Fix test log dumps

.tests/e2e/test_full_run.py

@@ -1,6 +1,7 @@
 import pytest
 import shutil
 import subprocess as sp
+import sys
 import tempfile
 from pathlib import Path
 
@@ -39,19 +40,30 @@ def setup():
 @pytest.fixture
 def run_sunbeam(setup):
     temp_dir, project_dir = setup
-
-    # Run the test job.
-    sp.check_output(
-        [
-            "sunbeam",
-            "run",
-            "--profile",
-            project_dir,
-            "all_template",
-            "--directory",
-            temp_dir,
-        ]
-    )
+    output_fp = project_dir / "sunbeam_output"
+    log_fp = output_fp / "logs"
+    stats_fp = project_dir / "stats"
+
+    # Run the test job
+    try:
+        sp.check_output(
+            [
+                "sunbeam",
+                "run",
+                "--profile",
+                project_dir,
+                "all_template",
+                "--directory",
+                temp_dir,
+            ]
+        )
+    except sp.CalledProcessError as e:
+        shutil.copytree(log_fp, "logs/")
+        shutil.copytree(stats_fp, "stats/")
+        sys.exit(e)
+
+    shutil.copytree(log_fp, "logs/")
+    shutil.copytree(stats_fp, "stats/")
 
     output_fp = project_dir / "sunbeam_output"
     benchmarks_fp = project_dir / "stats/"

README.md

@@ -32,7 +32,7 @@ The dependency .yml file can be named whatever you want, as long as you refer to
 
 ### .github/
 
-This directory contains CI workflows for GitHub to run automatically on PRs, including tests and linting. If the linter raises errors, you can fix them by running `snakefmt` on any snakemake files and `black` on any python files.
+This directory contains CI workflows for GitHub to run automatically on PRs, including tests and linting. If the linter raises errors, you can fix them by running `snakefmt` on any snakemake files and `black` on any python files. The release workflow will build and push a docker image for each environment in the extension.
 
 ### .tests/
 
@@ -42,6 +42,10 @@ This directory contains tests, broken down into types such as end-to-end (e2e) a
 
 This directory contains scripts that can be run by rules. Use this for any rules that need to run python, R, etc code.
 
+### envs/*.Dockerfile
+
+The Dockerfiles provided with conda env specifications allow for containerized runs of sunbeam (meaning they use docker containers to run each rule rather than conda envs).
+
 (You can delete everything above this line)
 -----------------------------------------------------------------