macos-14, read from census

ryan-williams · Oct 28, 2024 · 1f382e1 · 1f382e1
1 parent 5d4b536
commit 1f382e1
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Showing 2 changed files with 18 additions and 6 deletions.
diff --git a/.github/workflows/scratchwork.yml b/.github/workflows/scratchwork.yml
@@ -4,12 +4,13 @@ on:
     inputs:
       runs-on:
         description: 'Select a runner ("macos-latest" = Intel, "macos-latest-xlarge" = M1)'
-        default: 'macos-latest-xlarge'
+        default: 'macos-14'
         type: choice
         options:
-          - macos-latest
-          - macos-latest-xlarge
-          - ubuntu-latest
+          - macos-13
+          - macos-14
+          - ubuntu-20
+          - ubuntu-22
           # - windows-latest
       ref:
         description: 'Branch or tag clone/install/test (leave blank to install latest version from PyPI)'
@@ -50,6 +51,8 @@ jobs:
       - name: 'Run with `import tiledb` before `import tiledbsoma` (sometimes segfaults)'
         env:
           IMPORT_TILEDB: 1
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
         run: |
           ./segfault-repro.py
           rv=$?

diff --git a/segfault-repro.py b/segfault-repro.py
@@ -7,7 +7,16 @@
     print("Importing `tiledb` before `tiledbsoma`")
     import tiledb
 
+print("Importing tiledbsoma")
 import tiledbsoma
+print("Imported tiledbsoma")
+import tiledb
+print("Imported tiledb")
 
-
-print(tiledbsoma.Experiment.open("pbmc-small"))
+soma_ctx = tiledbsoma.SOMATileDBContext(tiledb_config={
+    "vfs.s3.no_sign_request": "true",
+    "vfs.s3.region": "us-west-2",
+})
+uri = f"s3://cellxgene-census-public-us-west-2/cell-census/2024-07-01/soma/census_data/homo_sapiens"
+exp = tiledbsoma.open(uri, context=soma_ctx)
+print(exp)