diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 6a9d23ee4..b9fcc01ad 100755 --- a/.github/CONTRIBUTING.md +++ b/.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). diff --git a/CHANGELOG.md b/CHANGELOG.md index 121cdbde2..2089609b8 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/INSTALLATION.md b/INSTALLATION.md index 6d2161926..f5718fae2 100644 --- a/INSTALLATION.md +++ b/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): ``` diff --git a/README.md b/README.md index f5b2b9728..d80fecf74 100644 --- a/README.md +++ b/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 diff --git a/lumispy/release_info.py b/lumispy/release_info.py index 5a7f88986..849536960 100644 --- a/lumispy/release_info.py +++ b/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" diff --git a/lumispy/signals/cl_spectrum.py b/lumispy/signals/cl_spectrum.py index 2cf381f95..3c69f40e5 100644 --- a/lumispy/signals/cl_spectrum.py +++ b/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: diff --git a/lumispy/signals/luminescence_spectrum.py b/lumispy/signals/luminescence_spectrum.py index e32fbec06..712eb4869 100644 --- a/lumispy/signals/luminescence_spectrum.py +++ b/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]) diff --git a/lumispy/utils/axes.py b/lumispy/utils/axes.py index ba712e923..6bbdf2376 100644 --- a/lumispy/utils/axes.py +++ b/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$^{-1}$": diff --git a/releasing_guide.md b/releasing_guide.md index 2a20fdc47..9ebbdddb2 100644 --- a/releasing_guide.md +++ b/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