From 6461a5c0c8f797ed3ace9909e3e66348d9aef78b Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Fri, 9 Aug 2024 10:57:51 +0200 Subject: [PATCH] Fix integration environments (#292) * New mamba action Signed-off-by: zethson * Fix integration environments Signed-off-by: zethson * Fix integration environments Signed-off-by: zethson * Fix integration environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson * Fix compositional environments Signed-off-by: zethson --------- Signed-off-by: zethson --- jupyter-book/conditions/compositional.yml | 26 ++++++++----------- .../advanced_integration.yml | 2 +- .../paired_integration.yml | 2 +- 3 files changed, 13 insertions(+), 17 deletions(-) diff --git a/jupyter-book/conditions/compositional.yml b/jupyter-book/conditions/compositional.yml index b4dbf6df..7acb57bc 100644 --- a/jupyter-book/conditions/compositional.yml +++ b/jupyter-book/conditions/compositional.yml @@ -1,22 +1,18 @@ name: compositional channels: - - anaconda - conda-forge - bioconda + - anaconda dependencies: - - conda-forge::jupyterlab=3.5.0 - - conda-forge::scanpy=1.9.1 - - anaconda::git - - r-base==4.0.5 - - bioconductor-edger==3.32.1 - - rpy2==3.4.2 - - notebook - - schist==0.7.15 - - conda-forge::r-statmod==1.4.37 + - conda-forge::python=3.11.9 + - conda-forge::git + - conda-forge::jupyterlab + - conda-forge::r-statmod + - r-base=4.3.1 + - bioconductor-edger + - conda-forge::rpy2=3.5.11 + - conda-forge::notebook + - conda-forge::schist=0.8.4 - pip - pip: - - altair==4.2.0 - - pertpy==0.3.0 - - toytree==2.0.1 - - scvi-tools==0.17.1 - - git+https://github.com/emdann/milopy.git@master + - pertpy==0.8.0 diff --git a/jupyter-book/multimodal_integration/advanced_integration.yml b/jupyter-book/multimodal_integration/advanced_integration.yml index 7d0a663c..0c04beb2 100644 --- a/jupyter-book/multimodal_integration/advanced_integration.yml +++ b/jupyter-book/multimodal_integration/advanced_integration.yml @@ -15,7 +15,7 @@ dependencies: - conda-forge::rpy2=3.5.6 - bioconda::anndata2ri=1.1 - conda-forge::r-spatstat.core - - conda-forge::pip + - conda-forge::pip<24.1 - pip: - scvi-tools==0.19.0 - multigrate==0.0.2 diff --git a/jupyter-book/multimodal_integration/paired_integration.yml b/jupyter-book/multimodal_integration/paired_integration.yml index 641023fa..61c1ee70 100644 --- a/jupyter-book/multimodal_integration/paired_integration.yml +++ b/jupyter-book/multimodal_integration/paired_integration.yml @@ -12,7 +12,7 @@ dependencies: - conda-forge::notebook - conda-forge::rpy2=3.5.6 - bioconda::anndata2ri=1.1 - - conda-forge::pip + - conda-forge::pip<24.1 - pip: - muon - pysam