Merge pull request LumiSpy#91 from LumiSpy/jlaehne-patch-1

Update installation guide to RELEASE_next_minor

.github/CONTRIBUTING.md

@@ -4,6 +4,6 @@ The [issue tracker](https://github.com/lumispy/lumispy/issues) can be used to re
 - give a minimal example demonstrating the bug,
 - copy and paste the error traceback.
 
-## Contribute
+## Pull Requests
 
-If you want to contribute to the HyperSpy source code, you can send us a [pull requests](https://github.com/lumispy/lumispy/pulls). For more information, please refer to the [HyperSpy developer guide](http://hyperspy.org/hyperspy-doc/current/dev_guide/index.html).
+If you want to contribute to the LumiSpy source code, you can send us a [pull request](https://github.com/lumispy/lumispy/pulls). For more information, please refer to the [HyperSpy developer guide](http://hyperspy.org/hyperspy-doc/current/dev_guide/intro.html).

CHANGELOG.md

@@ -5,6 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## UNRELEASED
+### Changed
+- Mentions of the now deleted `non_uniform_axes` branch in HyperSpy updated to `RELEASE_next_minor`
+- Change 'master' to 'main' branch
+- Updated/corrected badges in README.md
 
 ## 2021-08-22 - version 0.1.2
 ### Added

INSTALLATION.md

@@ -5,8 +5,8 @@
 LumiSpy requires Python 3 and conda -- we suggest using the Python 3 version 
 of [Miniconda](https://conda.io/miniconda.html).
 
-We recommend creating a new environment for the lumispy package (or installing 
-it in the hyperspy environment, if you have one already). To create a new 
+We recommend creating a new environment for the LumiSpy package (or installing 
+it in the HyperSpy environment, if you have one already). To create a new 
 environment:
 
 1. Load the anaconda prompt.
@@ -18,7 +18,7 @@ environment:
 
 ### 2) Installing the package in the new environment
 
-Now activate the lumispy environment and install the package using pip:
+Now activate the LumiSpy environment and install the package using pip:
 ```
     $ conda activate lumispy
     $ pip install lumispy
@@ -28,28 +28,28 @@ Installation is completed! To start using it, check the next section.
 
 #### OPTIONAL: Working with eV instead of wavelength units
 
-In order to convert your signal luminescence axes (normally in wavelength in nanometers) to energy units, you will need to reinstall the `hyperspy` package to its developing branch `non-uniform-axes`. **If you skip this, all lumispy function will work, except the energy conversion functions.**
+In order to convert your signal luminescence axes (normally in wavelength in nanometers) to energy units, you will need to reinstall the `hyperspy` package to its developing branch `RELEASE_next_minor`. **If you skip this, all LumiSpy functions will work, except the energy conversion.**
 
 To do that, follow these steps:
 
 1. Load the anaconda prompt.
-2. Activate the lumispy environment using `conda activate lumispy`).
-5. Install `git` and reinstall the hyperspy package running:
+2. Activate the LumiSpy environment using `conda activate lumispy`).
+5. Install `git` and reinstall the HyperSpy package running:
 
 ```
     $ conda activate lumispy
     $ conda install git -y
     $ pip uninstall hyperspy -y
-    $ pip install git+git://github.com/hyperspy/hyperspy@non_uniform_axes
+    $ pip install git+git://github.com/hyperspy/hyperspy@RELEASE_next_minor
 ```
 
-Now you are ready to use all the functionalites of lumispy.
+Now you are ready to use all the functionalites of LumiSpy.
 
 ### 3) Getting Started
 
 To get started using LumiSpy, especially if you are unfamiliar with Python, we 
 recommend using [Jupyter notebooks](https://jupyter.org/). Having installed 
-lumispy as above, a Jupyter notebook can be opened using the following commands 
+LumiSpy as above, a Jupyter notebook can be opened using the following commands 
 entered into an anaconda prompt (from scratch):
 
 ```

README.md

@@ -16,7 +16,7 @@ provided by the [HyperSpy](http://hyperspy.org) library. It is aimed at helping
 with the analysis of luminescence spectroscopy data (cathodoluminescence, 
 photoluminescence, electroluminescence, Raman, SNOM).
 
-If analysis using LumiSpy forms a part of published work please consider 
+If analysis using LumiSpy forms a part of published work, please consider 
 recognising the code development by citing the project using the [Zenodo-DOI](https://doi.org/10.5281/zenodo.4640445).
 
 Instructions on how to install LumiSpy and get started: [installation guide](INSTALLATION.md).
@@ -26,7 +26,7 @@ have been curated as a series of Jupyter notebooks that you can work through
 and modify to perform many common analyses. Simply:
 
 1. Download the `lumispy_demos` repository in your desired folder
-2. Load lumispy (see [installation guide](INSTALLATION.md))
+2. Load LumiSpy (see [installation guide](INSTALLATION.md))
 3. In Jupyter lab, navigate to the folder and start using the notebook
 
 Everyone is welcome to contribute. Please read our

lumispy/release_info.py

@@ -7,7 +7,7 @@
 url = "http://lumispy.org"
 license = "GPLv3"
 platforms = ["Linux", "Mac OSX", "Windows XP/2000/NT", "Windows 95/98/ME"]
-maintainer = "Jordi Ferrer Orri, Jonas Lähnemann, Duncan Johnstone"
+maintainer = "Jordi Ferrer Orri, Jonas Lähnemann, Duncan Johnstone, Eric Prestat"
 email = "jf631@cam.ac.uk"
 status = "Development"
 

lumispy/signals/cl_spectrum.py

@@ -78,7 +78,7 @@ def remove_spikes(
         if not "threshold" in getfullargspec(self.spikes_removal_tool)[0]:
             raise ImportError(
                 "Spike removal works only "
-                "if the non_uniform_axis branch of HyperSpy is used."
+                "if the RELEASE_next_minor branch of HyperSpy is used."
             )
 
         if luminescence_roi is not None and signal_mask is not None:

lumispy/signals/luminescence_spectrum.py

@@ -84,7 +84,7 @@ def to_eV(self, inplace=True, jacobian=True):
 
         Note
         ----
-        Using a non-linear axis works only for the non_uniform_axis development
+        Using a non-linear axis works only for the RELEASE_next_minor development
         branch of HyperSpy.
 
         """
@@ -93,7 +93,7 @@ def to_eV(self, inplace=True, jacobian=True):
         if not "axis" in getfullargspec(DataAxis)[0]:
             raise ImportError(
                 "Conversion to energy axis works only "
-                "if the non_uniform_axis branch of HyperSpy is used."
+                "if the RELEASE_next_minor branch of HyperSpy is used."
             )
 
         evaxis, factor = axis2eV(self.axes_manager.signal_axes[0])
@@ -174,7 +174,7 @@ def to_invcm(self, inplace=True, jacobian=True):
 
         Note
         ----
-        Using a non-linear axis works only for the non_uniform_axis development
+        Using a non-linear axis works only for the RELEASE_next_minor development
         branch of HyperSpy.
 
         """
@@ -183,7 +183,7 @@ def to_invcm(self, inplace=True, jacobian=True):
         if not "axis" in getfullargspec(DataAxis)[0]:
             raise ImportError(
                 "Conversion to wavenumber axis works only"
-                " if the non_uniform_axis branch of HyperSpy is used."
+                " if the RELEASE_next_minor branch of HyperSpy is used."
             )
 
         invcmaxis, factor = axis2invcm(self.axes_manager.signal_axes[0])
@@ -267,7 +267,7 @@ def to_invcm_relative(self, laser, inplace=True, jacobian=True):
 
         Note
         ----
-        Using a non-linear axis works only for the non_uniform_axis development
+        Using a non-linear axis works only for the RELEASE_next_minor development
         branch of HyperSpy.
 
         """
@@ -276,7 +276,7 @@ def to_invcm_relative(self, laser, inplace=True, jacobian=True):
         if not "axis" in getfullargspec(DataAxis)[0]:
             raise ImportError(
                 "Conversion to wavenumber axis works only"
-                " if the non_uniform_axis branch of HyperSpy is used."
+                " if the RELEASE_next_minor branch of HyperSpy is used."
             )
 
         invcmaxis, factor = axis2invcm(self.axes_manager.signal_axes[0])

lumispy/utils/axes.py

@@ -90,7 +90,7 @@ def axis2eV(ax0):
     if not "axis" in getfullargspec(DataAxis)[0]:
         raise ImportError(
             "Conversion to energy axis works only "
-            "if the non_uniform_axis branch of HyperSpy is used."
+            "if the RELEASE_next_minor branch of HyperSpy is used."
         )
     if ax0.units == "eV":
         raise AttributeError("Signal unit is already eV.")
@@ -140,7 +140,7 @@ def axis2invcm(ax0):
     if not "axis" in getfullargspec(DataAxis)[0]:
         raise ImportError(
             "Conversion to energy axis works only "
-            "if the non_uniform_axis branch of HyperSpy is used."
+            "if the RELEASE_next_minor branch of HyperSpy is used."
         )
 
     if ax0.units == r"cm$^{-1}$":

releasing_guide.md

@@ -15,7 +15,7 @@ To publish a new LumiSpy release do the following steps:
 - Create a tag e.g. `git tag -a v0.1.1 -m "LumiSpy version 0.1.1"`
 - Push tag to user fork for a test run `git push origin v0.1.1`. Will run the release
   workflow without uploading to PyPi
-- Push tag to lumispy repository to trigger release `git push upstream v0.1.1`
+- Push tag to LumiSpy repository to trigger release `git push upstream v0.1.1`
   (this triggers the GitHub action to create the sdist and wheel and upload to
   PyPi automatically). :warning: this is a point of no return :warning:
 
@@ -27,5 +27,5 @@ To publish a new LumiSpy release do the following steps:
 
 ### Follow-up
 
-- Tidy up and close corresponding milestone
+- Tidy up and close corresponding milestone or project
 - A PR to the conda-forge feedstock will be created by the conda-forge bot