  - numpy >= 1.21.0
+  - numpy >= 1.23.0
   - openblas=*=*openmp*
   - openmpi
   - pip
@@ -37,7 +38,7 @@ dependencies:
   - pygobject
   - pylint
   - pytest
-  - python >= 3.9
+  - python >= 3.10
   - rich
   - scipy
   - tqdm

diff --git a/docs/numcosmo-docs.sgml b/docs/numcosmo-docs.sgml
@@ -77,9 +77,10 @@
     <section>
       <title>Power spectrum functions</title>
       <xi:include href="xml/ncm_powspec.xml"/>
+      <xi:include href="xml/ncm_powspec_corr3d.xml"/>
       <xi:include href="xml/ncm_powspec_filter.xml"/>
       <xi:include href="xml/ncm_powspec_sphere_proj.xml"/>
-      <xi:include href="xml/ncm_powspec_corr3d.xml"/>
+      <xi:include href="xml/ncm_powspec_spline2d.xml"/>
     </section>
     <section>
       <title>Harmonic Oscillator</title>
@@ -271,14 +272,15 @@
   <chapter>
     <title>Perturbations</title>
     <xi:include href="xml/nc_hipert.xml"/>
-    <xi:include href="xml/nc_hipert_bg_var.xml"/>
-    <xi:include href="xml/nc_hipert_wkb.xml"/>
     <xi:include href="xml/nc_hipert_adiab.xml"/>
-    <xi:include href="xml/nc_hipert_gw.xml"/>
-    <xi:include href="xml/nc_hipert_two_fluids.xml"/>
-    <xi:include href="xml/nc_hipert_boltzmann.xml"/>
+    <xi:include href="xml/nc_hipert_bg_var.xml"/>
     <xi:include href="xml/nc_hipert_boltzmann_std.xml"/>
+    <xi:include href="xml/nc_hipert_boltzmann.xml"/>
+    <xi:include href="xml/nc_hipert_em.xml"/>
     <xi:include href="xml/nc_hipert_first_order.xml"/>
+    <xi:include href="xml/nc_hipert_gw.xml"/>
+    <xi:include href="xml/nc_hipert_two_fluids.xml"/>
+    <xi:include href="xml/nc_hipert_wkb.xml"/>
     <section>
       <title>Gravitational theories</title>
       <xi:include href="xml/nc_hipert_grav.xml"/>
@@ -320,9 +322,9 @@
     <section>
       <title>Matter Power Spectrum</title>
       <xi:include href="xml/nc_powspec_ml.xml"/>
-      <xi:include href="xml/nc_powspec_ml_fix_spline.xml"/>
-      <xi:include href="xml/nc_powspec_ml_transfer.xml"/>
       <xi:include href="xml/nc_powspec_ml_cbe.xml"/>
+      <xi:include href="xml/nc_powspec_ml_spline.xml"/>
+      <xi:include href="xml/nc_powspec_ml_transfer.xml"/>
       <xi:include href="xml/nc_powspec_mnl.xml"/>
       <xi:include href="xml/nc_powspec_mnl_halofit.xml"/>
     </section>
@@ -434,6 +436,7 @@
     <xi:include href="xml/nc_data_dist_mu.xml"/>
     <xi:include href="xml/nc_data_snia_cov.xml"/>
     <xi:include href="xml/nc_data_cluster_ncount.xml"/>
+    <xi:include href="xml/nc_data_cluster_ncounts_gauss.xml"/>
     <xi:include href="xml/nc_data_cluster_pseudo_counts.xml"/>
     <xi:include href="xml/nc_data_cluster_wl.xml"/>
     <xi:include href="xml/nc_data_reduced_shear_cluster_mass.xml"/>

diff --git a/examples/example_exp_potential.py b/examples/example_exp_potential.py