diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c2bac4db..3ed521b9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -2,49 +2,22 @@ name: Continuous Integration on: push: - branches: - - '*' - tags: - - '*' pull_request: jobs: tests: - name: ${{ matrix.name }} - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - include: - - name: Python 3.6 - os: ubuntu-20.04 - python: '3.6' - - name: Python 3.7 - os: ubuntu-20.04 - python: '3.7' - - name: Python 3.8 - os: ubuntu-20.04 - python: '3.8' - - name: Python 3.9 - os: ubuntu-20.04 - python: '3.9' - - name: Python 3.10 - os: ubuntu-20.04 - python: '3.10' - steps: - - name: Checkout code - uses: actions/checkout@v2 - with: - submodules: 'true' - fetch-depth: 0 - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python }} - - name: Install HDF5 and MPI - if: startsWith(matrix.os, 'ubuntu') - run: sudo apt-get install libhdf5-serial-dev libmpich-dev - - name: Install tox - run: pip install tox - - name: Run tests - run: tox -e test-bitlevel + uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1 + with: + libraries: | + apt: + - libhdf5-serial-dev + - libmpich-dev + envs: | + - linux: py37-test-bitlevel + runs-on: ubuntu-20.04 + - linux: py38-test-bitlevel + runs-on: ubuntu-20.04 + - linux: py39-test-bitlevel + runs-on: ubuntu-20.04 + - linux: py310-test-bitlevel + runs-on: ubuntu-20.04 diff --git a/.gitignore b/.gitignore index eb62bdaa..5b9a0edf 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ +hyperion/_version.py hyperion/data/* build docs/_build @@ -15,4 +16,5 @@ build_cmake .vscode dist Hyperion.egg-info - +*.so +pip-wheel-metadata diff --git a/docs/tutorials/tutorial_quantities_yt.rst b/docs/tutorials/tutorial_quantities_yt.rst index 24e0de42..1bccad24 100644 --- a/docs/tutorials/tutorial_quantities_yt.rst +++ b/docs/tutorials/tutorial_quantities_yt.rst @@ -26,7 +26,7 @@ where ``pf`` is a ``StaticOutput`` yt object! This can then be used as a normal dataset in yt. For example, we can easily make projections of density and temperature along the y-axis:: - from yt.mods import ProjectionPlot + from yt import ProjectionPlot prj = ProjectionPlot(pf, 'y', ['density', 'temperature'], center=[0.0, 0.0, 0.0]) diff --git a/hyperion/densities/ulrich_envelope.py b/hyperion/densities/ulrich_envelope.py index 34858831..c2a1f4cc 100644 --- a/hyperion/densities/ulrich_envelope.py +++ b/hyperion/densities/ulrich_envelope.py @@ -20,10 +20,10 @@ def delta_neg(r, q): rho = np.sqrt(-q.real ** 3) theta = np.arccos(r.real / rho) - s = (rho ** (1. / 3.) * np.cos(theta / 3.)).astype(np.complex) + s = (rho ** (1. / 3.) * np.cos(theta / 3.)).astype(complex) s.imag = rho ** (1. / 3.) * np.sin(theta / 3.) - t = (rho ** (1. / 3.) * np.cos(-theta / 3.)).astype(np.complex) + t = (rho ** (1. / 3.) * np.cos(-theta / 3.)).astype(complex) t.imag = rho ** (1. / 3.) * np.sin(-theta / 3.) return s, t @@ -49,8 +49,8 @@ def cubic(c, d): Solve x**3 + c * x + d = 0 ''' - c = c.astype(np.complex) - d = d.astype(np.complex) + c = c.astype(complex) + d = d.astype(complex) q = c / 3. r = - d / 2. @@ -59,8 +59,8 @@ def cubic(c, d): pos = delta >= 0. - s = np.zeros(c.shape, dtype=np.complex) - t = np.zeros(c.shape, dtype=np.complex) + s = np.zeros(c.shape, dtype=complex) + t = np.zeros(c.shape, dtype=complex) if np.sum(pos) > 0: s[pos], t[pos] = delta_pos(r[pos], delta[pos]) @@ -69,8 +69,8 @@ def cubic(c, d): s[~pos], t[~pos] = delta_neg(r[~pos], q[~pos]) x1 = s + t - x2 = - (s + t) / 2. + np.sqrt(3.) / 2. * (s - t) * np.complex(0., 1.) - x3 = - (s + t) / 2. - np.sqrt(3.) / 2. * (s - t) * np.complex(0., 1.) + x2 = - (s + t) / 2. + np.sqrt(3.) / 2. * (s - t) * complex(0., 1.) + x3 = - (s + t) / 2. - np.sqrt(3.) / 2. * (s - t) * complex(0., 1.) return x1, x2, x3 diff --git a/hyperion/dust/emissivities.py b/hyperion/dust/emissivities.py index e9c59ba6..8d4e930f 100644 --- a/hyperion/dust/emissivities.py +++ b/hyperion/dust/emissivities.py @@ -151,9 +151,9 @@ def hash(self): h = hashlib.md5() h.update(str(self.is_lte).encode('utf-8')) h.update(self.var_name.encode('utf-8')) - h.update(self.var.tostring()) - h.update(self.nu.tostring()) - h.update(self.jnu.tostring()) + h.update(self.var.tobytes()) + h.update(self.nu.tobytes()) + h.update(self.jnu.tobytes()) return h.hexdigest() def __setattr__(self, attribute, value): diff --git a/hyperion/dust/mean_opacities.py b/hyperion/dust/mean_opacities.py index 4c47952a..dc80d901 100644 --- a/hyperion/dust/mean_opacities.py +++ b/hyperion/dust/mean_opacities.py @@ -171,12 +171,12 @@ def plot(self, figure, subplot): def hash(self): h = hashlib.md5() - h.update(self.temperature.tostring()) - h.update(self.specific_energy.tostring()) - h.update(self.chi_planck.tostring()) - h.update(self.kappa_planck.tostring()) - h.update(self.chi_inv_planck.tostring()) - h.update(self.kappa_inv_planck.tostring()) - h.update(self.chi_rosseland.tostring()) - h.update(self.kappa_rosseland.tostring()) + h.update(self.temperature.tobytes()) + h.update(self.specific_energy.tobytes()) + h.update(self.chi_planck.tobytes()) + h.update(self.kappa_planck.tobytes()) + h.update(self.chi_inv_planck.tobytes()) + h.update(self.kappa_inv_planck.tobytes()) + h.update(self.chi_rosseland.tobytes()) + h.update(self.kappa_rosseland.tobytes()) return h.hexdigest() diff --git a/hyperion/dust/optical_properties.py b/hyperion/dust/optical_properties.py index 36d22a05..111dfb3f 100644 --- a/hyperion/dust/optical_properties.py +++ b/hyperion/dust/optical_properties.py @@ -383,14 +383,14 @@ def plot(self, figure, subplots): def hash(self): h = hashlib.md5() - h.update(self.nu.tostring()) - h.update(self.chi.tostring()) - h.update(self.albedo.tostring()) - h.update(self.mu.tostring()) - h.update(self.P1.tostring()) - h.update(self.P2.tostring()) - h.update(self.P3.tostring()) - h.update(self.P4.tostring()) + h.update(self.nu.tobytes()) + h.update(self.chi.tobytes()) + h.update(self.albedo.tobytes()) + h.update(self.mu.tobytes()) + h.update(self.P1.tobytes()) + h.update(self.P2.tobytes()) + h.update(self.P3.tobytes()) + h.update(self.P4.tobytes()) return h.hexdigest() def __setattr__(self, attribute, value): diff --git a/hyperion/grid/amr_grid.py b/hyperion/grid/amr_grid.py index 2ee8a200..783c999b 100644 --- a/hyperion/grid/amr_grid.py +++ b/hyperion/grid/amr_grid.py @@ -602,7 +602,7 @@ def from_yt(cls, ds, quantity_mapping={}): >>> ds = load('DD0010/moving7_0010') >>> def _dust_density(field, data): ... return data[('gas', 'density')].in_units('g/cm**3') * 0.01 - >>> ds.add_field(('gas', 'dust_density'), function=_dust_density, units='g/cm**3') + >>> ds.add_field(('gas', 'dust_density'), function=_dust_density, units='g/cm**3', sampling_type='cell') >>> amr = AMRGrid.from_yt(ds, quantity_mapping={'density':('gas', 'dust_density')}) """ diff --git a/hyperion/grid/cartesian_grid.py b/hyperion/grid/cartesian_grid.py index 52ad7492..12b735f0 100644 --- a/hyperion/grid/cartesian_grid.py +++ b/hyperion/grid/cartesian_grid.py @@ -392,9 +392,9 @@ def write_single_array(self, group, name, array, copy=True, absolute_paths=False def get_geometry_id(self): geo_hash = hashlib.md5() - geo_hash.update(self.x_wall.tostring()) - geo_hash.update(self.y_wall.tostring()) - geo_hash.update(self.z_wall.tostring()) + geo_hash.update(self.x_wall.tobytes()) + geo_hash.update(self.y_wall.tobytes()) + geo_hash.update(self.z_wall.tobytes()) return geo_hash.hexdigest() def __getitem__(self, item): diff --git a/hyperion/grid/cylindrical_polar_grid.py b/hyperion/grid/cylindrical_polar_grid.py index 2fc8cff5..73cfbb63 100644 --- a/hyperion/grid/cylindrical_polar_grid.py +++ b/hyperion/grid/cylindrical_polar_grid.py @@ -420,9 +420,9 @@ def write_single_array(self, group, name, array, copy=True, absolute_paths=False def get_geometry_id(self): geo_hash = hashlib.md5() - geo_hash.update(self.w_wall.tostring()) - geo_hash.update(self.z_wall.tostring()) - geo_hash.update(self.p_wall.tostring()) + geo_hash.update(self.w_wall.tobytes()) + geo_hash.update(self.z_wall.tobytes()) + geo_hash.update(self.p_wall.tobytes()) return geo_hash.hexdigest() def __getitem__(self, item): diff --git a/hyperion/grid/octree_grid.py b/hyperion/grid/octree_grid.py index 651db7c2..b77e070a 100644 --- a/hyperion/grid/octree_grid.py +++ b/hyperion/grid/octree_grid.py @@ -196,7 +196,7 @@ def refined(self, value): def _validate(self, value): - value_hash = hashlib.md5(value.tostring()).hexdigest() + value_hash = hashlib.md5(value.tobytes()).hexdigest() if value_hash in self._validate_cache: return value @@ -205,7 +205,7 @@ def _validate(self, value): # Check that refined array reduces to a single False if removing all # levels of refinement. - refined_str = value.tostring() + refined_str = value.tobytes() previous = '' while True: refined_str = refined_str.replace(b'\x01\x00\x00\x00\x00\x00\x00\x00\x00', b'\x00') @@ -491,7 +491,7 @@ def get_geometry_id(self): geo_hash.update(struct.pack('>d', self.dx)) geo_hash.update(struct.pack('>d', self.dy)) geo_hash.update(struct.pack('>d', self.dz)) - geo_hash.update(self.refined.tostring()) + geo_hash.update(self.refined.tobytes()) return geo_hash.hexdigest() def __getitem__(self, item): diff --git a/hyperion/grid/spherical_polar_grid.py b/hyperion/grid/spherical_polar_grid.py index 5b0f67b5..d6637486 100644 --- a/hyperion/grid/spherical_polar_grid.py +++ b/hyperion/grid/spherical_polar_grid.py @@ -430,9 +430,9 @@ def write_single_array(self, group, name, array, copy=True, absolute_paths=False def get_geometry_id(self): geo_hash = hashlib.md5() - geo_hash.update(self.r_wall.tostring()) - geo_hash.update(self.t_wall.tostring()) - geo_hash.update(self.p_wall.tostring()) + geo_hash.update(self.r_wall.tobytes()) + geo_hash.update(self.t_wall.tobytes()) + geo_hash.update(self.p_wall.tobytes()) return geo_hash.hexdigest() def __getitem__(self, item): diff --git a/hyperion/grid/tests/test_yt.py b/hyperion/grid/tests/test_yt.py index 645c982d..c11220b0 100644 --- a/hyperion/grid/tests/test_yt.py +++ b/hyperion/grid/tests/test_yt.py @@ -75,7 +75,7 @@ def setup_method(self, method): @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES) def test_to_yt(self, tmpdir, grid_type): - from yt.mods import ProjectionPlot + from yt import ProjectionPlot g = self.grid[grid_type] g['density'] = [] @@ -101,7 +101,7 @@ def test_from_yt(tmpdir): def _dust_density(field, data): return data["density"].in_units('g/cm**3') * 0.01 - ds.add_field(("gas", "dust_density"), function=_dust_density, units='g/cm**3') + ds.add_field(("gas", "dust_density"), function=_dust_density, units='g/cm**3', sampling_type='cell') amr = AMRGrid.from_yt(ds, quantity_mapping={'density': ('gas', 'dust_density')}) @@ -147,7 +147,7 @@ def test_axis_ordering_cartesian(): g['density'] = [] g['density'].append(density) - from yt.mods import ProjectionPlot, SlicePlot + from yt import ProjectionPlot, SlicePlot pf = g.to_yt() @@ -177,7 +177,7 @@ def test_axis_ordering_amr(): grid.quantities['density'] = [] grid.quantities['density'].append(np.arange(grid.nz)[:, None, None] * np.ones((grid.nz, grid.ny, grid.nx))) - from yt.mods import ProjectionPlot, SlicePlot + from yt import ProjectionPlot, SlicePlot pf = g.to_yt() diff --git a/hyperion/grid/voronoi_grid.py b/hyperion/grid/voronoi_grid.py index bfc4c52f..97f64ccf 100644 --- a/hyperion/grid/voronoi_grid.py +++ b/hyperion/grid/voronoi_grid.py @@ -527,9 +527,9 @@ def write_single_array(self, group, name, array, copy=True, absolute_paths=False def get_geometry_id(self): # The grid is uniquely defined by the points and the bounds geo_hash = hashlib.md5() - geo_hash.update(self.x.tostring()) - geo_hash.update(self.y.tostring()) - geo_hash.update(self.z.tostring()) + geo_hash.update(self.x.tobytes()) + geo_hash.update(self.y.tobytes()) + geo_hash.update(self.z.tobytes()) geo_hash.update(struct.pack('>d', self.xmin)) geo_hash.update(struct.pack('>d', self.xmax)) geo_hash.update(struct.pack('>d', self.ymin)) diff --git a/hyperion/grid/yt3_wrappers.py b/hyperion/grid/yt3_wrappers.py index 32c0beea..5c9aa426 100644 --- a/hyperion/grid/yt3_wrappers.py +++ b/hyperion/grid/yt3_wrappers.py @@ -107,7 +107,7 @@ def amr_grid_to_yt_stream(levels, dust_id=0): bbox = np.array([[xmin, xmax], [ymin, ymax], [zmin, zmax]]) - from yt.mods import load_amr_grids + from yt import load_amr_grids spf = load_amr_grids(grid_data, domain_dimensions, bbox=bbox, geometry=('cartesian', ('x', 'y', 'z'))) @@ -154,7 +154,7 @@ def octree_grid_to_yt_stream(grid, dust_id=0): zmin = grid.z - grid.dz zmax = grid.z + grid.dz - from yt.mods import load_octree + from yt import load_octree quantities = {} for field in grid.quantities: @@ -183,7 +183,7 @@ def cartesian_grid_to_yt_stream(grid, xmin, xmax, ymin, ymax, zmin, zmax, dust_i data[field] = grid.quantities[field][dust_id].transpose(), '' # Load cartesian grid into yt - from yt.mods import load_uniform_grid + from yt import load_uniform_grid spf = load_uniform_grid(data=data, domain_dimensions=np.array(grid.shape[::-1], dtype=np.int32), bbox=np.array([(xmin, xmax), (ymin, ymax), (zmin, zmax)]), @@ -240,7 +240,7 @@ def yt_dataset_to_amr_grid(ds, quantity_mapping={}): >>> ds = load('DD0010/moving7_0010') >>> def _dust_density(field, data): ... return data[('gas', 'density')].in_units('g/cm**3') * 0.01 - >>> ds.add_field(('gas', 'dust_density'), function=_dust_density, units='g/cm**3') + >>> ds.add_field(('gas', 'dust_density'), function=_dust_density, units='g/cm**3', sampling_type='cell') >>> amr = yt_dataset_to_amr_grid(ds, quantity_mapping={'density':('gas', 'dust_density')}) """ diff --git a/hyperion/model/tests/data/test_pascucci.tau=0.1.rtout b/hyperion/model/tests/data/test_pascucci.tau=0.1.rtout index 83e3d553..8dc5ea57 100644 Binary files a/hyperion/model/tests/data/test_pascucci.tau=0.1.rtout and b/hyperion/model/tests/data/test_pascucci.tau=0.1.rtout differ diff --git 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a/hyperion/model/tests/data/test_specific_energy.grid_type=sph.sample_sources_evenly=True.multiple_densities=True.rtout and b/hyperion/model/tests/data/test_specific_energy.grid_type=sph.sample_sources_evenly=True.multiple_densities=True.rtout differ diff --git a/hyperion/model/tests/test_amr_checks.py b/hyperion/model/tests/test_amr_checks.py index 5e4245b8..bbc3d976 100644 --- a/hyperion/model/tests/test_amr_checks.py +++ b/hyperion/model/tests/test_amr_checks.py @@ -224,7 +224,7 @@ def test_shadowing_regression(tmpdir): m.write(tmpdir.join(random_id()).strpath) mo = m.run(tmpdir.join(random_id()).strpath) - from yt.mods import SlicePlot + from yt import SlicePlot g = mo.get_quantities() diff --git a/hyperion/util/interpolate.py b/hyperion/util/interpolate.py index df330bdf..e68475a0 100644 --- a/hyperion/util/interpolate.py +++ b/hyperion/util/interpolate.py @@ -58,7 +58,7 @@ def interp1d_fast(x, y, xval): if x.dtype != float or y.dtype != float: x, y = x.astype(float), y.astype(float) if np.isscalar(xval): - return interp1d_linear_scalar(x, y, np.float(xval)) + return interp1d_linear_scalar(x, y, float(xval)) else: if xval.ndim > 1: return interp1d_linear_array(x, y, xval.flatten()).reshape(xval.shape) @@ -74,7 +74,7 @@ def interp1d_fast_loglog(x, y, xval): if x.dtype != float or y.dtype != float: x, y = x.astype(float), y.astype(float) if np.isscalar(xval): - return interp1d_loglog_scalar(x, y, np.float(xval)) + return interp1d_loglog_scalar(x, y, float(xval)) else: if xval.ndim > 1: return interp1d_loglog_array(x, y, xval.flatten()).reshape(xval.shape) @@ -90,7 +90,7 @@ def interp1d_fast_linlog(x, y, xval): if x.dtype != float or y.dtype != float: x, y = x.astype(float), y.astype(float) if np.isscalar(xval): - return interp1d_linlog_scalar(x, y, np.float(xval)) + return interp1d_linlog_scalar(x, y, float(xval)) else: if xval.ndim > 1: return interp1d_linlog_array(x, y, xval.flatten()).reshape(xval.shape) @@ -106,7 +106,7 @@ def interp1d_fast_loglin(x, y, xval): if x.dtype != float or y.dtype != float: x, y = x.astype(float), y.astype(float) if np.isscalar(xval): - return interp1d_loglin_scalar(x, y, np.float(xval)) + return interp1d_loglin_scalar(x, y, float(xval)) else: if xval.ndim > 1: return interp1d_loglin_array(x, y, xval.flatten()).reshape(xval.shape) diff --git a/tox.ini b/tox.ini index 3bc99f8b..b28b5f12 100644 --- a/tox.ini +++ b/tox.ini @@ -8,10 +8,14 @@ isolated_build = true [testenv] changedir = .tmp/{envname} +deps = + numpy==1.21.* extras = test: test allowlist_externals = + {toxinidir}/configure make + mv commands = pip freeze {toxinidir}/configure --prefix={envdir}