Port update reference data pipeline to GitHub Actions (#2249)

* Create new workflow

* Patch for arepo tests

* Restore deleted parameter

* Black format; Add missing skip reason

* Fix typo in comment

* Add more comments

* Create slash command dispatcher

* Changes to dispatcher

* Black format

* Adapt workflow to run on workflow dispatch; create pull request step

* Black format

* Minor fixes

* Add bot comments after result

* Remove Azure Pipelines YAML file

* Do not push .lfs-assets-id on pull request

.github/workflows/dispatcher.yml

@@ -0,0 +1,21 @@
+name: slash-command
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  dispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Slash Command Dispatcher
+        uses: peter-evans/slash-command-dispatch@v3
+        with:
+          token: ${{ secrets.BOT_TOKEN }}
+          commands: |
+            compare-refdata
+            update-refdata
+          repository: tardis-sn/tardis
+          issue-type: pull-request
+          permission: triage
+          reaction-token: ${{ secrets.BOT_TOKEN }}
+          allow-edits: true

.github/workflows/update-refdata.yml

@@ -0,0 +1,150 @@
+#  For more information about TARDIS pipelines, please refer to:
+#
+#    https://tardis-sn.github.io/tardis/development/continuous_integration.html
+
+name: update-refdata
+
+on:
+  repository_dispatch:
+    types: [update-refdata-command]
+
+env:
+  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --generate-reference
+  CACHE_NUMBER: 1  # increase to reset cache manually
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  pr-open:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout pull/${{ github.event.client_payload.pull_request.number }}
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.client_payload.pull_request.head.sha }}
+
+      - uses: actions/checkout@v3
+        with:
+          repository: tardis-sn/tardis-refdata
+          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
+
+      - name: Restore LFS cache
+        uses: actions/cache@v3
+        id: lfs-cache
+        with:
+          path: tardis-refdata/.git/lfs
+          key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v${{ env.CACHE_NUMBER }}
+
+      - name: Pull LFS objects
+        run: git lfs pull
+        working-directory: tardis-refdata
+        if: steps.lfs-cache.outputs.cache-hit != 'true'
+
+      - name: Checkout LFS repository
+        run: git lfs checkout
+        working-directory: tardis-refdata
+        if: steps.lfs-cache.outputs.cache-hit == 'true'
+
+      - name: Setup environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+            activate-environment: tardis
+            use-mamba: true
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/share/miniconda3/envs/tardis
+          key: conda-linux-64-${{ hashFiles('conda-linux-64.lock') }}-v${{ env.CACHE_NUMBER }}
+        id: cache-conda
+
+      - name: Update environment
+        run: mamba update -n tardis --file conda-linux-64.lock
+        if: steps.cache-conda.outputs.cache-hit != 'true'
+
+      - name: Install package
+        run: pip install -e .
+
+      - name: Generate new reference data
+        run: pytest tardis ${{ env.PYTEST_FLAGS }}
+
+      - name: Remove unwanted files
+        run: rm .lfs-assets-id
+
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v4
+        with:
+          path: tardis-refdata
+          token: ${{ secrets.BOT_TOKEN }}
+          committer: TARDIS Bot <[email protected]>
+          author: TARDIS Bot <[email protected]>
+          branch: pr-${{ github.event.client_payload.pull_request.number }}
+          base: master
+          push-to-fork: tardis-bot/tardis-refdata
+          commit-message: Automated update (tardis pr-${{ github.event.client_payload.pull_request.number }})
+          title: Automated update (tardis pr-${{ github.event.client_payload.pull_request.number }})
+          body: |
+            *\*beep\* \*bop\**
+
+            Hi, human.
+
+            These are the changes made by https://github.com/tardis-sn/tardis/pull/${{ github.event.client_payload.pull_request.number }}, please be careful before merging this pull request.
+        id: create-pr
+
+      - name: Find comment
+        uses: peter-evans/find-comment@v2
+        id: fc
+        with:
+          issue-number: ${{ github.event.client_payload.pull_request.number }}
+          body-includes: Hi, human.
+        if: always()
+
+      - name: Post comment (success)
+        uses: peter-evans/create-or-update-comment@v2
+        with:
+          token:  ${{ secrets.BOT_TOKEN }}
+          issue-number: ${{ github.event.client_payload.pull_request.number }}
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          edit-mode: replace
+          body: |
+            *\*beep\* \*bop\**
+
+            Hi, human.
+
+            The **`${{ github.workflow }}`** workflow has **succeeded** :heavy_check_mark:
+
+            [**Click here**](${{ env.URL }}) to see your results.
+        env:
+          URL: https://github.com/tardis-sn/tardis-refdata/pull/${{ github.event.client_payload.pull_request.number }}
+        if: success()
+
+      - name: Post comment (failure)
+        uses: peter-evans/create-or-update-comment@v2
+        with:
+          token:  ${{ secrets.BOT_TOKEN }}
+          issue-number: ${{ github.event.number }}
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          edit-mode: replace
+          body: |
+            *\*beep\* \*bop\**
+
+            Hi, human.
+
+            The **`${{ github.workflow }}`** workflow has **failed** :x:
+
+            [**Click here**](${{ env.URL }}) to see the build log.
+        env:
+          URL: https://github.com/${{ github.repository_owner }}/${{ github.event.repository.name }}/actions/runs/${{ github.run_id }}?check_suite_focus=true
+        if: failure()

tardis/conftest.py

@@ -51,6 +51,14 @@ def pytest_configure(config):
         packagename = os.path.basename(os.path.dirname(__file__))
         TESTED_VERSIONS[packagename] = __version__
 
+    # Create a marker to ignore the `--generate-reference` flag. A use case for this
+    # marker is when there is data in the reference data repository that can't be
+    # generated by TARDIS, like the Arepo snapshots.
+    config.addinivalue_line(
+        "markers",
+        "ignore_generate: mark test to not generate new reference data",
+    )
+
 
 # Uncomment the last two lines in this block to treat all DeprecationWarnings as
 # exceptions. For Astropy v2.0 or later, there are 2 additional keywords,
@@ -100,6 +108,15 @@ def pytest_addoption(parser):
     )
 
 
+# Required by the `ignore_generate` marker
+def pytest_collection_modifyitems(config, items):
+    if config.getoption("--generate-reference"):
+        skip_generate = pytest.mark.skip(reason="Skip generate reference data")
+        for item in items:
+            if "ignore_generate" in item.keywords:
+                item.add_marker(skip_generate)
+
+
 # -------------------------------------------------------------------------
 # project specific fixtures
 # -------------------------------------------------------------------------

tardis/io/tests/test_arepo_parser.py

@@ -118,9 +118,11 @@ def get_full_reference_data():
     return data
 
 
+@pytest.mark.ignore_generate
 def test_cone_profile(get_cone_csvy_model, get_cone_reference_data):
     assert get_cone_csvy_model == get_cone_reference_data
 
 
+@pytest.mark.ignore_generate
 def test_full_profile(get_full_csvy_model, get_full_reference_data):
     assert get_full_csvy_model == get_full_reference_data