[FIX] Update packages

Author: eseiler

.github/workflows/pages.yml

@@ -45,7 +45,7 @@ jobs:
           tar xf ${{ github.workspace }}/.github/data/data.tar.zst -C ${{ github.workspace }}/results/raw_data
 
       - name: Run snakemake
-        run: snakemake --use-conda --conda-frontend mamba --cores $(nproc)
+        run: snakemake --use-conda --cores $(nproc)
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3

workflow/envs/bokeh.yml

@@ -2,4 +2,4 @@ name: bokeh
 channels:
   - conda-forge
 dependencies:
-  - bokeh=3.4.1
+  - bokeh=3.7.3

workflow/envs/landingpage.yml

@@ -2,4 +2,4 @@ name: landingpage
 channels:
   - conda-forge
 dependencies:
-  - html2image=2.0.4.3
+  - html2image=2.0.7

workflow/envs/lint.yml

@@ -2,7 +2,7 @@ name: lint
 channels:
   - conda-forge
 dependencies:
-  - black=24.4.0
-  - isort=5.13.2
-  - pylint=3.1.0
-  - bioconda::snakefmt=0.10.1
+  - black=24.10.0
+  - isort=6.0.1
+  - pylint=3.3.8
+  - bioconda::snakefmt=0.11.0

workflow/envs/r.yml

@@ -2,7 +2,7 @@ name: r
 channels:
   - conda-forge
 dependencies:
-  - r-base=4.3.3
+  - r-base=4.4.3
   - r-here
   - r-yaml
   - r-tidyr

workflow/envs/snakemake.yml

@@ -2,4 +2,4 @@ name: snakemake
 channels:
   - conda-forge
 dependencies:
-  - bioconda::snakemake=8.10.7
+  - bioconda::snakemake=9.9.0