Simplify CI, fix mybinder.org build, bump python (and other) versions

.binder/environment.yml

@@ -2,42 +2,42 @@ channels:
 - conda-forge
 - nodefaults
 dependencies:
-# !! you can only use single `=` to set a version. Otherwise it will break the update job
-- invoke=2.2.0
-- packaging
-- pyyaml
+- ruamel.yaml
 # applications
-- jupyterlab=4.1.8
-- jupyter-collaboration=2.1.1
-- nbconvert=7.16.4
-- notebook=7.1.3
+- jupyterlab
+- jupyter-collaboration
+- nbconvert
+- notebook
 # extensions
-- jupyter-offlinenotebook=0.3.1
-- jupyterlab-fasta=3.3
-- jupyterlab-geojson=3.4
+- jupyter-offlinenotebook
+- jupyterlab-fasta
+- jupyterlab-geojson
+# R kernel
+- r-irkernel
+- r-ggplot2
 # Python Kernel
-- ipykernel=6.29.3
-- xeus-python=0.14.3
-- ipywidgets=8
-- ipyleaflet=0.19.1
-- altair=5.3.0
-- bqplot=0.12.43
-- dask=2024.5.0
-- matplotlib-base=3.8.4
-- pandas=2.2.2
-- python=3.9
-- scikit-image=0.22.0
-- scikit-learn=1.4.2
-- seaborn-base=0.13.2
-- tensorflow=2.11.0
-- sympy=1.12
-- traittypes=0.2.1
+- ipykernel
+- xeus-python
+- ipywidgets
+- ipyleaflet
+- altair
+- bqplot
+- dask
+- matplotlib-base
+- pandas
+- python=3.12
+- scikit-image
+- scikit-learn
+- seaborn-base
+- tensorflow
+- sympy
+- traittypes
 # C++ Kernel
-- xeus-cling=0.13.0
-- xtensor=0.23.10
-- xtensor-blas=0.19.2
-- xwidgets=0.26.1
-- xleaflet=0.16.0
+# - xeus-cling
+# - xtensor
+# - xtensor-blas
+# - xwidgets
+# - xleaflet
 # CLI tools
 - pip
 - vim

.binder/postBuild

@@ -1,8 +1,7 @@
 set -ex
 
-# invoke r --env-name=notebook
-invoke demofiles
-invoke talk -t demo
+python build.py
+
 rm -rf demofiles
 rm -rf notebooks
 rm -rf narrative

.github/workflows/main.yml

@@ -15,38 +15,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Cache conda
-        uses: actions/cache@v3
-        env:
-          # Increase this value to reset cache if .binder/environment.yml has not changed
-          CACHE_NUMBER: 0
+      - name: Install mamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.binder/environment.yml') }}
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          mamba-version: ">=1.4.0"
-          # Defaults is added automatically
-          channels: conda-forge
-          channel-priority: "strict"
-          activate-environment: jupyterlab-demo
+          micromamba-version: '1.5.1-0'
           environment-file: .binder/environment.yml
-          # The following option is blocking the environment resolution (newer versions are not found)
-          # use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          environment-name: jupyterlab-demo
+          cache-environment: true
       - run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
+          micromamba info
+          micromamba list
+          micromamba config sources
+          micromamba config list
           printenv | sort
       - run: |
-          invoke r --env-name=jupyterlab-demo
           jupyter nbconvert --to notebook --execute  --ExecutePreprocessor.timeout=60 --stdout notebooks/Data.ipynb > /dev/null;
           jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=60 --stdout notebooks/Fasta.ipynb > /dev/null;
           jupyter nbconvert --to notebook --execute  --ExecutePreprocessor.timeout=60 --stdout notebooks/R.ipynb > /dev/null;
-          invoke demofiles
-          invoke talk -t demo
-          jupyter lab workspaces import .binder/workspace.json
-          python -m jupyterlab.browser_check
-          invoke clean
+          python build.py

README.md

@@ -13,84 +13,15 @@ generation user interface of Project Jupyter.
 The demo requires `mamba`, available as part of [Mambaforge](https://github.com/conda-forge/miniforge) and the package
  requirements are described in `environment.yml`
 
-To install the environment and demofiles, we use [pyinvoke](http://pyinvoke.org). To install pyinvoke with `mamba` call:
-```bash
-mamba install -c conda-forge invoke packaging pyyaml
-```
-
-### Create the environment
-
-To create the conda environment with all the dependencies and jupyterlab extensions for the demo, run:
-
-```bash
-invoke environment  # optionally --env-name=my-env-name
-```
-
-The default environment name is `jupyterlab-demo`.
-
-To create the environment and remove previous installation, call:
-
-```bash
-invoke environment --clean
-```
-
-### Activate/deactivate the environment
-
-To activate the conda environment, run:
-
-```bash
-source activate jupyterlab-demo
-```
-
-To deactivate the conda environment, run:
-
-```bash
-source deactivate
-```
-
-### Additional demo files
-
-The demo includes files from a number of other repositories. To install these files,
-run:
-
-```bash
-invoke demofiles
-```
-
-To remove demofiles and download again all:
-```
-invoke demofiles --clean
-```
-
-### R Language support
-
-To add R language support, run:
-
-```bash
-invoke r
-```
-
-### Julia Language support
-
-To add Julia language support follow the instructions [here](https://github.com/JuliaLang/IJulia.jl#installation).
-
-
-### Uninstalling
-
-To uninstall the demofiles and enviornment, call:
-
-```
-invoke clean
-```
+TODO: More installation instructions
 
 # Demo guide
 
 The basic outline of the JupyterLab demo is described in the file `jupyterlab.md`.
 
-
 # External Repositories
 
-Our `invoke demofiles` clones repos from other authors.  The details of these repos are as follows:
+Our `build.py` clones repos from other authors.  The details of these repos are as follows:
 
 | Name  | Author |License |
 |---|---|---|

build.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python3
+from pathlib import Path
+import subprocess
+from ruamel.yaml import YAML
+import shutil
+import os
+
+yaml = YAML()
+
+DEMO_FOLDER = "demofiles"
+
+def setup_talks():
+    """
+    Reads yaml file talks.yml and moves files and folders specified in yaml
+    file to the a folder matching the name of the talk Args: talk_name: name
+    of talk in talks.yml Note: yaml file is assumed to be a dict of dicts of
+    lists and dict with the following python format:
+    {'talk_name':
+        {'folders':
+            {'src0': 'dest0', 'src1': 'dest1']
+        'files':
+            ['file0', file1']
+    'rename':
+    {'oldname': 'newname'}
+        }
+    }
+    or in yaml format:
+    talk_name:
+        folders:
+            src0: dest0
+            src1: dest1
+        files:
+            - file0
+            - file1
+        rename:
+            oldname: newname
+    """
+    with open("talks.yml", "r") as stream:
+        talks = yaml.load(stream)
+    for talk_name in talks:
+        Path(talk_name).mkdir(parents=True, exist_ok=True)
+
+        if "files" in talks[talk_name]:
+            for f in talks[talk_name]["files"]:
+                copied_path = os.path.join(talk_name, os.path.basename(f))
+                shutil.copy(f, copied_path)
+                assert os.path.isfile(copied_path), f"{f} failed to copy into {talk_name}"
+
+        if "folders" in talks[talk_name]:
+            for src, dst in talks[talk_name]["folders"].items():
+                dst = os.path.join(talk_name, dst)
+                if not os.path.exists(dst):
+                    shutil.copytree(src, dst)
+
+        if "rename" in talks[talk_name]:
+            for old_file, new_file in talks[talk_name]["rename"].items():
+                moved_file = os.path.join(talk_name, os.path.basename(old_file))
+                if os.path.isfile(moved_file):
+                    os.rename(moved_file, os.path.join(talk_name, new_file))
+                elif os.path.isfile(old_file):
+                    shutil.copy(old_file, os.path.join(talk_name, new_file))
+
+def setup_demofiles():
+    print("creating demofolder")
+    demo_folder = Path("demofiles")
+    demo_folder.mkdir(parents=True, exist_ok=True)
+
+    # list of repos used in demo
+    print(f"cloning repos into demo folder {demo_folder}")
+    reponames = [
+        "jakevdp/PythonDataScienceHandbook",
+        "swissnexSF/Urban-Data-Challenge",
+        "altair-viz/altair",
+        "QuantEcon/QuantEcon.notebooks",
+        "theandygross/TCGA",
+        "aymericdamien/TensorFlow-Examples",
+        "bloomberg/bqplot",
+    ]
+    for repo in reponames:
+        target_path = demo_folder / Path(repo.split("/")[1])
+        if not target_path.is_dir():
+            subprocess.check_call([
+                "git", "clone", "--depth", "1",
+                f"https://github.com/{repo}.git"
+            ], cwd=demo_folder)
+    # This empty file and empty folder are for showing drag and drop in jupyterlab
+    Path("move_this_file.txt").touch()
+    Path("move_it_here").mkdir(exist_ok=True)
+
+def main():
+    setup_demofiles()
+    setup_talks()
+
+
+if __name__ == "__main__":
+    main()