Merge pull request #8 from Wytamma/pyLangevitour

Python interface for langevitour contributed by Wytamma Wirth.

.gitignore

@@ -47,3 +47,8 @@ inst/doc
 docs
 /doc/
 /Meta/
+
+# python 
+*.pyc
+dist
+.ipynb_checkpoints/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: langevitour
 Title: Langevin Tour
-Version: 0.5.2
+Version: 0.5.5
 Authors@R: 
     person("Paul", "Harrison", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-3980-268X"))

README.md

@@ -1,6 +1,6 @@
 # langevitour
 
-langevitour is an HTML widget that randomly tours projections of a high-dimensional dataset with an animated scatter-plot. The user can manipulate the plot to use specified axes, or turn on Guided Tour mode to perform [projection pursuit](https://en.wikipedia.org/wiki/Projection_pursuit), finding an informative projection of the data. Groups within the data can be hidden or shown, as can particular axes. Known projections of interest can be added as "extra axes" and also manipulated. The widget can be used from within R, or included in a self-contained Rmarkdown document, or a Shiny app, or used directly from Javascript.
+langevitour is an HTML widget that randomly tours projections of a high-dimensional dataset with an animated scatter-plot. The user can manipulate the plot to use specified axes, or turn on Guided Tour mode to perform [projection pursuit](https://en.wikipedia.org/wiki/Projection_pursuit), finding an informative projection of the data. Groups within the data can be hidden or shown, as can particular axes. Known projections of interest can be added as "extra axes" and also manipulated. The widget can be used from within R or Python, or included in a self-contained Rmarkdown document, or a Shiny app, or used directly from Javascript.
 
 <a href="https://logarithmic.net/langevitour/2022-abacbs/" style="display: block; margin: 5px; border: 1px solid #000; float: right">
 <img src="https://logarithmic.net/langevitour/2022-abacbs/abacbs-langevitour-poster-2022-small.png" width=300>
@@ -20,6 +20,8 @@ langevitour is a twist on the "tour" concept from software such as [XGobi](http:
 
 * [Javascript example](https://pfh.github.io/langevitour/example.html)
 
+* [Python example](https://colab.research.google.com/github/Wytamma/pyLangevitour/blob/main/examples/notebook.ipynb)
+
 <br>
 
 ## R installation
@@ -108,6 +110,53 @@ For example, to define a new guide you would:
 
 <br>
 
+## Python installation 
+```bash
+pip install langevitour
+```
+
+## Python usage 
+
+```python
+import numpy as np
+
+from langevitour import Langevitour
+
+# Generate a sample dataset
+X = []
+group = []
+n = 20000
+
+def r():
+    return np.random.normal(0, 0.02)
+
+for i in range(n):
+    a = i/n * np.pi * 2
+    X.append([
+        10 + np.sin(a)/3 + r(),
+        20 + np.sin(a*2)/3 + r(),
+        30 + np.sin(a*3)/3,
+        40 + np.sin(a*4)/3,
+        50 + np.sin(a*5)/3
+    ])
+    group.append(int(i*4/n))
+
+# Extra axes (specified as columns of a matrix)
+extra_axes = [[1], [2], [0], [0], [0]]
+extra_axes_names = ["V1+2*V2"]
+
+tour = Langevitour(
+    X,
+    group=group,
+    extra_axes=extra_axes,
+    extra_axes_names=extra_axes_names,
+    point_size=1,
+)
+tour.write_html("langevitour_plot.html")
+```
+
+langevitour also works in [jupyter notebooks](https://colab.research.google.com/github/pfh/langevitour/blob/main/py/examples/langevitour.ipynb).
+
 ## Copyright
 
 Langevitour is free software made available under the [MIT license](https://github.com/pfh/langevitour/blob/main/LICENSE.md). Included libraries [jStat](https://github.com/jstat/jstat) and [SVD-JS](https://github.com/danilosalvati/svd-js) are also provided under the MIT license. Included library [D3](https://github.com/d3/d3) is provided under the [ISC license](https://github.com/d3/d3/blob/main/LICENSE).

inst/htmlwidgets/langevitour.yaml

@@ -1,6 +1,6 @@
 dependencies:
  - name: langevitour
-   version: "0.5.2"
+   version: "0.5.5"
    src: htmlwidgets/lib/
    script:
    - langevitour-pack.js

package.json

@@ -1,19 +1,21 @@
 {
   "name": "langevitour",
-  "version": "0.5.2",
+  "version": "0.5.5",
   "description": "An HTML widget that randomly tours 2D projections of numerical data.",
   "type": "module",
   "main": "lib/langevitour.js",
   "sideEffects": false,
   "scripts": {
     "test": "echo \"Error: no test specified\" && exit 1",
-    "sync-versions": "VERSION=$(grep '^Version:' DESCRIPTION | cut -d' ' -f2) && sed -i '/^  \\\"version\\\"/ c\\  \\\"version\\\": \\\"'$VERSION'\\\",' package.json && sed -i '/^   version:/ c\\   version: \\\"'$VERSION'\\\"' inst/htmlwidgets/langevitour.yaml",
+    "sync-versions": "VERSION=$(grep '^Version:' DESCRIPTION | cut -d' ' -f2) && sed -i '/^  \\\"version\\\"/ c\\  \\\"version\\\": \\\"'$VERSION'\\\",' package.json && sed -i '/^   version:/ c\\   version: \\\"'$VERSION'\\\"' inst/htmlwidgets/langevitour.yaml && hatch version $VERSION",
     "js-build": "npx tsc && npx webpack",
     "js-build-quick": "npx tsc && npx webpack --mode=development",
     "js-docs": "npx typedoc src/langevitour.ts --out docs/jsdoc/ --excludeNotDocumented --readme none",
     "r-document": "Rscript -e 'devtools::document()'",
     "r-docs": "npm run r-document && Rscript -e 'pkgdown::build_site()'",
-    "build": "npm run sync-versions && npm run js-build && npm run js-docs && npm run r-docs",
+    "py-build": "cp inst/htmlwidgets/lib/langevitour-pack.js py/langevitour/static/langevitour-pack.js && hatch build",
+    "py-publish": "hatch publish",
+    "build": "npm run sync-versions && npm run js-build && npm run js-docs && npm run r-docs && npm run py-build",
     "r-install": "Rscript -e 'devtools::install()'",
     "r-install-quick": "Rscript -e 'devtools::install(quick=TRUE)'"
   },

py/README.md

@@ -0,0 +1,56 @@
+# langevitour for Python
+
+[![PyPI - Version](https://img.shields.io/pypi/v/langevitour.svg)](https://pypi.org/project/langevitour)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/langevitour.svg)](https://pypi.org/project/langevitour)
+
+Python interface for [langevitour](https://github.com/pfh/langevitour/) a HTML widget that randomly tours projections of a high-dimensional dataset with an animated scatter-plot.
+
+For more information see the langevitour [Github repo](https://github.com/pfh/langevitour) or [website](https://logarithmic.net/langevitour/).
+
+## Installation
+
+```bash
+pip install langevitour
+```
+
+## Python usage 
+
+```python
+import numpy as np
+
+from langevitour import Langevitour
+
+# Generate a sample dataset
+X = []
+group = []
+n = 20000
+
+def r():
+    return np.random.normal(0, 0.02)
+
+for i in range(n):
+    a = i/n * np.pi * 2
+    X.append([
+        10 + np.sin(a)/3 + r(),
+        20 + np.sin(a*2)/3 + r(),
+        30 + np.sin(a*3)/3,
+        40 + np.sin(a*4)/3,
+        50 + np.sin(a*5)/3
+    ])
+    group.append(int(i*4/n))
+
+# Extra axes (specified as columns of a matrix)
+extra_axes = [[1], [2], [0], [0], [0]]
+extra_axes_names = ["V1+2*V2"]
+
+tour = Langevitour(
+    X,
+    group=group,
+    extra_axes=extra_axes,
+    extra_axes_names=extra_axes_names,
+    point_size=1,
+)
+tour.write_html("langevitour_plot.html")
+```
+
+langevitour also works in [jupyter notebooks](https://colab.research.google.com/github/pfh/langevitour/blob/main/py/examples/langevitour.ipynb).

py/examples/tour.py

@@ -0,0 +1,35 @@
+import numpy as np
+
+from langevitour import Langevitour
+
+# Generate a sample dataset
+X = []
+group = []
+n = 20000
+
+def r():
+    return np.random.normal(0, 0.02)
+
+for i in range(n):
+    a = i/n * np.pi * 2
+    X.append([
+        10 + np.sin(a)/3 + r(),
+        20 + np.sin(a*2)/3 + r(),
+        30 + np.sin(a*3)/3,
+        40 + np.sin(a*4)/3,
+        50 + np.sin(a*5)/3
+    ])
+    group.append(int(i*4/n))
+
+# Extra axes (specified as columns of a matrix)
+extra_axes = [[1], [2], [0], [0], [0]]
+extra_axes_names = ["V1+2*V2"]
+
+tour = Langevitour(
+    X,
+    group=group,
+    extra_axes=extra_axes,
+    extra_axes_names=extra_axes_names,
+    point_size=1,
+)
+tour.write_html("langevitour_plot.html")

py/langevitour/__about__.py

@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2023-present Wytamma Wirth <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+__version__ = "0.5.5"

py/langevitour/__init__.py

@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2023-present Wytamma Wirth <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+from .langevitour import Langevitour