country roads

* added setup function Signed-off-by: Asish Kumar <[email protected]> * refactor geometry calculate distances Signed-off-by: Asish Kumar <[email protected]> * Refactor montecarlo estimators in benchmark code Signed-off-by: Asish Kumar <[email protected]> * add cache and setup functions Signed-off-by: Asish Kumar <[email protected]> * add cache and setup functions Signed-off-by: Asish Kumar <[email protected]> * ran ruff linter Signed-off-by: Asish Kumar <[email protected]> * Thou hath vanquished the redundant variables and functions Signed-off-by: Asish Kumar <[email protected]> * fix bugs Signed-off-by: Asish Kumar <[email protected]> * change benchmark yml Signed-off-by: Asish Kumar <[email protected]> * repeat in class Signed-off-by: Asish Kumar <[email protected]> * Benchmark run_tardis with track_rpacket enabled (tardis-sn#2720) * Benchmark run_tardis with track_rpacket enabled * Update config to resemble time_run_tardis config * Fix Benchmark error * Cache Benchmark Property * Remove Cached Property decorator * rounds in benchmarks Signed-off-by: Asish Kumar <[email protected]> * fix Signed-off-by: Asish Kumar <[email protected]> * fix error in formal integral Signed-off-by: Asish Kumar <[email protected]> * more cache Signed-off-by: Asish Kumar <[email protected]> * sort by ratio Signed-off-by: Asish Kumar <[email protected]> * Donot run docs, benchmarks and stardis tests on draft PRs. (tardis-sn#2761) * Add ready to review to run tests * Add if condition to check PR status * Running stardis tests only on push to master * Removing osx-64 from workflows * Add Extend Array Function (tardis-sn#2771) * Add Extend Array Function * Fix Typo and restructure * Restructure * Doc string update * Was expecting numpy arrays to be passed by reference but it is not so updating it * Add test for the extend array function * Opacity state slice (tardis-sn#2758) * Added basic sliing operation to opacitystate and set the transport solver to use the bounds of the gemoetry indices * Reformatted the slicing index * Added slicing operation with __getitem__ * Added docstring * removed old slice method * Ran black * Added back the 'slice' method because __getitem__ is wacky * added missing argument * fixed missing argument * ran black * fixed the tests * ran black * Updated the slice to use __getitem__ again and modified the opacitystate object defined in the opacities module * Removed old slice method and print statements * removed print statement from the test * added type annotation to OpacityState getitem * updated numba interface * Fixes black formatting * Release Pipeline Fixes (tardis-sn#2767) * Fix zenodo badge * Pick from the website * update badge in credits.rst * Use the all versions DOI * Inherit secrets * Change triggers for testing * Reset Triggers * Fix ruff comments issue (tardis-sn#2762) * Fix ruff comments issue * Only check files changed * Testing triggers * Fix bash commands * No pager * fetch depth * Reset all changes * cache in setup function Signed-off-by: Asish Kumar <[email protected]> * change benchmark yml Signed-off-by: Asish Kumar <[email protected]> --------- Signed-off-by: Asish Kumar <[email protected]> Co-authored-by: Sumit Gupta <[email protected]> Co-authored-by: KasukabeDefenceForce <[email protected]> Co-authored-by: Jack O'Brien <[email protected]> Co-authored-by: Andrew Fullard <[email protected]> Co-authored-by: Atharva Arya <[email protected]>
officialasishkumar · Aug 2, 2024 · aa7cd19 · aa7cd19
1 parent 4f0ab22
commit aa7cd19
Show file tree

Hide file tree

Showing 18 changed files with 187 additions and 54 deletions.
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -14,6 +14,7 @@ on:
       - reopened
       - synchronize
       - labeled # benchmarks label required
+      - ready_for_review
   workflow_dispatch:
 
 env: 
@@ -70,8 +71,8 @@ jobs:
       - name: Run benchmarks for last 4 commits if not PR
         if: github.event_name != 'pull_request_target'
         run: |
-          git log -n 1  --pretty=format:"%H" >> tag_commits.txt
-          asv run -a rounds=1 HASHFILE:tag_commits.txt --bench transport_montecarlo_single_packet_loop | tee asv-output.log
+          git log -n 1 --pretty=format:"%H" >> tag_commits.txt
+          asv run HASHFILE:tag_commits.txt --quick | tee asv-output.log
           if grep -q failed asv-output.log; then 
             echo "Some benchmarks have failed!"   
             exit 1

diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
@@ -18,6 +18,7 @@ on:
       - reopened
       - synchronize
       - labeled # requires the `build-docs` label
+      - ready_for_review
 
   workflow_dispatch: # manual trigger
 
@@ -37,6 +38,7 @@ defaults:
 jobs:
   check-for-changes:
     runs-on: ubuntu-latest
+    if: ${{ !github.event.pull_request.draft }}
     outputs:
       trigger-check-outcome: ${{ steps.trigger_check.outcome }}
       docs-check-outcome: ${{ steps.docs_check.outcome }}

diff --git a/.github/workflows/codestyle.yml b/.github/workflows/codestyle.yml
@@ -7,8 +7,7 @@ name: codestyle
 on:
   push:
     branches:
-      - "*"
-
+      - master
   pull_request_target:
     branches:
       - master
@@ -37,6 +36,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Download Lock File
         run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
@@ -57,12 +58,22 @@ jobs:
           cache-downloads: true
 
       - name: Show statistics
-        run: ruff check  --statistics  --show-fixes . | tee ruff_stats.txt
-        id: ruff_stats
+        run: ruff check  --statistics  --show-fixes $(git --no-pager diff --name-only ${{ github.event.pull_request.base.sha }}  ${{ github.event.pull_request.head.sha }} --) | tee ruff_stats.txt
 
       - name: Show entire output
-        run: ruff check . --output-format=full | tee ruff_full.txt
-        id: ruff_complete
+        run: ruff check --output-format=concise $(git --no-pager diff --name-only ${{ github.event.pull_request.base.sha }}  ${{ github.event.pull_request.head.sha }} --) | tee ruff_full.txt
+
+      - name: Statistics output read
+        id: ruff_stats
+        uses: juliangruber/[email protected]
+        with:
+          path: ruff_stats.txt
+
+      - name: Entire output read
+        id: ruff_complete 
+        uses: juliangruber/[email protected]
+        with:
+          path: ruff_full.txt
 
       - name: Find Comment
         if: always() && github.event_name == 'pull_request_target'

diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
@@ -143,5 +143,6 @@ jobs:
 
   pip_tests:
     uses: ./.github/workflows/tests.yml
+    secrets: inherit
     with:
       pip_git: true
diff --git a/.github/workflows/stardis-tests.yml b/.github/workflows/stardis-tests.yml
@@ -3,12 +3,17 @@ name: stardis-tests
 on:
   push:
     branches:
-    - '*'
+    - master
 
   pull_request:
     branches:
     - '*'
 
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
   workflow_dispatch:
 
 defaults:
@@ -22,18 +27,15 @@ jobs:
   build:
     strategy:
       matrix:
-        label: [osx-64, linux-64]
+        label: [linux-64]
         include:
           - os: ubuntu-latest
             label: linux-64
             prefix: /usr/share/miniconda3/envs/stardis
 
-          - os: macos-latest
-            label: osx-64
-            prefix: /Users/runner/miniconda3/envs/stardis
-
     name: ${{ matrix.label }}
     runs-on: ${{ matrix.os }}
+    if: ${{ !github.event.pull_request.draft }}
     steps:     
       - uses: actions/checkout@v4
         with:

diff --git a/README.rst b/README.rst
@@ -112,8 +112,9 @@ The following BibTeX entries are needed for the references:
 
 .. |CITATION| replace:: kerzendorf_2023_10207663
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.3_10207663-blue
-                 :target: https://doi.org/10.5281/zenodo.3_10207663
+.. |DOI_BADGE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592480.svg
+                :target: https://doi.org/10.5281/zenodo.592480
+
 
 .. code-block:: bibtex
 

diff --git a/benchmarks/benchmark_base.py b/benchmarks/benchmark_base.py
@@ -62,7 +62,8 @@ def config_rpacket_tracking(self):
     @functools.cached_property
     def tardis_ref_path(self):
         ref_data_path = Path(
-            Path(__file__).parent.parent, "tardis-refdata"
+            Path(__file__).parent.parent,
+            "tardis-refdata"
         ).resolve()
         return ref_data_path
 

diff --git a/benchmarks/run_tardis.py b/benchmarks/run_tardis.py
@@ -6,7 +6,6 @@
 from tardis import run_tardis
 from tardis.io.atom_data import AtomData
 
-
 class BenchmarkRunTardis(BenchmarkBase):
     """
     Class to benchmark the `run tardis` function.

diff --git a/benchmarks/spectrum_formal_integral.py b/benchmarks/spectrum_formal_integral.py
@@ -8,8 +8,11 @@
 
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.spectrum import formal_integral
+
 config.THREADING_LAYER = "workqueue"
 
+
+
 class BenchmarkTransportMontecarloFormalIntegral(BenchmarkBase):
     """
     Class to benchmark the numba formal integral function.

diff --git a/benchmarks/transport_montecarlo_interaction.py b/benchmarks/transport_montecarlo_interaction.py
@@ -16,6 +16,15 @@ class BenchmarkTransportMontecarloInteraction(BenchmarkBase):
 
     repeat = 3
 
+    def setup(self):
+        self.Packet = self.packet
+        self.time_explosion = self.verysimple_time_explosion
+        self.enable_full_relativity = self.verysimple_enable_full_relativity
+        self.opacity_state = self.verysimple_opacity_state
+
+    repeat = 3 
+
+    @functools.cache
     def setup(self):
         self.Packet = self.packet
         self.time_explosion = self.verysimple_time_explosion

diff --git a/benchmarks/transport_montecarlo_packet_trackers.py b/benchmarks/transport_montecarlo_packet_trackers.py
@@ -26,6 +26,7 @@ def time_rpacket_trackers_to_dataframe(self, num_packets, length):
         packet_trackers.rpacket_trackers_to_dataframe(
             self.TransportState.rpacket_tracker
         )
+
     def time_generate_rpacket_tracker_list(self, num_packets, length):
         packet_trackers.generate_rpacket_tracker_list(num_packets, length)
 

diff --git a/docs/resources/credits.rst b/docs/resources/credits.rst
@@ -76,8 +76,8 @@ The following BibTeX entries are needed for the references:
 
 .. |CITATION| replace:: kerzendorf_2023_10207663
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.3_10207663-blue
-                 :target: https://doi.org/10.5281/zenodo.3_10207663
+.. |DOI_BADGE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592480.svg
+                :target: https://doi.org/10.5281/zenodo.592480
 
 .. code-block:: bibtex
 

diff --git a/tardis/opacities/opacity_state.py b/tardis/opacities/opacity_state.py
@@ -106,6 +106,41 @@ def __init__(
         self.photo_ion_activation_idx = photo_ion_activation_idx
         self.k_packet_idx = k_packet_idx
 
+    def __getitem__(self, i: slice):
+        """Get a shell or slice of shells of the attributes of the opacity state
+
+        Args:
+            i (slice): shell slice.  Will fail if slice is int since class only supports array types
+
+        Returns:
+            OpacityState : a shallow copy of the current instance
+        """
+        # NOTE: This currently will not work with continuum processes since it does not slice those arrays
+        return OpacityState(
+            self.electron_density[i],
+            self.t_electrons[i],
+            self.line_list_nu,
+            self.tau_sobolev[:, i],
+            self.transition_probabilities[:, i],
+            self.line2macro_level_upper,
+            self.macro_block_references,
+            self.transition_type,
+            self.destination_level_id,
+            self.transition_line_id,
+            self.bf_threshold_list_nu,
+            self.p_fb_deactivation,
+            self.photo_ion_nu_threshold_mins,
+            self.photo_ion_nu_threshold_maxs,
+            self.photo_ion_block_references,
+            self.chi_bf,
+            self.x_sect,
+            self.phot_nus,
+            self.ff_opacity_factor,
+            self.emissivities,
+            self.photo_ion_activation_idx,
+            self.k_packet_idx,
+        )
+
 
 def opacity_state_initialize(
     plasma,

diff --git a/tardis/transport/montecarlo/base.py b/tardis/transport/montecarlo/base.py
@@ -23,7 +23,7 @@
 from tardis.transport.montecarlo.montecarlo_transport_state import (
     MonteCarloTransportState,
 )
-from tardis.transport.montecarlo.numba_interface import (
+from tardis.opacities.opacity_state import (
     opacity_state_initialize,
 )
 from tardis.transport.montecarlo.packet_trackers import (
@@ -110,16 +110,21 @@ def initialize_transport_state(
         packet_collection = self.packet_source.create_packets(
             no_of_packets, seed_offset=iteration
         )
-        estimators = initialize_estimator_statistics(
-            plasma.tau_sobolevs.shape, gamma_shape
-        )
 
         geometry_state = simulation_state.geometry.to_numba()
         opacity_state = opacity_state_initialize(
             plasma,
             self.line_interaction_type,
             self.montecarlo_configuration.DISABLE_LINE_SCATTERING,
         )
+        opacity_state = opacity_state[
+            simulation_state.geometry.v_inner_boundary_index : simulation_state.geometry.v_outer_boundary_index
+        ]
+
+        estimators = initialize_estimator_statistics(
+            opacity_state.tau_sobolev.shape, gamma_shape
+        )
+
         transport_state = MonteCarloTransportState(
             packet_collection,
             estimators,

diff --git a/tardis/transport/montecarlo/numba_interface.py b/tardis/transport/montecarlo/numba_interface.py
@@ -112,6 +112,41 @@ def __init__(
         self.photo_ion_activation_idx = photo_ion_activation_idx
         self.k_packet_idx = k_packet_idx
 
+    def __getitem__(self, i: slice):
+        """Get a shell or slice of shells of the attributes of the opacity state
+
+        Args:
+            i (slice): shell slice.  Will fail if slice is int since class only supports array types
+
+        Returns:
+            OpacityState : a shallow copy of the current instance
+        """
+        # NOTE: This currently will not work with continuum processes since it does not slice those arrays
+        return OpacityState(
+            self.electron_density[i],
+            self.t_electrons[i],
+            self.line_list_nu,
+            self.tau_sobolev[:, i],
+            self.transition_probabilities[:, i],
+            self.line2macro_level_upper,
+            self.macro_block_references,
+            self.transition_type,
+            self.destination_level_id,
+            self.transition_line_id,
+            self.bf_threshold_list_nu,
+            self.p_fb_deactivation,
+            self.photo_ion_nu_threshold_mins,
+            self.photo_ion_nu_threshold_maxs,
+            self.photo_ion_block_references,
+            self.chi_bf,
+            self.x_sect,
+            self.phot_nus,
+            self.ff_opacity_factor,
+            self.emissivities,
+            self.photo_ion_activation_idx,
+            self.k_packet_idx,
+        )
+
 
 def opacity_state_initialize(
     plasma,

diff --git a/tardis/transport/montecarlo/packet_trackers.py b/tardis/transport/montecarlo/packet_trackers.py
@@ -16,6 +16,7 @@
     ("shell_id", int64[:]),
     ("interaction_type", int64[:]),
     ("num_interactions", int64),
+    ("extend_factor", int64),
 ]
 
 
@@ -47,6 +48,8 @@ class RPacketTracker(object):
             Type of interaction the rpacket undergoes
         num_interactions : int
             Internal counter for the interactions that a particular RPacket undergoes
+        extend_factor : int
+            The factor by which to extend the properties array when the size limit is reached
     """
 
     def __init__(self, length):
@@ -61,34 +64,27 @@ def __init__(self, length):
         self.shell_id = np.empty(self.length, dtype=np.int64)
         self.interaction_type = np.empty(self.length, dtype=np.int64)
         self.num_interactions = 0
+        self.extend_factor = 2
+
+    def extend_array(self, array, array_length):
+        temp_array = np.empty(
+            array_length * self.extend_factor, dtype=array.dtype
+        )
+        temp_array[:array_length] = array
+        return temp_array
 
     def track(self, r_packet):
         if self.num_interactions >= self.length:
-            temp_length = self.length * 2
-            temp_status = np.empty(temp_length, dtype=np.int64)
-            temp_r = np.empty(temp_length, dtype=np.float64)
-            temp_nu = np.empty(temp_length, dtype=np.float64)
-            temp_mu = np.empty(temp_length, dtype=np.float64)
-            temp_energy = np.empty(temp_length, dtype=np.float64)
-            temp_shell_id = np.empty(temp_length, dtype=np.int64)
-            temp_interaction_type = np.empty(temp_length, dtype=np.int64)
-
-            temp_status[: self.length] = self.status
-            temp_r[: self.length] = self.r
-            temp_nu[: self.length] = self.nu
-            temp_mu[: self.length] = self.mu
-            temp_energy[: self.length] = self.energy
-            temp_shell_id[: self.length] = self.shell_id
-            temp_interaction_type[: self.length] = self.interaction_type
-
-            self.status = temp_status
-            self.r = temp_r
-            self.nu = temp_nu
-            self.mu = temp_mu
-            self.energy = temp_energy
-            self.shell_id = temp_shell_id
-            self.interaction_type = temp_interaction_type
-            self.length = temp_length
+            self.status = self.extend_array(self.status, self.length)
+            self.r = self.extend_array(self.r, self.length)
+            self.nu = self.extend_array(self.nu, self.length)
+            self.mu = self.extend_array(self.mu, self.length)
+            self.energy = self.extend_array(self.energy, self.length)
+            self.shell_id = self.extend_array(self.shell_id, self.length)
+            self.interaction_type = self.extend_array(
+                self.interaction_type, self.length
+            )
+            self.length = self.length * self.extend_factor
 
         self.index = r_packet.index
         self.seed = r_packet.seed