Migrate to Regression Data Completely

.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:

.github/workflows/build-docs.yml

@@ -92,15 +92,15 @@ 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
         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 .

.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:
 
             <br>
 
-            > :warning: **WARNING:** 
+            > :warning: **WARNING:**
             >
             > This pull request should be auto-merged. **Do not merge manually if any check fails**.
             >
@@ -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

.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-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:
   run:
     shell: bash -l {0}
- 
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
   cancel-in-progress: true
-    
+
 
 jobs:
   tests:
@@ -65,38 +65,39 @@ 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" 
-      
-      - name: Refdata Generation tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" 
+        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "${{ 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 ${{ matrix.rpacket_tracking }} rpacket_tracking"
         if: contains(github.event.pull_request.labels.*.name, 'run-generation-tests') || github.ref == 'refs/heads/master'
-      
+
       - run: mv .coverage .coverage.${{ strategy.job-index }}
 
       - uses: actions/upload-artifact@v4
         with:
           name: coverage-${{ matrix.continuum }}-continuum-${{ matrix.rpacket_tracking }}-rpacket_tracking-${{ matrix.os }}
+          include-hidden-files: true
           path: |
             .coverage*
             !.coveragerc
-    
+
   combine_coverage_reports:
     needs: [tests]
     if: github.repository_owner == 'tardis-sn'
@@ -110,16 +111,16 @@ 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
 

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"
         }
     }
 }

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 model:

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 model:

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 model:

tardis/conftest.py

@@ -1,4 +1,5 @@
 import os
+from copy import deepcopy
 from pathlib import Path
 
 import pytest
@@ -91,9 +92,6 @@ 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,
@@ -141,17 +139,20 @@ 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_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")

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-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)"
    ]

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

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 csvy_model: csvy_full.csvy

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

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 csvy_model: branch85_csvy.csvy

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 csvy_model: csvy_model_to_test_abundances.csvy

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 csvy_model: exponential_csvy.csvy

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 

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-data repository
 atom_data: kurucz_cd23_chianti_H_He.h5
 
 csvy_model: model_full_csvy.csvy