change pulling tests from hello looper dev branch instead of dev-deriv

.gitignore

@@ -64,7 +64,7 @@ open_pipelines/
 .coverage*
 .pytest_cache
 .vscode/
-/tests/data/hello_looper-dev_derive/.gitignore
+/tests/data/hello_looper-dev/.gitignore
 
 # Reserved files for comparison
 *RESERVE*

tests/conftest.py

@@ -199,7 +199,7 @@ def prep_temp_pep(example_pep_piface_path):
 
     # Get Path to local copy of hello_looper
     hello_looper_dir_path = os.path.join(
-        example_pep_piface_path, "hello_looper-dev_derive"
+        example_pep_piface_path, "hello_looper-dev"
     )
 
     # Make local temp copy of hello_looper
@@ -217,14 +217,14 @@ def prep_temp_pep_basic(example_pep_piface_path):
 
     # Get Path to local copy of hello_looper
     hello_looper_dir_path = os.path.join(
-        example_pep_piface_path, "hello_looper-dev_derive"
+        example_pep_piface_path, "hello_looper-dev"
     )
 
     # Make local temp copy of hello_looper
     d = tempfile.mkdtemp()
     shutil.copytree(hello_looper_dir_path, d, dirs_exist_ok=True)
 
-    advanced_dir = os.path.join(d, "basic")
+    advanced_dir = os.path.join(d, "intermediate")
     path_to_looper_config = os.path.join(advanced_dir, ".looper.yaml")
 
     return path_to_looper_config
@@ -235,7 +235,7 @@ def prep_temp_pep_csv(example_pep_piface_path):
 
     # Get Path to local copy of hello_looper
     hello_looper_dir_path = os.path.join(
-        example_pep_piface_path, "hello_looper-dev_derive"
+        example_pep_piface_path, "hello_looper-dev"
     )
 
     # Make local temp copy of hello_looper
@@ -275,7 +275,7 @@ def prep_temp_pep_pipestat(example_pep_piface_path):
     # Get Path to local copy of hello_looper
 
     hello_looper_dir_path = os.path.join(
-        example_pep_piface_path, "hello_looper-dev_derive"
+        example_pep_piface_path, "hello_looper-dev"
     )
 
     # Make local temp copy of hello_looper
@@ -294,7 +294,7 @@ def prep_temp_pep_pipestat_advanced(example_pep_piface_path):
     # Get Path to local copy of hello_looper
 
     hello_looper_dir_path = os.path.join(
-        example_pep_piface_path, "hello_looper-dev_derive"
+        example_pep_piface_path, "hello_looper-dev"
     )
 
     # Make local temp copy of hello_looper
@@ -313,7 +313,7 @@ def prep_temp_pep_pephub(example_pep_piface_path):
     # Get Path to local copy of hello_looper
 
     hello_looper_dir_path = os.path.join(
-        example_pep_piface_path, "hello_looper-dev_derive"
+        example_pep_piface_path, "hello_looper-dev"
     )
 
     # Make local temp copy of hello_looper

tests/data/hello_looper-dev_derive/README.md → tests/data/hello_looper-dev/README.md

@@ -4,10 +4,12 @@ This repository provides minimal working examples for the [looper pipeline submi
 
 This repository contains examples
 
-1. `/basic` - A basic example pipeline and project.
-2. `/pephub` - Example of how to point looper to PEPhub.
-3. `/pipestat` - Example of a pipeline that uses pipestat for recording results.
-4. `/csv` - How to use a pipeline with a CSV sample table (no YAML config)
+1. `/minimal` - A basic example pipeline and project.
+2. `/intermediate` - An intermediate example pipeline and project with a couple extra options.
+3. `/advanced` - A more advanced example, showcasing the capabilities of Looper.
+4. `/pephub` - Example of how to point looper to PEPhub.
+5. `/pipestat` - Example of a pipeline that uses pipestat for recording results.
+6. `/csv` - How to use a pipeline with a CSV sample table (no YAML config)
 
 Each example contains:
 

tests/data/hello_looper-dev/minimal/.looper.yaml

@@ -0,0 +1,5 @@
+pep_config: project/project_config.yaml # local path to pep config
+# pep_config: pepkit/hello_looper:default  # you can also use a pephub registry path
+output_dir: "results"
+pipeline_interfaces:
+  sample: pipeline/pipeline_interface.yaml

tests/data/hello_looper-dev/minimal/project/project_config.yaml

@@ -0,0 +1,2 @@
+pep_version: 2.0.0
+sample_table: sample_annotation.csv

tests/data/hello_looper-dev/minimal/project/sample_annotation.csv

@@ -0,0 +1,3 @@
+sample_name,library,file,toggle
+frog_1,anySampleType,data/frog_1.txt,1
+frog_2,anySampleType,data/frog_2.txt,1

tests/data/hello_looper-dev/pephub/pipeline/count_lines.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+linecount=`wc -l $1 | sed -E 's/^[[:space:]]+//' | cut -f1 -d' '`
+echo "Number of lines: $linecount"

tests/data/hello_looper-dev/pephub/pipeline/pipeline_interface.yaml

@@ -0,0 +1,6 @@
+pipeline_name: count_lines
+pipeline_type: sample
+var_templates:
+  pipeline: '{looper.piface_dir}/count_lines.sh'
+command_template: >
+  {pipeline.var_templates.pipeline} {sample.file}

tests/data/hello_looper-dev/pipestat/data/frog_1.txt

@@ -0,0 +1,4 @@
+ribbit
+ribbit
+ribbit
+CROAK!

tests/data/hello_looper-dev/pipestat/data/frog_2.txt

@@ -0,0 +1,7 @@
+ribbit
+ribbit
+ribbit
+
+ribbit, ribbit
+ribbit, ribbit
+CROAK!

tests/update_test_data.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-branch='dev_derive'
+branch='dev'
 
 wget https://github.com/pepkit/hello_looper/archive/refs/heads/${branch}.zip
 mv ${branch}.zip data/