From e6b61e3283c2e017c05fdc39e049a8b917b59fe0 Mon Sep 17 00:00:00 2001
From: VasuJ <145879890+vjaganat90@users.noreply.github.com>
Date: Tue, 20 Aug 2024 12:33:29 -0400
Subject: [PATCH 1/2] 'search_paths_cwl' when compile fail (#264)

* 'search_paths_cwl' when compile fail

* indent the global_config.json

---------

Co-authored-by: Vasu Jaganath <vasu.jaganath@axleinfo.com>
---
 src/sophios/compiler.py     | 2 +-
 src/sophios/input_output.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/sophios/compiler.py b/src/sophios/compiler.py
index 90f81ce8..f3abb0fb 100644
--- a/src/sophios/compiler.py
+++ b/src/sophios/compiler.py
@@ -319,7 +319,7 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                 # Use auto-discovery mechanism (with run tag)
                 tool_i = tools[stepid_runtag]
             else:
-                msg = f'Error! Neither {stepid.stem} nor {stepid_runtag.stem} found!'
+                msg = f"Error! Neither {stepid.stem} nor {stepid_runtag.stem} found!, check your 'search_paths_cwl' in global_config.json"
                 raise Exception(msg)
             # Programmatically modify tool_i here
             graph_dummy = graph  # Just use anything here to satisfy mypy
diff --git a/src/sophios/input_output.py b/src/sophios/input_output.py
index 6bf5c809..7c486051 100644
--- a/src/sophios/input_output.py
+++ b/src/sophios/input_output.py
@@ -138,7 +138,7 @@ def write_config_to_disk(config: Json, config_file: Path) -> None:
     # make the full path if it doesn't exist
     config_dir.mkdir(parents=True, exist_ok=True)
     with open(config_file, 'w', encoding='utf-8') as f:
-        json.dump(config, f)
+        json.dump(config, f, indent=4, sort_keys=True)
 
 
 def get_config(config_file: Path, default_config_file: Path) -> Json:

From d8834377883196f5c22de6d5c40da3d774956a51 Mon Sep 17 00:00:00 2001
From: sameeul <sameeul@gmail.com>
Date: Tue, 20 Aug 2024 12:37:46 -0400
Subject: [PATCH 2/2] Update pyproject.toml for release

---
 pyproject.toml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4990bb38..88d80b08 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -104,11 +104,6 @@ runners = [
     "toil[cwl]",
     "cwl-utils",
 ]
-runners-src = [
-    "toil[cwl] @ git+https://github.com/sameeul/toil.git",
-    "cwltool @ git+https://github.com/sameeul/cwltool.git",
-    "cwl-utils @ git+https://github.com/sameeul/cwl-utils.git",
-]
 # See docs/requirements.txt
 doc = [
     "sphinx",
@@ -118,7 +113,6 @@ doc = [
 plots = ["matplotlib"]
 cyto = ["ipycytoscape"] # only for DAG visualization
 all_except_runner_src = ["sophios[test,doc,plots,cyto,mypy-types]"]
-all = ["sophios[test,doc,plots,cyto,runners-src,mypy-types]"]
 
 [project.scripts]
 sophios = "sophios.main:main"