diff --git a/.github/workflows/test-pr.yaml b/.github/workflows/test-pr.yaml index 74aea250b..bb98480d9 100644 --- a/.github/workflows/test-pr.yaml +++ b/.github/workflows/test-pr.yaml @@ -37,9 +37,7 @@ jobs: - name: Installing Dependencies run: | - python3 -m pip install --upgrade pip - python3 -m pip install --upgrade pandocfilters jupyter - python3 -m pip install --upgrade -r requirements.txt + $CONDA/bin/conda env update --file environment.yml --name base - name: Generating notebooks diff --git a/environment.yml b/environment.yml index 62b85c0a0..a7ca22119 100644 --- a/environment.yml +++ b/environment.yml @@ -1,10 +1,11 @@ name: binder-env +channels: + - conda-forge + - bioconda + - openms dependencies: -- python=3.10 -#- bioconda::pyopenms maybe not needed because we install it in a post-build event -- pip - -- pip: + - python=3.10 + - pyopenms - matplotlib - plotly - pandas @@ -16,4 +17,6 @@ dependencies: - holoviews - pyviz_comms - jupyter-server-proxy - - massql + - pip + - pip: + - massql diff --git a/postBuild b/postBuild deleted file mode 100644 index d18037d92..000000000 --- a/postBuild +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -python3 -m pip install --index-url https://pypi.cs.uni-tuebingen.de/simple/ pyopenms - -# Those should be enabled by default on binder. For serving -#jupyter serverextension enable --sys-prefix jupyter_server_proxy -#jupyter labextension install @jupyterlab/server-proxy - -mkdir -p ~/.jupyter/ && cp jupyter_notebook_config.py ~/.jupyter/