Enhancement/Remove Anaconda Defaults Channel (#145)

* remove anaconda defaults channel * sanity testing gh actions * pin down version of mkl * disable reference tests for gha testing * disable results checking for gha testing * reactivate reference results checking tests * pin mkl version in regular deeprvat env file --------- Co-authored-by: Brian Clarke <[email protected]> Co-authored-by: Marcel Mück <[email protected]>
PMBio · Oct 25, 2024 · 54e9057 · 54e9057
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commit 54e9057
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diff --git a/.github/workflows/pipeline-tests.yml b/.github/workflows/pipeline-tests.yml
@@ -111,7 +111,6 @@ jobs:
       prerun_cmd: cp ./tests/deeprvat/regenie/pretrained/deeprvat_config.yaml ./example/
       dry_run: false
       download_regenie_outputs: true
-      #run_burden_results_check: true
       run_regenie_association_results_check: true
 
   # Association Testing Training

diff --git a/deeprvat_annotations.yml b/deeprvat_annotations.yml
@@ -1,7 +1,6 @@
 name: deeprvat_annotations
 channels:
   - conda-forge
-  - defaults
   - bioconda
 dependencies:
   - python=3.9.16

diff --git a/deeprvat_env.yaml b/deeprvat_env.yaml
@@ -4,13 +4,13 @@ channels:
   - nvidia
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - click=8.1
   - cudatoolkit=11.8
   - dask=2023.5
   - fastparquet=0.5
   - h5py=3.1
+  - mkl==2022.1.0
   - numcodecs=0.11
   - numpy=1.21
   - optuna=2.10

diff --git a/deeprvat_env_no_gpu.yml b/deeprvat_env_no_gpu.yml
@@ -3,13 +3,12 @@ channels:
   - pytorch
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - click=8.1
   - dask=2023.5
   - fastparquet=0.5
   - h5py=3.1
-  - mkl!=2024.1.0
+  - mkl==2022.1.0
   - numcodecs=0.11
   - numpy=1.21
   - optuna=2.10