From 287b202cfcbca10e5c430844e7350b089f75be4b Mon Sep 17 00:00:00 2001
From: Wytamma Wirth <wytamma.wirth@me.com>
Date: Wed, 31 Jan 2024 23:39:32 +1100
Subject: [PATCH] Allow pass SnkConfig to CLI

---
 snk/cli/cli.py                     | 13 ++++++++-----
 snk/cli/subcommands/run.py         |  2 +-
 tests/test_cli/test_subcommands.py | 30 ++++++++++++++++--------------
 tests/test_dynamic_typer.py        |  2 +-
 4 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/snk/cli/cli.py b/snk/cli/cli.py
index 4ee8c74..9f49c0b 100644
--- a/snk/cli/cli.py
+++ b/snk/cli/cli.py
@@ -32,8 +32,8 @@ class CLI(DynamicTyper):
       >>> CLI(Path('/path/to/workflow'))
     """
 
-    def __init__(self, workflow_dir_path: Path = None) -> None:
-        if not workflow_dir_path:
+    def __init__(self, workflow_dir_path: Path = None, snk_config: SnkConfig = None) -> None:
+        if workflow_dir_path is None:
             # get the calling frame (the frame of the function that called this function)
             calling_frame = inspect.currentframe().f_back
             # get the file path from the calling frame
@@ -42,9 +42,12 @@ def __init__(self, workflow_dir_path: Path = None) -> None:
             workflow_dir_path = workflow_dir_path.parent
         self.workflow = Workflow(path=workflow_dir_path)
         self.snakemake_config = load_workflow_snakemake_config(workflow_dir_path)
-        self.snk_config = SnkConfig.from_workflow_dir(
-            workflow_dir_path, create_if_not_exists=True
-        )
+        if snk_config is None:
+            self.snk_config = SnkConfig.from_workflow_dir(
+                workflow_dir_path, create_if_not_exists=True
+            )
+        else:
+            self.snk_config = snk_config
         if self.snk_config.version:
             self.version = self.snk_config.version
         else: 
diff --git a/snk/cli/subcommands/run.py b/snk/cli/subcommands/run.py
index 93c9a5c..02679d6 100644
--- a/snk/cli/subcommands/run.py
+++ b/snk/cli/subcommands/run.py
@@ -256,7 +256,7 @@ def run(
         if configs:
             args.extend(["--config", *configs])
         if verbose:
-            typer.secho(f"snakemake {' '.join(args)}\n", fg=typer.colors.MAGENTA, secho=True)
+            typer.secho(f"snakemake {' '.join(args)}\n", fg=typer.colors.MAGENTA, err=True)
         if not keep_snakemake and Path(".snakemake").exists():
             keep_snakemake = True
         try:
diff --git a/tests/test_cli/test_subcommands.py b/tests/test_cli/test_subcommands.py
index 0d82ddb..8fa5fe0 100644
--- a/tests/test_cli/test_subcommands.py
+++ b/tests/test_cli/test_subcommands.py
@@ -1,19 +1,21 @@
 import pytest
 
-@pytest.mark.parametrize("cmd,expected_in_response", [
-    (["script", "run", "hello.py"], ["hello world"]),
-    (["script", "list"], ["hello.py"]),
-    (["script", "show", "hello.py"], ["print('hello world')"]),
-    (["env", "list"], ["python"]),
-    (["env", "show", "python"], ["python"]),
-    (["env", "create"], ["All conda environments created!"]),
-    (["env", "create", "python"], ["Created environment python!"]),
-    (["env", "run", "-v", "python", "which python"], [".snakemake"]),
-    (["env", "activate", "python"], ["Activating python environment...", "Exiting python environment..."]),
-    (["env", "remove", "-f"], ["Deleted"]),
+@pytest.mark.parametrize("cmd,expected_in_stdout,expected_in_stderr", [
+    (["script", "run", "hello.py"], ["hello world"], []),
+    (["script", "list"], ["hello.py"], []),
+    (["script", "show", "hello.py"], ["print('hello world')"], []),
+    (["env", "list"], ["python"], []),
+    (["env", "show", "python"], ["python"], []),
+    (["env", "create"], ["All conda environments created!"], []),
+    (["env", "create", "python"], ["Created environment python!"], []),
+    (["env", "run", "-v", "python", "which python"], [".snakemake"], []),
+    (["env", "activate", "python"], [], ["Activating python environment...", "Exiting python environment..."]),
+    (["env", "remove", "-f"], ["Deleted"], []),
 ])
-def test_snk_cli_command(local_runner, cmd, expected_in_response):
+def test_snk_cli_command(local_runner, cmd, expected_in_stdout, expected_in_stderr):
     res = local_runner(cmd)
     assert res.code == 0, res.stderr
-    for expected in expected_in_response:
-        assert expected in res.stdout, res.stderr
\ No newline at end of file
+    for expected in expected_in_stdout:
+        assert expected in res.stdout, res.stderr
+    for expected in expected_in_stderr:
+        assert expected in res.stderr, res.stderr
\ No newline at end of file
diff --git a/tests/test_dynamic_typer.py b/tests/test_dynamic_typer.py
index 98d4490..562d3ef 100644
--- a/tests/test_dynamic_typer.py
+++ b/tests/test_dynamic_typer.py
@@ -126,6 +126,6 @@ def test_error(dynamic_typer, cli_runner):
 
 
 def test_log(dynamic_typer, cli_runner, capsys):
-    dynamic_typer.log("Log message")
+    dynamic_typer.log("Log message", stderr=False)
     captured = capsys.readouterr()
     assert "Log message" in captured.out