From c30ed9fcaa43b9a691b39d7d0d4107f2a5d47e26 Mon Sep 17 00:00:00 2001
From: Neil Shephard <n.shephard@sheffield.ac.uk>
Date: Tue, 7 May 2024 11:09:06 +0100
Subject: [PATCH] chore: topofileformats > AFMReader for module and update
 imports

+ Forgot the `topofileformats` directory that holds package needs renaming to `AFMReader`.
+ Updates all imports to work with new package name.
---
 {topofileformats => AFMReader}/__init__.py | 0
 {topofileformats => AFMReader}/asd.py      | 4 ++--
 {topofileformats => AFMReader}/ibw.py      | 4 ++--
 {topofileformats => AFMReader}/io.py       | 0
 {topofileformats => AFMReader}/jpk.py      | 4 ++--
 {topofileformats => AFMReader}/logging.py  | 0
 {topofileformats => AFMReader}/spm.py      | 4 ++--
 pyproject.toml                             | 3 ++-
 8 files changed, 10 insertions(+), 9 deletions(-)
 rename {topofileformats => AFMReader}/__init__.py (100%)
 rename {topofileformats => AFMReader}/asd.py (99%)
 rename {topofileformats => AFMReader}/ibw.py (96%)
 rename {topofileformats => AFMReader}/io.py (100%)
 rename {topofileformats => AFMReader}/jpk.py (97%)
 rename {topofileformats => AFMReader}/logging.py (100%)
 rename {topofileformats => AFMReader}/spm.py (97%)

diff --git a/topofileformats/__init__.py b/AFMReader/__init__.py
similarity index 100%
rename from topofileformats/__init__.py
rename to AFMReader/__init__.py
diff --git a/topofileformats/asd.py b/AFMReader/asd.py
similarity index 99%
rename from topofileformats/asd.py
rename to AFMReader/asd.py
index 7e496b5..f36094f 100644
--- a/topofileformats/asd.py
+++ b/AFMReader/asd.py
@@ -12,8 +12,8 @@
 from matplotlib import animation
 
 
-from topofileformats.logging import logger
-from topofileformats.io import (
+from AFMReader.logging import logger
+from AFMReader.io import (
     read_int32,
     read_int16,
     read_float,
diff --git a/topofileformats/ibw.py b/AFMReader/ibw.py
similarity index 96%
rename from topofileformats/ibw.py
rename to AFMReader/ibw.py
index 07cbffc..8a884f2 100644
--- a/topofileformats/ibw.py
+++ b/AFMReader/ibw.py
@@ -6,7 +6,7 @@
 import numpy as np
 from igor2 import binarywave
 
-from topofileformats.logging import logger
+from AFMReader.logging import logger
 
 logger.enable(__package__)
 
@@ -66,7 +66,7 @@ def load_ibw(file_path: Path | str, channel: str) -> tuple[np.ndarray, float]:
     Load the image and pixel to nanometre scaling factor - 'HeightTracee' is the default channel name (the extra 'e' is
     not a typo!).
 
-    >>> from topofileformats.ibw import load_ibw
+    >>> from AFMReader.ibw import load_ibw
     >>> image, pixel_to_nanometre_scaling_factor = load_ibw(file_path="./my_ibw_file.ibw", channel="HeightTracee")
     """
     logger.info(f"Loading image from : {file_path}")
diff --git a/topofileformats/io.py b/AFMReader/io.py
similarity index 100%
rename from topofileformats/io.py
rename to AFMReader/io.py
diff --git a/topofileformats/jpk.py b/AFMReader/jpk.py
similarity index 97%
rename from topofileformats/jpk.py
rename to AFMReader/jpk.py
index 382c832..3776081 100644
--- a/topofileformats/jpk.py
+++ b/AFMReader/jpk.py
@@ -6,7 +6,7 @@
 import numpy as np
 import tifffile
 
-from topofileformats.logging import logger
+from AFMReader.logging import logger
 
 logger.enable(__package__)
 
@@ -63,7 +63,7 @@ def load_jpk(file_path: Path | str, channel: str) -> tuple[np.ndarray, float]:
     --------
     Load height trace channel from the .jpk file. 'height_trace' is the default channel name.
 
-    >>> from topofileformats.jpk import load_jpk
+    >>> from AFMReader.jpk import load_jpk
     >>> image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk", channel="height_trace")
     """
     logger.info(f"Loading image from : {file_path}")
diff --git a/topofileformats/logging.py b/AFMReader/logging.py
similarity index 100%
rename from topofileformats/logging.py
rename to AFMReader/logging.py
diff --git a/topofileformats/spm.py b/AFMReader/spm.py
similarity index 97%
rename from topofileformats/spm.py
rename to AFMReader/spm.py
index 603d64a..e5d554c 100644
--- a/topofileformats/spm.py
+++ b/AFMReader/spm.py
@@ -6,7 +6,7 @@
 import pySPM
 import numpy as np
 
-from topofileformats.logging import logger
+from AFMReader.logging import logger
 
 logger.enable(__package__)
 
@@ -72,7 +72,7 @@ def load_spm(file_path: Path | str, channel: str) -> tuple:
     Load the image and pixel to nanometre scaling factor, available channels are 'Height', 'ZSensor' and 'Height
     Sensor'.
 
-    >>> from topofileformats.spm import load_spm
+    >>> from AFMReader.spm import load_spm
     >>> image, pixel_to_nm = load_spm(file_path="path/to/file.spm", channel="Height")
     ```
     """
diff --git a/pyproject.toml b/pyproject.toml
index 42049e4..d3d8755 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,7 +48,8 @@ dev = [
   "pytest",
   "pytest-cov",
   "pylint",
-  "ruff"
+  "ruff",
+  "setuptools_scm[toml]",
 ]
 
 [project.urls]