Merge pull request #852 from AFM-SPM/ns-rse/851-afmreader

docs/installation.md

@@ -64,7 +64,7 @@ pip install topostats==2.0.0
 For more information on using `pip` to install and manage packages please refer to the [pip
 documentation](https://pip.pypa.io/en/stable/user_guide/).
 
-### Cloning from GitHub
+### Installing from GitHub
 
 You may wish to consider cloning and installing TopoStats from GitHub if...
 
@@ -73,42 +73,45 @@ You may wish to consider cloning and installing TopoStats from GitHub if...
 - If you have found an issue in a released version and want to see if it has been fixed in the unreleased version.
 - If you wish to develop and extend TopoStats with new features yourself.
 
-If you do not have Git already installed please see [Git](installation#git). If you intend to contribute to the
-development of TopoStats please read through the [contributing](contributing) section.
+There are two options to install from GitHub, which you use will depend on what you want to do.
 
-If you are familiar with the command line then you can clone and install TopoStats with the following _after_ activating
-your virtual environment.
+1. Using PyPI to install directly.
+2. Clone the repository and install from there.
+
+If all you want to do is use the development version of TopoStats then you can use option 1. If you wish to change the
+underlying code you should use option 2.
+
+#### Installing from GitHub using PyPI
+
+[`pip`][pip] supports [installing packages from GitHub][pip_github]. To install the `main` branch of TopoStats use the
+following in your Virtual Environment.
 
 ```bash
-git clone https://github.com/AFM-SPM/TopoStats.git
-# If you have SSH access configured to GitHub then you can use
-git clone [email protected]:AFM-SPM/TopoStats.git
+pip install git+https://github.com/AFM-SPM/TopoStats.git@main
 ```
 
-#### Cloning Using GitKraken
-
-If you are using GitKraken you can clone the repository by selecting "Clone" and then "GitHub.com" and typing
-`TopoStats` into the box next to "Repository to Clone" and you should be presented with the option of selecting
-"TopoStats" from the AFM-SPM organisation.
+You can install any branch on GitHub by modifying the last argument (`@main`) to the branch you wish to install,
+e.g. `@another_branch` would install the `another_branch` (if it existed).
 
-Alternatively you can "Clone with URL" and enter `https://github.com/AFM-SPM/TopoStats.git` as the URL to clone from,
-selecting a destination to clone to.
+#### Cloning the Repository and installing
 
-#### Installing TopoStats from the Cloned Repository
+If you do not have Git already installed please see [Git](installation#git). If you intend to contribute to the
+development of TopoStats please read through the [contributing](contributing) section.
 
-Once cloned you will have to open a Terminal and navigate to the directory you cloned and _after_ activating your
-virtual environment install TopoStats with the following.
+If you are familiar with the command line then you can clone and install TopoStats with the following _after_ activating
+your virtual environment. By installing in editable mode (with the `-e` flag) switching branches will make the branch
+available.
 
 ```bash
-cd /path/to/where/topostats/was/cloned/TopoStats
-pip install .
+cd ~/where/to/clone
+git clone [email protected]:AFM-SPM/TopoStats.git
+cd TopoStats
+pip install -e .
 ```
 
-If you wish to make changes to the code and test then make a `git branch`, make your changes and install in editable mode,
-i.e. `pip install -e .`.
-
 If you plan to contribute to development by adding features or address an existing
-[issue](https://github.com/AFM-SPM/TopoStats/issues) please refer to the [contributing](contributing) section.
+[issue](https://github.com/AFM-SPM/TopoStats/issues) please refer to the [contributing](contributing) section and pay
+particular attention to the section about installing additional dependencies.
 
 We include [notebooks](notebooks) which show how to use different aspects of TopoStats. If you wish to try these out the
 [Jupyter Noteooks](https://jupyter.org/) then you can install the dependencies that are required from the cloned
@@ -118,12 +121,19 @@ TopoStats repository using...
 pip install ".[notebooks]"
 ```
 
+#### Cloning Using GitKraken
+
+If you are using GitKraken you can clone the repository by selecting "Clone" and then "GitHub.com" and typing
+`TopoStats` into the box next to "Repository to Clone" and you should be presented with the option of selecting
+"TopoStats" from the AFM-SPM organisation. Once cloned follow the above instructions to install with `pip` under your
+virtual environment.
+
 ## Tests
 
 One of the major changes in the refactoring is the introduction of unit tests. These require certain packages to be
 installed which are not installed to your virtual environment by
 [setuptools](https://setuptools.pypa.io/en/latest/setuptools.html) in the above steps. If you are intending to modify or
-contribute to the development of TopoStats and making changes to the code base you will likely want to be able to run
+contribute to the development of TopoStats or make changes to the code base you will likely want to be able to run
 the tests. Install the necessary dependencies to do so with...
 
 ```bash
@@ -135,9 +145,13 @@ pytest
 
 ## Git
 
-[Git](https://git.vc) is a version control system for managing software development and is required to be installed on
+[Git][git] is a version control system for managing software development and is required to be installed on
 your computer in order to clone the TopoStats repository. Instructions on installing Git can be found at [Git Guides -
 install git](https://github.com/git-guides/install-git).
 
 A nice Graphical User Interface for working with Git is [GitKraken](https://www.gitkraken.com/) which includes
 everything you need.
+
+[git]: https://git.vc
+[pip]: https://pypi.org/project/pip/
+[pip_github]: https://pip.pypa.io/en/stable/getting-started/#install-a-package-from-github

pyproject.toml

@@ -36,6 +36,7 @@ keywords = [
 ]
 requires-python = ">=3.9"
 dependencies = [
+  "AFMReader",
   "h5py",
   "igor2",
   "matplotlib",
@@ -51,7 +52,6 @@ dependencies = [
   "seaborn",
   "snoop",
   "tifffile",
-  "topofileformats",
   "tqdm",
 ]
 

tests/test_io.py

@@ -561,7 +561,7 @@ def test_load_scan_asd(load_scan_asd: LoadScans) -> None:
     frames, px_to_nm_scaling = load_scan_asd.load_asd()
     assert isinstance(frames, np.ndarray)
     assert frames.shape == (197, 200, 200)
-    assert frames.sum() == -71724923530211.84
+    assert frames.sum() == -1368044348.3393068
     assert isinstance(px_to_nm_scaling, float)
     assert px_to_nm_scaling == 2.0
 
@@ -698,12 +698,14 @@ def test__spm_pixel_to_nm_scaling(
 @pytest.mark.parametrize(
     ("load_scan_object", "length", "image_shape", "image_sum", "filename", "pixel_to_nm_scaling"),
     [
-        ("load_scan_spm", 1, (1024, 1024), 30695369.188316286, "minicircle", 0.4940029296875),
-        ("load_scan_ibw", 1, (512, 512), -218091520.0, "minicircle2", 1.5625),
-        ("load_scan_jpk", 1, (256, 256), 286598232.9308627, "file", 1.2770176335964876),
-        ("load_scan_gwy", 1, (512, 512), 33836850.232917726, "file", 0.8468632812499975),
-        ("load_scan_topostats", 1, (1024, 1024), 184140.8593819073, "file", 0.4940029296875),
-        ("load_scan_asd", 197, (200, 200), -673381139990.2344, "file_122", 2.0),
+        pytest.param("load_scan_spm", 1, (1024, 1024), 30695369.188316286, "minicircle", 0.4940029296875, id="spm"),
+        pytest.param("load_scan_ibw", 1, (512, 512), -218091520.0, "minicircle2", 1.5625, id="ibw"),
+        pytest.param("load_scan_jpk", 1, (256, 256), 286598232.9308627, "file", 1.2770176335964876, id="jpk"),
+        pytest.param("load_scan_gwy", 1, (512, 512), 33836850.232917726, "file", 0.8468632812499975, id="gwy"),
+        pytest.param(
+            "load_scan_topostats", 1, (1024, 1024), 184140.8593819073, "file", 0.4940029296875, id="topostats"
+        ),
+        pytest.param("load_scan_asd", 197, (200, 200), -12843725.967220962, "file_122", 2.0, id="asd"),
     ],
 )
 def test_load_scan_get_data(

topostats/io.py

@@ -19,9 +19,9 @@
 import pandas as pd
 import pySPM
 import tifffile
+from AFMReader import asd
 from igor2 import binarywave
 from ruamel.yaml import YAML, YAMLError
-from topofileformats import asd
 
 from topostats.logs.logs import LOGGER_NAME
 
@@ -1026,6 +1026,7 @@ def get_data(self) -> None:
                     self.image, self.pixel_to_nm_scaling = suffix_to_loader[suffix]()
                 except Exception as e:
                     if "Channel" in str(e) and "not found" in str(e):
+                        LOGGER.warning(e)  # log the specific error message
                         LOGGER.warning(f"[{self.filename}] Channel {self.channel} not found, skipping image.")
                     else:
                         raise