Adding github actions support (#107)

* adding minimal workflow to test installation process

* adding numpy

* installing cfitsio

* oups

* oups (again)

* new try with correct name

* add fftw

* minimal unit test

* add pspy vs. namaster test

* adding more python version and removing deprectaed travis file

* remove macos

.github/workflows/testing.yml

@@ -0,0 +1,35 @@
+name: Testing
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Ubuntu dependencies
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get install -y libcfitsio-dev libfftw3-dev
+
+    - name: Install dependencies via pip
+      run: |
+        python -m pip install --upgrade pip numpy
+        python -m pip install .
+
+    - name: Testing pspipe
+      run: |
+        python -m unittest pspipe/tests/test_pspipe.py
+        python -m unittest pspipe/tests/test_pspy_namaster.py

pspipe/tests/test_pspipe.py

@@ -0,0 +1,17 @@
+import unittest
+
+
+class PSPipeTest(unittest.TestCase):
+    def test_dependencies(self):
+        def _assert_import(pkg_name):
+            try:
+                import importlib
+                importlib.import_module(pkg_name)
+            except:
+                assert False, "Import of '{}' fails".format(pkg_name)
+
+        _assert_import("camb")
+        _assert_import("mflike")
+        _assert_import("pixell")
+        _assert_import("pspy")
+        _assert_import("pymaster")

pspipe/tests/test_pspy_namaster.py

@@ -0,0 +1,109 @@
+import os
+import tempfile
+
+import camb
+import healpy as hp
+import numpy as np
+import pymaster as nmt
+from pspy import pspy_utils, so_map, so_mcm, so_spectra, so_window, sph_tools
+
+lon, lat = 30, 50
+radius = 25
+nside = 512
+ncomp = 3
+niter = 3
+spectra = ["TT", "TE", "TB", "ET", "BT", "EE", "EB", "BE", "BB"]
+
+template_healpix = so_map.healpix_template(ncomp, nside=nside)
+binary_healpix = so_map.healpix_template(ncomp=1, nside=nside)
+vec = hp.ang2vec(lon, lat, lonlat=True)
+disc = hp.query_disc(nside, vec, radius=np.deg2rad(radius))
+binary_healpix.data[disc] = 1
+
+
+lmin, lmax = 2, 10**4
+l = np.arange(lmin, lmax)
+cosmo_params = {
+    "H0": 67.5,
+    "As": 1e-10 * np.exp(3.044),
+    "ombh2": 0.02237,
+    "omch2": 0.1200,
+    "ns": 0.9649,
+    "Alens": 1.0,
+    "tau": 0.0544,
+}
+pars = camb.set_params(**cosmo_params)
+pars.set_for_lmax(lmax, lens_potential_accuracy=1)
+results = camb.get_results(pars)
+powers = results.get_cmb_power_spectra(pars, CMB_unit="muK")
+
+
+output_dir = os.path.join(tempfile.gettempdir(), "test_pspy_namaster")
+os.makedirs(output_dir, exist_ok=True)
+cl_file = os.path.join(output_dir, "cl_camb.dat")
+np.savetxt(cl_file, np.hstack([l[:, np.newaxis], powers["total"][lmin:lmax]]))
+
+
+cmb = template_healpix.synfast(cl_file)
+noise = so_map.white_noise(cmb, rms_uKarcmin_T=20, rms_uKarcmin_pol=np.sqrt(2) * 20)
+cmb.data += noise.data
+
+
+window = so_window.create_apodization(binary_healpix, apo_type="C1", apo_radius_degree=1)
+mask = so_map.simulate_source_mask(binary_healpix, n_holes=10, hole_radius_arcmin=30)
+mask = so_window.create_apodization(mask, apo_type="C1", apo_radius_degree=1)
+window.data *= mask.data
+window = (window, window)
+
+lmax = 3 * nside - 1
+
+
+def run_pspy():
+    binning_file = os.path.join(output_dir, "binning.dat")
+    pspy_utils.create_binning_file(bin_size=40, n_bins=100, file_name=binning_file)
+    mbb_inv, Bbl = so_mcm.mcm_and_bbl_spin0and2(
+        window, binning_file, lmax=lmax, type="Cl", niter=niter
+    )
+    alms = sph_tools.get_alms(cmb, window, niter=niter, lmax=lmax)
+    ell, ps = so_spectra.get_spectra(alms, spectra=spectra)
+    lb, Clb = so_spectra.bin_spectra(
+        ell, ps, binning_file, lmax, type="Cl", mbb_inv=mbb_inv, spectra=spectra
+    )
+    return lb, Clb
+
+
+def run_namaster():
+    field_0 = nmt.NmtField(window[0].data, [cmb.data[0]])
+    field_2 = nmt.NmtField(window[1].data, [cmb.data[1], cmb.data[2]])
+    nlb = 40
+    b = nmt.NmtBin(nside, nlb=nlb)
+    lb = b.get_effective_ells()
+    wsp = nmt.NmtWorkspace()
+    wsp.compute_coupling_matrix(field_0, field_2, b, is_teb=True, n_iter=niter, lmax_mask=lmax)
+    cl_coupled_00 = nmt.compute_coupled_cell(field_0, field_0)
+    cl_coupled_02 = nmt.compute_coupled_cell(field_0, field_2)
+    cl_coupled_22 = nmt.compute_coupled_cell(field_2, field_2)
+    cls_coupled = np.array(
+        [
+            cl_coupled_00[0],  # TT
+            cl_coupled_02[0],  # TE
+            cl_coupled_02[1],  # TB
+            cl_coupled_22[0],  # EE
+            cl_coupled_22[1],  # EB
+            cl_coupled_22[2],  # BE
+            cl_coupled_22[3],  # BB
+        ]
+    )
+    cls_uncoupled = wsp.decouple_cell(cls_coupled)
+    Clb = {k: cls_uncoupled[i] for i, k in enumerate(["TT", "TE", "TB", "EE", "EB", "BE", "BB"])}
+    Clb["ET"] = Clb["TE"]
+    Clb["BT"] = Clb["TB"]
+    return lb, Clb
+
+
+lb_pspy, Clb_pspy = run_pspy()
+lb_nmt, Clb_nmt = run_namaster()
+
+for spec in spectra:
+    msg = f"Testing {spec} spectrum"
+    np.testing.assert_almost_equal(Clb_pspy[spec], Clb_nmt[spec], err_msg=msg, decimal=12)