BioLizardStylePython 0.1.0__tar.gz → 0.2.0__tar.gz

{biolizardstylepython-0.1.0 → biolizardstylepython-0.2.0}/.gitignore

@@ -1,12 +1,16 @@
-.Rhistory
-.DS_Store
-.Rproj.user
-.RData
-.Ruserdata
-.Rproj.user
-BioLizardStyleR/.RData
-BioLizardStyleR/.Rhistory
-BioLizardStyleR/.Rproj.user
-BioLizardStylePython/.idea/*
-.idea
-
+.Rhistory
+.DS_Store
+.Rproj.user
+.RData
+.Ruserdata
+.Rproj.user
+BioLizardStyleR/.RData
+BioLizardStyleR/.Rhistory
+BioLizardStyleR/.Rproj.user
+BioLizardStylePython/.idea/*
+.idea
+
+#pytest and unittest
+.pytest_cache
+__pycache__
+result_images

biolizardstylepython-0.2.0/CHANGELOG.md

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+# Changelog
+
+<!--next-version-placeholder-->
+
+## v0.2.0 (2024-04-10)
+
+### Feature
+
+- Switched from Nunito to Lato font
+- Automated clearing of matplotlib cache upon loading the module
+- Added infromative error messages in case colorspace or lato are not installed
+
+
+### Fix
+
+- fix bug in discrete qualitative fill scale
+- update default lizard_style colorscale to show colors in teh same ortder as discrete palette
+
+
+### Tests
+
+- Added new tests to all package modules
+
+### Documentation
+
+- Added readme and usage examples
+
+## v0.1.0 (2023-09-08)
+
+- First release of `BioLizardStylePython`

{biolizardstylepython-0.1.0 → biolizardstylepython-0.2.0}/LICENSE

@@ -1,22 +1,22 @@
- Copyright (c) 2023 BioLizard
-
- Permission is hereby granted, free of charge, to any person
- obtaining a copy of this software and associated documentation
- files (the "Software"), to deal in the Software without
- restriction, including without limitation the rights to use,
- copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the
- Software is furnished to do so, subject to the following
- conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ Copyright (c) 2023 BioLizard
+
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use,
+ copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following
+ conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  OTHER DEALINGS IN THE SOFTWARE.

biolizardstylepython-0.2.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: BioLizardStylePython
+Version: 0.2.0
+Summary: Enhance plots with the signature Biolizard aesthetic for matplotlib and seaborn.
+Project-URL: Homepage, https://github.com/lizard-bio/nature-grade-visualization-playground/tree/main
+Author: Robbe Neirynck
+Author-email: BioLizard <contact@lizard.bio>, Aniko Meijer <aniko.meijer@lizard.bio>
+Maintainer-email: Alexander Koch <alexander.koch@lizard.bio>, Aniko Meijer <aniko.meijer@lizard.bio>
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.9
+Requires-Dist: font-lato>=0.0.1
+Requires-Dist: fonts>=0.0.3
+Requires-Dist: matplotlib>=3.7.1
+Requires-Dist: pillow>=9.4.0
+Description-Content-Type: text/markdown
+
+# BioLizardStylePython
+
+Enhance plots with the signature Biolizard aesthetic for matplotlib and seaborn.
+
+## install
+
+### 1. Extra requirements
+`BioLizardStylePython` relies on the colorspace package, which is not available on the Python Package Index (PyPI). However, it is hosted on GitHub and needs to be installed directly from there. To install the `colorspace` package, please run the following command in your terminal:
+```
+pip install git+https://github.com/retostauffer/python-colorspace.git
+```
+Once you've successfully installed `colorspace`, you can proceed with the installation and usage of `BioLizardStylePython`.
+
+### 2. Package Installation
+
+The BioLizardStylePython package is available on PyPI and can be easily installed using:
+```
+pip install BioLizardStylePython
+```
+
+### 3. Font Installation
+
+The BioLizardStyleR package makes use of the signature BioLizard font 'Lato'. This font can be found on Google Fonts under an open font license.
+
+If you don't have the Lato font locally installed, you can download and install it from GitHub.
+
+1. **Download Fonts**: Download the two font files from the GitHub repository [Nature Grade Visualization Playground](https://github.com/lizard-bio/nature-grade-visualization-playground/tree/main).
+2. **Install Fonts**: Install the downloaded fonts on your system.
+3. **Complete**: Once the installation is done, you're all set to use the font.
+
+## usage
+
+### 1. Styling Function: `lizard_style()`
+
+This function applies a BioLizard aesthetic to your matplotlib or seaborn plots. The aim is to ensure that plots maintain a uniform look, irrespective of whether they were made in R or Python.
+
+### 2. BioLizard Color Palettes
+
+These are qualitative, sequential, and divergent color maps that can be applied to your plots. The palettes are designed using BioLizard's house colors, keeping perceptual uniformity and color-blind friendliness in mind. For more information, consult the help documentation specific to each function.
+
+### 3. Finalizing and Exporting Plots: `finalise_lizardplot()`
+
+This function adds a BioLizard footer beneath your graph and exports it to a specified format such as PNG or PDF. The footer includes the BioLizard logo at the bottom right corner and leaves room for source text.
+
+## Contributing and Feedback
+
+Contributions and feedback are very welcome and much appreciated. 
+
+Issues can be reported [on github](https://github.com/lizard-bio/nature-grade-visualization-playground/issues).
+

biolizardstylepython-0.2.0/README.md

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+# BioLizardStylePython
+
+Enhance plots with the signature Biolizard aesthetic for matplotlib and seaborn.
+
+## install
+
+### 1. Extra requirements
+`BioLizardStylePython` relies on the colorspace package, which is not available on the Python Package Index (PyPI). However, it is hosted on GitHub and needs to be installed directly from there. To install the `colorspace` package, please run the following command in your terminal:
+```
+pip install git+https://github.com/retostauffer/python-colorspace.git
+```
+Once you've successfully installed `colorspace`, you can proceed with the installation and usage of `BioLizardStylePython`.
+
+### 2. Package Installation
+
+The BioLizardStylePython package is available on PyPI and can be easily installed using:
+```
+pip install BioLizardStylePython
+```
+
+### 3. Font Installation
+
+The BioLizardStyleR package makes use of the signature BioLizard font 'Lato'. This font can be found on Google Fonts under an open font license.
+
+If you don't have the Lato font locally installed, you can download and install it from GitHub.
+
+1. **Download Fonts**: Download the two font files from the GitHub repository [Nature Grade Visualization Playground](https://github.com/lizard-bio/nature-grade-visualization-playground/tree/main).
+2. **Install Fonts**: Install the downloaded fonts on your system.
+3. **Complete**: Once the installation is done, you're all set to use the font.
+
+## usage
+
+### 1. Styling Function: `lizard_style()`
+
+This function applies a BioLizard aesthetic to your matplotlib or seaborn plots. The aim is to ensure that plots maintain a uniform look, irrespective of whether they were made in R or Python.
+
+### 2. BioLizard Color Palettes
+
+These are qualitative, sequential, and divergent color maps that can be applied to your plots. The palettes are designed using BioLizard's house colors, keeping perceptual uniformity and color-blind friendliness in mind. For more information, consult the help documentation specific to each function.
+
+### 3. Finalizing and Exporting Plots: `finalise_lizardplot()`
+
+This function adds a BioLizard footer beneath your graph and exports it to a specified format such as PNG or PDF. The footer includes the BioLizard logo at the bottom right corner and leaves room for source text.
+
+## Contributing and Feedback
+
+Contributions and feedback are very welcome and much appreciated. 
+
+Issues can be reported [on github](https://github.com/lizard-bio/nature-grade-visualization-playground/issues).
+

biolizardstylepython-0.2.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

biolizardstylepython-0.2.0/docs/_build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 54eda93c4de205dc457ab623e162c12e
+tags: 645f666f9bcd5a90fca523b33c5a78b7