Plot-configurations for scientific publications, purely based on matplotlib

Last update: Jan 08, 2023

Related tags

Data Visualization tueplots

Overview

TUEplots

Plot-configurations for scientific publications, purely based on matplotlib.

Usage

Please have a look at the examples in the example/ directory.

Contribution

Tests are run with pytest. You can use tox (you only have to install tox once):

pip install tox 
tox

The CI checks for compliance of the code with black and isort, and runs the tests and the notebooks. To automatically satisfy the former, there is a pre-commit that can be used (do this once):

pip install pre-commit
pre-commit install

From then on, your code will be checked for isort and black compatibility automatically.

Comments

Colors

Feature request: I would like to propose to store the colors in colors.py not as a tuple, but as an np.array.

Reasoning: I'm planning to add the entire Uni Tü color palette. If they're stored as np.arrays, that makes it easier to interpolate between colors, in particular to create lighter versions of existing colors.

opened by philipphennig 7
Add list of supported venues to README and docs

First time users might be interested in a quick overview of whether their targeted venue is supported by tueplots. While this information can be found in the API docs, I think it would be good to provide an overview on the "landing page" of this package, i.e., either the GitHub README file or the docs index file.

opened by braun-steven 5
Font seems off
Hi,

I tried using tueplots but encountered some weird bug, where my plot got from this: to this: just by removing defined figsize and adding:

from tueplots import bundles plt.rcParams.update(bundles.neurips2021(usetex=False, ncols=2, nrows=1))

Example code can be found here.

Is this a bug or am I missing something?
opened by dmandic17 4

mathit in beamer_moml is too fat

beamer_moml uses Roboto Condensed, which matches our style for beamer. But math variables (i.e. the \mathit font) is set in regular roboto.

MWE:

import numpy as np
from matplotlib import pyplot as plt
from tueplots import bundles

plt.rcParams.update({"figure.dpi": 150})
plt.rcParams.update(bundles.beamer_moml())

def f_b(x):
    return 2 ** (x / 2 - 2)


fig, ax = plt.subplots()

x = np.linspace(0, 12, num=120)
ax.plot(x, f_b(x), "-k")

ax.set_xlabel("$x$ (note that text is fine, mathit is not)")
ax.set_ylabel("$\log f(x)=6$")

I have no clue how to fix this. Anyone?

bug enhancement

opened by philipphennig 2

Related packages
It could be useful to add information about related packages somewhere (to the readme?). This way we can mix and match (and also explain what we are doing differently)

There are for instance:

Seaborn: https://seaborn.pydata.org/index.html

ProPlot: https://proplot.readthedocs.io/en/latest/cycles.html

SciencePlots: https://github.com/garrettj403/SciencePlots

Any others?
opened by pnkraemer 2
Fix pre-commit error on buggy black version
This resolves the error below:

ImportError: cannot import name '_unicodefun' from 'click'

See https://github.com/psf/black/issues/2964

Validation of fix:

pre-commit clean pre-commit run --all-files tox -e black
opened by kianmeng 1

Fontsize flexibility

Currently, most of the fontsizes are computed via

def _from_base(*, base):
    return {
        "font.size": base - 1,
        "axes.labelsize": base - 1,
        "legend.fontsize": base - 3,
        "xtick.labelsize": base - 3,
        "ytick.labelsize": base - 3,
        "axes.titlesize": base - 1,
    }

which has some fairly generic defaults. It would be very useful for me to be able to change the "1" and "3" values in my application. For example, via

def _from_base(*, base, normalsize_offset=1, small_offset=3):
    return {
        "font.size": base - normalsize_offset,
        "axes.labelsize": base - normalsize_offset,
        "legend.fontsize": base - small_offset,
        "xtick.labelsize": base - small_offset,
        "ytick.labelsize": base - small_offset,
        "axes.titlesize": base - normalsize_offset,
    }

opened by pnkraemer 1

Windows compatibility and doctests
It seems that tueplots is not windows compatible, likely because byexample is not.

This can be fixed rather easily. The steps could be:

[x] Add windows-latest and macos-latest platforms to tests (to detect those issues)

[x] Replace byexample runs with doctest (it can do the same, but should be compatible with all platforms)

bug
opened by pnkraemer 1
_Inches_per_Point is inverted

The Variable _INCHES_PER_POINT = 1.0 * 72.27 in line 5 of figsizes.py is the wrong way round. It should either be renamed to _POINTS_PER_INCH or be set to 1.0 / 72.27.
invalid

opened by philipphennig 1
Font types
Often, conference and journal style files require Type-1 fonts. Per default, matplotlib uses type 3 fonts.

One thing that one could do would be to change the rcparams to pdf.fonttype=42,

plt.rcParams["pdf.fonttype"] = 42 # alternative would be 3

which generates type 42 fonts. It is not clear entirely whether this is sufficient for the type 1 rule. That would require checking, though.
enhancement question
opened by pnkraemer 1
Font and figure size update for beamer moml
I propose two changes, exclusively to the beamer bundle:

Introduced an explicit beamer_moml(), which is set to from_base(10) (Otherwise the fonts are too large)

Changed figsize.beamer(): I removed the rows argument, which doesn't make sense in the beamer context, and instead introduced rel_width and rel_height. In beamer slides, the typical use-case is that you know how much of the slide you want the figure to take up. This can now be achieved by setting those two parameters. Their default values are 1, which corresponds to the whole slide.
opened by philipphennig 1
ICML 2023

I would happily review a PR including a contribution of the ICML 2023 files. The call for papers (including a style file) is out now: https://icml.cc/Conferences/2023/CallForPapers.

Most, if not all of the configurations should be the same as in the last year(s).
enhancement good first issue

opened by pnkraemer 0
Readme images not displayed on PyPi

The images in tueplots' readme are not displayed on pypi:

It would be good to fix this. Maybe along the lines of what is explained here:

https://stackoverflow.com/questions/41983209/how-do-i-add-images-to-a-pypi-readme-that-works-on-github
documentation

opened by pnkraemer 0
Notebook quality assurance

The linters (black, isort, pylint) can be applied to the example notebooks via nbqa: https://github.com/nbQA-dev/nbQA This will enforce the same code quality for the notebooks as for the rest of the code.
documentation

opened by pnkraemer 1

Releases(v0.0.5)

v0.0.5(Sep 16, 2022)
What's Changed

light face for roboto in beamer_moml by @philipphennig in https://github.com/pnkraemer/tueplots/pull/95

Update the figsize notebook to be more explicit about ncols and nrows by @nathanaelbosch in https://github.com/pnkraemer/tueplots/pull/96

Fontsize-offset parameters by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/98

Fixed a few typos by @pitmonticone in https://github.com/pnkraemer/tueplots/pull/99

Tight(er) whitespace around figure when saving by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/101

AISTATS 2023 style by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/102

ICLR 2023 by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/105

New Contributors

@nathanaelbosch made their first contribution in https://github.com/pnkraemer/tueplots/pull/96

@pitmonticone made their first contribution in https://github.com/pnkraemer/tueplots/pull/99

Full Changelog: https://github.com/pnkraemer/tueplots/compare/v0.0.4...v0.0.5
Source code(tar.gz)
Source code(zip)
v0.0.4(Apr 12, 2022)
What's Changed

Correct links readme by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/75

Manual trigger for pypi workflow by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/79

fixed _Inches_per_Point by @philipphennig in https://github.com/pnkraemer/tueplots/pull/82

Notebook linting by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/83

Add rel_width argument for figsizes by @marvinpfoertner in https://github.com/pnkraemer/tueplots/pull/84

fix typo by @tdsimao in https://github.com/pnkraemer/tueplots/pull/86

Troubleshooting by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/87

Add Neurips 2022 Style by @ltatzel in https://github.com/pnkraemer/tueplots/pull/89

Execute CI on MacOS, Linux, and Windows as part of the workflow by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/92

Set default font families in bundles to mimic paper body font. by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/93

New Contributors

@marvinpfoertner made their first contribution in https://github.com/pnkraemer/tueplots/pull/84

@tdsimao made their first contribution in https://github.com/pnkraemer/tueplots/pull/86

@ltatzel made their first contribution in https://github.com/pnkraemer/tueplots/pull/89

Full Changelog: https://github.com/pnkraemer/tueplots/compare/v0.0.3...v0.0.4
Source code(tar.gz)
Source code(zip)
v0.0.3(Jan 21, 2022)
What's Changed

simplified publishing action by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/52

Beamer moml updates by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/54

Ph color by @philipphennig in https://github.com/pnkraemer/tueplots/pull/55

Height width ratio by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/57

Test improvements by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/58

fixed readme install by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/60

Aistats by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/61

Single column figsize width by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/62

Moved all requirements to setup.cfg by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/66

ICML updates by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/67

Figsize refactor by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/68

Sphinx by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/69

sphinx requirements by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/70

Change badge-style of licence by @not-a-feature in https://github.com/pnkraemer/tueplots/pull/73

Readthedocs configuration by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/72

Improve docs by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/74

New Contributors

@not-a-feature made their first contribution in https://github.com/pnkraemer/tueplots/pull/73

Full Changelog: https://github.com/pnkraemer/tueplots/compare/v0.0.2...v0.0.3a1

What's Changed

simplified publishing action by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/52

Beamer moml updates by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/54

Ph color by @philipphennig in https://github.com/pnkraemer/tueplots/pull/55

Height width ratio by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/57

Test improvements by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/58

fixed readme install by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/60

Aistats by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/61

Single column figsize width by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/62

Moved all requirements to setup.cfg by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/66

ICML updates by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/67

Figsize refactor by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/68

Sphinx by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/69

sphinx requirements by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/70

Change badge-style of licence by @not-a-feature in https://github.com/pnkraemer/tueplots/pull/73

Readthedocs configuration by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/72

Improve docs by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/74

New Contributors

@not-a-feature made their first contribution in https://github.com/pnkraemer/tueplots/pull/73

Full Changelog: https://github.com/pnkraemer/tueplots/compare/v0.0.2...v0.0.3a

What's Changed

simplified publishing action by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/52

Beamer moml updates by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/54

Ph color by @philipphennig in https://github.com/pnkraemer/tueplots/pull/55

Height width ratio by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/57

Test improvements by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/58

fixed readme install by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/60

Aistats by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/61

Single column figsize width by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/62

Moved all requirements to setup.cfg by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/66

ICML updates by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/67

Figsize refactor by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/68

Sphinx by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/69

sphinx requirements by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/70

Change badge-style of licence by @not-a-feature in https://github.com/pnkraemer/tueplots/pull/73

Readthedocs configuration by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/72

Improve docs by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/74

New Contributors

@not-a-feature made their first contribution in https://github.com/pnkraemer/tueplots/pull/73

Full Changelog: https://github.com/pnkraemer/tueplots/compare/v0.0.2...v0.0.3
Source code(tar.gz)
Source code(zip)
v0.0.2(Jan 11, 2022)

Source code(tar.gz)
Source code(zip)
v0.0.1b(Jan 11, 2022)
What's Changed

Improved publish by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/51

Full Changelog: https://github.com/pnkraemer/tueplots/compare/v0.0.1...v0.0.1b
Source code(tar.gz)
Source code(zip)
v0.0.1(Jan 11, 2022)
What's Changed

CI by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/1

tutorial for font sizes by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/2

added fontsizes for JMLR by @philipphennig in https://github.com/pnkraemer/tueplots/pull/3

Color cycles by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/5

CI for linting/tests (with tox) and running notebooks by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/10

Fonts by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/11

Axes by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/12

Colors as constants by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/13

Template with years by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/14

context managers by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/15

Markers by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/18

Readme by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/21

Added the University of Tübingen colors (with tests) by @philipphennig in https://github.com/pnkraemer/tueplots/pull/17

Constants restructured by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/22

Bundles by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/23

PIp by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/25

larger timeout by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/26

Fonts default by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/29

Tex bundles by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/31

Related packages in readme by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/32

Pylint by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/33

legends by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/34

Font troubleshoot and parameter update by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/35

Badges in readme by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/39

Readme by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/41

Jmlr updates by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/44

Line base ratio and axes module by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/45

Font and figure size update for beamer moml by @philipphennig in https://github.com/pnkraemer/tueplots/pull/46

Teaser images in readme by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/48

Module names by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/49

Publishing workflow by @pnkraemer in https://github.com/pnkraemer/tueplots/pull/50

New Contributors

@pnkraemer made their first contribution in https://github.com/pnkraemer/tueplots/pull/1

@philipphennig made their first contribution in https://github.com/pnkraemer/tueplots/pull/3

Full Changelog: https://github.com/pnkraemer/tueplots/commits/v0.0.1
Source code(tar.gz)
Source code(zip)

Owner

Nicholas Krämer

I am a PhD student in machine learning at the University of Tübingen and former MSc student of mathematics at the University of Bonn.

GitHub Repository

Create HTML profiling reports from pandas DataFrame objects

Pandas Profiling Documentation | Slack | Stack Overflow Generates profile reports from a pandas DataFrame. The pandas df.describe() function is great

10k Jan 01, 2023

HM02: Visualizing Interesting Datasets

HM02: Visualizing Interesting Datasets This is a homework assignment for CSCI 40 class at Claremont McKenna College. Go to the project page to learn m

11 Oct 26, 2021

script to generate HeN ipfs app exports of GLSL shaders

HeNerator A simple script to generate HeN ipfs app exports from any frag shader created with: GlslViewer GlslEditor The Book of Shaders glslCanvas VS

22 Dec 21, 2022

A simple code for plotting figure, colorbar, and cropping with python

Python Plotting Tools This repository provides a python code to generate figures (e.g., curves and barcharts) that can be used in the paper to show th

134 Jan 02, 2023

Simple python implementation with matplotlib to manually fit MIST isochrones to Gaia DR2 color-magnitude diagrams

7 Oct 22, 2022

Sci palettes for matplotlib/seaborn

sci palettes for matplotlib/seaborn Installation python3 -m pip install sci-palettes Usage import seaborn as sns import matplotlib.pyplot as plt impor

2 Jun 07, 2022

Fast 1D and 2D histogram functions in Python

About Sometimes you just want to compute simple 1D or 2D histograms with regular bins. Fast. No nonsense. Numpy's histogram functions are versatile, a

237 Dec 18, 2022

Generate SVG (dark/light) images visualizing (private/public) GitHub repo statistics for profile/website.

Generate daily updated visualizations of GitHub user and repository statistics from the GitHub API using GitHub Actions for any combination of private and public repositories, whether owned or contri

2 Dec 16, 2022

The Metabolomics Integrator (MINT) is a post-processing tool for liquid chromatography-mass spectrometry (LCMS) based metabolomics.

MINT (Metabolomics Integrator) The Metabolomics Integrator (MINT) is a post-processing tool for liquid chromatography-mass spectrometry (LCMS) based m

0 May 04, 2022

This is a super simple visualization toolbox (script) for transformer attention visualization ✌

Trans_attention_vis This is a super simple visualization toolbox (script) for transformer attention visualization ✌ 1. How to prepare your attention m

3 Jul 09, 2022

股票行情实时数据接口-A股,完全免费的沪深证券股票数据-中国股市,python最简封装的API接口

股票行情实时数据接口-A股,完全免费的沪深证券股票数据-中国股市,python最简封装的API接口,包含日线,历史K线,分时线,分钟线,全部实时采集，系统包括新浪腾讯双数据核心采集获取，自动故障切换，STOCK数据格式成DataFrame格式,可用来查询研究量化分析，股票程序自动化交易系统.为量化研究者在数据获取方面极大地减轻工作量，更加专注于策略和模型的研究与实现。

572 Jan 08, 2023

Drug design and development team HackBio internship is a virtual bioinformatics program that introduces students and professional to advanced practical bioinformatics and its applications globally.

-Nyokong. Drug design and development team HackBio internship is a virtual bioinformatics program that introduces students and professional to advance

4 Aug 04, 2022

Plot-configurations for scientific publications, purely based on matplotlib

Related tags

Overview

TUEplots

Usage

Contribution

Comments

Releases(v0.0.5)

v0.0.5(Sep 16, 2022)

What's Changed

New Contributors

v0.0.4(Apr 12, 2022)

What's Changed

New Contributors

v0.0.3(Jan 21, 2022)

What's Changed

New Contributors

What's Changed

New Contributors

What's Changed

New Contributors

v0.0.2(Jan 11, 2022)

v0.0.1b(Jan 11, 2022)

What's Changed

v0.0.1(Jan 11, 2022)

What's Changed

New Contributors

Owner

Nicholas Krämer

Create HTML profiling reports from pandas DataFrame objects

HM02: Visualizing Interesting Datasets

script to generate HeN ipfs app exports of GLSL shaders

A simple code for plotting figure, colorbar, and cropping with python

Simple python implementation with matplotlib to manually fit MIST isochrones to Gaia DR2 color-magnitude diagrams

Sci palettes for matplotlib/seaborn

Fast 1D and 2D histogram functions in Python

Generate SVG (dark/light) images visualizing (private/public) GitHub repo statistics for profile/website.

The Metabolomics Integrator (MINT) is a post-processing tool for liquid chromatography-mass spectrometry (LCMS) based metabolomics.

This is a super simple visualization toolbox (script) for transformer attention visualization ✌

股票行情实时数据接口-A股,完全免费的沪深证券股票数据-中国股市,python最简封装的API接口

Drug design and development team HackBio internship is a virtual bioinformatics program that introduces students and professional to advanced practical bioinformatics and its applications globally.

🎨 Python3 binding for `@AntV/G2Plot` Plotting Library .

A small script written in Python3 that generates a visual representation of the Mandelbrot set.

在原神中使用围栏绘图

Visualization of numerical optimization algorithms

Simple addon for snapping active object to mesh ground

An intuitive library to add plotting functionality to scikit-learn objects.

Python support for Godot 🐍🐍🐍

Declarative statistical visualization library for Python