viscose 0.1.0__tar.gz

viscose-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 BojarLab
+
+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.

viscose-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: viscose
+Version: 0.1.0
+Summary: Scientific plots that are pieces of art: palettes with their own special effects, drawn without matplotlib
+Author-email: Daniel Bojar <daniel.bojar@gu.se>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/BojarLab/viscose
+Project-URL: Bug Tracker, https://github.com/BojarLab/viscose/issues
+Keywords: plotting,visualization,figures,palettes,glycowork
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: glycorender>=0.5.4
+Provides-Extra: cluster
+Requires-Dist: scipy; extra == "cluster"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: scipy; extra == "dev"
+Requires-Dist: pandas; extra == "dev"
+Dynamic: license-file
+
+<h1 align="center">viscose</h1>
+
+<p align="center"><strong>Scientific plots that are pieces of art.</strong><br>
+Pick a palette. It brings its own colors, type, axes, and special effects.</p>
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/hero.png" alt="Ridgeline plots in all four palettes, above an embedding, a clustermap, a volcano plot, and a line and bar figure" width="100%"></p>
+
+```bash
+pip install viscose              # numpy and glycorender are all it needs
+pip install "viscose[cluster]"   # adds scipy for clustermaps
+```
+
+## One word changes everything
+
+```python
+import viscose as vc
+
+fig, ax = vc.subplots(palette = 'aura')
+fig.suptitle('Differential abundance', 'Tumor vs. healthy tissue, 412 glycans')
+ax.scatter(x, y, hue = direction)
+ax.axhline(2)
+ax.set_xlabel('log_{2} fold change')
+ax.set_ylabel('-log_{10} adjusted p')
+fig.save('volcano.pdf')
+```
+
+Same data, same code, and only `palette` changes. Spheres become rings, gradients become solid shapes, hairline axes become
+heavy rounded ones, and titles go from light and wide to bold and tight. No styling code, no `rcParams`, and no theme files.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/one_word.png" alt="The same volcano plot in Lumen, Couture, Poster, and Aura" width="100%"></p>
+
+## Four palettes, four personalities
+
+Each palette has two hues in four shades, and effects to match. Few colors, in shades of those few colors, on white: figures
+that look composed in a paper and striking on a slide.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/palettes.png" alt="A sample scene and eight shades for each palette" width="100%"></p>
+
+### `lumen`: peacock and marigold
+
+Gradients run through the marks, points are glossy spheres, lines glow, and everything rests on soft shadows.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/lumen.png" alt="An embedding, a line and bar figure, and a ridgeline plot in Lumen" width="100%"></p>
+
+### `couture`: plum and gold
+
+Hairline axes held away from the data, slender needle bars, large light titles, and spaced capitals.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/couture.png" alt="A mass spectrum, stacked bars, and a volcano plot in Couture" width="100%"></p>
+
+### `poster`: forest and vermilion
+
+Heavy rounded axes, big bold type, and thick solid marks cut apart by crisp white gaps.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/poster.png" alt="A volcano plot, stacked bars, and a ridgeline plot in Poster" width="100%"></p>
+
+### `aura`: burgundy and teal
+
+Marks float on soft shadows in their own color, above rounded heatmap cells, with no axis lines at all.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/aura.png" alt="A clustermap, a line and bar figure, and an embedding in Aura" width="100%"></p>
+
+## Out of the box
+
+The same data and the same labels, with no styling on either side: matplotlib and seaborn on the left, viscose on the right.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/versus.png" alt="A volcano plot from matplotlib and seaborn defaults beside the same plot from viscose in Aura" width="100%"></p>
+
+## Glycans in your plots
+
+viscose shares its renderer with [glycowork](https://github.com/BojarLab/glycowork)'s GlycoDraw, so a plot can carry real SNFG
+drawings as sharp as the rest of the figure, in PNG, PDF, and SVG.
+
+```python
+from glycowork.motif.draw import annotate_figure
+
+ax.annotate('Neu5Ac(a2-6)Gal(b1-4)GlcNAc', (x, y), offset = (12, 0), svg_label = True)
+fig.save('volcano.svg')
+annotate_figure('volcano.svg', filepath = 'volcano.pdf', compact = True)
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/glycans.png" alt="A volcano plot and a biosynthetic network with SNFG glycan drawings as labels" width="100%"></p>
+
+## Everything you reach for
+
+`hue`, `style`, and `size` take one value per point and build the legend for you, as seaborn does.
+
+```python
+ax.scatter(x, y, hue = stage, style = source, size = abundance,
+           hue_label = 'Stage', style_label = 'Source', size_label = 'Abundance')
+ax.text(0.02, 0.98, 'F = 4.2\np = 0.003', axes_fraction = True, va = 'top')
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/hue_style_size.png" alt="A scatter plot with color, shape, and size mapped to data, with a three-part legend" width="80%"></p>
+
+Clustermaps come with both dendrograms and a color bar. Hand over a DataFrame and it brings its own labels.
+
+```python
+fig, heat = vc.clustermap(df, palette = 'aura', title = 'Glycan abundance by tissue', colorbar_label = 'z-score')
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/clustermap.png" alt="A clustermap of glycan abundance across tissues in Aura" width="80%"></p>
+
+| | |
+|---|---|
+| **Plots** | `plot`, `scatter`, `bar`, `barh`, `stacked_bar`, `hist`, `fill_between`, `errorbar`, `stem`, `hlines`, `arrow`, `heatmap`, `ridgeline`, `dendrogram`, `axhline`, `axvline`, and `vc.clustermap` |
+| **Markers** | `o`, `s`, `D`, `^`, `v`, `X`, `P`, and `*`, all with the palette's effects |
+| **Annotation** | `text`, `annotate`, `legend`, and `colorbar`, with `_{sub}` and `^{super}` in any text |
+| **Layout** | Colliding tick labels turn and thin themselves, labels move to the side with room, legends wrap, and the page grows for anything that needs it |
+| **Output** | `fig.save` writes PNG, PDF, or SVG from the same geometry, with marks, gradients, and text as real vectors in PDF and SVG |
+| **Display** | `fig.show()` works inline in Jupyter and slate, and in the system's image viewer from a terminal, with CI and coding agents kept silent |
+| **SVG hooks** | `gid` on `arrow` and `scatter` names elements for hover text and scripting |
+| **State** | None hidden: a figure is an object, with no current figure and nothing to close |
+
+## Light and quick
+
+No compiled plotting stack, no backends, and no font cache. For vector output, viscose is often many times faster than
+matplotlib and seaborn, and its files can be far smaller. At 300 dpi, in Poster:
+
+| | matplotlib and seaborn | viscose |
+|---|---|---|
+| Dependencies | Nine extra packages, 42.5 MB | numpy and glycorender, with 0.11 MB of its own code |
+| Clustermap, 300 x 100, PDF | 1.57 s, 587 kB | **0.02 s, 79 kB** |
+| Clustermap, 300 x 100, SVG | 1.40 s, 5,943 kB | **0.02 s, 182 kB** |
+| Clustermap, 26 x 16, PDF | 0.11 s, 22 kB | **0.01 s**, 26 kB |
+| Three lines with a legend, PDF | 0.03 s, 12 kB | **under 0.01 s**, 13 kB |
+| Scatter, 100,000 points, PDF | 0.96 s, 1,524 kB | **0.19 s, 644 kB** |
+| Scatter, 412 points, PNG | 0.18 s, 147 kB | 0.20 s, 180 kB |
+
+matplotlib's compiled rasterizer is still about twice as fast on most PNGs,
+and the soft shadows of Lumen and Aura add about half a second. To rerun the full comparison, wins and losses alike, use
+[benchmarks/compare_matplotlib.py](https://github.com/BojarLab/viscose/blob/main/benchmarks/compare_matplotlib.py).
+
+## Make it yours
+
+`vc.set_palette('aura')` changes the default for every figure. A library that builds on viscose calls `vc.default_palette('aura')`
+instead, which gives way to the choice of whoever uses it. In any palette, refer to its shades as `a0` to `a3` and `b0` to `b3`, dark
+to pale, or as `ink`, `muted`, and `faint`; hex and CSS color names work too. `fig.pal.groups(3, 2)` gives categories grouped by hue,
+here three shades of one and two of the other, and `fig.pal.contrast(n)` alternates between the hues for categories that have to stand
+apart, as `scatter(hue = ...)` does.
+
+A palette of your own is two hues, three text colors, and whichever effects you like:
+
+```python
+vc.register_palette(vc.Palette('midnight', ['#14213D', '#27477E', '#5C85C5', '#C4D5EE'], ['#8F5B00', '#D08C00', '#F2B83B', '#FBE5B0'],
+                               '#14213D', '#5A6478', '#E6EAF1', point = 'sphere', bar = 'deep', shadow = 0.4))
+fig, ax = vc.subplots(palette = 'midnight')
+```
+
+Century Gothic is used where it is installed, and glycorender's bundled Comfortaa elsewhere.
+
+## More
+
+[examples/gallery.py](https://github.com/BojarLab/viscose/blob/main/examples/gallery.py) draws seven standard figures in every palette, [examples/features.py](https://github.com/BojarLab/viscose/blob/main/examples/features.py)
+draws one sheet of features per palette, and [examples/readme_figures.py](https://github.com/BojarLab/viscose/blob/main/examples/readme_figures.py) draws every image on this page.

viscose-0.1.0/README.md

@@ -0,0 +1,155 @@
+<h1 align="center">viscose</h1>
+
+<p align="center"><strong>Scientific plots that are pieces of art.</strong><br>
+Pick a palette. It brings its own colors, type, axes, and special effects.</p>
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/hero.png" alt="Ridgeline plots in all four palettes, above an embedding, a clustermap, a volcano plot, and a line and bar figure" width="100%"></p>
+
+```bash
+pip install viscose              # numpy and glycorender are all it needs
+pip install "viscose[cluster]"   # adds scipy for clustermaps
+```
+
+## One word changes everything
+
+```python
+import viscose as vc
+
+fig, ax = vc.subplots(palette = 'aura')
+fig.suptitle('Differential abundance', 'Tumor vs. healthy tissue, 412 glycans')
+ax.scatter(x, y, hue = direction)
+ax.axhline(2)
+ax.set_xlabel('log_{2} fold change')
+ax.set_ylabel('-log_{10} adjusted p')
+fig.save('volcano.pdf')
+```
+
+Same data, same code, and only `palette` changes. Spheres become rings, gradients become solid shapes, hairline axes become
+heavy rounded ones, and titles go from light and wide to bold and tight. No styling code, no `rcParams`, and no theme files.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/one_word.png" alt="The same volcano plot in Lumen, Couture, Poster, and Aura" width="100%"></p>
+
+## Four palettes, four personalities
+
+Each palette has two hues in four shades, and effects to match. Few colors, in shades of those few colors, on white: figures
+that look composed in a paper and striking on a slide.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/palettes.png" alt="A sample scene and eight shades for each palette" width="100%"></p>
+
+### `lumen`: peacock and marigold
+
+Gradients run through the marks, points are glossy spheres, lines glow, and everything rests on soft shadows.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/lumen.png" alt="An embedding, a line and bar figure, and a ridgeline plot in Lumen" width="100%"></p>
+
+### `couture`: plum and gold
+
+Hairline axes held away from the data, slender needle bars, large light titles, and spaced capitals.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/couture.png" alt="A mass spectrum, stacked bars, and a volcano plot in Couture" width="100%"></p>
+
+### `poster`: forest and vermilion
+
+Heavy rounded axes, big bold type, and thick solid marks cut apart by crisp white gaps.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/poster.png" alt="A volcano plot, stacked bars, and a ridgeline plot in Poster" width="100%"></p>
+
+### `aura`: burgundy and teal
+
+Marks float on soft shadows in their own color, above rounded heatmap cells, with no axis lines at all.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/aura.png" alt="A clustermap, a line and bar figure, and an embedding in Aura" width="100%"></p>
+
+## Out of the box
+
+The same data and the same labels, with no styling on either side: matplotlib and seaborn on the left, viscose on the right.
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/versus.png" alt="A volcano plot from matplotlib and seaborn defaults beside the same plot from viscose in Aura" width="100%"></p>
+
+## Glycans in your plots
+
+viscose shares its renderer with [glycowork](https://github.com/BojarLab/glycowork)'s GlycoDraw, so a plot can carry real SNFG
+drawings as sharp as the rest of the figure, in PNG, PDF, and SVG.
+
+```python
+from glycowork.motif.draw import annotate_figure
+
+ax.annotate('Neu5Ac(a2-6)Gal(b1-4)GlcNAc', (x, y), offset = (12, 0), svg_label = True)
+fig.save('volcano.svg')
+annotate_figure('volcano.svg', filepath = 'volcano.pdf', compact = True)
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/glycans.png" alt="A volcano plot and a biosynthetic network with SNFG glycan drawings as labels" width="100%"></p>
+
+## Everything you reach for
+
+`hue`, `style`, and `size` take one value per point and build the legend for you, as seaborn does.
+
+```python
+ax.scatter(x, y, hue = stage, style = source, size = abundance,
+           hue_label = 'Stage', style_label = 'Source', size_label = 'Abundance')
+ax.text(0.02, 0.98, 'F = 4.2\np = 0.003', axes_fraction = True, va = 'top')
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/hue_style_size.png" alt="A scatter plot with color, shape, and size mapped to data, with a three-part legend" width="80%"></p>
+
+Clustermaps come with both dendrograms and a color bar. Hand over a DataFrame and it brings its own labels.
+
+```python
+fig, heat = vc.clustermap(df, palette = 'aura', title = 'Glycan abundance by tissue', colorbar_label = 'z-score')
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/BojarLab/viscose/main/examples/readme/clustermap.png" alt="A clustermap of glycan abundance across tissues in Aura" width="80%"></p>
+
+| | |
+|---|---|
+| **Plots** | `plot`, `scatter`, `bar`, `barh`, `stacked_bar`, `hist`, `fill_between`, `errorbar`, `stem`, `hlines`, `arrow`, `heatmap`, `ridgeline`, `dendrogram`, `axhline`, `axvline`, and `vc.clustermap` |
+| **Markers** | `o`, `s`, `D`, `^`, `v`, `X`, `P`, and `*`, all with the palette's effects |
+| **Annotation** | `text`, `annotate`, `legend`, and `colorbar`, with `_{sub}` and `^{super}` in any text |
+| **Layout** | Colliding tick labels turn and thin themselves, labels move to the side with room, legends wrap, and the page grows for anything that needs it |
+| **Output** | `fig.save` writes PNG, PDF, or SVG from the same geometry, with marks, gradients, and text as real vectors in PDF and SVG |
+| **Display** | `fig.show()` works inline in Jupyter and slate, and in the system's image viewer from a terminal, with CI and coding agents kept silent |
+| **SVG hooks** | `gid` on `arrow` and `scatter` names elements for hover text and scripting |
+| **State** | None hidden: a figure is an object, with no current figure and nothing to close |
+
+## Light and quick
+
+No compiled plotting stack, no backends, and no font cache. For vector output, viscose is often many times faster than
+matplotlib and seaborn, and its files can be far smaller. At 300 dpi, in Poster:
+
+| | matplotlib and seaborn | viscose |
+|---|---|---|
+| Dependencies | Nine extra packages, 42.5 MB | numpy and glycorender, with 0.11 MB of its own code |
+| Clustermap, 300 x 100, PDF | 1.57 s, 587 kB | **0.02 s, 79 kB** |
+| Clustermap, 300 x 100, SVG | 1.40 s, 5,943 kB | **0.02 s, 182 kB** |
+| Clustermap, 26 x 16, PDF | 0.11 s, 22 kB | **0.01 s**, 26 kB |
+| Three lines with a legend, PDF | 0.03 s, 12 kB | **under 0.01 s**, 13 kB |
+| Scatter, 100,000 points, PDF | 0.96 s, 1,524 kB | **0.19 s, 644 kB** |
+| Scatter, 412 points, PNG | 0.18 s, 147 kB | 0.20 s, 180 kB |
+
+matplotlib's compiled rasterizer is still about twice as fast on most PNGs,
+and the soft shadows of Lumen and Aura add about half a second. To rerun the full comparison, wins and losses alike, use
+[benchmarks/compare_matplotlib.py](https://github.com/BojarLab/viscose/blob/main/benchmarks/compare_matplotlib.py).
+
+## Make it yours
+
+`vc.set_palette('aura')` changes the default for every figure. A library that builds on viscose calls `vc.default_palette('aura')`
+instead, which gives way to the choice of whoever uses it. In any palette, refer to its shades as `a0` to `a3` and `b0` to `b3`, dark
+to pale, or as `ink`, `muted`, and `faint`; hex and CSS color names work too. `fig.pal.groups(3, 2)` gives categories grouped by hue,
+here three shades of one and two of the other, and `fig.pal.contrast(n)` alternates between the hues for categories that have to stand
+apart, as `scatter(hue = ...)` does.
+
+A palette of your own is two hues, three text colors, and whichever effects you like:
+
+```python
+vc.register_palette(vc.Palette('midnight', ['#14213D', '#27477E', '#5C85C5', '#C4D5EE'], ['#8F5B00', '#D08C00', '#F2B83B', '#FBE5B0'],
+                               '#14213D', '#5A6478', '#E6EAF1', point = 'sphere', bar = 'deep', shadow = 0.4))
+fig, ax = vc.subplots(palette = 'midnight')
+```
+
+Century Gothic is used where it is installed, and glycorender's bundled Comfortaa elsewhere.
+
+## More
+
+[examples/gallery.py](https://github.com/BojarLab/viscose/blob/main/examples/gallery.py) draws seven standard figures in every palette, [examples/features.py](https://github.com/BojarLab/viscose/blob/main/examples/features.py)
+draws one sheet of features per palette, and [examples/readme_figures.py](https://github.com/BojarLab/viscose/blob/main/examples/readme_figures.py) draws every image on this page.

viscose-0.1.0/pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "viscose"
+version = "0.1.0"
+description = "Scientific plots that are pieces of art: palettes with their own special effects, drawn without matplotlib"
+readme = "README.md"
+authors = [
+    {name = "Daniel Bojar", email = "daniel.bojar@gu.se"}
+]
+license = "MIT"
+license-files = ["LICENSE"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+keywords = ["plotting", "visualization", "figures", "palettes", "glycowork"]
+dependencies = ["numpy", "glycorender>=0.5.4"]
+requires-python = ">=3.11"
+
+[project.optional-dependencies]
+cluster = ["scipy"]
+dev = ["pytest", "scipy", "pandas"]
+
+[project.urls]
+"Homepage" = "https://github.com/BojarLab/viscose"
+"Bug Tracker" = "https://github.com/BojarLab/viscose/issues"
+
+[tool.setuptools]
+packages = ["viscose"]
+
+[tool.pytest.ini_options]
+pythonpath = ["."]

viscose-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+