Use new extension logger

Author: Ulthran

.github/workflows/tests.yml

@@ -22,9 +22,9 @@ jobs:
       - name: Dump Logs
         shell: bash
         if: always()
-        run: tail -n +1 logs/*
+        run: tail -n +1 logs/* || true
 
       - name: Dump Stats
         shell: bash
         if: always()
-        run: cat stats/*
+        run: cat stats/* || true

.tests/data/README.md

@@ -0,0 +1,5 @@
+# Test data
+
+## reads
+
+From sunbeam/tests/data

.tests/e2e/test_full_run.py

@@ -7,12 +7,10 @@
 
 
 @pytest.fixture
-def setup():
-    temp_dir = Path(tempfile.mkdtemp())
-
+def setup(tmp_path):
     reads_fp = Path(".tests/data/reads/").resolve()
 
-    project_dir = temp_dir / "project/"
+    project_dir = tmp_path / "project/"
 
     sp.check_output(["sunbeam", "init", "--data_fp", reads_fp, project_dir])
 
@@ -30,14 +28,14 @@ def setup():
         ]
     )
 
-    yield temp_dir, project_dir
+    yield tmp_path, project_dir
 
-    shutil.rmtree(temp_dir)
+    shutil.rmtree(tmp_path)
 
 
 @pytest.fixture
 def run_sunbeam(setup):
-    temp_dir, project_dir = setup
+    tmp_path, project_dir = setup
     output_fp = project_dir / "sunbeam_output"
     log_fp = output_fp / "logs"
     stats_fp = project_dir / "stats"
@@ -50,7 +48,7 @@ def run_sunbeam(setup):
             project_dir,
             "all_template",
             "--directory",
-            temp_dir,
+            tmp_path,
         ],
         capture_output=True,
         text=True,

sbx_template.smk

@@ -4,6 +4,19 @@ except NameError:
     # For backwards compatibility with older versions of Sunbeam
     SBX_TEMPLATE_VERSION = "0.0.0"
 
+try:
+    logger = get_extension_logger("sbx_template")
+except NameError:
+    # For backwards compatibility with older versions of Sunbeam
+    import logging
+
+    logger = logging.getLogger("sunbeam.pipeline.extensions.sbx_template")
+
+
+logger.info("Doing some extension specific setup...")
+logger.info(f"Using sbx_template version {SBX_TEMPLATE_VERSION}.")
+logger.error("Don't worry, this isn't a real error.")
+
 
 localrules:
     all_template,
@@ -31,7 +44,7 @@ rule example_rule:
     container:
         f"docker://sunbeamlabs/sbx_template:{SBX_TEMPLATE_VERSION}"
     shell:
-        "cat {params.opts} {input} >> {output} 2> {log}"
+        "(cat {params.opts} {input} > {output}) > {log} 2>&1"
 
 
 rule example_with_script: