Basic Regression Data Setup

.github/actions/setup_env/action.yml

@@ -0,0 +1,31 @@
+name: "Setup environment"
+description: "Sets up environment for stardis and caches it"
+
+inputs:
+  os-label:
+    description: "os label for lock file, default linux"
+    required: true
+    default: "linux-64"
+
+runs:
+  using: "composite"
+  steps:
+      - name: Download Lock File
+        run:  wget -q https://raw.githubusercontent.com/tardis-sn/stardis/main/conda-${{ inputs.os-label }}.lock
+        shell: bash
+
+      - name: Generate Cache Key
+        run: | 
+          file_hash=$(cat conda-${{ inputs.os-label }}.lock | shasum -a 256 | cut -d' ' -f1)
+          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
+        id: cache-environment-key
+        shell: bash
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: conda-${{ inputs.os-label }}.lock
+          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
+          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
+          environment-name: stardis
+          cache-environment: true
+          cache-downloads: true

.github/actions/setup_lfs/action.yml

@@ -0,0 +1,52 @@
+name: "Setup LFS"
+description: "Pull LFS repositories and caches them"
+
+
+inputs:
+  regression-data-repo:
+    description: "stardis regression data repository"
+    required: false
+    default: "tardis-sn/stardis-regression-data"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Clone tardis-sn/stardis-regression-data
+      uses: actions/checkout@v4
+      with:
+        repository: ${{ inputs.regression-data-repo }}
+        path: stardis-regression-data
+
+    - name: Create LFS file list
+      run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
+      working-directory: stardis-regression-data
+      shell: bash
+
+    - name: Restore LFS cache
+      uses: actions/cache/restore@v4
+      id: lfs-cache-regression-data
+      with:
+        path: stardis-regression-data/.git/lfs
+        key: ${{ runner.os }}-lfs-${{ hashFiles('stardis-regression-data/.lfs-assets-id') }}-v1
+
+    - name: Git LFS Pull
+      run: git lfs pull
+      working-directory: stardis-regression-data
+      if: steps.lfs-cache-regression-data.outputs.cache-hit != 'true'
+      shell: bash
+
+    - name: Git LFS Checkout
+      run: git lfs checkout
+      working-directory: stardis-regression-data
+      if: steps.lfs-cache-regression-data.outputs.cache-hit == 'true'
+      shell: bash
+
+    - name: Save LFS cache if not found
+      # uses fake ternary
+      # for reference: https://github.com/orgs/community/discussions/26738#discussioncomment-3253176
+      if: ${{ steps.lfs-cache-regression-data.outputs.cache-hit != 'true' && !contains(github.ref, 'merge') && always() || false }}
+      uses: actions/cache/save@v4
+      id: lfs-cache-regression-data-save
+      with:
+        path: stardis-regression-data/.git/lfs
+        key: ${{ runner.os }}-lfs-${{ hashFiles('stardis-regression-data/.lfs-assets-id') }}-v1

.github/workflows/tests.yml

@@ -2,12 +2,16 @@ name: tests
 
 on:
   push:
+    branches:
+      - main
   pull_request:
+    branches:
+      - main
   workflow_dispatch:
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
-  PYTEST_FLAGS: --cov=stardis --cov-report=xml --cov-report=html
+  PYTEST_FLAGS: --cov=stardis --cov-report=xml --cov-report=html --stardis-regression-data=${{ github.workspace }}/stardis-regression-data
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
 defaults:
@@ -16,19 +20,16 @@ defaults:
 
 jobs:
   build:
-    # if: github.repository_owner == 'tardis-sn'
+    if: github.repository_owner == 'tardis-sn'
     strategy:
       matrix:
         include:
-
         - os: ubuntu-latest
           label: linux-64
           prefix: /usr/share/miniconda3/envs/stardis
-
         # - os: ubuntu-latest
         #   label: linux-64-cuda
         #   prefix: /usr/share/miniconda3/envs/stardis
-
         - os: macos-latest
           label: osx-64
           prefix: /Users/runner/miniconda3/envs/stardis
@@ -37,39 +38,23 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v2
-
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: stardis
-          use-mamba: true
+      - uses: actions/checkout@v4
 
-
-      - name: Cache lockfile
-        uses: actions/cache@v2
+      - name: Setup LFS
+        uses: ./.github/actions/setup_lfs
+
+      - name: Setup STARDIS
+        uses: ./.github/actions/setup_env
         with:
-          path: ${{ matrix.prefix }}
-          key: conda-${{ matrix.label }}-${{ hashFiles(format('conda-{0}.lock', matrix.label)) }}-${{ env.CACHE_NUMBER }}
-        id: cache-conda
-
-      - name: Update Conda Environment
-        id: update-env
-        run: |
-          mamba update -n stardis --file conda-${{ matrix.label }}.lock
-        if: steps.cache-conda.outputs.cache-hit != 'true'
+          os-label: ${{ matrix.label }}
 
       - name: Install TARDIS
         id: install-tardis
-        # shell: bash -l {0}
         run: |
           pip install git+https://github.com/tardis-sn/tardis.git@release-2024.08.25
 
       - name: Install STARDIS
         id: install-stardis
-        # shell: bash -l {0}
         run: |
           pip install -e .[test]
 

stardis/conftest.py

@@ -1,10 +1,11 @@
+import os
 import pytest
 from pathlib import Path
 import numpy as np
 from astropy import units as u
 
 from tardis.io.atom_data.base import AtomData
-from tardis.io.atom_data.util import download_atom_data
+from tardis.io.atom_data import download_atom_data
 from tardis.io.configuration.config_validator import validate_yaml
 from tardis.io.configuration.config_reader import Configuration
 from stardis.io.model.marcs import read_marcs_model
@@ -15,6 +16,8 @@
 from stardis.radiation_field.source_functions.blackbody import blackbody_flux_at_nu
 from stardis import STARDISOutput
 from stardis.io.base import SCHEMA_PATH
+from stardis.util import regression_data
+
 
 EXAMPLE_CONF_PATH = Path(__file__).parent / "tests" / "stardis_test_config.yml"
 EXAMPLE_CONF_PATH_BROADENING = (
@@ -24,6 +27,27 @@
     Path(__file__).parent / "tests" / "stardis_test_config_parallel.yml"
 )
 
+# ensuring that regression_data is not removed by ruff
+assert regression_data is not None
+
+pytest_plugins = [
+    "stardis.util.regression_data",
+]
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--stardis-regression-data",
+        default=None,
+        help="Path to the stardis regression data directory",
+    )
+    parser.addoption(
+        "--generate-reference",
+        action="store_true",
+        default=False,
+        help="generate reference data instead of testing",
+    )
+
 
 @pytest.fixture(scope="session")
 def example_tracing_nus():
@@ -281,3 +305,12 @@ def example_stardis_output_parallel(
         example_stellar_plasma,
         example_stellar_radiation_field_parallel,
     )
+
+
+@pytest.fixture(scope="session")
+def stardis_regression_path(request):
+    stardis_regression_path = request.config.getoption("--stardis-regression-data")
+    if stardis_regression_path is None:
+        pytest.skip("--stardis-regression-data was not specified")
+    else:
+        return Path(os.path.expandvars(os.path.expanduser(stardis_regression_path)))

stardis/model/base.py

@@ -1,4 +1,7 @@
-class StellarModel:
+from tardis.io.util import HDFWriterMixin
+
+
+class StellarModel(HDFWriterMixin):
     """
     Class containing information about the stellar model.
 
@@ -20,6 +23,8 @@ class StellarModel:
         Class attribute to be easily accessible for initializing arrays that need to match the shape of the model.
     """
 
+    hdf_properties = ["temperatures", "geometry", "composition"]
+
     def __init__(self, temperatures, geometry, composition):
         self.temperatures = temperatures
         self.geometry = geometry

stardis/model/geometry/radial1d.py

@@ -1,5 +1,7 @@
-class Radial1DGeometry:
+from tardis.io.util import HDFWriterMixin
+
 
+class Radial1DGeometry:
     """
     Holds information about model geometry (distribution of depth points) for radial 1D models.
 
@@ -15,6 +17,8 @@ class Radial1DGeometry:
         distance to the next depth point
     """
 
+    hdf_properties = ["r"]
+
     def __init__(self, r):
         self.r = r
 

stardis/radiation_field/base.py

@@ -4,9 +4,10 @@
 from stardis.radiation_field.opacities.opacities_solvers import calc_alphas
 from stardis.radiation_field.radiation_field_solvers import raytrace
 from stardis.radiation_field.source_functions.blackbody import blackbody_flux_at_nu
+from tardis.io.util import HDFWriterMixin
 
 
-class RadiationField:
+class RadiationField(HDFWriterMixin):
     """
     Class containing information about the radiation field.
     ###TODO Radiation field temperature should be a separate attribute, for the case of differing gas and radiation.
@@ -30,6 +31,8 @@ class RadiationField:
         Radiation field fluxes at each frequency at each depth point. Initialized as zeros and calculated by a solver.
     """
 
+    hdf_properties = ["frequencies", "opacities", "F_nu"]
+
     def __init__(self, frequencies, source_function, stellar_model):
         self.frequencies = frequencies
         self.source_function = source_function

stardis/tests/stardis_test_config.yml

@@ -14,3 +14,7 @@ opacity:
         disable: False
         broadening: []
 no_of_thetas: 1
+result_options:
+    return_model: true
+    return_plasma: true
+    return_radiation_field: true

stardis/tests/test_stardis_regression.py

@@ -0,0 +1,95 @@
+import numpy as np
+import pandas as pd
+
+plasma_properties = [
+    "alpha_line",
+    "beta_rad",
+    "electron_densities",
+    "g",
+    "g_electron",
+    "general_level_boltzmann_factor",
+    "ion_number_density",
+    "ionization_data",
+    "level_boltzmann_factor",
+    "level_number_density",
+    "levels",
+    "lines",
+    "lines_lower_level_index",
+    "lines_upper_level_index",
+    "metastability",
+    "nlte_excitation_species",
+    "nlte_ionization_species",
+    "nu",
+    "number_density",
+    "partition_function",
+    "phi",
+    "selected_atoms",
+    "stimulated_emission_factor",
+    "t_electrons",
+    "t_rad",
+    "wavelength_cm",
+]
+
+plasma_properties_complex = []
+
+
+def test_stardis_stellar_model(example_stardis_output, regression_data):
+    actual = example_stardis_output.stellar_model
+    expected = regression_data.sync_hdf_store(actual)
+
+    np.testing.assert_allclose(
+        actual.temperatures.value, expected["/stellar_model/temperatures"]
+    )
+
+
+def test_stardis_stellar_model_geometry(example_stardis_output, regression_data):
+    actual = example_stardis_output.stellar_model.geometry.r.value
+    expected = regression_data.sync_ndarray(actual)
+    np.testing.assert_allclose(actual, expected)
+
+
+def test_stardis_plasma(example_stardis_output, regression_data):
+    expected = regression_data.sync_hdf_store(example_stardis_output.stellar_plasma)
+    actual_plasma = example_stardis_output.stellar_plasma
+    for item in plasma_properties:
+        actual_item = getattr(actual_plasma, item)
+        expected_item = expected[f"plasma/{item}"]
+        if isinstance(actual_item, list):
+            actual_item = np.ndarray(actual_item)
+
+        if any(
+            isinstance(actual_item, object_type)
+            for object_type in [pd.MultiIndex, pd.Index]
+        ):
+            expected_item = expected[f"plasma/{item}"].values.flatten()
+            np.testing.assert_array_equal(actual_item.values, expected_item)
+
+        elif isinstance(actual_item, np.ndarray):
+            np.testing.assert_allclose(
+                actual=actual_item,
+                desired=expected_item,
+                err_msg=f"Error encountered when comparing regression data for property- {item}",
+            )
+        elif isinstance(actual_item, pd.DataFrame):
+            pd.testing.assert_frame_equal(actual_item, expected_item)
+        elif isinstance(actual_item, pd.Series):
+            pd.testing.assert_series_equal(actual_item, expected_item)
+        else:
+            plasma_properties_complex.append(item)
+    if plasma_properties_complex:
+        raise AssertionError(
+            f"These properties were not tested- {plasma_properties_complex}"
+        )
+
+
+def test_stardis_radiation_field(example_stardis_output, regression_data):
+    expected = regression_data.sync_hdf_store(
+        example_stardis_output.stellar_radiation_field
+    )
+    actual = example_stardis_output.stellar_radiation_field
+
+    np.testing.assert_allclose(
+        expected["/radiation_field/frequencies"].values, actual.frequencies.value
+    )
+
+    np.testing.assert_allclose(expected["/radiation_field/F_nu"].values, actual.F_nu)