Benchmarks oct 23 fix (#37)

* Allow Simulation Tests to Run Independently  (tardis-sn#2407)

* Modify test_packet_source.py so that sim and tardis/tests can run

* remove BasePacketSource

* format

* Add docstrings

* Pre-release 2023.09.17 (tardis-sn#2411)

Automated changes for pre-release 2023.09.17

* upgrading env in 2022 (tardis-sn#2410)

* fix several bugs related to upgrade

* fix the get function in pandas

* fixed several incompatibilities for new libraries

* fixed up the changes in pandas testing and other reindexing issues

* fix other bugs with new environment

* blackify tardis

* updated the conda-lock file

* add lock files

* update cache number

* fix simulation tests

* remove units for testing

* blackify

* Update tardis/visualization/tools/tests/test_sdec_plot.py

good catch

Co-authored-by: Atharva Arya <[email protected]>

* add assert

* reset caches

---------

Co-authored-by: Atharva Arya <[email protected]>

* In gamma ray code : Changed times to np.geomspace (tardis-sn#2415)

* Changed times to np.geomspace

* Added myself to mailmap

* rename RadialModel1D to SimulationState (tardis-sn#2417)

* rename RadialModel1D to SimulationState

* black files

* rename simulation_state2 (tardis-sn#2421)

* fixup of many files to make them pass the tests

* change model for typo

* Ignore tests in docstr coverage (tardis-sn#2424)

ignore tests in docstr coverage

* Disabled formal integral for continuum interaction (tardis-sn#2426)

Disabled formal integral

Co-authored-by: Alexander Holas <alexander.holas@h-its>

* add linelist exposure to atom data and reader, built on current (tardis-sn#2428)

* add linelist exposure to atom data and reader, built on current

* add josh to mailmap

* Modified how setup input energy takes isotope name. Earlier it was ga… (tardis-sn#2425)

Modified how setup input energy takes isotope name. Earlier it was gamma_ray_lines.Isotope

* Added a function to calculate shell masses (tardis-sn#2434)

* Added a function to calculate shell masses

* Added a function to calculate shell masses

* changed shell masses with the new function

* Fix duplicate entries in continuum line list (tardis-sn#2443)

* Workaround list access

* Formatting

* Added error if duplicate

* Remove duplicates

* Fix typo, add comment

* Remove bandaid fix

* Cleanup

* More cleanup

* Fix numba parallel issues (tardis-sn#2447)

* Enabled parallel

* Fix the mistake

* Update docs

* Change glob patterns in `setup.cfg`  (tardis-sn#2441)

* Fix package_data in setup.cfg, mainly io and viz

* more folders

* Test pip installation

* Remove test step

* Fix more folders

* restructure of geometry (tardis-sn#2422)

* restructure of geometry

* add radial1d boundary logic

* black format

* several fixes

* fix epsilon

* add testing of boundaries

* change the r_inner_active

* first integration with `from_config` working

* hunting down density indexing bug

* all model tests (without csvy) pass

* more fixes

* fix of model to simulation_state

* fix inner boundary packet error

* fix some leftovers

* final fix for csvy

* blackify

* restructure to readers and remove some leftover code

* further cleanup

* first start of the restructure

* add comment about removing quantitiness

* add velocity check

* add new abundance functions

* remove default units

* Add FAQ section to documentation (tardis-sn#2450)

* Add faq

* Added Overview

* Fix typo

* Remove lock file creation from pre release workflow (tardis-sn#2432)

* Install latest version of mamba

* Unpin conda lock installatiion

* Split lockfilee creation to separate workflow

* change docs installation- put a warning for conda forge installation and comment out install from package

* fix

* delete create lockfiles

* download llock file

* Pre-release 2023.10.20 (tardis-sn#2452)

Automated changes for pre-release 2023.10.20

* Add verbose assert to NLTE rate equation (tardis-sn#2457)

* add verbose assert

* formatting

* Fix bug in relativistic packet source (tardis-sn#2453)

* Fix bug in relativistic packet source

* Add initial test for BlackBodySimpleSourceRelativistic

* Remove incorrect docstring

* Update tardis/montecarlo/tests/test_packet_source.py

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Update tardis/montecarlo/tests/test_packet_source.py

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Rename all occurences of blackbodysimplesourcerelativistic

* Do not hardcore blackbody_simplesource_relativistic.beta

---------

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Enable nlte ionization as plasma component (tardis-sn#2458)

* Rename nlte ion and electron

* Enable NLTE

* Fix typo

* Add docs

* Fix transitionprob dtype

* dtype conversion

* dtype for sparse matrix

* Typing in numba

* Fix test variable name

* Add missing electron density case

* Fix typo

* Update docstr-cov.yml to fix failing action (tardis-sn#2462)

* Update docstr-cov.yml to fix failing action

* Explicitly install setuptools

* NLTE Ionization solver polish (tardis-sn#2461)

* assertion for first guess

* Add checks to decay

* Fix greater equal

* Fix deprecated series index

* Pre-release 2023.11.05 (tardis-sn#2466)

Automated changes for pre-release 2023.11.05

* Tests Plasma Using Syrupy (tardis-sn#2413)

* Add syrupy classes to conftest

* Add syrupy to env file

* Another folder for syrupy data

* Save as npy instead of txt

* Use syrupy fixtures

* Different assertion functions for pandas dataframes and series

* Zeta data fix

* Blackify

* Blackify conftest

* test_hdf_plasmas using syrupy

* Install syrupy with conda

* Remove additional line adding syrupy as a plugin

* Set update snapshots config option when generate reference is selected

* Remove old refdata code from test plasmas complete

* Create plasma conftest file

* Text based snapshot fixture with custom location

* Snapshot path

* tardis regressions my fork

* Refactor test_hdf_plasmas.py

* Format using black

* test nlte excitation using syrupy

* nlte solver

* plasma continuum

* test tardis model density config

* Lock files

* Increase cache no

* format using black

* cleanup- sort dependencies, delete comments

* Documentation to run these tests

* remove commented out fixtures which are not used anywhere

* docs code render fix

* tests final cleanup

* renaming files, yet to deal with ambr snapshot extension and curly brackets

* renaming snapshots

* Add comments

* Add astropy import guard (tardis-sn#2470)

* Add astropy import guard

* mailmap

* Reading in decay radiation data in atom data (tardis-sn#2471)

* Reading in decay radiation data in atom data

* Added docstring

* Fixes the checksum

* Pre-release 2023.11.26 (tardis-sn#2477)

Automated changes for pre-release 2023.11.26

* Update plasma configuration documentation (tardis-sn#2459)

* update plasma docs

* Update mailmap

* Fix typo

* Add ruff rules and docs (tardis-sn#2478)

* Add ruff rules and docs

* Update pyproject.toml

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* rebuild docs

---------

Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Decay energy chain (tardis-sn#2448)

* Added a function to calculate shell masses

* Added a function to calculate shell masses

* changed shell masses with the new function

* Changed mass fraction to masses in to_inventories()

* Co-authored-by: Wolfgang Kerzendorf <[email protected]>

* Added a function to calculate total decays

* Added a function to calculate energies from gamma rays and positrons.

* added a function to calculate average energies of gamma rays and positrons

* Added a fucntion to calculate each decay chain energies

* Added dictionaries to handle multiple isotopes

* Changed value to values

* added tests for gamma_ray_transport

* Added tests for calculating activity

* Added test for activity

* Added tests for two isotope

* Changed Ni_isotope_mass

* Added pytest paramterize

* Added test for calculating shell masses

* Ran test for checking activity of parent nuclide with analytical solution.

* The function test_activity matches with the radioactivedecay output upto 14 decimal places. The Avogadro's number used in radioactivedecay is not from astropy.

* Added tests for checking if iso_dict is returning the right key.

* Added test for inventories dictionary.

* Added a test to check if the calculate_average_energy function passes the right list ahead.

* Added new function for testing energy budget from each decay chain.

* Added a new function for energy per mass

* Reading in decay radiation data in atom data

* Add

* Added tests for gamma ray transport.

* Added tests for all functions for gamma_ray_transport. Added docstrings.

* Changing decay energy chain

* Added a function to get taus

* Added tests for multiple isotopes

* Fixes the test calculate shell masses with hand calculated values

* Use Mamba instead of conda

* Run asv for last 5 commits

* Add pull request trigger temporarily

* Reset

---------

Co-authored-by: tardis-bot <[email protected]>
Co-authored-by: Wolfgang Kerzendorf <[email protected]>
Co-authored-by: Anirban <[email protected]>
Co-authored-by: Alexander Holas <[email protected]>
Co-authored-by: Alexander Holas <alexander.holas@h-its>
Co-authored-by: Joshua Shields <[email protected]>
Co-authored-by: Anirban <[email protected]>
Co-authored-by: Christian Vogl <[email protected]>
Co-authored-by: Andrew <[email protected]>

.github/workflows/benchmarks.yml

@@ -4,9 +4,11 @@ on:
   push:
     branches:
       - master
+
   pull_request_target:
     branches:
-      - '*'
+      - master
+
     types:
       - opened
       - reopened
@@ -38,10 +40,10 @@ jobs:
       - name: Checkout pull/${{ github.event.number }}
         uses: actions/checkout@v3
         with:
-          ref: ${{ github.event.pull_request.head.sha }}
+          ref: ${{ github.sha }}
           fetch-depth: 0
         if: github.event_name == 'pull_request_target'
-      
+
       - name: Restore Atom Data
         uses: actions/cache/restore@v3
         id: atom-data-restore
@@ -62,24 +64,34 @@ jobs:
         with:
           path: benchmarks/data/kurucz_cd23_chianti_H_He.h5
           key: atom-data
+
+      - name: Setup Mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: benchmark
+          init-shell: >-
+            bash
+          create-args: >-
+            python
+            asv
+            mamba
 
       - name: Install asv
-        run: pip install asv==0.5.*
+        run: pip install asv
 
       - name: Accept all asv questions
         run: asv machine --yes
 
       - name: Run benchmarks for last 5 commits if not PR
         if: github.event_name != 'pull_request_target'
-        continue-on-error: true
         run: |
           git log -n 5  --pretty=format:"%H" >> tag_commits.txt
           asv run HASHFILE:tag_commits.txt | tee asv-output.log  
           if grep -q failed asv-output.log; then 
             echo "Some benchmarks have failed!"
             exit 1
           fi
-          
+
       - name: Generate Graphs and HTML
         if: github.event_name != 'pull_request_target'
         run: asv publish

asv.conf.json

@@ -10,7 +10,7 @@
         "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
     ],
     "branches": ["master"],
-    "environment_type": "conda",
+    "environment_type": "mamba",
     "show_commit_url": "https://github.com/tardis-sn/tardis/commit",
     "conda_environment_file": "tardis_env3.yml",
     "benchmark_dir": "benchmarks",