From 883715038c7007f621163e74ab94a5d49273efe1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 8 Aug 2024 16:57:35 -0400
Subject: [PATCH] feat: add shell_run() and exec_in_context() + basic tests

---
 pyproject.toml         |  3 ++-
 src/ccbr_tools/util.py | 20 ++++++++++++++++++++
 tests/test_cli.py      |  9 +++++++--
 tests/test_util.py     |  5 +++++
 4 files changed, 34 insertions(+), 3 deletions(-)
 create mode 100644 src/ccbr_tools/util.py
 create mode 100644 tests/test_util.py

diff --git a/pyproject.toml b/pyproject.toml
index 6c5ae50..5e9e1c1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,8 +34,9 @@ classifiers = [
 requires-python = ">=3.10"
 dependencies = [
     "biopython",
-    "pandas",
     "Click >= 8.1.3",
+    "pandas",
+    "requests"
 ]
 
 [project.optional-dependencies]
diff --git a/src/ccbr_tools/util.py b/src/ccbr_tools/util.py
new file mode 100644
index 0000000..8a24ee8
--- /dev/null
+++ b/src/ccbr_tools/util.py
@@ -0,0 +1,20 @@
+""" Miscellaneous utility functions """
+import contextlib
+import io
+import subprocess
+
+
+def shell_run(command_str):
+    """Run a shell command and return stdout/stderr"""
+    out = subprocess.run(command_str, capture_output=True, shell=True, text=True)
+    return "\n".join([out.stdout, out.stderr])
+
+
+def exec_in_context(func, *args, **kwargs):
+    """Execute a function in a context manager to capture stdout/stderr"""
+    with contextlib.redirect_stdout(io.StringIO()) as out_f, contextlib.redirect_stderr(
+        io.StringIO()
+    ) as err_f:
+        func(*args, **kwargs)
+        out_combined = "\n".join([out_f.getvalue(), err_f.getvalue()])
+    return out_combined
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 813df60..aae7598 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,2 +1,7 @@
-def test_example():
-    assert True
+from ccbr_tools.util import shell_run
+
+
+def test_help_jobby():
+    assert "Will take your job(s)... and display their information!" in shell_run(
+        "jobby -h"
+    )
diff --git a/tests/test_util.py b/tests/test_util.py
new file mode 100644
index 0000000..bd1ea28
--- /dev/null
+++ b/tests/test_util.py
@@ -0,0 +1,5 @@
+from ccbr_tools.util import exec_in_context
+
+
+def test_exec():
+    assert exec_in_context(print, "hello", "world") == "hello world\n\n"