Fix integration environments (#292)

* New mamba action Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix integration environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix integration environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix integration environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> * Fix compositional environments Signed-off-by: zethson <lukas.heumos@posteo.net> --------- Signed-off-by: zethson <lukas.heumos@posteo.net>
theislab · Aug 9, 2024 · 6461a5c · 6461a5c
1 parent e45ea77
commit 6461a5c
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diff --git 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
@@ -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
@@ -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