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Brew Cask Install Conda

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Install brew if necessary, and then run: brew install saulpw/vd/visidata Linux - Debian/Ubuntu apt install visidata Linux - NixOS nix-env -i visidata Linux - GNU Guix guix install visidata Conda conda install -channel conda-forge visidata Python v3.6+ pip3 install visidata Unreleased Bleeding Edge. Using Pip: pip3 install git+https://github. Jul 19, 2019 Once miniconda is installed via brew cask the conda executable will be available at which point conda init should be run so that conda can setup its own environment for the shell that you are using (e.g. Bash, zsh, etc.) I think this is what conda activate prompts the user to do when it's run without first having conda init run. If you don't have wget on OSX, try installing homebrew and then run brew install wget. If you get a new Apple machine, you might need to run xcode-select -install first. If you installed conda but which python still points to the system python location, run the following commands to enable it. See full list on gully.github.io.

Released:

Format Matplotlib for scientific plotting

Project description

Matplotlib styles for scientific figures

This repo has Matplotlib styles to format your figures for scientific papers, presentations and theses.

Getting Started

The easiest way to install SciencePlots is by using pip:

The pip installation will automatically move all of the Matplotlib style files *.mplstyle into the appropriate directory on your computer.

Notes:

  • SciencePlots requires Latex (see Latex installation instructions).
  • If you would like to use CJK fonts, you will need to install these font separately (see CJK font installation instructions).

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Please see the FAQ section for more information and troubleshooting.

Using the Styles

'science' is the main style from this repo. Whenever you want to use it, simply add the following to the top of your python script:

You can also combine multiple styles together by:

In this case, the ieee style will override some of the parameters from the science style in order to configure the plot for IEEE papers (column width, fontsizes, etc.).

To use any of the styles temporarily, you can use:

Examples

The science style:

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The science + grid styles:

The science + ieee styles for IEEE papers:

  • IEEE requires figures to be readable when printed in black and white. The ieee style also sets the figure width to fit within one column of an IEEE paper.

The science + nature styles for Nature articles:

  • Nature recommends sans-serif fonts.

The science + scatter styles for scatter plots:

The science + notebook styles for Jupyter notebooks:

You can also combine these styles with the other styles that come with Matplotlib. For example, the dark_background + science + high-vis styles:

Note: See the examples/ directory for more!

CJK Fonts

Brew Cask Install Conda

Traditional Chinese (science + no-latex + cjk-tc-font):

Simplified Chinese (science + no-latex + cjk-sc-font):

Japanese (science + no-latex + cjk-jp-font):

Korean (science + no-latex + cjk-kr-font):

See the FAQ for information on installing CJK fonts.

Color Blind Safe Color Cycles

The bright color cycle (7 colors):

The vibrant color cycle (7 colors):

The muted color cycle (10 colors):

The high-contrast color cycle (3 colors):

The light color cycle (9 colors):

Note: These color cycles are from Paul Tol's website.

Other Color Cycles

The std-colors color cycle (used to override other color cycles, e.g., the color cycle from ieee):

The high-vis color cycle:

The retro color cycle:

Help and Contributing

Please feel free to contribute to the SciencePlots repo! For example, it would be good to add new styles for different journals and add new color cycles. Before starting a new style or making any changes, please create an issue through the GitHub issue tracker. That way we can discuss if the changes are necessary and the best approach.

If you need any help with SciencePlots, please first check the FAQ and search through the previous GitHub issues. If you can't find an answer, create a new issue through the GitHub issue tracker.

You can checkout Matplotlib's documentation for more information on plotting settings.

FAQ

  1. Installing Latex:

    • SciencePlots requires Latex to be installed on your machine.

      • On MacOS, I recommend MacTex. Make sure that this Latex installation is added to your path enviroment variable. See this issue for more troubleshooting tips.

      • On Windows, I recommend MikTex. Again, you have to add Latex to your path enviroment variable. See this issue for more troubleshooting tips.

      • On Linux (Ubuntu), you can install Tex Live and the other requirements using:

    • Please see Matplotlib's guide to using Latex for more troubleshooting tips.

    • If you don't want to install Latex, you can disable Latex by using:

  2. Installing CJK fonts

    • To use Chinese, Japanese or Korean fonts, you first need to install Noto CJK Fonts. You can download and install these fonts from the given link or you can install them with a package manager:

    • For Windows Subsystem for Linux (WSL), you will need to manually download and install the fonts by following these instructions.

    • Note that matplotlib may not find the fonts correctly. You can refresh the font cache by running:

    • See this issue for more information.

  3. Installing SciencePlots manually:

    • If you like, you can install the *.mplstyle files manually. First, clone the repository and then copy all of the *.mplstyle files into your Matplotlib style directory. If you're not sure where this is, in an interactive python console type:

    • You should get back something like /home/garrett/.matplotlib. You would then put the *.mplstyle files in /home/garrett/.matplotlib/stylelib/ (you may need to create the stylelib directory):

  4. Using different fonts:

    • SciencePlots uses the default serif font. If you would like to specify a different font, you can use:

    • If you would like to use Times New Roman specifically, please see the discussion in this issue.

  5. Installing SciencePlots within Google Colab, IPython, Jupyter Notebooks, etc.:

    • After installing SciencePlots within one of these environments, you may need to reload the Matplotlib style library. For example:

SciencePlots in Academic Papers

The following papers use SciencePlots:

  • Y. Liu, X. Liu, Y. Sun, 'QGrain: An open-source and easy-to-use software for the comprehensive analysis of grain size distributions', Sedimentary Geology, vol. 423, 105980, Aug. 2021.

  • J. Garrett, and E. Tong, 'A Dispersion-Compensated Algorithm for the Analysis of Electromagnetic Waveguides,'IEEE Signal Process. Lett., vol. 28, pp. 1175-1179, Jun. 2021.

  • G. Jegannathan, et al., 'Current-Assisted SPAD with Improved p-n Junction and Enhanced NIR Performance', Sensors, Dec 2020. (open access)

  • H. Tian, et al., 'ivis Dimensionality Reduction Framework for Biomacromolecular Simulations', J. Chem. Inf. Model., Aug 2020. (open access)

  • P. Stoltz, et al., 'A new simple algorithm for space charge limited emission,'Phys. Plasmas, vol. 27, no. 9, pp. 093103, Sep. 2020. (open access)

  • J. Garrett, et al., 'A Nonlinear Transmission Line Model for Simulating Distributed SIS Frequency Multipliers,'IEEE Trans. THz Sci. Technol., vol. 10, no. 3, pp. 246-255, May 2020. (open access)

  • J. Garrett, et al., 'Simulating the Behavior of a 230 GHz SIS Mixer Using Multi-Tone Spectral Domain Analysis,'IEEE Trans. THz Sci. Technol., vol. 9, no. 9, pp. 540-548, Nov. 2019. (open access)

  • J. Garrett, et al., 'A Compact and Easy to Fabricate E-plane Waveguide Bend,'IEEE Microw. Wireless Compon. Lett., vol. 29, no. 8, pp. 529-531, Aug. 2019. (open access)

  • J. Garrett, 'A 230 GHz Focal Plane Array Using a Wide IF Bandwidth SIS Receiver,' DPhil thesis, University of Oxford, Oxford, UK, 2018. (open access)

If you use SciencePlots in your paper/thesis, feel free to add it to the list!

Citing SciencePlots

You don't have to cite SciencePlots if you use it but it's nice if you do:

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Conda

I’m always using the Homebrew to install the dependencies needed. For recent studies, I need Anaconda for learning python developments. So the first step is trying to install Anaconda with homebrew via brewcaskinstallanaconda, but get this warn information while installing:

To fix this bug, you need to add the /usr/local/anaconda3/bin directory to the PATH environment variable. Simply run this command in terminal if you’re using bash:

or, if you use zsh instead of bash, command like this:

Then, full restart terminal and run:

Install

condainit is available in conda versions 4.6.12 and later.

Anaconda will configure the environment automatically for you. Example of configurations on my Mac looks like this after execute the above command:

I would highly recommend you to use zsh to get a more interactive terminal interface, read this post for setting up zsh. On newer macOS such as bigSur, zsh is now the default shell application.

The same works for miniconda. If you installed it using Homebrew with brewcaskinstallminiconda, you need to set source of the PATH to .zshrc, for example.

Then, still in a zsh shell:

That’s it, miniconda will set responding configs automatically. After that, you can comment out the exportPATH='$PATH:/opt/miniconda3/bin' in .zshrc file.

Update conda

If you run condaupdate--all for the first time, it may warn:

To fix this issue, we can change the ownership of the above directory with:

If you come across other issues, please leave your comments below…

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