Remove binder

.github/workflows/build.yml

@@ -0,0 +1,27 @@
+# Builds the repository using mamba
+
+---
+name: build
+
+on: 
+  push:
+  pull_request:
+  schedule:
+      - cron: '0 0 * * 0'
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        envs: [binder/environment.yml]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      - name: Install Conda environment for ${{ matrix.envs }} with Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ${{ matrix.envs }}

README.md

@@ -1,5 +1,4 @@
 # Guide on how to integrate CellProfiler and OMERO
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ome/omero-guide-cellprofiler/master?filepath=notebooks/idr0002.ipynb)
 [![Documentation Status](https://readthedocs.org/projects/omero-guide-cellprofiler/badge/?version=latest)](https://omero-guides.readthedocs.io/en/latest/cellprofiler/docs/index.html)
 [![Actions Status](https://github.com/ome/omero-guide-cellprofiler/workflows/repo2docker/badge.svg)](https://github.com/ome/omero-guide-cellprofiler/actions)
 
@@ -12,11 +11,6 @@ This repository contains documentation and notebooks.
 
 ## Run the notebooks
 
-### Running on cloud resources
-
-[![Binder](https://mybinder.org/v2/gh/ome/omero-guide-cellprofiler/master?filepath=notebooks)
-
-The OMERO server used will need to have [websockets support](https://docs.openmicroscopy.org/omero/latest/sysadmins/websockets.html) enabled.
 
 ### Running in Docker
 
@@ -31,13 +25,17 @@ tool to run this repository as a local Docker instance:
 ### Running locally
 
 Finally, if you would like to install the necessary requirements locally,
-we suggest using conda.
+we suggest using mamba.
 
 Then, create the environment:
 
     $ git clone https://github.com/ome/omero-guide-cellprofiler
     $ cd omero-guide-cellprofiler
-    $ conda env create -n omero-guide-cellprofiler -f binder/environment.yml
+    $ mamba env create -f binder/environment.yml
+
+For OS X arm64 Apple Silicon
+
+    $ CONDA_SUBDIR=osx-64 mamba env create -f binder/environment.yml
 
 and activate the newly created environment:
 
@@ -51,7 +49,6 @@ The following steps are only required if you want to run the notebooks
   * To register the environment, run ``python -m ipykernel install --user --name omero-guide-cellprofiler``
   * Select the notebook you wish to run and select the ``Kernel>Change kernel>Python [conda env:omero-guide-cellprofiler]`` or ``Kernel>Change kernel>omero-guide-cellprofiler``
 * If Anaconda is not installed:
-  * In the environment, install ``jupyter`` e.g. ``pip install jupyter``
   * Add the virtualenv as a jupyter kernel i.e. ``ipython kernel install --name "omero-guide-cellprofiler" --user``
   * Open jupyter notebook i.e. ``jupyter notebook`` and select the ``omero-guide-cellprofiler`` kernel or ``[conda env:omero-guide-cellprofiler]`` according to what is available
 

binder/environment.yml

@@ -1,11 +1,12 @@
+name: omero-guide-cellprofiler
 channels:
   - defaults
   - anaconda
   - bioconda
   - conda-forge
   - ome
 dependencies:
-  - zeroc-ice36-python
+  - ome::zeroc-ice36-python==3.6.5
   - h5py==3.7.0
   - pandas==1.5.3
   - pip
@@ -21,5 +22,6 @@ dependencies:
   - scikit-learn==1.2.2
   - mysqlclient==1.4.6
   - pip:
+    - jupyter==1.0.0
     - ome-zarr
-    - git+https://github.com/CellProfiler/CellProfiler.git@v4.2.4
+    - git+https://github.com/CellProfiler/CellProfiler.git@v4.2.6