From 6e30643c344a3fe932cdc970da2d340182b7f088 Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Wed, 14 Dec 2022 14:15:55 +0100 Subject: [PATCH 1/5] Update environment.yml --- environment.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/environment.yml b/environment.yml index 62b85c0a0..856e34663 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 From 5a70a64e4f0f61ccfde8e49796995fc15eb4f450 Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Wed, 14 Dec 2022 14:17:37 +0100 Subject: [PATCH 2/5] Delete requirements.txt --- requirements.txt | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 633720b90..000000000 --- a/requirements.txt +++ /dev/null @@ -1,13 +0,0 @@ -pyopenms -matplotlib -plotly -pandas -adjustText -scikit-learn -requests -bokeh -datashader -holoviews -pyviz_comms -jupyter-server-proxy -massql From 544981a116ad611bc8c0c07e06978fcd7ee1306b Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Wed, 14 Dec 2022 14:17:55 +0100 Subject: [PATCH 3/5] Delete postBuild --- postBuild | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 postBuild diff --git a/postBuild b/postBuild deleted file mode 100644 index d2dac98b3..000000000 --- a/postBuild +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -wget https://nightly.link/OpenMS/OpenMS/workflows/pyopenms-wheels/nightly/Linux-wheels.zip\?status\=completed -mv Linux-wheels.zip\?status=completed Linux-wheels.zip -unzip Linux-wheels.zip -pip install pyopenms_nightly-*-cp310-cp310*.whl - -# Those should be enabled by default on binder. For serving -#jupyter serverextension enable --sys-prefix jupyter_server_proxy -#jupyter labextension install @jupyterlab/server-proxy From 522b142b56398d6136b0c2976078001e592a148e Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Wed, 14 Dec 2022 14:25:46 +0100 Subject: [PATCH 4/5] Update environment.yml --- environment.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 856e34663..a7ca22119 100644 --- a/environment.yml +++ b/environment.yml @@ -17,4 +17,6 @@ dependencies: - holoviews - pyviz_comms - jupyter-server-proxy - - massql + - pip + - pip: + - massql From 650b98a2f73b39da715fb9443b430409e41fa79b Mon Sep 17 00:00:00 2001 From: Samuel Wein Date: Wed, 1 Nov 2023 13:27:39 +0100 Subject: [PATCH 5/5] Update test-pr.yaml to use conda --- .github/workflows/test-pr.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/test-pr.yaml b/.github/workflows/test-pr.yaml index 37709757b..892695dd8 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