A syrupy replacement

.github/workflows/tests.yml

@@ -15,7 +15,7 @@ on:
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
-  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-snapshot-data=${{ github.workspace }}/tardis-regressions
+  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-regression-data=${{ github.workspace }}/tardis-regression-data
                 --cov=tardis --cov-report=xml --cov-report=html 
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -62,36 +62,68 @@ jobs:
 
       - name: Restore LFS cache
         uses: actions/cache/restore@v3
-        id: lfs-cache
+        id: lfs-cache-refdata
         with:
           path: tardis-refdata/.git/lfs
           key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
 
       - name: Git LFS Pull
         run: git lfs pull
         working-directory: tardis-refdata
-        if: steps.lfs-cache.outputs.cache-hit != 'true'
+        if: steps.lfs-cache-refdata.outputs.cache-hit != 'true'
 
       - name: Git LFS Checkout
         run: git lfs checkout
         working-directory: tardis-refdata
-        if: steps.lfs-cache.outputs.cache-hit == 'true'
+        if: steps.lfs-cache-refdata.outputs.cache-hit == 'true'
 
       - 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.outputs.cache-hit != 'true'  && always() || false }}
         uses: actions/cache/save@v3
-        id: lfs-cache-save
+        id: lfs-cache-refdata-save
         with:
           path: tardis-refdata/.git/lfs
           key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
 
-      - name: Clone tardis-sn/tardis-regressions
+      - name: Clone tardis-sn/tardis-regression-data
         uses: actions/checkout@v4
         with:
-          repository: tardis-sn/tardis-regressions
-          path: tardis-regressions
+          repository: tardis-sn/tardis-regression-data
+          path: tardis-regression-data
+
+      - name: Create LFS file list
+        run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
+        working-directory: tardis-refdata
+
+      - name: Restore LFS cache
+        uses: actions/cache/restore@v3
+        id: lfs-cache-regression-data
+        with:
+          path: tardis-regression-data/.git/lfs
+          key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-regression-data/.lfs-assets-id') }}-v1
+
+      - name: Git LFS Pull
+        run: git lfs pull
+        working-directory: tardis-regression-data
+        if: steps.lfs-cache-regression-data.outputs.cache-hit != 'true'
+
+      - name: Git LFS Checkout
+        run: git lfs checkout
+        working-directory: tardis-regression-data
+        if: steps.lfs-cache-regression-data.outputs.cache-hit == 'true'
+
+      - 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.outputs.cache-hit != 'true'  && always() || false }}
+        uses: actions/cache/save@v3
+        id: lfs-cache-regression-data-save
+        with:
+          path: tardis-regression-data/.git/lfs
+          key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-regression-data/.lfs-assets-id') }}-v1
+
 
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v2

tardis/conftest.py

@@ -1,3 +1,19 @@
+import os
+from pathlib import Path
+
+import pandas as pd
+import pytest
+from astropy.version import version as astropy_version
+
+from tardis.io.configuration.config_reader import Configuration
+from tardis.io.util import YAMLLoader, yaml_load_file
+from tardis.simulation import Simulation
+from tardis.tests.fixtures.atom_data import *
+from tardis.tests.fixtures.regression_data import regression_data
+
+# ensuring that regression_data is not removed by ruff
+assert regression_data is not None
+
 """Configure Test Suite.
 
 This file is used to configure the behavior of pytest when using the Astropy
@@ -7,10 +23,6 @@
 
 """
 
-import os
-from pathlib import Path
-
-from astropy.version import version as astropy_version
 
 # For Astropy 3.0 and later, we can use the standalone pytest plugin
 if astropy_version < "3.0":
@@ -70,32 +82,24 @@ def pytest_configure(config):
 # To ignore some specific deprecation warning messages for Python version
 # MAJOR.MINOR or later, add:
 #     warnings_to_ignore_by_pyver={(MAJOR, MINOR): ['Message to ignore']}
-# from astropy.tests.helper import enable_deprecations_as_exceptions  # noqa
+# from astropy.tests.helper import enable_deprecations_as_exceptions
 # enable_deprecations_as_exceptions()
 
 # -------------------------------------------------------------------------
 # Here the TARDIS testing stuff begins
 # -------------------------------------------------------------------------
 
-import re
-import pytest
-import pandas as pd
-from tardis.io.util import yaml_load_file, YAMLLoader
-from tardis.io.configuration.config_reader import Configuration
-from tardis.simulation import Simulation
-from tardis.util.syrupy_extensions import (
-    SingleFileSanitizedNames,
-    NumpySnapshotExtenstion,
-    PandasSnapshotExtenstion,
-)
-
-pytest_plugins = "syrupy"
-
 
 def pytest_addoption(parser):
     parser.addoption(
         "--tardis-refdata", default=None, help="Path to Tardis Reference Folder"
     )
+    parser.addoption(
+        "--tardis-regression-data",
+        default=None,
+        help="Path to the TARDIS regression data directory",
+    )
+
     parser.addoption(
         "--integration-tests",
         dest="integration-tests",
@@ -108,13 +112,6 @@ def pytest_addoption(parser):
         default=False,
         help="generate reference data instead of testing",
     )
-
-    parser.addoption(
-        "--tardis-snapshot-data",
-        default=None,
-        help="Path to Tardis Snapshot Folder",
-    )
-
     parser.addoption(
         "--less-packets",
         action="store_true",
@@ -168,9 +165,6 @@ def tardis_snapshot_path(request):
         )
 
 
-from tardis.tests.fixtures.atom_data import *
-
-
 @pytest.yield_fixture(scope="session")
 def tardis_ref_data(tardis_ref_path, generate_reference):
     if generate_reference:
@@ -238,23 +232,3 @@ def simulation_verysimple(config_verysimple, atomic_dataset):
     sim = Simulation.from_config(config_verysimple, atom_data=atomic_data)
     sim.iterate(4000)
     return sim
-
-
-# -------------------------------------------------------------------------
-# fixtures and plugins for syrupy/regression data testing
-# -------------------------------------------------------------------------
-
-
-@pytest.fixture
-def pandas_snapshot_extention():
-    return PandasSnapshotExtenstion
-
-
-@pytest.fixture
-def numpy_snapshot_extension():
-    return NumpySnapshotExtenstion
-
-
-@pytest.fixture
-def singlefilesanitized():
-    return SingleFileSanitizedNames

tardis/montecarlo/montecarlo_numba/tests/test_base.py

@@ -1,10 +1,7 @@
-import pytest
-import pandas as pd
-import os
-import numpy.testing as npt
 from copy import deepcopy
-from tardis.base import run_tardis
-from pandas.testing import assert_frame_equal
+
+import numpy.testing as npt
+import pytest
 
 from tardis.montecarlo import (
     montecarlo_configuration as montecarlo_configuration,
@@ -35,8 +32,7 @@ def montecarlo_main_loop_config(
 
 def test_montecarlo_main_loop(
     montecarlo_main_loop_config,
-    tardis_ref_path,
-    request,
+    regression_data,
     atomic_dataset,
 ):
     atomic_dataset = deepcopy(atomic_dataset)
@@ -48,26 +44,21 @@ def test_montecarlo_main_loop(
     montecarlo_main_loop_simulation.run_convergence()
     montecarlo_main_loop_simulation.run_final()
 
-    compare_fname = os.path.join(
-        tardis_ref_path, "montecarlo_1e5_compare_data.h5"
+    expected_hdf_store = regression_data.sync_hdf_store(
+        montecarlo_main_loop_simulation
     )
-    if request.config.getoption("--generate-reference"):
-        montecarlo_main_loop_simulation.to_hdf(compare_fname, overwrite=True)
 
     # Load compare data from refdata
-    expected_nu = pd.read_hdf(
-        compare_fname, key="/simulation/transport/output_nu"
-    ).values
-    expected_energy = pd.read_hdf(
-        compare_fname, key="/simulation/transport/output_energy"
-    ).values
-    expected_nu_bar_estimator = pd.read_hdf(
-        compare_fname, key="/simulation/transport/nu_bar_estimator"
-    ).values
-    expected_j_estimator = pd.read_hdf(
-        compare_fname, key="/simulation/transport/j_estimator"
-    ).values
 
+    expected_nu = expected_hdf_store["/simulation/transport/output_nu"]
+    expected_energy = expected_hdf_store["/simulation/transport/output_energy"]
+    expected_nu_bar_estimator = expected_hdf_store[
+        "/simulation/transport/nu_bar_estimator"
+    ]
+    expected_j_estimator = expected_hdf_store[
+        "/simulation/transport/j_estimator"
+    ]
+    expected_hdf_store.close()
     actual_energy = montecarlo_main_loop_simulation.transport.output_energy
     actual_nu = montecarlo_main_loop_simulation.transport.output_nu
     actual_nu_bar_estimator = (
@@ -84,11 +75,9 @@ def test_montecarlo_main_loop(
     npt.assert_allclose(actual_nu.value, expected_nu, rtol=1e-13)
 
 
-@pytest.mark.xfail(reason="need to store virtual packet data in hdf5")
 def test_montecarlo_main_loop_vpacket_log(
     montecarlo_main_loop_config,
-    tardis_ref_path,
-    request,
+    regression_data,
     atomic_dataset,
 ):
     atomic_dataset = deepcopy(atomic_dataset)
@@ -102,25 +91,24 @@ def test_montecarlo_main_loop_vpacket_log(
     montecarlo_main_loop_simulation.run_convergence()
     montecarlo_main_loop_simulation.run_final()
 
-    compare_fname = os.path.join(
-        tardis_ref_path, "montecarlo_1e5_compare_data.h5"
+    expected_hdf_store = regression_data.sync_hdf_store(
+        montecarlo_main_loop_simulation
     )
-    if request.config.getoption("--generate-reference"):
-        montecarlo_main_loop_simulation.to_hdf(compare_fname, overwrite=True)
 
-    # Load compare data from refdata
-    expected_nu = pd.read_hdf(
-        compare_fname, key="/simulation/transport/output_nu"
-    ).values
-    expected_energy = pd.read_hdf(
-        compare_fname, key="/simulation/transport/output_energy"
-    ).values
-    expected_nu_bar_estimator = pd.read_hdf(
-        compare_fname, key="/simulation/transport/nu_bar_estimator"
-    ).values
-    expected_j_estimator = pd.read_hdf(
-        compare_fname, key="/simulation/transport/j_estimator"
-    ).values
+    expected_nu = expected_hdf_store["/simulation/transport/output_nu"]
+    expected_energy = expected_hdf_store["/simulation/transport/output_energy"]
+    expected_nu_bar_estimator = expected_hdf_store[
+        "/simulation/transport/nu_bar_estimator"
+    ]
+    expected_j_estimator = expected_hdf_store[
+        "/simulation/transport/j_estimator"
+    ]
+    expected_vpacket_log_nus = expected_hdf_store[
+        "/simulation/transport/virt_packet_nus"
+    ]
+    expected_vpacket_log_energies = expected_hdf_store[
+        "/simulation/transport/virt_packet_energies"
+    ]
 
     transport = montecarlo_main_loop_simulation.transport
     actual_energy = transport.output_energy
@@ -129,11 +117,27 @@ def test_montecarlo_main_loop_vpacket_log(
     actual_j_estimator = montecarlo_main_loop_simulation.transport.j_estimator
     actual_vpacket_log_nus = transport.virt_packet_nus
     actual_vpacket_log_energies = transport.virt_packet_energies
-
+    expected_hdf_store.close()
     # Compare
     npt.assert_allclose(
-        actual_nu_bar_estimator, expected_nu_bar_estimator, rtol=1e-13
+        actual_nu_bar_estimator,
+        expected_nu_bar_estimator,
+        rtol=1e-12,
+        atol=1e-15,
+    )
+    npt.assert_allclose(
+        actual_j_estimator, expected_j_estimator, rtol=1e-12, atol=1e-15
+    )
+    npt.assert_allclose(
+        actual_energy.value, expected_energy, rtol=1e-12, atol=1e-15
+    )
+    npt.assert_allclose(actual_nu.value, expected_nu, rtol=1e-12, atol=1e-15)
+    npt.assert_allclose(
+        actual_vpacket_log_nus, expected_vpacket_log_nus, rtol=1e-12, atol=1e-15
+    )
+    npt.assert_allclose(
+        actual_vpacket_log_energies,
+        expected_vpacket_log_energies,
+        rtol=1e-12,
+        atol=1e-15,
     )
-    npt.assert_allclose(actual_j_estimator, expected_j_estimator, rtol=1e-13)
-    npt.assert_allclose(actual_energy.value, expected_energy, rtol=1e-13)
-    npt.assert_allclose(actual_nu.value, expected_nu, rtol=1e-13)