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pgljupyter\n\nPlantGL & L-Py jupyter widgets\n\n## Install with pip - inside conda env\n\n```bash\nconda create -y -n pgljupyter -c fredboudon -c conda-forge \\\n    'openalea.lpy>=3.4.0' 'jupyterlab>=2.2.0' 'ipywidgets>=7.5.0'\nconda activate pgljupyter\npip install pgljupyter\njupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager\njupyter lab build && jupyter lab\n```\n\n## Build, install and run from source\n\n - install lpy, plantgl, jupyterlab, widgets and widgetsextension\n\n```bash\nconda create -y -n pgljupyter -c fredboudon -c conda-forge \\\n    'openalea.lpy>=3.4.0' 'jupyterlab>=2.2.0' 'ipywidgets>=7.5.0'\nconda activate pgljupyter\njupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager\n```\n\n - install emsdk: https://emscripten.org/docs/getting_started/downloads.html\n\n```bash\ngit clone https://github.com/emscripten-core/emsdk.git\ncd emsdk\n./emsdk install latest\n./emsdk activate latest\nsource ./emsdk_env.sh\ncd ..\n```\n\n 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pgljupyter\n\nPlantGL & L-Py jupyter widgets\n\n## Install with pip - inside conda env\n\n```bash\nconda create -y -n pgljupyter -c fredboudon -c conda-forge \\\n    'openalea.lpy>=3.4.0' 'jupyterlab>=2.2.0' 'ipywidgets>=7.5.0'\nconda activate pgljupyter\npip install pgljupyter\njupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager\njupyter lab build && jupyter lab\n```\n\n## Build, install and run from source\n\n - install lpy, plantgl, jupyterlab, widgets and widgetsextension\n\n```bash\nconda create -y -n pgljupyter -c fredboudon -c conda-forge \\\n    'openalea.lpy>=3.4.0' 'jupyterlab>=2.2.0' 'ipywidgets>=7.5.0'\nconda activate pgljupyter\njupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager\n```\n\n - install emsdk: https://emscripten.org/docs/getting_started/downloads.html\n\n```bash\ngit clone https://github.com/emscripten-core/emsdk.git\ncd emsdk\n./emsdk install latest\n./emsdk activate latest\nsource ./emsdk_env.sh\ncd ..\n```\n\n 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['fredboudon'](https://anaconda.org/fredboudon/openalea.lpy).\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fredboudon/plantgl-jupyter/HEAD?labpath=%2Fexamples%2Fbroccoli.ipynb)\n\n\n![Leuvenberg](docs/lpy_leuwenberg.gif)\n\n\n[![DOI](https://zenodo.org/badge/252633303.svg)](https://zenodo.org/badge/latestdoi/252633303)\n\n## Quick Examples\n\n### PlantGL\n\n- simple PlantGL shapes - spheres [@nbviewer](https://nbviewer.jupyter.org/github/jvail/plantgl-jupyter/blob/master/examples/spheres.ipynb)\n\n### L-Py\n\n- a tree model - leuwenberg [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/lpy/leuwenberg/leuwenberg.ipynb)\n\n- plot magic - leuwenberg [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/lpy/leuwenberg/lpy_plot_magic.ipynb)\n\n- champignon [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/magic_champignon.ipynb)\n\n- magics with scalar parameters - broccoli [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/broccoli.ipynb)\n\n- magics with curve parameters - sweep surface [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/lpy/sweep_surface/sweep_surface.ipynb)\n\n\n\n## Usage\n\n```python\nfrom pgljupyter import SceneWidget, LsystemWidget\n```\n\n**SceneWidget**\n\nRenderer for PlantGL Scenes, Shapes, Geometries\n\nArguments:\n\n- `arg0` list | plantgl.Shape | plantgl.Scene: a list of shapes or scenes or a single object\n- `position` tuple (float, float, float): x, y, z position of arg0 (default (0, 0, 0))\n- `scale` float: scale factor for arg0 (default 1)\n- `size_display` tuple (int, int): width and height of the canvas (minimum 400)\n- `size_world` float: extend on the 3D scene in all directions\n\nExample:\n\n```python\nfrom openalea.plantgl.all import Scene, Sphere\nfrom pgljupyter import SceneWidget\n\ns = Scene([Sphere()])\nsw = SceneWidget(s)\nsw\n```\nTutorial:\n-  Display of spheres [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/spheres.ipynb)\n\n**LsystemWidget**\n\nRenderer for lpy.Lstrings derived from lpy.Lsystem code\n\nArguments:\n\n- `arg0` string: file name / path of lpy code file\n- `unit` string enum: the unit used in the Lsystem model ('m', 'dm', 'cm', 'mm', default 'm')\n- `scale` float: scale factor for arg0 (default 1)\n- `animate` bool: if `True` runs animation automatically\n- `size_display` tuple (int, int): width and height of the canvas (minimum 400)\n- `size_world` float: extend on the 3D scene in all directions\n\nImportant property/methods:\n- `editor` : display an editor of the graphical parameters\n- `get_lstring(self)` : return the lstring corresponding to the current step of the simulation display in the widget.\n- `get_namespace(self)` : return the namespace of variables of the simulation\n\nExample:\n\n```python\nfrom pgljupyter import LsystemWidget\n\nlw = LsystemWidget('myfile.lpy')\nlw\n```\n```python\nlw.editor\n```\n\nTutorial:\n- Display of the simulation of a lpy file :  [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/lpy/leuwenberg/leuwenberg.ipynb)\n\n**%%lpy**\n\nA cell magic to inline L-Py code in a notebook\n\nArguments:\n\n- `--size`, `-s` int,int: same as `size_display`\n- `--world`, `-w` float: same as `size_world`\n- `--unit`, `-u` enum: same as `unit`\n- `--params`, `-p` LsystemParameters: name of LsystemParameters instance\n- `--animate`, `-a` True: runs animation automatically\n- `--extended-editor`, `-e` False: show/hide all parameter controls\n\nExample:\n\n```python\n# activated by importing pgljupyter\nimport pgljupyter\n```\n\n```python\n%%lpy -u cm\nfrom openalea.plantgl.all import *\nAxiom: ;(1)+(10)_(2)F(10);(0)@g(Paraboloid(10,10,2,False))\nderivation length: 100\nproduction:\nF(x) --> F(x+0.2)\n@g(p) --> @g(Paraboloid(p.radius + 0.15, p.height + 0.2, 2, False))\n_(x) --> _(x+0.02)\n```\n\nExample with graphical parameters:\n\n```python\n# activated by importing pgljupyter\nimport pgljupyter\nfrom openalea.lpy.lsysparameters import LsystemParameters\n```\n\n```python\nlp = LsystemParameters()\nlp.add_scalar(name='a', value=1, minvalue=0, maxvalue=100)\nlp.add_function(name='b') # default graphical function created\n```\n\n```python\n%%lpy -p lp\n\nAxiom: SetGuide(b,a)F(a)\n```\n\nTutorials:\n- simple L-systems [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/magic_champignon.ipynb)\n- graphical scalar parameters - broccoli [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/broccoli.ipynb)\n- graphical curve parameters - sweep surface [@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/lpy/sweep_surface/sweep_surface.ipynb)\n\n\n**%lpy_plot**\n\nA line magic to plot all derivation steps of an Lsystem on a square plane\n\nArguments:\n\n- `arg0`, string: L-Py file\n- `--size`, `-s` int,int: width and hight of the canvas\n- `--cell`, `-c` float: size of cell for a single derivation step\n- `--derive`, `-d` int[,int[,int]]: start, stop, step derivation\n\nExample:\n\n```python\n# activated by importing pgljupyter\nimport pgljupyter\n```\n\n```python\n%lpy_plot myfile.lpy\n```\nTutorial:\n- Display of the simulation from a lpy file :[@nbviewer](https://nbviewer.jupyter.org/github/fredboudon/plantgl-jupyter/blob/master/examples/lpy/leuwenberg/lpy_plot_magic.ipynb)\n\n## Installation\n\n### Install with pip - inside conda environment\n\nSome examples also require `matplotlib`, `xarray-simlab` and `rpy2`.\n\n```bash\nconda create -y -n pgl -c fredboudon -c conda-forge \\\n    openalea.lpy jupyterlab ipywidgets pip\n```\n\n```bash\nconda activate pgl\npip install pgljupyter\n```\n\n### Development install\n\n - install lpy, plantgl, jupyterlab, widgets and widgetsextension\n\n```bash\nmamba env create -f environment-dev.yml\nconda activate pgljupyter-dev\n```\n\n - install emsdk: https://emscripten.org/docs/getting_started/downloads.html\n\n```bash\ngit clone https://github.com/emscripten-core/emsdk.git\ncd emsdk\n./emsdk install 2.0.29\n./emsdk activate 2.0.29\nsource ./emsdk_env.sh\ncd ..\n```\n\n - get pgljupyter source\n\n```bash\ngit clone https://github.com/jvail/plantgl-jupyter.git\ncd plantgl-jupyter\n```\n\n - fetch plantgl and install pgljs deps\n\n```bash\ngit submodule update --init --recursive\ncd src/pgljs\nnpm install\ncd ../..\n```\n\n - install pgljupyter deps and build (requires activated emsdk i.e. source ./emsdk_env.sh)\n\n```bash\nnpm install\nnpm run build:all\npip install -e .\njupyter labextension develop . --overwrite\n```\n - run lab\n\n```bash\njupyter lab --notebook-dir=./examples\n```\n\n### Development uninstall\n\n```bash\npip uninstall pgljupyter\n```\n\nIn development mode, you will also need to remove the symlink created by `jupyter labextension develop`\ncommand. To find its location, you can run `jupyter labextension list` to figure out where the `labextensions`\nfolder is located. Then you can remove the symlink named `pgljupyter` within that folder.\n","readmeFilename":"README.md"}