Merge branch 'tardis-sn:master' into line-interaction-radius

.github/actions/setup_env/action.yml

@@ -0,0 +1,32 @@
+name: "Setup environment"
+description: "Sets up environment for tardis and caches it"
+
+inputs:
+  os-label:
+    description: "os label for lock file, default linux"
+    required: true
+    default: "linux"
+
+runs:
+  using: "composite"
+  steps:
+      - name: Download Lock File
+        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-${{ inputs.os-label }}.lock
+        if: matrix.pip == true
+        shell: bash
+
+      - name: Generate Cache Key
+        run: | 
+          file_hash=$(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: tardis
+          cache-environment: true
+          cache-downloads: true

.github/workflows/build-docs.yml

@@ -88,28 +88,18 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
         if: github.event_name == 'pull_request_target'
 
-      - name: Generate Cache Key
-        run: |
-          file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
+
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: linux-64
 
       - name: Copy atom_data
         run: |
           mkdir -p ~/Downloads/tardis-data && cp -a ./tardis-refdata/atom_data/. ~/Downloads/tardis-data
 
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-linux-64.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
-
       - name: Install package
         run: pip install -e .
 

.github/workflows/pre-release.yml

@@ -27,23 +27,10 @@ jobs:
         env:
           KEY_SECRET_JSON: ${{ secrets.ZENODO_KEY_SECRET_JSON }}
 
-      - name: Download Lock File
-        run: wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
-
-      - name: Generate Cache Key
-        run: |
-          file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-linux-64.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: linux-64
 
       - name: Run Notebook
         run: jupyter nbconvert gather_data.ipynb --to html --execute --ExecutePreprocessor.timeout=6000

.github/workflows/tests.yml

@@ -22,7 +22,7 @@ on:
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
   PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-regression-data=${{ github.workspace }}/tardis-regression-data
-                --cov=tardis --cov-report=xml --cov-report=html 
+                --cov=tardis --cov-report=xml --cov-report=html
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
 concurrency:
@@ -39,9 +39,9 @@ jobs:
     strategy:
       matrix:
         pip: [true, false]
-        label: [osx-64, linux-64]
+        label: [osx-arm64, linux-64]
         include:
-          - label: osx-64
+          - label: osx-arm64
             os: macos-latest
             prefix: /Users/runner/miniconda3/envs/tardis
 
@@ -56,25 +56,11 @@ jobs:
 
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
-
-      - name: Download Lock File
-        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-${{ matrix.label }}.lock
-        if: matrix.pip == true
 
-      - name: Generate Cache Key
-        run: | 
-          file_hash=$(cat conda-${{ matrix.label }}.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-${{ matrix.label }}.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: ${{ matrix.label }}
 
       - name: Install package editable
         run: |
@@ -100,7 +86,12 @@ jobs:
           echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
 
       - name: Run tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }}
+        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "not continuum"
+        working-directory: ${{ env.TARDIS_PIP_PATH }}
+        if: always()
+
+      - name: Run continuum tests
+        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m continuum
         working-directory: ${{ env.TARDIS_PIP_PATH }}
         if: always()
 

.github/workflows/update-refdata.yml

@@ -32,23 +32,10 @@ jobs:
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
 
-      - name: Download Lock File
-        run: wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
-
-      - name: Generate Cache Key
-        run: |
-          file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-linux-64.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: linux-64
 
       - name: Install package
         run: pip install -e .

.mailmap

@@ -14,6 +14,7 @@ Alice Harpole <[email protected]>
 Alice Harpole <[email protected]> Alice Harpole <[email protected]>
 
 Aman Kumar <[email protected]>
+Asish Kumar <[email protected]>
 
 Andreas Flörs <[email protected]>
 Andreas Flörs <[email protected]> Andreas Flörs <[email protected]>

benchmarks/benchmark_base.py

@@ -5,25 +5,26 @@
 
 import astropy.units as u
 import numpy as np
-import pandas as pd
 from numba import njit
 
 from benchmarks.util.nlte import NLTE
+from tardis import run_tardis
 from tardis.io.atom_data import AtomData
 from tardis.io.configuration import config_reader
 from tardis.io.configuration.config_reader import Configuration
 from tardis.io.util import YAMLLoader, yaml_load_file
 from tardis.model import SimulationState
+from tardis.model.geometry.radial1d import NumbaRadial1DGeometry
 from tardis.simulation import Simulation
 from tardis.tests.fixtures.atom_data import DEFAULT_ATOM_DATA_UUID
 from tardis.tests.fixtures.regression_data import RegressionData
-from tardis.transport.montecarlo import RPacket
-from tardis.transport.montecarlo.numba_interface import (
-    opacity_state_initialize,
-)
+from tardis.transport.montecarlo import RPacket, montecarlo_configuration
+from tardis.transport.montecarlo.estimators import radfield_mc_estimators
+from tardis.transport.montecarlo.numba_interface import opacity_state_initialize
 from tardis.transport.montecarlo.packet_collections import (
     VPacketCollection,
 )
+from tardis.transport.montecarlo.packet_trackers import RPacketTracker
 
 
 class BenchmarkBase:
@@ -350,13 +351,66 @@ def generate_reference(self):
             return option
 
     @property
-    def tardis_ref_data(self):
-        # TODO: This function is not working in the benchmarks.
-        if self.generate_reference:
-            mode = "w"
-        else:
-            mode = "r"
-        with pd.HDFStore(
-            f"{self.tardis_ref_path}/unit_test_data.h5", mode=mode
-        ) as store:
-            yield store
+    def verysimple_radfield_mc_estimators(self):
+        plasma = self.nb_simulation_verysimple.plasma
+        return radfield_mc_estimators.initialize_estimator_statistics(
+            plasma.tau_sobolevs.shape, plasma.gamma.shape
+        )
+
+    @property
+    def montecarlo_configuration(self):
+        return montecarlo_configuration.MonteCarloConfiguration()
+
+    @property
+    def rpacket_tracker(self): 
+        return RPacketTracker(0)
+
+    @property
+    def transport_state(self):
+        return self.nb_simulation_verysimple.transport.transport_state
+
+    @property
+    def simulation_rpacket_tracking_enabled(self):
+        config_verysimple = self.config_verysimple
+        config_verysimple.montecarlo.iterations = 3
+        config_verysimple.montecarlo.no_of_packets = 4000
+        config_verysimple.montecarlo.last_no_of_packets = -1
+        config_verysimple.spectrum.virtual.virtual_packet_logging = True
+        config_verysimple.montecarlo.no_of_virtual_packets = 1
+        config_verysimple.montecarlo.tracking.track_rpacket = True
+        config_verysimple.spectrum.num = 2000
+        atomic_data = deepcopy(self.atomic_dataset)
+        sim = run_tardis(
+            config_verysimple,
+            atom_data=atomic_data,
+            show_convergence_plots=False,
+        )
+        return sim
+
+    @property
+    def geometry(self):
+        return NumbaRadial1DGeometry(
+            r_inner=np.array([6.912e14, 8.64e14], dtype=np.float64),
+            r_outer=np.array([8.64e14, 1.0368e15], dtype=np.float64),
+            v_inner=np.array([-1, -1], dtype=np.float64),
+            v_outer=np.array([-1, -1], dtype=np.float64),
+        )
+
+
+    @property
+    def estimators(self):
+        return radfield_mc_estimators.RadiationFieldMCEstimators(
+            j_estimator=np.array([0.0, 0.0], dtype=np.float64),
+            nu_bar_estimator=np.array([0.0, 0.0], dtype=np.float64),
+            j_blue_estimator=np.array(
+                [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], dtype=np.float64
+            ),
+            Edotlu_estimator=np.array(
+                [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0]], dtype=np.float64
+            ),
+            photo_ion_estimator=np.empty((0, 0), dtype=np.float64),
+            stim_recomb_estimator=np.empty((0, 0), dtype=np.float64),
+            bf_heating_estimator=np.empty((0, 0), dtype=np.float64),
+            stim_recomb_cooling_estimator=np.empty((0, 0), dtype=np.float64),
+            photo_ion_estimator_statistics=np.empty((0, 0), dtype=np.int64),
+        )

benchmarks/run_tardis.py

@@ -4,8 +4,6 @@
 
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis import run_tardis
-from tardis.io.configuration.config_reader import Configuration
-
 
 class BenchmarkRunTardis(BenchmarkBase):
     """
@@ -14,12 +12,8 @@ class BenchmarkRunTardis(BenchmarkBase):
 
     def __init__(self):
         super().__init__()
-        self.config = None
-
-    def setup(self):
         filename = "data/tardis_configv1_benchmark.yml"
-        path = self.get_relative_path(filename)
-        self.config = Configuration.from_yaml(path)
+        self.path = self.get_relative_path(filename)
 
     def time_run_tardis(self):
-        run_tardis(self.config, log_level="ERROR", show_progress_bars=False)
+        run_tardis(self.path, log_level="ERROR", show_progress_bars=False)

benchmarks/transport_geometry_calculate_distances.py

@@ -0,0 +1,68 @@
+from asv_runner.benchmarks.mark import parameterize
+
+import tardis.transport.frame_transformations as frame_transformations
+import tardis.transport.geometry.calculate_distances as calculate_distances
+from benchmarks.benchmark_base import BenchmarkBase
+
+
+class BenchmarkTransportGeometryCalculateDistances(BenchmarkBase):
+    """
+    Class to benchmark the calculate distances function.
+    """
+
+    @property
+    def model(self):
+        return 5.2e7
+
+    def time_calculate_distance_boundary(self):
+        mu = 0.3
+        r = 7.5e14
+
+        calculate_distances.calculate_distance_boundary(
+            r, mu, self.geometry.r_inner[0], self.geometry.r_outer[0]
+        )
+
+    @parameterize(
+        {
+            "Parameters": [
+                {
+                    "packet": {
+                        "nu_line": 0.1,
+                        "is_last_line": True
+                    },
+                    "enable_full_relativity": True,
+                },
+                {
+                    "packet": {
+                        "nu_line": 0.2,
+                        "is_last_line": False
+                    },
+                    "enable_full_relativity": True,
+                }
+            ]
+        }
+    )
+    def time_calculate_distance_line(self, parameters):
+        packet_params = parameters["packet"]
+        nu_line = packet_params["nu_line"]
+        is_last_line = packet_params["is_last_line"]
+        enable_full_relativity = parameters["enable_full_relativity"]
+
+        time_explosion = self.model
+
+        doppler_factor = frame_transformations.get_doppler_factor(
+            self.static_packet.r,
+            self.static_packet.mu,
+            time_explosion,
+            enable_full_relativity
+        )
+        comov_nu = self.static_packet.nu * doppler_factor
+
+        calculate_distances.calculate_distance_line(
+            self.static_packet,
+            comov_nu,
+            is_last_line,
+            nu_line,
+            time_explosion,
+            enable_full_relativity
+        )