From 91e7fdd4b41263ec40752dcad3bcdf7ec848211c Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Sun, 7 Jul 2024 12:39:54 -0700
Subject: [PATCH 01/26] Updated rename wells functionality at CLI level, fixed
 style errors

---
 iohub/cli/cli.py | 59 ++++++++++++++++++++++++++++++++++++++++++++++++
 iohub/ngff.py    | 44 ++++++++++++++++++++++++++++++++++++
 2 files changed, 103 insertions(+)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 901b92a9..ed70585e 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -1,9 +1,11 @@
+import csv
 import pathlib
 
 import click
 
 from iohub._version import __version__
 from iohub.convert import TIFFConverter
+from iohub.ngff import open_ome_zarr
 from iohub.reader import print_info
 
 VERSION = __version__
@@ -87,3 +89,60 @@ def convert(input, output, grid_layout, chunks):
         chunks=chunks,
     )
     converter()
+
+
+@click.command()
+@click.help_option("-h", "--help")
+@click.argument(
+    "csvfile",
+    type=click.File("r"),
+)
+@click.argument(
+    "zarrfile",
+    type=click.Path(
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        resolve_path=True,
+        path_type=pathlib.Path,
+    ),
+)
+def rename_wells_cli(csvfile, zarrfile):
+    """Rename wells based on CSV file
+
+    The CSV file should have two columns: old_well_path and new_well_path.
+    """
+    names = []
+
+    csvreader = csv.reader(csvfile)
+    for row in csvreader:
+        if len(row) != 2:
+            raise ValueError(
+                f"Invalid row format: {row}."
+                f"Each row must have two columns."
+            )
+        names.append([row[0], row[1]])
+
+    plate = open_ome_zarr(zarrfile, mode="a")
+
+    modified = {}
+    modified["wells"] = []
+    modified["rows"] = []
+    modified["columns"] = []
+
+    well_paths = [
+        plate.metadata.wells[i].path for i in range(len(plate.metadata.wells))
+    ]
+
+    for old_well_path, new_well_path in names:
+        if old_well_path not in well_paths:
+            raise ValueError(
+                f"Old well path '{old_well_path}' not found "
+                f"in the plate metadata."
+            )
+        for well in plate.metadata.wells:
+            if well.path == old_well_path and well not in modified["wells"]:
+                plate.rename_well(
+                    plate, well, old_well_path, new_well_path, modified, False
+                )
+                modified["wells"].append(well)
diff --git a/iohub/ngff.py b/iohub/ngff.py
index d5a307e0..698215c5 100644
--- a/iohub/ngff.py
+++ b/iohub/ngff.py
@@ -1565,6 +1565,50 @@ def positions(self) -> Generator[tuple[str, Position], None, None]:
             for _, position in well.positions():
                 yield position.zgroup.path, position
 
+    def rename_well(
+        self,
+        well,
+        old_well_path: str,
+        new_well_path: str,
+        modified={},
+        single_well=True,
+    ):
+        """Rename a well.
+
+        Parameters
+        ----------
+        old_well_path : str
+            Old name of well
+        new_well_path : str
+            New name of well
+        modified : dict, optional
+            Tracks modified wells
+        single well: bool, optional
+            True: renaming one well, False: renaming multiple wells
+        """
+        old_row, old_column = old_well_path.split("/")
+        new_row, new_column = new_well_path.split("/")
+
+        if well.path == old_well_path:
+            well.path = new_well_path  # update well metadata
+            zarr.storage.rename(
+                self.zgroup._store, old_well_path, new_well_path
+            )  # update well paths
+
+        for column in self.metadata.columns:
+            if column.name == old_column and column not in modified["columns"]:
+                column.name = new_column  # update column metadata
+                if not single_well:
+                    modified["columns"].append(column)
+
+        for row in self.metadata.rows:
+            if row.name == old_row and row not in modified["rows"]:
+                row.name = new_row  # update row metadata
+                if not single_well:
+                    modified["rows"].append(row)
+
+        self.dump_meta()
+
 
 def open_ome_zarr(
     store_path: StrOrBytesPath,

From d336cd85997be29043c3c2489104b8bc7fd1d247 Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Tue, 9 Jul 2024 11:43:18 -0700
Subject: [PATCH 02/26] CLI changes

---
 iohub/cli/cli.py | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index ed70585e..fef0b69b 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -91,23 +91,23 @@ def convert(input, output, grid_layout, chunks):
     converter()
 
 
-@click.command()
+@cli.command()
 @click.help_option("-h", "--help")
-@click.argument(
-    "csvfile",
-    type=click.File("r"),
+@click.option(
+    "-i",
+    "input.zarr",
+    type=click.Path(exists=True, file_okay=True, dir_okay=False),
+    required=True,
+    help="Path to the input Zarr file.",
 )
-@click.argument(
-    "zarrfile",
-    type=click.Path(
-        exists=True,
-        file_okay=True,
-        dir_okay=False,
-        resolve_path=True,
-        path_type=pathlib.Path,
-    ),
+@click.option(
+    "-c",
+    "names.csv",
+    type=click.File("r"),
+    required=True,
+    help="Path to the CSV file containing well names.",
 )
-def rename_wells_cli(csvfile, zarrfile):
+def rename_wells(csvfile, zarrfile):
     """Rename wells based on CSV file
 
     The CSV file should have two columns: old_well_path and new_well_path.
@@ -143,6 +143,6 @@ def rename_wells_cli(csvfile, zarrfile):
         for well in plate.metadata.wells:
             if well.path == old_well_path and well not in modified["wells"]:
                 plate.rename_well(
-                    plate, well, old_well_path, new_well_path, modified, False
+                    well, old_well_path, new_well_path, modified, False
                 )
                 modified["wells"].append(well)

From e3f70298cbbf4ac0ddd0164c3ce30f0cbd0e328e Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Tue, 9 Jul 2024 16:50:24 -0700
Subject: [PATCH 03/26] fix click options

---
 iohub/cli/cli.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index fef0b69b..260e2ad9 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -95,14 +95,14 @@ def convert(input, output, grid_layout, chunks):
 @click.help_option("-h", "--help")
 @click.option(
     "-i",
-    "input.zarr",
+    "--input",
     type=click.Path(exists=True, file_okay=True, dir_okay=False),
     required=True,
     help="Path to the input Zarr file.",
 )
 @click.option(
     "-c",
-    "names.csv",
+    "--csv",
     type=click.File("r"),
     required=True,
     help="Path to the CSV file containing well names.",

From 4fb8b03c9cd75f8c8b4114840e69c11175d8a181 Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Tue, 9 Jul 2024 16:55:39 -0700
Subject: [PATCH 04/26] basic test for help message

---
 tests/cli/test_cli.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index b8ddf9c7..c6e8ede0 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -104,3 +104,13 @@ def test_cli_convert_ome_tiff(grid_layout, tmpdir):
     result = runner.invoke(cli, cmd)
     assert result.exit_code == 0, result.output
     assert "Converting" in result.output
+
+
+def test_rename_wells_help():
+    runner = CliRunner()
+    cmd = ["rename-wells"]
+    for option in ("-h", "--help"):
+        cmd.append(option)
+        result = runner.invoke(cli, cmd)
+        assert result.exit_code == 0
+        assert "containing well names" in result.output

From 1f27a194d2f1bf6adb064c5c2d92a882b6acbb43 Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Thu, 11 Jul 2024 13:57:21 -0700
Subject: [PATCH 05/26] Updated decorator

---
 iohub/cli/cli.py |  9 +++++----
 iohub/ngff.py    | 38 ++++++++++++++++++++------------------
 2 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 260e2ad9..b01b0f67 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -108,6 +108,10 @@ def convert(input, output, grid_layout, chunks):
     help="Path to the CSV file containing well names.",
 )
 def rename_wells(csvfile, zarrfile):
+    rename_wells_cli(csvfile, zarrfile)
+
+
+def rename_wells_cli(csvfile, zarrfile):
     """Rename wells based on CSV file
 
     The CSV file should have two columns: old_well_path and new_well_path.
@@ -125,10 +129,7 @@ def rename_wells(csvfile, zarrfile):
 
     plate = open_ome_zarr(zarrfile, mode="a")
 
-    modified = {}
-    modified["wells"] = []
-    modified["rows"] = []
-    modified["columns"] = []
+    modified = []
 
     well_paths = [
         plate.metadata.wells[i].path for i in range(len(plate.metadata.wells))
diff --git a/iohub/ngff.py b/iohub/ngff.py
index 698215c5..460e00fb 100644
--- a/iohub/ngff.py
+++ b/iohub/ngff.py
@@ -1570,8 +1570,6 @@ def rename_well(
         well,
         old_well_path: str,
         new_well_path: str,
-        modified={},
-        single_well=True,
     ):
         """Rename a well.
 
@@ -1589,25 +1587,29 @@ def rename_well(
         old_row, old_column = old_well_path.split("/")
         new_row, new_column = new_well_path.split("/")
 
-        if well.path == old_well_path:
-            well.path = new_well_path  # update well metadata
-            zarr.storage.rename(
-                self.zgroup._store, old_well_path, new_well_path
-            )  # update well paths
+        well_paths = [well.path for well in self.metadata.wells]
 
-        for column in self.metadata.columns:
-            if column.name == old_column and column not in modified["columns"]:
-                column.name = new_column  # update column metadata
-                if not single_well:
-                    modified["columns"].append(column)
+        if old_well_path not in well_paths:
+            raise ValueError(f"Well '{old_well_path}' not found in plate.")
 
-        for row in self.metadata.rows:
-            if row.name == old_row and row not in modified["rows"]:
-                row.name = new_row  # update row metadata
-                if not single_well:
-                    modified["rows"].append(row)
+        else:
+            well = self[old_well_path]
 
-        self.dump_meta()
+            if well.path == old_well_path:
+                well.path = new_well_path  # update well metadata
+                zarr.storage.rename(
+                    self.zgroup._store, old_well_path, new_well_path
+                )  # update well paths
+
+            for column in self.metadata.columns:
+                if column.name == old_column:
+                    column.name = new_column  # update column metadata
+
+            for row in self.metadata.rows:
+                if row.name == old_row:
+                    row.name = new_row  # update row metadata
+
+            self.dump_meta()
 
 
 def open_ome_zarr(

From 66e5d12c41640b98bca206bfe04da3472aacfb6a Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@cpu-e-1.clusternet>
Date: Thu, 11 Jul 2024 16:06:48 -0700
Subject: [PATCH 06/26] Exception changes

---
 iohub/cli/cli.py | 22 ++++++++--------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index b01b0f67..52f5dca5 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -131,19 +131,13 @@ def rename_wells_cli(csvfile, zarrfile):
 
     modified = []
 
-    well_paths = [
-        plate.metadata.wells[i].path for i in range(len(plate.metadata.wells))
-    ]
-
     for old_well_path, new_well_path in names:
-        if old_well_path not in well_paths:
-            raise ValueError(
-                f"Old well path '{old_well_path}' not found "
-                f"in the plate metadata."
-            )
         for well in plate.metadata.wells:
-            if well.path == old_well_path and well not in modified["wells"]:
-                plate.rename_well(
-                    well, old_well_path, new_well_path, modified, False
-                )
-                modified["wells"].append(well)
+            if well.path == old_well_path and well not in modified:
+                try:
+                    plate.rename_well(
+                        well, old_well_path, new_well_path, modified, False
+                    )
+                    modified.append(well)
+                except ValueError as e:
+                    click.echo(f"Error: {e}", err=True)

From 75a9327043476d2e8673bc5188976d5d4c9da128 Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Fri, 12 Jul 2024 11:17:40 -0700
Subject: [PATCH 07/26] Updated rename wells and testing

---
 iohub/cli/cli.py      | 18 ++++++++++++------
 iohub/ngff.py         | 10 ++++------
 tests/cli/test_cli.py | 32 +++++++++++++++++++++++++++++---
 3 files changed, 45 insertions(+), 15 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 52f5dca5..993d3864 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -96,13 +96,15 @@ def convert(input, output, grid_layout, chunks):
 @click.option(
     "-i",
     "--input",
-    type=click.Path(exists=True, file_okay=True, dir_okay=False),
+    "zarrfile",
+    type=click.Path(exists=True, file_okay=True, dir_okay=True),
     required=True,
     help="Path to the input Zarr file.",
 )
 @click.option(
     "-c",
     "--csv",
+    "csvfile",
     type=click.File("r"),
     required=True,
     help="Path to the CSV file containing well names.",
@@ -116,6 +118,7 @@ def rename_wells_cli(csvfile, zarrfile):
 
     The CSV file should have two columns: old_well_path and new_well_path.
     """
+
     names = []
 
     csvreader = csv.reader(csvfile)
@@ -131,13 +134,16 @@ def rename_wells_cli(csvfile, zarrfile):
 
     modified = []
 
-    for old_well_path, new_well_path in names:
+    print(f"names: {names}")
+
+    for name in names:
+        old_well_path, new_well_path = name[0], name[1]
         for well in plate.metadata.wells:
-            if well.path == old_well_path and well not in modified:
+            if str(well.path) == str(old_well_path) and well not in modified:
+                print(f"Renaming {old_well_path} to {new_well_path}...")
                 try:
-                    plate.rename_well(
-                        well, old_well_path, new_well_path, modified, False
-                    )
+                    plate.rename_well(well, old_well_path, new_well_path)
                     modified.append(well)
+                    print(f"Well {old_well_path} renamed to {new_well_path}")
                 except ValueError as e:
                     click.echo(f"Error: {e}", err=True)
diff --git a/iohub/ngff.py b/iohub/ngff.py
index 460e00fb..23c143ee 100644
--- a/iohub/ngff.py
+++ b/iohub/ngff.py
@@ -1579,10 +1579,6 @@ def rename_well(
             Old name of well
         new_well_path : str
             New name of well
-        modified : dict, optional
-            Tracks modified wells
-        single well: bool, optional
-            True: renaming one well, False: renaming multiple wells
         """
         old_row, old_column = old_well_path.split("/")
         new_row, new_column = new_well_path.split("/")
@@ -1592,8 +1588,10 @@ def rename_well(
         if old_well_path not in well_paths:
             raise ValueError(f"Well '{old_well_path}' not found in plate.")
 
-        else:
-            well = self[old_well_path]
+        elif old_well_path in well_paths:
+            well = next(
+                w for w in self.metadata.wells if w.path == old_well_path
+            )
 
             if well.path == old_well_path:
                 well.path = new_well_path  # update well metadata
diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index c6e8ede0..19e980db 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -1,17 +1,17 @@
+import csv
 import re
 from unittest.mock import patch
 
-from click.testing import CliRunner
 import pytest
+from click.testing import CliRunner
 
 from iohub._version import __version__
 from iohub.cli.cli import cli
-
 from tests.conftest import (
+    hcs_ref,
     mm2gamma_ome_tiffs,
     ndtiff_v2_datasets,
     ndtiff_v3_labeled_positions,
-    hcs_ref,
 )
 
 
@@ -114,3 +114,29 @@ def test_rename_wells_help():
         result = runner.invoke(cli, cmd)
         assert result.exit_code == 0
         assert "containing well names" in result.output
+
+
+def test_rename_wells_basic():
+    runner = CliRunner()
+    test_zarr = "/hpc/mydata/joseph.schull/stitched_phase.zarr"
+    test_csv = "/hpc/mydata/joseph.schull/update_well_names.csv"
+    cmd = ["rename-wells", "-i", test_zarr, "-c", test_csv]
+    result = runner.invoke(cli, cmd)
+    print(result.output)
+    assert result.exit_code == 0
+
+
+def test_rename_wells_completion():
+    runner = CliRunner()
+    test_zarr = "/hpc/mydata/joseph.schull/stitched_phase.zarr"
+    test_csv = "/hpc/mydata/joseph.schull/update_well_names.csv"
+    cmd = ["rename-wells", "-i", test_zarr, "-c", test_csv]
+    result = runner.invoke(cli, cmd)
+    with open(test_csv, mode="r") as infile:
+        reader = csv.reader(infile)
+        names = list(reader)
+    for oldname, newname in names:
+        expected_message = f"Well {oldname} renamed to {newname}"
+        assert (
+            expected_message in result.output
+        ), f"Missing expected message: {expected_message}"

From f256cfe55ba3956d312f1896a962ec58263ea00c Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Fri, 12 Jul 2024 11:34:38 -0700
Subject: [PATCH 08/26] Updated test

---
 iohub/cli/cli.py      | 3 +--
 tests/cli/test_cli.py | 9 ---------
 2 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 993d3864..399c3e65 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -136,8 +136,7 @@ def rename_wells_cli(csvfile, zarrfile):
 
     print(f"names: {names}")
 
-    for name in names:
-        old_well_path, new_well_path = name[0], name[1]
+    for old_well_path, new_well_path in names:
         for well in plate.metadata.wells:
             if str(well.path) == str(old_well_path) and well not in modified:
                 print(f"Renaming {old_well_path} to {new_well_path}...")
diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index 19e980db..8af74943 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -122,16 +122,7 @@ def test_rename_wells_basic():
     test_csv = "/hpc/mydata/joseph.schull/update_well_names.csv"
     cmd = ["rename-wells", "-i", test_zarr, "-c", test_csv]
     result = runner.invoke(cli, cmd)
-    print(result.output)
     assert result.exit_code == 0
-
-
-def test_rename_wells_completion():
-    runner = CliRunner()
-    test_zarr = "/hpc/mydata/joseph.schull/stitched_phase.zarr"
-    test_csv = "/hpc/mydata/joseph.schull/update_well_names.csv"
-    cmd = ["rename-wells", "-i", test_zarr, "-c", test_csv]
-    result = runner.invoke(cli, cmd)
     with open(test_csv, mode="r") as infile:
         reader = csv.reader(infile)
         names = list(reader)

From 65a039498a3a5638384c70d74b0359db568137b9 Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Sun, 14 Jul 2024 17:00:00 -0700
Subject: [PATCH 09/26] Updated test

---
 iohub/cli/cli.py      | 11 +++++++--
 tests/cli/test_cli.py | 57 ++++++++++++++++++++++++++++++++++++++++---
 2 files changed, 62 insertions(+), 6 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 399c3e65..8d445caf 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -132,9 +132,11 @@ def rename_wells_cli(csvfile, zarrfile):
 
     plate = open_ome_zarr(zarrfile, mode="a")
 
-    modified = []
+    print(
+        f"Initial well paths: {[well.path for well in plate.metadata.wells]}"
+    )
 
-    print(f"names: {names}")
+    modified = []
 
     for old_well_path, new_well_path in names:
         for well in plate.metadata.wells:
@@ -146,3 +148,8 @@ def rename_wells_cli(csvfile, zarrfile):
                     print(f"Well {old_well_path} renamed to {new_well_path}")
                 except ValueError as e:
                     click.echo(f"Error: {e}", err=True)
+
+    print(
+        f"Process completed"
+        f"Final well paths: {[well.path for well in plate.metadata.wells]}"
+    )
diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index 8af74943..ae422054 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -116,11 +116,60 @@ def test_rename_wells_help():
         assert "containing well names" in result.output
 
 
-def test_rename_wells_basic():
+def test_rename_wells_basic(tmpdir):
     runner = CliRunner()
-    test_zarr = "/hpc/mydata/joseph.schull/stitched_phase.zarr"
-    test_csv = "/hpc/mydata/joseph.schull/update_well_names.csv"
-    cmd = ["rename-wells", "-i", test_zarr, "-c", test_csv]
+    test_csv = tmpdir / "well_names.csv"
+    csv_data = [
+        ["B/03", "B/03modified"],
+    ]
+    with open(test_csv, mode="w", newline="") as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerows(csv_data)
+
+    cmd = ["rename-wells", "-i", hcs_ref, "-c", str(test_csv)]
+    result = runner.invoke(cli, cmd)
+
+    print(result.output)
+    assert result.exit_code == 0
+
+    final_well_paths = None
+
+    for line in result.output.split("\n"):
+        if line.startswith("Process completed. Final well paths:"):
+            final_well_paths = eval(line.split(": ")[1])
+            break
+
+    assert (
+        final_well_paths is not None
+    ), "Final well paths not found in the output"
+
+    new_well_paths = [row[1] for row in csv_data]
+    old_well_paths = [row[0] for row in csv_data]
+
+    for new_path in new_well_paths:
+        assert (
+            new_path in final_well_paths
+        ), f"Expected {new_path} in final well paths"
+
+    for old_path in old_well_paths:
+        assert (
+            old_path not in final_well_paths
+        ), f"Did not expect {old_path} in final well paths"
+
+
+def test_rename_wells_renaming_message(tmpdir):
+    runner = CliRunner()
+    test_csv = tmpdir / "well_names.csv"
+
+    csv_data = [
+        ["B/03", "B/03"],
+    ]
+
+    with open(test_csv, mode="w", newline="") as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerows(csv_data)
+
+    cmd = ["rename-wells", "-i", hcs_ref, "-c", str(test_csv)]
     result = runner.invoke(cli, cmd)
     assert result.exit_code == 0
     with open(test_csv, mode="r") as infile:

From 01132dcb819f4d8b6ad77e178f330ef834cb84cd Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Sun, 14 Jul 2024 17:20:49 -0700
Subject: [PATCH 10/26] test_rename_wells_basic

---
 iohub/cli/cli.py      |  5 +----
 tests/cli/test_cli.py | 29 ++---------------------------
 2 files changed, 3 insertions(+), 31 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 8d445caf..00e87888 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -149,7 +149,4 @@ def rename_wells_cli(csvfile, zarrfile):
                 except ValueError as e:
                     click.echo(f"Error: {e}", err=True)
 
-    print(
-        f"Process completed"
-        f"Final well paths: {[well.path for well in plate.metadata.wells]}"
-    )
+    print(f"Final well paths: {[well.path for well in plate.metadata.wells]}")
diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index ae422054..349f20ae 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -120,7 +120,7 @@ def test_rename_wells_basic(tmpdir):
     runner = CliRunner()
     test_csv = tmpdir / "well_names.csv"
     csv_data = [
-        ["B/03", "B/03modified"],
+        ["B/03", "B/03test"],
     ]
     with open(test_csv, mode="w", newline="") as csvfile:
         writer = csv.writer(csvfile)
@@ -135,7 +135,7 @@ def test_rename_wells_basic(tmpdir):
     final_well_paths = None
 
     for line in result.output.split("\n"):
-        if line.startswith("Process completed. Final well paths:"):
+        if line.startswith("Final well paths:"):
             final_well_paths = eval(line.split(": ")[1])
             break
 
@@ -155,28 +155,3 @@ def test_rename_wells_basic(tmpdir):
         assert (
             old_path not in final_well_paths
         ), f"Did not expect {old_path} in final well paths"
-
-
-def test_rename_wells_renaming_message(tmpdir):
-    runner = CliRunner()
-    test_csv = tmpdir / "well_names.csv"
-
-    csv_data = [
-        ["B/03", "B/03"],
-    ]
-
-    with open(test_csv, mode="w", newline="") as csvfile:
-        writer = csv.writer(csvfile)
-        writer.writerows(csv_data)
-
-    cmd = ["rename-wells", "-i", hcs_ref, "-c", str(test_csv)]
-    result = runner.invoke(cli, cmd)
-    assert result.exit_code == 0
-    with open(test_csv, mode="r") as infile:
-        reader = csv.reader(infile)
-        names = list(reader)
-    for oldname, newname in names:
-        expected_message = f"Well {oldname} renamed to {newname}"
-        assert (
-            expected_message in result.output
-        ), f"Missing expected message: {expected_message}"

From c7c42edddc75abc35c4ff6c542a281e086496782 Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Sun, 14 Jul 2024 18:23:18 -0700
Subject: [PATCH 11/26] Updated tests, converting well names back to original

---
 tests/cli/test_cli.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index 349f20ae..f9720cf6 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -116,7 +116,7 @@ def test_rename_wells_help():
         assert "containing well names" in result.output
 
 
-def test_rename_wells_basic(tmpdir):
+def test_rename_wells(tmpdir):
     runner = CliRunner()
     test_csv = tmpdir / "well_names.csv"
     csv_data = [
@@ -155,3 +155,15 @@ def test_rename_wells_basic(tmpdir):
         assert (
             old_path not in final_well_paths
         ), f"Did not expect {old_path} in final well paths"
+    
+    test_csv_2 = tmpdir / "well_names_2.csv"
+    csv_data = [
+        ["B/03test", "B/03"],
+    ]
+    with open(test_csv_2, mode="w", newline="") as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerows(csv_data)
+
+    cmd = ["rename-wells", "-i", hcs_ref, "-c", str(test_csv_2)]
+    result = runner.invoke(cli, cmd)
+    print(result.output)

From 452f8ed010d8febf3dfc1a4afb436cf849e68afb Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Sun, 14 Jul 2024 19:58:06 -0700
Subject: [PATCH 12/26] Context manager update

---
 iohub/cli/cli.py | 45 +++++++++++++++++++++++++--------------------
 1 file changed, 25 insertions(+), 20 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 00e87888..723e368b 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -130,23 +130,28 @@ def rename_wells_cli(csvfile, zarrfile):
             )
         names.append([row[0], row[1]])
 
-    plate = open_ome_zarr(zarrfile, mode="a")
-
-    print(
-        f"Initial well paths: {[well.path for well in plate.metadata.wells]}"
-    )
-
-    modified = []
-
-    for old_well_path, new_well_path in names:
-        for well in plate.metadata.wells:
-            if str(well.path) == str(old_well_path) and well not in modified:
-                print(f"Renaming {old_well_path} to {new_well_path}...")
-                try:
-                    plate.rename_well(well, old_well_path, new_well_path)
-                    modified.append(well)
-                    print(f"Well {old_well_path} renamed to {new_well_path}")
-                except ValueError as e:
-                    click.echo(f"Error: {e}", err=True)
-
-    print(f"Final well paths: {[well.path for well in plate.metadata.wells]}")
+    with open_ome_zarr(zarrfile, mode="a") as plate:
+        well_paths = [well.path for well in plate.metadata.wells]
+        print(f"Initial well paths: {well_paths}")
+
+        modified = []
+
+        for old_well_path, new_well_path in names:
+            for well in plate.metadata.wells:
+                if (
+                    str(well.path) == str(old_well_path)
+                    and well not in modified
+                ):
+                    print(f"Renaming {old_well_path} to {new_well_path}...")
+                    try:
+                        plate.rename_well(well, old_well_path, new_well_path)
+                        modified.append(well)
+                        print(
+                            f"Well {old_well_path} renamed to {new_well_path}"
+                        )
+                    except ValueError as e:
+                        click.echo(f"Error: {e}", err=True)
+
+        print(
+            f"Final well paths: {[well.path for well in plate.metadata.wells]}"
+        )

From c753a87fbc1f29bc8c11f464376a4fa6bab97a77 Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Wed, 17 Jul 2024 16:39:36 -0700
Subject: [PATCH 13/26] well-mapping.csv

---
 docs/examples/well-mapping.csv | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 docs/examples/well-mapping.csv

diff --git a/docs/examples/well-mapping.csv b/docs/examples/well-mapping.csv
new file mode 100644
index 00000000..6ebe5570
--- /dev/null
+++ b/docs/examples/well-mapping.csv
@@ -0,0 +1,4 @@
+0/0,0/A
+0/1,0/B
+0/2,0/C
+0/3,0/D

From 6851360beb9e05ea76d278f2b1fc98cab81f0563 Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Sat, 20 Jul 2024 19:43:47 -0700
Subject: [PATCH 14/26] Updating row and column indices

---
 iohub/ngff.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/iohub/ngff.py b/iohub/ngff.py
index 23c143ee..8f4e5e5b 100644
--- a/iohub/ngff.py
+++ b/iohub/ngff.py
@@ -1,4 +1,4 @@
-# TODO: remove this in the future (PEP deferred for 3.11, now 3.12?)
+c# TODO: remove this in the future (PEP deferred for 3.11, now 3.12?)
 from __future__ import annotations
 
 import logging
@@ -1595,6 +1595,8 @@ def rename_well(
 
             if well.path == old_well_path:
                 well.path = new_well_path  # update well metadata
+                well.row_index = new_row  
+                well.column_index = new_column
                 zarr.storage.rename(
                     self.zgroup._store, old_well_path, new_well_path
                 )  # update well paths

From ce70316c2359dac6fd78de39c7a48a4276a3cf1e Mon Sep 17 00:00:00 2001
From: Joseph Schull <joseph.schull@login-01.clusternet>
Date: Sat, 20 Jul 2024 19:47:48 -0700
Subject: [PATCH 15/26] Style changes

---
 iohub/ngff.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/iohub/ngff.py b/iohub/ngff.py
index 8f4e5e5b..11113aa0 100644
--- a/iohub/ngff.py
+++ b/iohub/ngff.py
@@ -1,4 +1,4 @@
-c# TODO: remove this in the future (PEP deferred for 3.11, now 3.12?)
+# TODO: remove this in the future (PEP deferred for 3.11, now 3.12?)
 from __future__ import annotations
 
 import logging
@@ -1595,7 +1595,7 @@ def rename_well(
 
             if well.path == old_well_path:
                 well.path = new_well_path  # update well metadata
-                well.row_index = new_row  
+                well.row_index = new_row
                 well.column_index = new_column
                 zarr.storage.rename(
                     self.zgroup._store, old_well_path, new_well_path

From 31888c6d6761a6e7dad621d78eb8fddd087a3e46 Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Thu, 19 Sep 2024 10:13:47 -0700
Subject: [PATCH 16/26] rework API with `self.zgroup.move`

---
 iohub/ngff/nodes.py | 74 +++++++++++++++++++++++----------------------
 1 file changed, 38 insertions(+), 36 deletions(-)

diff --git a/iohub/ngff/nodes.py b/iohub/ngff/nodes.py
index ee9070fa..965df379 100644
--- a/iohub/ngff/nodes.py
+++ b/iohub/ngff/nodes.py
@@ -1575,49 +1575,51 @@ def positions(self) -> Generator[tuple[str, Position], None, None]:
 
     def rename_well(
         self,
-        well,
-        old_well_path: str,
-        new_well_path: str,
+        old: str,
+        new: str,
     ):
-        """Rename a well.
+        """Rename a well. 
 
         Parameters
         ----------
-        old_well_path : str
-            Old name of well
-        new_well_path : str
-            New name of well
+        old : str
+            Old name of well, e.g. "A/1"
+        new : str
+            New name of well, e.g. "B/2"
         """
-        old_row, old_column = old_well_path.split("/")
-        new_row, new_column = new_well_path.split("/")
-
-        well_paths = [well.path for well in self.metadata.wells]
-
-        if old_well_path not in well_paths:
-            raise ValueError(f"Well '{old_well_path}' not found in plate.")
-
-        elif old_well_path in well_paths:
-            well = next(
-                w for w in self.metadata.wells if w.path == old_well_path
-            )
-
-            if well.path == old_well_path:
-                well.path = new_well_path  # update well metadata
-                well.row_index = new_row
-                well.column_index = new_column
-                zarr.storage.rename(
-                    self.zgroup._store, old_well_path, new_well_path
-                )  # update well paths
-
-            for column in self.metadata.columns:
-                if column.name == old_column:
-                    column.name = new_column  # update column metadata
 
-            for row in self.metadata.rows:
-                if row.name == old_row:
-                    row.name = new_row  # update row metadata
+        old_row, old_column = old.split("/")
+        new_row, new_column = new.split("/")
+        
+        # raises ValueError if old well does not exist
+        # or if new well already exists
+        self.zgroup.move(old, new)
+
+        # update well metadata
+        old_well_index = [well_name.path for well_name in self.metadata.wells].index(old)
+        self.metadata.wells[old_well_index].path = new
+        new_well_names = [well.path for well in self.metadata.wells]
+
+        # update row/col metadata
+        # check for new row/col        
+        if new_row not in [row.name for row in self.metadata.rows]:
+            self.metadata.rows.append(PlateAxisMeta(name=new_row))
+        if new_column not in [col.name for col in self.metadata.columns]:
+            self.metadata.columns.append(PlateAxisMeta(name=new_column))
+
+        # check for empty row/col
+        if old_row not in [well.split("/")[0] for well in new_well_names]:
+            # delete empty row from zarr
+            del self.zgroup[old_row] 
+            self.metadata.rows = [
+                row for row in self.metadata.rows if row.name != old_row
+            ]
+        if old_column not in [well.split("/")[1] for well in new_well_names]:
+            self.metadata.columns = [
+                col for col in self.metadata.columns if col.name != old_column
+            ]
 
-            self.dump_meta()
+        self.dump_meta()
 
 
 def open_ome_zarr(

From 5b59dec0417482b66d59c7adcc1b397f9063534e Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Thu, 19 Sep 2024 10:14:11 -0700
Subject: [PATCH 17/26] test API

---
 tests/ngff/test_ngff.py | 77 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)

diff --git a/tests/ngff/test_ngff.py b/tests/ngff/test_ngff.py
index d1701529..1bc3436d 100644
--- a/tests/ngff/test_ngff.py
+++ b/tests/ngff/test_ngff.py
@@ -182,6 +182,39 @@ def _temp_ome_zarr(
         dataset.close()
         temp_dir.cleanup()
 
+@contextmanager
+def _temp_ome_zarr_plate(
+    image_5d: NDArray, channel_names: list[str], arr_name: str, position_list: list[tuple[str, str, str]], **kwargs   
+):
+    """Helper function to generate a temporary OME-Zarr store.
+
+    Parameters
+    ----------
+    image_5d : NDArray
+    channel_names : list[str]
+    arr_name : str
+    position_list : list[tuple[str, str, str]]
+
+    Yields
+    ------
+    Position
+    """
+    try:
+        temp_dir = TemporaryDirectory()
+        dataset = open_ome_zarr(
+            os.path.join(temp_dir.name, "ome.zarr"),
+            layout="hcs",
+            mode="a",
+            channel_names=channel_names,
+        )
+        for position in position_list:
+            pos = dataset.create_position(position[0], position[1], position[2])
+            pos.create_image(arr_name, image_5d, **kwargs)
+        yield dataset
+    finally:
+        dataset.close()
+        temp_dir.cleanup()
+
 
 @given(
     channels_and_random_5d=_channels_and_random_5d(),
@@ -290,6 +323,50 @@ def test_rename_channel(channels_and_random_5d, arr_name, new_channel):
         assert new_channel in dataset.channel_names
         assert dataset.metadata.omero.channels[0].label == new_channel
 
+@given(
+    channels_and_random_5d=_channels_and_random_5d(),
+    arr_name=short_alpha_numeric,
+)
+def test_rename_well(channels_and_random_5d, arr_name):
+    """Test `iohub.ngff.Position.rename_well()`"""
+    channel_names, random_5d = channels_and_random_5d
+
+    position_list = [["A", "1", "0"], ["C", "4", "0"]]
+    with _temp_ome_zarr_plate(random_5d, channel_names, arr_name, position_list) as dataset:
+        assert dataset.zgroup["A/1"]
+        with pytest.raises(KeyError):
+            dataset.zgroup["B/2"]
+        assert "A" in [r[0] for r in dataset.rows()]
+        assert "B" not in [r[0] for r in dataset.rows()]
+        assert "A" in [row.name for row in dataset.metadata.rows]
+        assert "B" not in [row.name for row in dataset.metadata.rows]
+        assert "1" in [col.name for col in dataset.metadata.columns]
+        assert "2" not in [col.name for col in dataset.metadata.columns]
+        assert "C" in [row.name for row in dataset.metadata.rows]
+        assert "4" in [col.name for col in dataset.metadata.columns]
+
+        dataset.rename_well("A/1", "B/2")
+
+        assert dataset.zgroup["B/2"]
+        with pytest.raises(KeyError):
+            dataset.zgroup["A/1"]
+        assert "A" not in [r[0] for r in dataset.rows()]
+        assert "B" in [r[0] for r in dataset.rows()]
+        assert "A" not in [row.name for row in dataset.metadata.rows]
+        assert "B" in [row.name for row in dataset.metadata.rows]
+        assert "1" not in [col.name for col in dataset.metadata.columns]
+        assert "2" in [col.name for col in dataset.metadata.columns]
+        assert "C" in [row.name for row in dataset.metadata.rows]
+        assert "4" in [col.name for col in dataset.metadata.columns]
+
+        # destination exists
+        with pytest.raises(ValueError):
+            dataset.rename_well("B/2", "C/4")
+
+        # source doesn't exist
+        with pytest.raises(ValueError):
+            dataset.rename_well("Q/1", "Q/2")
+
 
 @given(
     channels_and_random_5d=_channels_and_random_5d(),

From fb0685a4936a032de710923079c32e28fbdd84da Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Thu, 19 Sep 2024 10:14:33 -0700
Subject: [PATCH 18/26] simplify and document CLI

---
 iohub/cli/cli.py | 53 +++++++++++++++++-------------------------------
 1 file changed, 19 insertions(+), 34 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 723e368b..2a851b2d 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -107,20 +107,22 @@ def convert(input, output, grid_layout, chunks):
     "csvfile",
     type=click.File("r"),
     required=True,
-    help="Path to the CSV file containing well names.",
+    help="Path to the CSV file containing old and new well names.",
 )
-def rename_wells(csvfile, zarrfile):
-    rename_wells_cli(csvfile, zarrfile)
+def rename_wells(zarrfile, csvfile):
+    """Rename wells in an plate.
 
+    >> iohub rename-wells -i plate.zarr -c names.csv
 
-def rename_wells_cli(csvfile, zarrfile):
-    """Rename wells based on CSV file
-
-    The CSV file should have two columns: old_well_path and new_well_path.
+    The CSV file must have two columns with old and new names in the form:
+    ```
+    A/1,B/2
+    A/2,B/2
+    ```
     """
 
-    names = []
-
+    # read and check csv
+    name_pair_list = []
     csvreader = csv.reader(csvfile)
     for row in csvreader:
         if len(row) != 2:
@@ -128,30 +130,13 @@ def rename_wells_cli(csvfile, zarrfile):
                 f"Invalid row format: {row}."
                 f"Each row must have two columns."
             )
-        names.append([row[0], row[1]])
+        name_pair_list.append([row[0], row[1]])
 
+    # rename each well while catching errors
     with open_ome_zarr(zarrfile, mode="a") as plate:
-        well_paths = [well.path for well in plate.metadata.wells]
-        print(f"Initial well paths: {well_paths}")
-
-        modified = []
-
-        for old_well_path, new_well_path in names:
-            for well in plate.metadata.wells:
-                if (
-                    str(well.path) == str(old_well_path)
-                    and well not in modified
-                ):
-                    print(f"Renaming {old_well_path} to {new_well_path}...")
-                    try:
-                        plate.rename_well(well, old_well_path, new_well_path)
-                        modified.append(well)
-                        print(
-                            f"Well {old_well_path} renamed to {new_well_path}"
-                        )
-                    except ValueError as e:
-                        click.echo(f"Error: {e}", err=True)
-
-        print(
-            f"Final well paths: {[well.path for well in plate.metadata.wells]}"
-        )
+        for old, new in name_pair_list:
+            print(f"Renaming {old} to {new}")
+            try:
+                plate.rename_well(old, new)
+            except ValueError as e:
+                print(f"Error renaming {old} to {new}: {e}")
\ No newline at end of file

From 410f482dff9224b2af8eb6ac2a020c15cb9867db Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Thu, 19 Sep 2024 10:14:55 -0700
Subject: [PATCH 19/26] test CLI w/ round trip

---
 tests/cli/test_cli.py | 107 ++++++++++++++++++++++--------------------
 1 file changed, 56 insertions(+), 51 deletions(-)

diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index f9720cf6..ef8c94dc 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -5,6 +5,7 @@
 import pytest
 from click.testing import CliRunner
 
+from iohub import open_ome_zarr
 from iohub._version import __version__
 from iohub.cli.cli import cli
 from tests.conftest import (
@@ -14,6 +15,8 @@
     ndtiff_v3_labeled_positions,
 )
 
+from ..ngff.test_ngff import _temp_copy
+
 
 def pytest_generate_tests(metafunc):
     if "mm2gamma_ome_tiff" in metafunc.fixturenames:
@@ -106,64 +109,66 @@ def test_cli_convert_ome_tiff(grid_layout, tmpdir):
     assert "Converting" in result.output
 
 
-def test_rename_wells_help():
+def test_cli_rename_wells_help():
     runner = CliRunner()
     cmd = ["rename-wells"]
     for option in ("-h", "--help"):
         cmd.append(option)
         result = runner.invoke(cli, cmd)
         assert result.exit_code == 0
-        assert "containing well names" in result.output
+        assert ">> iohub rename-wells" in result.output
 
 
-def test_rename_wells(tmpdir):
-    runner = CliRunner()
-    test_csv = tmpdir / "well_names.csv"
-    csv_data = [
-        ["B/03", "B/03test"],
-    ]
-    with open(test_csv, mode="w", newline="") as csvfile:
-        writer = csv.writer(csvfile)
-        writer.writerows(csv_data)
-
-    cmd = ["rename-wells", "-i", hcs_ref, "-c", str(test_csv)]
-    result = runner.invoke(cli, cmd)
+def test_cli_rename_wells(tmpdir):
+    with _temp_copy(hcs_ref) as store_path:
+        runner = CliRunner()
+        test_csv = tmpdir / "well_names.csv"
+        csv_data = [
+            ["B/03", "D/4"],
+        ]
+        with open(test_csv, mode="w", newline="") as csvfile:
+            writer = csv.writer(csvfile)
+            writer.writerows(csv_data)
+
+        cmd = ["rename-wells", "-i", str(store_path), "-c", str(test_csv)]
+        result = runner.invoke(cli, cmd)
+
+        assert result.exit_code == 0
+        assert "Renaming" in result.output
+
+        with open_ome_zarr(store_path, mode="r") as plate:
+            well_names = [well[0] for well in plate.wells()]
+            assert "D/4" in well_names
+            assert "B/03" not in well_names
+            assert len(plate.metadata.wells) == 1
+            assert len(plate.metadata.rows) == 1
+            assert len(plate.metadata.columns) == 1
+            assert plate.metadata.wells[0].path == "D/4"
+            assert plate.metadata.rows[0].name == "D"
+            assert plate.metadata.columns[0].name == "4"
+
+        # Test round trip
+        test_csv_2 = tmpdir / "well_names_2.csv"
+        csv_data = [
+            ["D/4", "B/03"],
+        ]
+        with open(test_csv_2, mode="w", newline="") as csvfile:
+            writer = csv.writer(csvfile)
+            writer.writerows(csv_data)
+
+        cmd = ["rename-wells", "-i", store_path, "-c", str(test_csv_2)]
+        result = runner.invoke(cli, cmd)
+
+        with open_ome_zarr(store_path, mode="r") as plate:
+            well_names = [well[0] for well in plate.wells()]
+            assert "D/4" not in well_names
+            assert "B/03" in well_names
+            assert len(plate.metadata.wells) == 1
+            assert len(plate.metadata.rows) == 1
+            assert len(plate.metadata.columns) == 1
+            assert plate.metadata.wells[0].path == "B/03"
+            assert plate.metadata.rows[0].name == "B"
+            assert plate.metadata.columns[0].name == "03"
+        
 
-    print(result.output)
-    assert result.exit_code == 0
 
-    final_well_paths = None
-
-    for line in result.output.split("\n"):
-        if line.startswith("Final well paths:"):
-            final_well_paths = eval(line.split(": ")[1])
-            break
-
-    assert (
-        final_well_paths is not None
-    ), "Final well paths not found in the output"
-
-    new_well_paths = [row[1] for row in csv_data]
-    old_well_paths = [row[0] for row in csv_data]
-
-    for new_path in new_well_paths:
-        assert (
-            new_path in final_well_paths
-        ), f"Expected {new_path} in final well paths"
-
-    for old_path in old_well_paths:
-        assert (
-            old_path not in final_well_paths
-        ), f"Did not expect {old_path} in final well paths"
-    
-    test_csv_2 = tmpdir / "well_names_2.csv"
-    csv_data = [
-        ["B/03test", "B/03"],
-    ]
-    with open(test_csv_2, mode="w", newline="") as csvfile:
-        writer = csv.writer(csvfile)
-        writer.writerows(csv_data)
-
-    cmd = ["rename-wells", "-i", hcs_ref, "-c", str(test_csv_2)]
-    result = runner.invoke(cli, cmd)
-    print(result.output)

From 5caa25751a545db6f62eab3fc22159284b0a7fd0 Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Thu, 19 Sep 2024 10:29:50 -0700
Subject: [PATCH 20/26] style

---
 iohub/cli/cli.py        |  2 +-
 iohub/ngff/nodes.py     | 12 +++++++-----
 tests/cli/test_cli.py   |  3 ---
 tests/ngff/test_ngff.py | 16 +++++++++++++---
 4 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 2a851b2d..7243f67b 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -139,4 +139,4 @@ def rename_wells(zarrfile, csvfile):
             try:
                 plate.rename_well(old, new)
             except ValueError as e:
-                print(f"Error renaming {old} to {new}: {e}")
\ No newline at end of file
+                print(f"Error renaming {old} to {new}: {e}")
diff --git a/iohub/ngff/nodes.py b/iohub/ngff/nodes.py
index 965df379..dba6edaf 100644
--- a/iohub/ngff/nodes.py
+++ b/iohub/ngff/nodes.py
@@ -1578,7 +1578,7 @@ def rename_well(
         old: str,
         new: str,
     ):
-        """Rename a well. 
+        """Rename a well.
 
         Parameters
         ----------
@@ -1590,18 +1590,20 @@ def rename_well(
 
         old_row, old_column = old.split("/")
         new_row, new_column = new.split("/")
-        
+
         # raises ValueError if old well does not exist
         # or if new well already exists
         self.zgroup.move(old, new)
 
         # update well metadata
-        old_well_index = [well_name.path for well_name in self.metadata.wells].index(old)
+        old_well_index = [
+            well_name.path for well_name in self.metadata.wells
+        ].index(old)
         self.metadata.wells[old_well_index].path = new
         new_well_names = [well.path for well in self.metadata.wells]
 
         # update row/col metadata
-        # check for new row/col        
+        # check for new row/col
         if new_row not in [row.name for row in self.metadata.rows]:
             self.metadata.rows.append(PlateAxisMeta(name=new_row))
         if new_column not in [col.name for col in self.metadata.columns]:
@@ -1610,7 +1612,7 @@ def rename_well(
         # check for empty row/col
         if old_row not in [well.split("/")[0] for well in new_well_names]:
             # delete empty row from zarr
-            del self.zgroup[old_row] 
+            del self.zgroup[old_row]
             self.metadata.rows = [
                 row for row in self.metadata.rows if row.name != old_row
             ]
diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index ef8c94dc..32ffd6fc 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -169,6 +169,3 @@ def test_cli_rename_wells(tmpdir):
             assert plate.metadata.wells[0].path == "B/03"
             assert plate.metadata.rows[0].name == "B"
             assert plate.metadata.columns[0].name == "03"
-        
-
-
diff --git a/tests/ngff/test_ngff.py b/tests/ngff/test_ngff.py
index 1bc3436d..8ea8786c 100644
--- a/tests/ngff/test_ngff.py
+++ b/tests/ngff/test_ngff.py
@@ -182,9 +182,14 @@ def _temp_ome_zarr(
         dataset.close()
         temp_dir.cleanup()
 
+
 @contextmanager
 def _temp_ome_zarr_plate(
-    image_5d: NDArray, channel_names: list[str], arr_name: str, position_list: list[tuple[str, str, str]], **kwargs   
+    image_5d: NDArray,
+    channel_names: list[str],
+    arr_name: str,
+    position_list: list[tuple[str, str, str]],
+    **kwargs,
 ):
     """Helper function to generate a temporary OME-Zarr store.
 
@@ -208,7 +213,9 @@ def _temp_ome_zarr_plate(
             channel_names=channel_names,
         )
         for position in position_list:
-            pos = dataset.create_position(position[0], position[1], position[2])
+            pos = dataset.create_position(
+                position[0], position[1], position[2]
+            )
             pos.create_image(arr_name, image_5d, **kwargs)
         yield dataset
     finally:
@@ -323,6 +330,7 @@ def test_rename_channel(channels_and_random_5d, arr_name, new_channel):
         assert new_channel in dataset.channel_names
         assert dataset.metadata.omero.channels[0].label == new_channel
 
+
 @given(
     channels_and_random_5d=_channels_and_random_5d(),
     arr_name=short_alpha_numeric,
@@ -332,7 +340,9 @@ def test_rename_well(channels_and_random_5d, arr_name):
     channel_names, random_5d = channels_and_random_5d
 
     position_list = [["A", "1", "0"], ["C", "4", "0"]]
-    with _temp_ome_zarr_plate(random_5d, channel_names, arr_name, position_list) as dataset:
+    with _temp_ome_zarr_plate(
+        random_5d, channel_names, arr_name, position_list
+    ) as dataset:
         assert dataset.zgroup["A/1"]
         with pytest.raises(KeyError):
             dataset.zgroup["B/2"]

From d1f763919259e1b589e08f6b729eef64c054069c Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Thu, 19 Sep 2024 11:17:21 -0700
Subject: [PATCH 21/26] make example typical

---
 docs/examples/well-mapping.csv | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/examples/well-mapping.csv b/docs/examples/well-mapping.csv
index 6ebe5570..da66e067 100644
--- a/docs/examples/well-mapping.csv
+++ b/docs/examples/well-mapping.csv
@@ -1,4 +1,4 @@
-0/0,0/A
-0/1,0/B
-0/2,0/C
-0/3,0/D
+0/0,A/1
+0/1,A/2
+0/2,B/1
+0/3,B/2

From 2c0c083e99db6bd87fa70c62005a8ca66d92d157 Mon Sep 17 00:00:00 2001
From: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Date: Mon, 30 Sep 2024 19:02:59 -0700
Subject: [PATCH 22/26] move rename_wells to its own file

---
 iohub/cli/cli.py           | 30 ++++----------------
 iohub/rename_wells.py      | 57 ++++++++++++++++++++++++++++++++++++++
 tests/cli/test_cli.py      | 52 +++++-----------------------------
 tests/conftest.py          | 26 +++++++++++++++++
 tests/test_rename_wells.py | 32 +++++++++++++++++++++
 5 files changed, 127 insertions(+), 70 deletions(-)
 create mode 100644 iohub/rename_wells.py
 create mode 100644 tests/test_rename_wells.py

diff --git a/iohub/cli/cli.py b/iohub/cli/cli.py
index 7243f67b..0c409a98 100644
--- a/iohub/cli/cli.py
+++ b/iohub/cli/cli.py
@@ -1,12 +1,11 @@
-import csv
 import pathlib
 
 import click
 
 from iohub._version import __version__
 from iohub.convert import TIFFConverter
-from iohub.ngff import open_ome_zarr
 from iohub.reader import print_info
+from iohub.rename_wells import rename_wells
 
 VERSION = __version__
 
@@ -91,7 +90,7 @@ def convert(input, output, grid_layout, chunks):
     converter()
 
 
-@cli.command()
+@cli.command(name="rename-wells")
 @click.help_option("-h", "--help")
 @click.option(
     "-i",
@@ -105,11 +104,11 @@ def convert(input, output, grid_layout, chunks):
     "-c",
     "--csv",
     "csvfile",
-    type=click.File("r"),
+    type=click.Path(exists=True, file_okay=True, dir_okay=False),
     required=True,
     help="Path to the CSV file containing old and new well names.",
 )
-def rename_wells(zarrfile, csvfile):
+def rename_wells_command(zarrfile, csvfile):
     """Rename wells in an plate.
 
     >> iohub rename-wells -i plate.zarr -c names.csv
@@ -120,23 +119,4 @@ def rename_wells(zarrfile, csvfile):
     A/2,B/2
     ```
     """
-
-    # read and check csv
-    name_pair_list = []
-    csvreader = csv.reader(csvfile)
-    for row in csvreader:
-        if len(row) != 2:
-            raise ValueError(
-                f"Invalid row format: {row}."
-                f"Each row must have two columns."
-            )
-        name_pair_list.append([row[0], row[1]])
-
-    # rename each well while catching errors
-    with open_ome_zarr(zarrfile, mode="a") as plate:
-        for old, new in name_pair_list:
-            print(f"Renaming {old} to {new}")
-            try:
-                plate.rename_well(old, new)
-            except ValueError as e:
-                print(f"Error renaming {old} to {new}: {e}")
+    rename_wells(zarrfile, csvfile)
diff --git a/iohub/rename_wells.py b/iohub/rename_wells.py
new file mode 100644
index 00000000..887f78b7
--- /dev/null
+++ b/iohub/rename_wells.py
@@ -0,0 +1,57 @@
+import csv
+from pathlib import Path
+
+from iohub.ngff import open_ome_zarr
+
+
+def rename_wells(zarr_store_path: str | Path, csv_file_path: str | Path):
+    """
+    Rename wells in a Zarr store based on a CSV file containing old and new
+    well names.
+
+    Parameters
+    ----------
+    zarr_store_path : str or Path
+        Path to the Zarr store.
+    csv_file_path : str or Path
+        Path to the CSV file containing the old and new well names.
+
+    Raises
+    ------
+    ValueError
+        If a row in the CSV file does not have exactly two columns.
+        If there is an error renaming a well in the Zarr store.
+
+    Notes
+    -----
+    The CSV file should have two columns:
+        - The first column contains the old well names.
+        - The second column contains the new well names.
+
+    Examples
+    --------
+    CSV file content:
+    A/1,B/2
+    A/2,B/2
+
+    """
+
+    # read and check csv
+    name_pair_list = []
+    with open(csv_file_path, "r") as csv_file:
+        for row in csv.reader(csv_file):
+            if len(row) != 2:
+                raise ValueError(
+                    f"Invalid row format: {row}."
+                    f"Each row must have two columns."
+                )
+            name_pair_list.append([row[0], row[1]])
+
+    # rename each well while catching errors
+    with open_ome_zarr(zarr_store_path, mode="a") as plate:
+        for old, new in name_pair_list:
+            print(f"Renaming {old} to {new}")
+            try:
+                plate.rename_well(old, new)
+            except ValueError as e:
+                print(f"Error renaming {old} to {new}: {e}")
diff --git a/tests/cli/test_cli.py b/tests/cli/test_cli.py
index 32ffd6fc..c464795b 100644
--- a/tests/cli/test_cli.py
+++ b/tests/cli/test_cli.py
@@ -1,11 +1,9 @@
-import csv
 import re
 from unittest.mock import patch
 
 import pytest
 from click.testing import CliRunner
 
-from iohub import open_ome_zarr
 from iohub._version import __version__
 from iohub.cli.cli import cli
 from tests.conftest import (
@@ -119,53 +117,17 @@ def test_cli_rename_wells_help():
         assert ">> iohub rename-wells" in result.output
 
 
-def test_cli_rename_wells(tmpdir):
+def test_cli_rename_wells(csv_data_file_1):
     with _temp_copy(hcs_ref) as store_path:
         runner = CliRunner()
-        test_csv = tmpdir / "well_names.csv"
-        csv_data = [
-            ["B/03", "D/4"],
+        cmd = [
+            "rename-wells",
+            "-i",
+            str(store_path),
+            "-c",
+            str(csv_data_file_1),
         ]
-        with open(test_csv, mode="w", newline="") as csvfile:
-            writer = csv.writer(csvfile)
-            writer.writerows(csv_data)
-
-        cmd = ["rename-wells", "-i", str(store_path), "-c", str(test_csv)]
         result = runner.invoke(cli, cmd)
 
         assert result.exit_code == 0
         assert "Renaming" in result.output
-
-        with open_ome_zarr(store_path, mode="r") as plate:
-            well_names = [well[0] for well in plate.wells()]
-            assert "D/4" in well_names
-            assert "B/03" not in well_names
-            assert len(plate.metadata.wells) == 1
-            assert len(plate.metadata.rows) == 1
-            assert len(plate.metadata.columns) == 1
-            assert plate.metadata.wells[0].path == "D/4"
-            assert plate.metadata.rows[0].name == "D"
-            assert plate.metadata.columns[0].name == "4"
-
-        # Test round trip
-        test_csv_2 = tmpdir / "well_names_2.csv"
-        csv_data = [
-            ["D/4", "B/03"],
-        ]
-        with open(test_csv_2, mode="w", newline="") as csvfile:
-            writer = csv.writer(csvfile)
-            writer.writerows(csv_data)
-
-        cmd = ["rename-wells", "-i", store_path, "-c", str(test_csv_2)]
-        result = runner.invoke(cli, cmd)
-
-        with open_ome_zarr(store_path, mode="r") as plate:
-            well_names = [well[0] for well in plate.wells()]
-            assert "D/4" not in well_names
-            assert "B/03" in well_names
-            assert len(plate.metadata.wells) == 1
-            assert len(plate.metadata.rows) == 1
-            assert len(plate.metadata.columns) == 1
-            assert plate.metadata.wells[0].path == "B/03"
-            assert plate.metadata.rows[0].name == "B"
-            assert plate.metadata.columns[0].name == "03"
diff --git a/tests/conftest.py b/tests/conftest.py
index 8d49c563..015a4951 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,9 @@
+import csv
 import shutil
 from pathlib import Path
 
 import fsspec
+import pytest
 from wget import download
 
 
@@ -100,3 +102,27 @@ def subdirs(parent: Path, name: str) -> list[Path]:
 
 
 ndtiff_v3_labeled_positions = test_datasets / "ndtiff_v3_labeled_positions"
+
+
+@pytest.fixture
+def csv_data_file_1(tmpdir):
+    test_csv_1 = tmpdir / "well_names_1.csv"
+    csv_data_1 = [
+        ["B/03", "D/4"],
+    ]
+    with open(test_csv_1, mode="w", newline="") as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerows(csv_data_1)
+    return test_csv_1
+
+
+@pytest.fixture
+def csv_data_file_2(tmpdir):
+    test_csv_2 = tmpdir / "well_names_2.csv"
+    csv_data_2 = [
+        ["D/4", "B/03"],
+    ]
+    with open(test_csv_2, mode="w", newline="") as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerows(csv_data_2)
+    return test_csv_2
diff --git a/tests/test_rename_wells.py b/tests/test_rename_wells.py
new file mode 100644
index 00000000..1df94f21
--- /dev/null
+++ b/tests/test_rename_wells.py
@@ -0,0 +1,32 @@
+from iohub import open_ome_zarr
+from iohub.rename_wells import rename_wells
+from tests.conftest import hcs_ref
+from tests.ngff.test_ngff import _temp_copy
+
+
+def test_cli_rename_wells(csv_data_file_1, csv_data_file_2):
+    with _temp_copy(hcs_ref) as store_path:
+        rename_wells(store_path, csv_data_file_1)
+        with open_ome_zarr(store_path, mode="r") as plate:
+            well_names = [well[0] for well in plate.wells()]
+            assert "D/4" in well_names
+            assert "B/03" not in well_names
+            assert len(plate.metadata.wells) == 1
+            assert len(plate.metadata.rows) == 1
+            assert len(plate.metadata.columns) == 1
+            assert plate.metadata.wells[0].path == "D/4"
+            assert plate.metadata.rows[0].name == "D"
+            assert plate.metadata.columns[0].name == "4"
+
+        # Test round trip
+        rename_wells(store_path, csv_data_file_2)
+        with open_ome_zarr(store_path, mode="r") as plate:
+            well_names = [well[0] for well in plate.wells()]
+            assert "D/4" not in well_names
+            assert "B/03" in well_names
+            assert len(plate.metadata.wells) == 1
+            assert len(plate.metadata.rows) == 1
+            assert len(plate.metadata.columns) == 1
+            assert plate.metadata.wells[0].path == "B/03"
+            assert plate.metadata.rows[0].name == "B"
+            assert plate.metadata.columns[0].name == "03"

From eb40820a72490aaa67bb393cdc345329164022a1 Mon Sep 17 00:00:00 2001
From: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Date: Mon, 30 Sep 2024 19:22:09 -0700
Subject: [PATCH 23/26] add checks for correct well names

---
 iohub/ngff/nodes.py   | 9 +++++++--
 iohub/rename_wells.py | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/iohub/ngff/nodes.py b/iohub/ngff/nodes.py
index dba6edaf..acfaac16 100644
--- a/iohub/ngff/nodes.py
+++ b/iohub/ngff/nodes.py
@@ -1588,8 +1588,13 @@ def rename_well(
             New name of well, e.g. "B/2"
         """
 
+        # normalize inputs
+        old = normalize_storage_path(old)
+        new = normalize_storage_path(new)
         old_row, old_column = old.split("/")
         new_row, new_column = new.split("/")
+        new_row_meta = PlateAxisMeta(name=new_row)
+        new_col_meta = PlateAxisMeta(name=new_column)
 
         # raises ValueError if old well does not exist
         # or if new well already exists
@@ -1605,9 +1610,9 @@ def rename_well(
         # update row/col metadata
         # check for new row/col
         if new_row not in [row.name for row in self.metadata.rows]:
-            self.metadata.rows.append(PlateAxisMeta(name=new_row))
+            self.metadata.rows.append(new_row_meta)
         if new_column not in [col.name for col in self.metadata.columns]:
-            self.metadata.columns.append(PlateAxisMeta(name=new_column))
+            self.metadata.columns.append(new_col_meta)
 
         # check for empty row/col
         if old_row not in [well.split("/")[0] for well in new_well_names]:
diff --git a/iohub/rename_wells.py b/iohub/rename_wells.py
index 887f78b7..a6ff018e 100644
--- a/iohub/rename_wells.py
+++ b/iohub/rename_wells.py
@@ -45,7 +45,7 @@ def rename_wells(zarr_store_path: str | Path, csv_file_path: str | Path):
                     f"Invalid row format: {row}."
                     f"Each row must have two columns."
                 )
-            name_pair_list.append([row[0], row[1]])
+            name_pair_list.append([row[0].strip(), row[1].strip()])
 
     # rename each well while catching errors
     with open_ome_zarr(zarr_store_path, mode="a") as plate:

From f9b6847e174d1d4e231444eabe4c4036e156c6e9 Mon Sep 17 00:00:00 2001
From: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Date: Mon, 30 Sep 2024 19:37:41 -0700
Subject: [PATCH 24/26] add tests for invalid well names

---
 tests/ngff/test_ngff.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/ngff/test_ngff.py b/tests/ngff/test_ngff.py
index 8b546976..39c42f07 100644
--- a/tests/ngff/test_ngff.py
+++ b/tests/ngff/test_ngff.py
@@ -377,6 +377,12 @@ def test_rename_well(channels_and_random_5d, arr_name):
         with pytest.raises(ValueError):
             dataset.rename_well("Q/1", "Q/2")
 
+        # invalid well names
+        with pytest.raises(ValueError):
+            dataset.rename_well("B/2", " A/1")
+        with pytest.raises(ValueError):
+            dataset.rename_well("B/2", "A/?")
+
 
 @given(
     channels_and_random_5d=_channels_and_random_5d(),

From 27cda8d9a1cccd995c27b1f0597f9acba32bf6c1 Mon Sep 17 00:00:00 2001
From: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Date: Thu, 3 Oct 2024 09:27:57 -0700
Subject: [PATCH 25/26] remove test_rename_wells deadline

---
 tests/ngff/test_ngff.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/ngff/test_ngff.py b/tests/ngff/test_ngff.py
index 35fae3ab..aff06a7d 100644
--- a/tests/ngff/test_ngff.py
+++ b/tests/ngff/test_ngff.py
@@ -335,6 +335,7 @@ def test_rename_channel(channels_and_random_5d, arr_name, new_channel):
     channels_and_random_5d=_channels_and_random_5d(),
     arr_name=short_alpha_numeric,
 )
+@settings(deadline=None)
 def test_rename_well(channels_and_random_5d, arr_name):
     """Test `iohub.ngff.Position.rename_well()`"""
     channel_names, random_5d = channels_and_random_5d

From 33a61a414dcb7822f3c583ab59d2e2fb12587554 Mon Sep 17 00:00:00 2001
From: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Date: Thu, 3 Oct 2024 15:16:17 -0700
Subject: [PATCH 26/26] remove test_set_scale deadline

---
 tests/ngff/test_ngff.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/ngff/test_ngff.py b/tests/ngff/test_ngff.py
index aff06a7d..4ec371a4 100644
--- a/tests/ngff/test_ngff.py
+++ b/tests/ngff/test_ngff.py
@@ -500,6 +500,7 @@ def test_set_transform_fov(ch_shape_dtype, arr_name):
 @given(
     ch_shape_dtype=_channels_and_random_5d_shape_and_dtype(),
 )
+@settings(deadline=None)
 def test_set_scale(ch_shape_dtype):
     channel_names, shape, dtype = ch_shape_dtype
     transform = [