⚡📝 make ci more robust to installation issues, update README for Mac …

…M1 chicps

.github/workflows/ci.yaml

@@ -69,17 +69,25 @@ jobs:
         mkdir runs
         papermill 04_1_train_pimms_models.ipynb runs/04_1_train_pimms_models.ipynb
         papermill 04_1_train_pimms_models.ipynb runs/04_1_train_pimms_models_no_val.ipynb -p sample_splits False
-    - name: Run demo workflow (integration test)
+    - name: Dry-Run demo workflow (integration test)
       continue-on-error: true
       run: | 
        cd project
        snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml -n
+    - name: Run demo workflow (integration test)
+      continue-on-error: true
+      run: | 
+       cd project
        snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml
     - name: Run demo workflow again (in case of installation issues)
+      continue-on-error: true
       run: | 
         cd project
-        snakemake -p -c1 -n --configfile config/single_dev_dataset/example/config.yaml
         snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml
+    - name: Run demo workflow again (in case of installation issues) - one thread
+      run: | 
+        cd project
+        snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml
     - name: Archive results
     # https://github.com/actions/upload-artifact
       uses: actions/upload-artifact@v4

.github/workflows/workflow_website.yaml

@@ -39,9 +39,15 @@ jobs:
         cd project
         snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c4 -k
     - name: Run demo workflow again (in case of installation issues)
+      continue-on-error: true
       run: | 
         cd project
         snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c4 -k
+    - name: Run demo workflow again (in case of installation issues) with one thread
+      continue-on-error: true
+      run: | 
+        cd project
+        snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c1 -k
     - name: Run differential analysis workflow
       run: | 
         cd project

README.md

@@ -127,23 +127,24 @@ mamba env create -n pimms -f environment.yml # faster, less then 5mins
 
 If on Mac M1, M2 or having otherwise issue using your accelerator (e.g. GPUs): Install the pytorch dependencies first, then the rest of the environment:
 
-### Install pytorch first (M-chips)
+### Install pytorch first
 
-> :warning: We currently see that fastai is not compatible with the M1 chip. M2 chips are working fine.
-> 
-> The ARM architecture seems to cause issues with some packages (fastai and potentiall others).
+> :warning: We currently see issues with some installations on M1 chips. A dependency
+> for one workflow is polars, which causes the issue. This should be [fixed now](https://github.com/RasmussenLab/njab/pull/13) 
+> for general use by delayed import 
+> of `mrmr-selection` in `njab`. If you encounter issues, please open an issue.
 
 Check how to install pytorch for your system [here](https://pytorch.org/get-started).
 
 - select the version compatible with your cuda version if you have an nvidia gpu or a Mac M-chip.
 
 ```bash
-conda create -n vaep python=3.9 pip
-conda activate vaep
+conda create -n pimms python=3.9 pip
+conda activate pimms
 # Follow instructions on https://pytorch.org/get-started: 
 # CUDA is not available on MacOS, please use default package
 # pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
-conda install pytorch::pytorch torchvision torchaudio fastai -c pytorch -c fastai
+conda install pytorch::pytorch torchvision torchaudio fastai -c pytorch -c fastai -y
 pip install pimms-learn
 pip install jupyterlab papermill # use run notebook interactively or as a script