From 9fa3464341515edafb27cf16b54ec2fd0df77eb4 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 10:21:24 +0530 Subject: [PATCH 01/11] Remove refdata reference from .py files, tests pass --- tardis/conftest.py | 15 +++++---------- .../io/model/readers/tests/test_arepo_parser.py | 4 ++-- tardis/plasma/tests/test_complete_plasmas.py | 4 ++-- tardis/tests/fixtures/atom_data.py | 8 ++++---- 4 files changed, 13 insertions(+), 18 deletions(-) diff --git a/tardis/conftest.py b/tardis/conftest.py index 8d5f6ad78b7..1c185a31de3 100644 --- a/tardis/conftest.py +++ b/tardis/conftest.py @@ -91,9 +91,6 @@ def pytest_configure(config): def pytest_addoption(parser): - parser.addoption( - "--tardis-refdata", default=None, help="Path to Tardis Reference Folder" - ) parser.addoption( "--tardis-regression-data", default=None, @@ -144,15 +141,13 @@ def generate_reference(request): else: return option - @pytest.fixture(scope="session") -def tardis_ref_path(request): - tardis_ref_path = request.config.getoption("--tardis-refdata") - if tardis_ref_path is None: - pytest.skip("--tardis-refdata was not specified") +def tardis_regression_path(request): + tardis_regression_path = request.config.getoption("--tardis-regression-data") + if tardis_regression_path is None: + pytest.skip("--tardis-regression-data was not specified") else: - return Path(os.path.expandvars(os.path.expanduser(tardis_ref_path))) - + return Path(os.path.expandvars(os.path.expanduser(tardis_regression_path))) @pytest.fixture(scope="session") def tardis_snapshot_path(request): diff --git a/tardis/io/model/readers/tests/test_arepo_parser.py b/tardis/io/model/readers/tests/test_arepo_parser.py index d205d9d90ed..7d831f3df3f 100644 --- a/tardis/io/model/readers/tests/test_arepo_parser.py +++ b/tardis/io/model/readers/tests/test_arepo_parser.py @@ -7,8 +7,8 @@ @pytest.fixture() -def arepo_snapshot_fname(tardis_ref_path): - return Path(tardis_ref_path) / "arepo_data" / "arepo_snapshot.json" +def arepo_snapshot_fname(tardis_regression_path): + return Path(tardis_regression_path) / "arepo_data" / "arepo_snapshot.json" @pytest.fixture diff --git a/tardis/plasma/tests/test_complete_plasmas.py b/tardis/plasma/tests/test_complete_plasmas.py index 60f9ae85abc..3b2b3cc866a 100644 --- a/tardis/plasma/tests/test_complete_plasmas.py +++ b/tardis/plasma/tests/test_complete_plasmas.py @@ -136,8 +136,8 @@ class TestPlasma: scalars_properties = ["time_explosion", "link_t_rad_t_electron"] @pytest.fixture(scope="class") - def chianti_he_db_fpath(self, tardis_ref_path): - return (tardis_ref_path / "atom_data" / "chianti_He.h5").absolute() + def chianti_he_db_fpath(self, tardis_regression_path): + return (tardis_regression_path / "atom_data" / "chianti_He.h5").absolute() @pytest.fixture(scope="class", params=CONFIG_LIST, ids=idfn) def config(self, request): diff --git a/tardis/tests/fixtures/atom_data.py b/tardis/tests/fixtures/atom_data.py index d2b4c7b084a..1a35d69a4b7 100644 --- a/tardis/tests/fixtures/atom_data.py +++ b/tardis/tests/fixtures/atom_data.py @@ -10,9 +10,9 @@ @pytest.fixture(scope="session") -def atomic_data_fname(tardis_ref_path): +def atomic_data_fname(tardis_regression_path): atomic_data_fname = ( - tardis_ref_path / "atom_data" / "kurucz_cd23_chianti_H_He.h5" + tardis_regression_path / "atom_data" / "kurucz_cd23_chianti_H_He.h5" ) atom_data_missing_str = ( @@ -44,11 +44,11 @@ def kurucz_atomic_data(atomic_dataset): @pytest.fixture # (scope="session") -def nlte_atomic_data_fname(tardis_ref_path): +def nlte_atomic_data_fname(tardis_regression_path): """ File name for the atomic data file used in NTLE ionization solver tests. """ - atomic_data_fname = tardis_ref_path / "nlte_atom_data" / "TestNLTE_He_Ti.h5" + atomic_data_fname = tardis_regression_path / "atom_data" / "nlte_atom_data" / "TestNLTE_He_Ti.h5" atom_data_missing_str = ( f"{atomic_data_fname} atomic datafiles " f"does not seem to exist" From 15c4ede33be8560269696d37c0d27347b6db523b Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 13:06:50 +0530 Subject: [PATCH 02/11] Error message fix --- tardis/io/model/parse_atom_data.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tardis/io/model/parse_atom_data.py b/tardis/io/model/parse_atom_data.py index 66b95fb4ffe..86665af0e4a 100644 --- a/tardis/io/model/parse_atom_data.py +++ b/tardis/io/model/parse_atom_data.py @@ -45,7 +45,7 @@ def parse_atom_data(config, atom_data=None): print( e, "Error might be from the use of an old-format of the atomic database, \n" - "please see https://github.com/tardis-sn/tardis-refdata/tree/master/atom_data" + "please see https://github.com/tardis-sn/tardis-regression-data/tree/master/atom_data" " for the most recent version.", ) raise From dd9ae5ae961c5548285ce0e8da77d5bf1581f1ea Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 13:16:01 +0530 Subject: [PATCH 03/11] Minor correction in config file comments --- .../configuration/components/models/data/config_init_trad.yml | 2 +- .../components/models/data/config_no_init_trad.yml | 2 +- .../resources/code_comparison/plasma_compare/tardis_example.yml | 2 +- tardis/energy_input/docs/working_gamma_ray_test.ipynb | 2 +- tardis/io/model/readers/tests/data/csvy_test_config.yml | 2 +- tardis/model/tests/data/branch85_csvy.yml | 2 +- tardis/model/tests/data/branch85_old_config.yml | 2 +- tardis/model/tests/data/csvy_model_to_test_abundances.yml | 2 +- tardis/model/tests/data/exponential_csvy.yml | 2 +- tardis/model/tests/data/exponential_old_config.yml | 2 +- tardis/model/tests/data/model_full_csvy.yml | 2 +- tardis/model/tests/data/model_full_old_config.yml | 2 +- tardis/model/tests/data/powerlaw_csvy.yml | 2 +- tardis/model/tests/data/powerlaw_old_config.yml | 2 +- tardis/model/tests/data/radiative_csvy.yml | 2 +- tardis/model/tests/data/radiative_old_config.yml | 2 +- tardis/model/tests/data/uniform_csvy.yml | 2 +- tardis/model/tests/data/uniform_old_config.yml | 2 +- tardis/plasma/tests/data/config_init_trad.yml | 2 +- 19 files changed, 19 insertions(+), 19 deletions(-) diff --git a/docs/io/configuration/components/models/data/config_init_trad.yml b/docs/io/configuration/components/models/data/config_init_trad.yml index cb4ecb5c1a7..dc333d59e8a 100755 --- a/docs/io/configuration/components/models/data/config_init_trad.yml +++ b/docs/io/configuration/components/models/data/config_init_trad.yml @@ -9,7 +9,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 model: diff --git a/docs/io/configuration/components/models/data/config_no_init_trad.yml b/docs/io/configuration/components/models/data/config_no_init_trad.yml index 1b1f2c1aad1..4d9b21160fa 100755 --- a/docs/io/configuration/components/models/data/config_no_init_trad.yml +++ b/docs/io/configuration/components/models/data/config_no_init_trad.yml @@ -9,7 +9,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 model: diff --git a/docs/resources/code_comparison/plasma_compare/tardis_example.yml b/docs/resources/code_comparison/plasma_compare/tardis_example.yml index 1cf7cab151d..e5ed31eac4b 100644 --- a/docs/resources/code_comparison/plasma_compare/tardis_example.yml +++ b/docs/resources/code_comparison/plasma_compare/tardis_example.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 13 day #distance: 24.2 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 model: diff --git a/tardis/energy_input/docs/working_gamma_ray_test.ipynb b/tardis/energy_input/docs/working_gamma_ray_test.ipynb index e952944ed1d..e8083cdbb6b 100644 --- a/tardis/energy_input/docs/working_gamma_ray_test.ipynb +++ b/tardis/energy_input/docs/working_gamma_ray_test.ipynb @@ -89,7 +89,7 @@ } ], "source": [ - "# Download the atom data file from tardis-refdata repo to run this cell.\n", + "# Download the atom data file from tardis-regression repo to run this cell.\n", "atom_data_file = 'kurucz_cd23_chianti_H_He.h5'\n", "atom_data = AtomData.from_hdf(atom_data_file)" ] diff --git a/tardis/io/model/readers/tests/data/csvy_test_config.yml b/tardis/io/model/readers/tests/data/csvy_test_config.yml index 3df6d499810..86cc8c6b79a 100644 --- a/tardis/io/model/readers/tests/data/csvy_test_config.yml +++ b/tardis/io/model/readers/tests/data/csvy_test_config.yml @@ -5,7 +5,7 @@ supernova: luminosity_requested: 8.770 log_lsun time_explosion: 16 day -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: csvy_full.csvy diff --git a/tardis/model/tests/data/branch85_csvy.yml b/tardis/model/tests/data/branch85_csvy.yml index 336d76344e3..34840195b3f 100644 --- a/tardis/model/tests/data/branch85_csvy.yml +++ b/tardis/model/tests/data/branch85_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: branch85_csvy.csvy diff --git a/tardis/model/tests/data/branch85_old_config.yml b/tardis/model/tests/data/branch85_old_config.yml index 1056660e91a..97721dd8fa2 100644 --- a/tardis/model/tests/data/branch85_old_config.yml +++ b/tardis/model/tests/data/branch85_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/csvy_model_to_test_abundances.yml b/tardis/model/tests/data/csvy_model_to_test_abundances.yml index 28828109bfd..8c39b85a221 100644 --- a/tardis/model/tests/data/csvy_model_to_test_abundances.yml +++ b/tardis/model/tests/data/csvy_model_to_test_abundances.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 4 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: csvy_model_to_test_abundances.csvy diff --git a/tardis/model/tests/data/exponential_csvy.yml b/tardis/model/tests/data/exponential_csvy.yml index 0712767be5f..2b5fbc25586 100644 --- a/tardis/model/tests/data/exponential_csvy.yml +++ b/tardis/model/tests/data/exponential_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: exponential_csvy.csvy diff --git a/tardis/model/tests/data/exponential_old_config.yml b/tardis/model/tests/data/exponential_old_config.yml index 64bba2d1124..4c8be171431 100644 --- a/tardis/model/tests/data/exponential_old_config.yml +++ b/tardis/model/tests/data/exponential_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/model_full_csvy.yml b/tardis/model/tests/data/model_full_csvy.yml index 642356c95e2..7352ffcd5d1 100644 --- a/tardis/model/tests/data/model_full_csvy.yml +++ b/tardis/model/tests/data/model_full_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: model_full_csvy.csvy diff --git a/tardis/model/tests/data/model_full_old_config.yml b/tardis/model/tests/data/model_full_old_config.yml index a88ea398c97..cd07a548fee 100644 --- a/tardis/model/tests/data/model_full_old_config.yml +++ b/tardis/model/tests/data/model_full_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/powerlaw_csvy.yml b/tardis/model/tests/data/powerlaw_csvy.yml index aa28f208a1a..6c3853367a9 100644 --- a/tardis/model/tests/data/powerlaw_csvy.yml +++ b/tardis/model/tests/data/powerlaw_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: powerlaw_csvy.csvy diff --git a/tardis/model/tests/data/powerlaw_old_config.yml b/tardis/model/tests/data/powerlaw_old_config.yml index 8713c040040..9139cd961fe 100644 --- a/tardis/model/tests/data/powerlaw_old_config.yml +++ b/tardis/model/tests/data/powerlaw_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/radiative_csvy.yml b/tardis/model/tests/data/radiative_csvy.yml index b3f33d3eea7..1c277a4ab85 100644 --- a/tardis/model/tests/data/radiative_csvy.yml +++ b/tardis/model/tests/data/radiative_csvy.yml @@ -5,7 +5,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: radiative_csvy.csvy diff --git a/tardis/model/tests/data/radiative_old_config.yml b/tardis/model/tests/data/radiative_old_config.yml index 97be58b892c..76e0a8ebd85 100644 --- a/tardis/model/tests/data/radiative_old_config.yml +++ b/tardis/model/tests/data/radiative_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/uniform_csvy.yml b/tardis/model/tests/data/uniform_csvy.yml index faa09f0ae1b..36c2dbff0e8 100644 --- a/tardis/model/tests/data/uniform_csvy.yml +++ b/tardis/model/tests/data/uniform_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: uniform_csvy.csvy diff --git a/tardis/model/tests/data/uniform_old_config.yml b/tardis/model/tests/data/uniform_old_config.yml index 9f494eaa96e..7831ad1a215 100644 --- a/tardis/model/tests/data/uniform_old_config.yml +++ b/tardis/model/tests/data/uniform_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/plasma/tests/data/config_init_trad.yml b/tardis/plasma/tests/data/config_init_trad.yml index a7ecefcd289..b2d8a384e4b 100755 --- a/tardis/plasma/tests/data/config_init_trad.yml +++ b/tardis/plasma/tests/data/config_init_trad.yml @@ -9,7 +9,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-refdata repository +# standard atomic data base; get it from the tardis-regression repository atom_data: kurucz_cd23_chianti_H_He.h5 model: From 825233e2b977f5d4c7980b2a09cf7cb5a44095b0 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 13:24:41 +0530 Subject: [PATCH 04/11] Remove refdata reference from tests --- .github/actions/setup_lfs/action.yml | 45 ---------------------------- .github/workflows/tests.yml | 4 +-- 2 files changed, 2 insertions(+), 47 deletions(-) diff --git a/.github/actions/setup_lfs/action.yml b/.github/actions/setup_lfs/action.yml index b3c76be7977..86a3b0464d4 100644 --- a/.github/actions/setup_lfs/action.yml +++ b/.github/actions/setup_lfs/action.yml @@ -3,10 +3,6 @@ description: "Pull LFS repositories and caches them" inputs: - refdata-repo: - description: "tardis refdata repository" - required: false - default: "tardis-sn/tardis-refdata" regression-data-repo: description: "tardis regression data repository" required: false @@ -15,47 +11,6 @@ inputs: runs: using: "composite" steps: - - name: Clone Refdata Repo - uses: actions/checkout@v4 - with: - repository: ${{ inputs.refdata-repo }} - path: tardis-refdata - lfs: false - - - name: Create LFS file list - run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id - working-directory: tardis-refdata - shell: bash - - - name: Restore LFS cache - uses: actions/cache/restore@v4 - 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-refdata.outputs.cache-hit != 'true' - shell: bash - - - name: Git LFS Checkout - run: git lfs checkout - working-directory: tardis-refdata - if: steps.lfs-cache-refdata.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-refdata.outputs.cache-hit != 'true' && !contains(github.ref, 'merge') && always() || false }} - uses: actions/cache/save@v4 - 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-regression-data uses: actions/checkout@v4 with: diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6ad45cb2015..b50fa4bf222 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -26,7 +26,7 @@ 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-append + PYTEST_FLAGS: --tardis-regression-data=${{ github.workspace }}/tardis-regression-data --cov=tardis --cov-report=xml --cov-report=html --cov-append CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} defaults: @@ -84,7 +84,7 @@ jobs: - name: Run tests run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" - - name: Refdata Generation tests + - name: Regression Data Generation tests run: pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" if: contains(github.event.pull_request.labels.*.name, 'run-generation-tests') || github.ref == 'refs/heads/master' From 0a61b6d3743aa6e320e6f4dde45f268dd0ec8e6e Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 14:17:21 +0530 Subject: [PATCH 05/11] Archive dispatcher for compare refdata, remove compare refdata from pre release, correct build docs workflow --- .github/workflows/{ => archive}/dispatcher.yml | 0 .github/workflows/build-docs.yml | 2 +- .github/workflows/pre-release.yml | 3 --- 3 files changed, 1 insertion(+), 4 deletions(-) rename .github/workflows/{ => archive}/dispatcher.yml (100%) diff --git a/.github/workflows/dispatcher.yml b/.github/workflows/archive/dispatcher.yml similarity index 100% rename from .github/workflows/dispatcher.yml rename to .github/workflows/archive/dispatcher.yml diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index 254c19ffbdd..a88e1f6ea03 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -100,7 +100,7 @@ jobs: - name: Copy atom_data run: | - mkdir -p ~/Downloads/tardis-data && cp -a ./tardis-refdata/atom_data/. ~/Downloads/tardis-data + mkdir -p ~/Downloads/tardis-data && cp -a ./tardis-regression-data/atom_data/. ~/Downloads/tardis-data - name: Install package run: pip install -e . diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml index 78b159e8b95..48339b7079f 100644 --- a/.github/workflows/pre-release.yml +++ b/.github/workflows/pre-release.yml @@ -138,9 +138,6 @@ jobs: merge-method: squash if: steps.create-pr.outputs.pull-request-operation == 'created' - compare_refdata: - uses: tardis-sn/tardis-refdata/.github/workflows/compare-refdata.yml@master - pip_tests: uses: ./.github/workflows/tests.yml secrets: inherit From b02680342e1ad7fe8e2cff40b453997956ea27e5 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 15:22:30 +0530 Subject: [PATCH 06/11] Apply ruff on workflow files --- .github/workflows/build-docs.yml | 4 ++-- .github/workflows/pre-release.yml | 8 ++++---- .github/workflows/tests.yml | 34 +++++++++++++++---------------- 3 files changed, 23 insertions(+), 23 deletions(-) diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index a88e1f6ea03..a630187331b 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -92,10 +92,10 @@ jobs: - name: Setup LFS uses: ./.github/actions/setup_lfs - + - name: Setup environment uses: ./.github/actions/setup_env - with: + with: os-label: linux-64 - name: Copy atom_data diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml index 48339b7079f..6dc7a8b8ace 100644 --- a/.github/workflows/pre-release.yml +++ b/.github/workflows/pre-release.yml @@ -30,14 +30,14 @@ jobs: - name: Download Lock File run: wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock shell: bash - + - name: Generate Cache Key - run: | + 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 shell: bash - + - uses: mamba-org/setup-micromamba@v1 with: environment-file: conda-linux-64.lock @@ -95,7 +95,7 @@ jobs:
- > :warning: **WARNING:** + > :warning: **WARNING:** > > This pull request should be auto-merged. **Do not merge manually if any check fails**. > diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b50fa4bf222..a1a8848383a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -7,16 +7,16 @@ name: tests on: push: branches: - - '*' + - '*' pull_request: branches: - - '*' + - '*' types: - opened - reopened - synchronize - labeled - workflow_call: # to be called by the pre release workflow + workflow_call: inputs: pip_git: description: "Whether or not to install tardis using git" @@ -26,17 +26,17 @@ on: env: CACHE_NUMBER: 0 # increase to reset cache manually - PYTEST_FLAGS: --tardis-regression-data=${{ github.workspace }}/tardis-regression-data --cov=tardis --cov-report=xml --cov-report=html --cov-append + PYTEST_FLAGS: --tardis-regression-data=${{ github.workspace }}/tardis-regression-data --cov=tardis --cov-report=xml --cov-report=html --cov-append CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} defaults: run: shell: bash -l {0} - + concurrency: group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} cancel-in-progress: true - + jobs: tests: @@ -65,29 +65,29 @@ jobs: - name: Setup LFS uses: ./.github/actions/setup_lfs - + - name: Setup environment uses: ./.github/actions/setup_env with: os-label: ${{ matrix.label }} - + - name: Install package editable if: ${{ !inputs.pip_git }} run: | pip install -e . --user - + - name: Install package git if: ${{ inputs.pip_git }} run: | pip install git+https://github.com/tardis-sn/tardis.git@master - name: Run tests - run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" - + run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" + - name: Regression Data Generation tests - run: pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" + run: pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" if: contains(github.event.pull_request.labels.*.name, 'run-generation-tests') || github.ref == 'refs/heads/master' - + - run: mv .coverage .coverage.${{ strategy.job-index }} - uses: actions/upload-artifact@v4 @@ -96,7 +96,7 @@ jobs: path: | .coverage* !.coveragerc - + combine_coverage_reports: needs: [tests] if: github.repository_owner == 'tardis-sn' @@ -110,16 +110,16 @@ jobs: # will download all artifacts(in this case all are coverage reports) - uses: actions/download-artifact@v4 - with: + with: path: . merge-multiple: true - + - name: Combine coverage reports run: | coverage combine coverage xml coverage html - + - name: Print report run: coverage report From bad18e3e2556fdd8745a9a1b5d8d561fbcf3b5b5 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 15:29:02 +0530 Subject: [PATCH 07/11] Apply black and ruff in python files --- tardis/conftest.py | 14 ++++++++++---- tardis/plasma/tests/test_complete_plasmas.py | 4 +++- tardis/tests/fixtures/atom_data.py | 7 ++++++- 3 files changed, 19 insertions(+), 6 deletions(-) diff --git a/tardis/conftest.py b/tardis/conftest.py index 1c185a31de3..e38c7eafa51 100644 --- a/tardis/conftest.py +++ b/tardis/conftest.py @@ -1,4 +1,5 @@ import os +from copy import deepcopy from pathlib import Path import pytest @@ -138,16 +139,21 @@ def generate_reference(request): option = request.config.getoption("--generate-reference") if option is None: return False - else: - return option + return option + @pytest.fixture(scope="session") def tardis_regression_path(request): - tardis_regression_path = request.config.getoption("--tardis-regression-data") + tardis_regression_path = request.config.getoption( + "--tardis-regression-data" + ) if tardis_regression_path is None: pytest.skip("--tardis-regression-data was not specified") else: - return Path(os.path.expandvars(os.path.expanduser(tardis_regression_path))) + return Path( + os.path.expandvars(os.path.expanduser(tardis_regression_path)) + ) + @pytest.fixture(scope="session") def tardis_snapshot_path(request): diff --git a/tardis/plasma/tests/test_complete_plasmas.py b/tardis/plasma/tests/test_complete_plasmas.py index 3b2b3cc866a..579dfaa52fb 100644 --- a/tardis/plasma/tests/test_complete_plasmas.py +++ b/tardis/plasma/tests/test_complete_plasmas.py @@ -137,7 +137,9 @@ class TestPlasma: @pytest.fixture(scope="class") def chianti_he_db_fpath(self, tardis_regression_path): - return (tardis_regression_path / "atom_data" / "chianti_He.h5").absolute() + return ( + tardis_regression_path / "atom_data" / "chianti_He.h5" + ).absolute() @pytest.fixture(scope="class", params=CONFIG_LIST, ids=idfn) def config(self, request): diff --git a/tardis/tests/fixtures/atom_data.py b/tardis/tests/fixtures/atom_data.py index 1a35d69a4b7..8cecbc44ffa 100644 --- a/tardis/tests/fixtures/atom_data.py +++ b/tardis/tests/fixtures/atom_data.py @@ -48,7 +48,12 @@ def nlte_atomic_data_fname(tardis_regression_path): """ File name for the atomic data file used in NTLE ionization solver tests. """ - atomic_data_fname = tardis_regression_path / "atom_data" / "nlte_atom_data" / "TestNLTE_He_Ti.h5" + atomic_data_fname = ( + tardis_regression_path + / "atom_data" + / "nlte_atom_data" + / "TestNLTE_He_Ti.h5" + ) atom_data_missing_str = ( f"{atomic_data_fname} atomic datafiles " f"does not seem to exist" From 214fdebbd1d92a820c910f5a4b637a4c1f33dca4 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 23 Aug 2024 19:24:33 +0530 Subject: [PATCH 08/11] Use full name of the repository --- .../configuration/components/models/data/config_init_trad.yml | 2 +- .../components/models/data/config_no_init_trad.yml | 2 +- .../resources/code_comparison/plasma_compare/tardis_example.yml | 2 +- tardis/energy_input/docs/working_gamma_ray_test.ipynb | 2 +- tardis/io/model/readers/tests/data/csvy_test_config.yml | 2 +- tardis/model/tests/data/branch85_csvy.yml | 2 +- tardis/model/tests/data/branch85_old_config.yml | 2 +- tardis/model/tests/data/csvy_model_to_test_abundances.yml | 2 +- tardis/model/tests/data/exponential_csvy.yml | 2 +- tardis/model/tests/data/exponential_old_config.yml | 2 +- tardis/model/tests/data/model_full_csvy.yml | 2 +- tardis/model/tests/data/model_full_old_config.yml | 2 +- tardis/model/tests/data/powerlaw_csvy.yml | 2 +- tardis/model/tests/data/powerlaw_old_config.yml | 2 +- tardis/model/tests/data/radiative_csvy.yml | 2 +- tardis/model/tests/data/radiative_old_config.yml | 2 +- tardis/model/tests/data/uniform_csvy.yml | 2 +- tardis/model/tests/data/uniform_old_config.yml | 2 +- tardis/plasma/tests/data/config_init_trad.yml | 2 +- 19 files changed, 19 insertions(+), 19 deletions(-) diff --git a/docs/io/configuration/components/models/data/config_init_trad.yml b/docs/io/configuration/components/models/data/config_init_trad.yml index dc333d59e8a..f8de5dc8149 100755 --- a/docs/io/configuration/components/models/data/config_init_trad.yml +++ b/docs/io/configuration/components/models/data/config_init_trad.yml @@ -9,7 +9,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 model: diff --git a/docs/io/configuration/components/models/data/config_no_init_trad.yml b/docs/io/configuration/components/models/data/config_no_init_trad.yml index 4d9b21160fa..33fe99b3ab1 100755 --- a/docs/io/configuration/components/models/data/config_no_init_trad.yml +++ b/docs/io/configuration/components/models/data/config_no_init_trad.yml @@ -9,7 +9,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 model: diff --git a/docs/resources/code_comparison/plasma_compare/tardis_example.yml b/docs/resources/code_comparison/plasma_compare/tardis_example.yml index e5ed31eac4b..d23c8e741a2 100644 --- a/docs/resources/code_comparison/plasma_compare/tardis_example.yml +++ b/docs/resources/code_comparison/plasma_compare/tardis_example.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 13 day #distance: 24.2 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 model: diff --git a/tardis/energy_input/docs/working_gamma_ray_test.ipynb b/tardis/energy_input/docs/working_gamma_ray_test.ipynb index e8083cdbb6b..77188813146 100644 --- a/tardis/energy_input/docs/working_gamma_ray_test.ipynb +++ b/tardis/energy_input/docs/working_gamma_ray_test.ipynb @@ -89,7 +89,7 @@ } ], "source": [ - "# Download the atom data file from tardis-regression repo to run this cell.\n", + "# Download the atom data file from tardis-regression-data repo to run this cell.\n", "atom_data_file = 'kurucz_cd23_chianti_H_He.h5'\n", "atom_data = AtomData.from_hdf(atom_data_file)" ] diff --git a/tardis/io/model/readers/tests/data/csvy_test_config.yml b/tardis/io/model/readers/tests/data/csvy_test_config.yml index 86cc8c6b79a..c22e9a40b91 100644 --- a/tardis/io/model/readers/tests/data/csvy_test_config.yml +++ b/tardis/io/model/readers/tests/data/csvy_test_config.yml @@ -5,7 +5,7 @@ supernova: luminosity_requested: 8.770 log_lsun time_explosion: 16 day -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: csvy_full.csvy diff --git a/tardis/model/tests/data/branch85_csvy.yml b/tardis/model/tests/data/branch85_csvy.yml index 34840195b3f..f1f4628caf0 100644 --- a/tardis/model/tests/data/branch85_csvy.yml +++ b/tardis/model/tests/data/branch85_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: branch85_csvy.csvy diff --git a/tardis/model/tests/data/branch85_old_config.yml b/tardis/model/tests/data/branch85_old_config.yml index 97721dd8fa2..de1d41159fc 100644 --- a/tardis/model/tests/data/branch85_old_config.yml +++ b/tardis/model/tests/data/branch85_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/csvy_model_to_test_abundances.yml b/tardis/model/tests/data/csvy_model_to_test_abundances.yml index 8c39b85a221..d4f1722d75d 100644 --- a/tardis/model/tests/data/csvy_model_to_test_abundances.yml +++ b/tardis/model/tests/data/csvy_model_to_test_abundances.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 4 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: csvy_model_to_test_abundances.csvy diff --git a/tardis/model/tests/data/exponential_csvy.yml b/tardis/model/tests/data/exponential_csvy.yml index 2b5fbc25586..96f170e9e9c 100644 --- a/tardis/model/tests/data/exponential_csvy.yml +++ b/tardis/model/tests/data/exponential_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: exponential_csvy.csvy diff --git a/tardis/model/tests/data/exponential_old_config.yml b/tardis/model/tests/data/exponential_old_config.yml index 4c8be171431..026bd218e69 100644 --- a/tardis/model/tests/data/exponential_old_config.yml +++ b/tardis/model/tests/data/exponential_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/model_full_csvy.yml b/tardis/model/tests/data/model_full_csvy.yml index 7352ffcd5d1..47a6d29beb5 100644 --- a/tardis/model/tests/data/model_full_csvy.yml +++ b/tardis/model/tests/data/model_full_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: model_full_csvy.csvy diff --git a/tardis/model/tests/data/model_full_old_config.yml b/tardis/model/tests/data/model_full_old_config.yml index cd07a548fee..925017a76ce 100644 --- a/tardis/model/tests/data/model_full_old_config.yml +++ b/tardis/model/tests/data/model_full_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/powerlaw_csvy.yml b/tardis/model/tests/data/powerlaw_csvy.yml index 6c3853367a9..a4af6bb592a 100644 --- a/tardis/model/tests/data/powerlaw_csvy.yml +++ b/tardis/model/tests/data/powerlaw_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: powerlaw_csvy.csvy diff --git a/tardis/model/tests/data/powerlaw_old_config.yml b/tardis/model/tests/data/powerlaw_old_config.yml index 9139cd961fe..5099d54f118 100644 --- a/tardis/model/tests/data/powerlaw_old_config.yml +++ b/tardis/model/tests/data/powerlaw_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/radiative_csvy.yml b/tardis/model/tests/data/radiative_csvy.yml index 1c277a4ab85..388cad75db3 100644 --- a/tardis/model/tests/data/radiative_csvy.yml +++ b/tardis/model/tests/data/radiative_csvy.yml @@ -5,7 +5,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: radiative_csvy.csvy diff --git a/tardis/model/tests/data/radiative_old_config.yml b/tardis/model/tests/data/radiative_old_config.yml index 76e0a8ebd85..e476e7346ce 100644 --- a/tardis/model/tests/data/radiative_old_config.yml +++ b/tardis/model/tests/data/radiative_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/model/tests/data/uniform_csvy.yml b/tardis/model/tests/data/uniform_csvy.yml index 36c2dbff0e8..693595a4fe6 100644 --- a/tardis/model/tests/data/uniform_csvy.yml +++ b/tardis/model/tests/data/uniform_csvy.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 csvy_model: uniform_csvy.csvy diff --git a/tardis/model/tests/data/uniform_old_config.yml b/tardis/model/tests/data/uniform_old_config.yml index 7831ad1a215..5273286c732 100644 --- a/tardis/model/tests/data/uniform_old_config.yml +++ b/tardis/model/tests/data/uniform_old_config.yml @@ -6,7 +6,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 diff --git a/tardis/plasma/tests/data/config_init_trad.yml b/tardis/plasma/tests/data/config_init_trad.yml index b2d8a384e4b..a48ff352f26 100755 --- a/tardis/plasma/tests/data/config_init_trad.yml +++ b/tardis/plasma/tests/data/config_init_trad.yml @@ -9,7 +9,7 @@ supernova: time_explosion: 16 day distance: 8.32 Mpc -# standard atomic data base; get it from the tardis-regression repository +# standard atomic data base; get it from the tardis-regression-data repository atom_data: kurucz_cd23_chianti_H_He.h5 model: From 2706faa2b7e6eca1ed08b98f72a036655cb2e269 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Mon, 26 Aug 2024 17:48:32 +0530 Subject: [PATCH 09/11] Turn spectrum tests into a module --- tardis/spectrum/tests/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 tardis/spectrum/tests/__init__.py diff --git a/tardis/spectrum/tests/__init__.py b/tardis/spectrum/tests/__init__.py new file mode 100644 index 00000000000..e69de29bb2d From 3b9ed177c9ea1ba0e63c5fb2dc0d64f39f4eb661 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 6 Sep 2024 12:14:56 +0530 Subject: [PATCH 10/11] Use regression data in asv config --- asv.conf.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/asv.conf.json b/asv.conf.json index 3fe4f4ec10f..f0157be649c 100644 --- a/asv.conf.json +++ b/asv.conf.json @@ -26,7 +26,7 @@ "html_dir": ".asv/html", "matrix": { "env": { - "TARDIS_REF_PATH": "tardis-refdata/atom_data" + "TARDIS_REF_PATH": "tardis-regression-data/atom_data" } } } \ No newline at end of file From ec55ece81a066810d427ca89a63f1be1017e5529 Mon Sep 17 00:00:00 2001 From: Atharva Arya Date: Fri, 6 Sep 2024 12:16:13 +0530 Subject: [PATCH 11/11] Upload hidden files --- .github/workflows/tests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a1a8848383a..a4915a2cbc8 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -93,6 +93,7 @@ jobs: - uses: actions/upload-artifact@v4 with: name: coverage-${{ matrix.continuum }}-continuum-${{ matrix.rpacket_tracking }}-rpacket_tracking-${{ matrix.os }} + include-hidden-files: true path: | .coverage* !.coveragerc