Merge pull request #59 from pwrose/master

upgrade to Python 3.11
jupyter-guide · Jun 21, 2024 · 3306b5f · 3306b5f
2 parents a756d05 + 04f0e17
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diff --git a/README.md b/README.md
@@ -31,18 +31,17 @@ This example demonstrates a reproducible 4-step workflow for predicting a protei
 
 ---
 
-**Rule 9: Design Your Notebooks to Be Read, Run, and Explored.** The nbviewer links below provide a non-interactive preview of notebooks and ![Binder](https://mybinder.org/badge_logo.svg) buttons launch
-Jupyter Notebook or Jupyter Lab in your web browser using the Binder ([mybinder.org](https://mybinder.org/)) server (may be slow!). (See the Binder website how to setup links to a Git repository.) The HTML links provide a permanent static record of the notebooks. All notebooks can also be launched directly from the links in the 0-Workflow.ipynb top-level notebook.
+**Rule 9: Design Your Notebooks to Be Read, Run, and Explored.** The nbviewer links below provide a static preview of notebooks. Click on the `launch binder` buttons to launch Jupyter Lab in your web browser using the Binder ([mybinder.org](https://mybinder.org/)) server (may be slow!). The HTML links provide a permanent static record of the notebooks. All notebooks can also be launched directly from the links in the 0-Workflow.ipynb top-level notebook.
 
 ---
 
-| Nbviewer | Jupyter Notebook | Jupyter Lab | HTML |
-| ---      | --               | ---         | ---  |
-| [0-Workflow.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/0-Workflow.html) |
-| [1-CreateDataset.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/1-CreateDataset.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F1-CreateDataset.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F1-CreateDataset.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/1-CreateDataset.html) |
-| [2-CalculateFeatures.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/2-CalculateFeatures.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F2-CalculateFeatures.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F2-CalculateFeatures.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/2-CalculateFeatures.html) |
-| [3-FitModel.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/3-FitModel.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F3-FitModel.ipynb) |[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F3-FitModel.ipynb)  | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/3-FitModel.html) |
-| [4-Predict.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/4-Predict.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F4-Predict.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F4-Predict.ipynb)| [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/4-Predict.html) |
+| Nbviewer | Jupyter Lab | HTML |
+| ---      | ---         | ---  |
+| [0-Workflow.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/0-Workflow.html) |
+| [1-CreateDataset.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/1-CreateDataset.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F1-CreateDataset.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/1-CreateDataset.html) |
+| [2-CalculateFeatures.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/2-CalculateFeatures.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F2-CalculateFeatures.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/2-CalculateFeatures.html) |
+| [3-FitModel.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/3-FitModel.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F3-FitModel.ipynb)  | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/3-FitModel.html) |
+| [4-Predict.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/4-Predict.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F4-Predict.ipynb)| [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/4-Predict.html) |
 
 ---
 
@@ -54,18 +53,62 @@ Jupyter Notebook or Jupyter Lab in your web browser using the Binder ([mybinder.
 
 This example demonstrates a reproducible 2-step workflow for simulating a phylogenetic tree and sequences.
 
-| Nbviewer | Jupyter Notebook | Jupyter Lab | HTML |
-| ---      | --               | ---         | ---  |
-| [0-Workflow.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example2%2F0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/0-Workflow.html) |
-| [1-SimulateTree.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/1-SimulateTree.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example2%2F1-SimulateTree.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F1-SimulateTree.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/1-SimulateTree.html) |
-| [2-SimulateSequences.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/2-SimulateSequences.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example2%2F2-SimulateSequences.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F2-SimulateSequences.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/2-SimulateSequences.html) |
+| Nbviewer | Jupyter Lab | HTML |
+| ---      | ---         | ---  |
+| [0-Workflow.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/0-Workflow.html) |
+| [1-SimulateTree.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/1-SimulateTree.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F1-SimulateTree.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/1-SimulateTree.html) |
+| [2-SimulateSequences.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/2-SimulateSequences.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F2-SimulateSequences.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/2-SimulateSequences.html) |
 
-## Runnning Jupyter Notebooks on CyVerse/VICE
-The new [VICE (Visual Interactive Computing Environment)](https://cyverse-visual-interactive-computing-environment.readthedocs-hosted.com/en/latest/index.html) in the [CyVerse Discovery Environment](https://www.cyverse.org/discovery%20environment) enables users to run Jupyter Lab in a production environment. To use VICE, sign up for a free [CyVerse account](https://www.cyverse.org/create-account).
+---
+
+## Run Jupyter Lab on a local Machine (Laptop, Desktop)
+Prerequisites: Miniconda3 (light-weight, preferred) or Anaconda3 and Mamba
+
+* Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html)
+* Install Mamba: ```conda install mamba -n base -c conda-forge```
+------
+
+1. Clone this git repository
+
+```
+git clone https://github.com/jupyter-guide/ten-rules-jupyter.git
+```
+
+2. Change into the directory
+
+```
+cd ten-rules-jupyter
+```
+
+3. Create CONDA environment
+
+```
+mamba env create -f environment.yml
+```
+4. Activate the CONDA environment
+
+```
+conda activate ten-rules-jupyter
+```
+5. Launch Jupyter Lab
+
+```
+jupyter lab
+```
+
+6. Deactivate the CONDA environment
+
+```
+conda deactivate
+```
+
+------
 
-[![Vice](vice/vice_badge.png)](https://de.cyverse.org/de/?type=apps&app-id=8ec235d8-f173-11e9-a56f-008cfa5ae621&system-id=de)
+> To remove the CONDA environment, run ```conda env remove -n ten-rules-jupyter```
+------
 
-[Follow these step to run Jupyter Lab on VICE](https://cyverse-visual-interactive-computing-environment.readthedocs-hosted.com/en/latest/user_guide/quick-jupyter.html)
+## Citation
+Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, et al. (2019) Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLOS Computational Biology 15(7): e1007007. [https://doi.org/10.1371/journal.pcbi.1007007](https://doi.org/10.1371/journal.pcbi.1007007)
 
 ## Contact Us
 If you encounter any problems with this repository, please report them [here](https://github.com/jupyter-guide/ten-rules-jupyter/issues).
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,21 @@
+name: ten-rules-jupyter 
+
+channels:
+  - conda-forge
+  - anaconda
+
+dependencies:
+  - python=3.11
+  - ipywidgets=8.0.6
+  - joblib=1.2.0
+  - jupyterlab=4.2.2
+  - pandas=2.0.2
+  - matplotlib=3.7.1
+  - seaborn=0.9.0
+  - scikit-learn=1.4.2
+  - watermark==1.6.1
+  - pip
+  - pip:
+    - Pyvolve==1.1.0 
+    - treesap==1.0.8
+    - treeswift==1.0.97
diff --git a/example1/0-Workflow.ipynb b/example1/0-Workflow.ipynb
@@ -202,21 +202,21 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPython 3.6.3\n",
-      "IPython 6.3.1\n",
+      "CPython 3.11.9\n",
+      "IPython 8.25.0\n",
       "\n",
-      "ipywidgets 7.4.0\n",
-      "matplotlib 2.2.2\n",
-      "numpy 1.14.5\n",
-      "pandas 0.22.0\n",
-      "sklearn 0.20.0\n",
+      "ipywidgets 8.0.6\n",
+      "matplotlib 3.7.1\n",
+      "numpy 1.26.4\n",
+      "pandas 2.0.2\n",
+      "sklearn 1.4.2\n",
       "\n",
-      "compiler   : GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)\n",
+      "compiler   : Clang 16.0.6 \n",
       "system     : Darwin\n",
-      "release    : 17.5.0\n",
+      "release    : 19.6.0\n",
       "machine    : x86_64\n",
       "processor  : i386\n",
-      "CPU cores  : 4\n",
+      "CPU cores  : 8\n",
       "interpreter: 64bit\n"
      ]
     }
@@ -240,7 +240,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -254,9 +254,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }