From 877dfb18894c8fb53ed0825db9d940e0b9bc262f Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Fri, 6 Feb 2026 16:02:49 +0100
Subject: [PATCH 1/2] remove cli.py

---
 src/openfe_analysis/cli.py | 29 -----------------------------
 1 file changed, 29 deletions(-)
 delete mode 100644 src/openfe_analysis/cli.py

diff --git a/src/openfe_analysis/cli.py b/src/openfe_analysis/cli.py
deleted file mode 100644
index c45c540..0000000
--- a/src/openfe_analysis/cli.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import json
-import pathlib
-
-import click
-
-from . import rmsd
-
-
-@click.group()
-def cli():
-    pass
-
-
-@cli.command(name="RFE_analysis")
-@click.argument(
-    "loc",
-    type=click.Path(
-        exists=True, readable=True, file_okay=False, dir_okay=True, path_type=pathlib.Path
-    ),
-)
-@click.argument("output", type=click.Path(writable=True, dir_okay=False, path_type=pathlib.Path))
-def rfe_analysis(loc, output):
-    pdb = loc / "hybrid_system.pdb"
-    trj = loc / "simulation.nc"
-
-    data = rmsd.gather_rms_data(pdb, trj)
-
-    with click.open_file(output, "w") as f:
-        f.write(json.dumps(data))

From 09e988a626ff50164ba40eb54f490f5b86d850a8 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Fri, 6 Feb 2026 16:10:04 +0100
Subject: [PATCH 2/2] remove cli from init

---
 src/openfe_analysis/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/openfe_analysis/__init__.py b/src/openfe_analysis/__init__.py
index 01c2bd8..b65c451 100644
--- a/src/openfe_analysis/__init__.py
+++ b/src/openfe_analysis/__init__.py
@@ -1,5 +1,5 @@
 from ._version import __version__  # isort: skip
-from . import cli, rmsd
+from . import rmsd
 from .reader import FEReader
 from .transformations import (
     Aligner,