🚧 switch mamba installation

.github/workflows/ci.yaml

@@ -18,38 +18,29 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest",
-             "macos-13",
+             #"macos-13",
              # "windows-latest" # rrcovNA cannot be build from source on windows-server
              ]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
     - name: Checkout
       uses: actions/checkout@v4
     - name: Set up Miniconda
-      # ! change action https://github.com/mamba-org/setup-micromamba
       uses: conda-incubator/setup-miniconda@v3
       with: 
-        miniforge-variant: Mambaforge
-        # miniforge-version: latest
-        use-mamba: true
-        channel-priority: disabled
         python-version: ${{ matrix.python-version }}
+        channel-priority: strict
         environment-file: snakemake_env.yml
         activate-environment: snakemake
         auto-activate-base: true
-        # auto-update-conda: true
+        auto-update-conda: true
     - name: inspect-conda-environment
       run: |
         conda info
         conda list
         conda env export --from-history --no-builds > environment.yml
         conda env export --no-builds
         conda env export --no-builds > environment_w_versions.yml
-    # - name: test-r-kernel-imports
-    #   run: |
-    #     Rscript -e "library(stringi)"
-    #     Rscript -e "library(stringr)"
-    #     Rscript -e "library(reshape2)"
     - name: Dry-Run demo workflow (integration test)
       run: | 
        cd project
@@ -59,6 +50,8 @@ jobs:
       run: | 
        cd project
        snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda
+    - name: Show current files in conda snakemake folder
+      run: ls -l project/.snakemake/conda/
     - name: Run demo workflow again (in case of installation issues)
       continue-on-error: true
       run: | 
@@ -75,35 +68,62 @@ jobs:
         name: ${{ matrix.os }}-${{ matrix.python-version }}-example-workflow-results
         path: |
           project/runs/example/
-          environment.yml
-          environment_w_versions.yml
+          snakemake_env
+          project/.snakemake/conda/
 
   run-unit-local-pip-installation:
     runs-on: ${{ matrix.os }}
     name: test-pip-installation
+    defaults:
+      run:
+        shell: bash -el {0}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: ["ubuntu-latest",]
+        # "macos-latest", "windows-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-tags: true
+          fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      # - uses: actions/setup-python@v5
+      #   with:
+      #     python-version: ${{ matrix.python-version }}
+
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
+          auto-update-conda: true
+          activate-environment: test
+          auto-activate-base: true
+
+      - name: check conda
+        run: |
+          conda info
+          conda list
+
+      - name: Install build dependencies explicitly
+        run: |
+          pip install setuptools_scm
+          conda list
 
       - name: install pimms
-        run: python -m pip install .
+        run: pip install .
+
+      - name: install njab
+        run: pip install njab
 
       - name: Install pytest
-        run: python -m pip install pytest pytest-cov
+        run: pip install pytest pytest-cov
 
       - name: Run pytest
         run: pytest .
 
       - name: Install papermill
-        run: python -m pip install papermill ipykernel
+        run: pip install papermill ipykernel
 
       - name: View papermill help message for notebooks (as scripts)
         run: |
@@ -141,4 +161,4 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/ci_workflow.yaml

@@ -2,8 +2,8 @@ name: run workflow with conda envs
 on:
   push:
     branches: [main, dev]
-  pull_request:
-    branches: [main, dev]
+  # pull_request:
+  #   branches: [main, dev]
   release:
     types: [published]
   schedule:

.github/workflows/test_pkg_on_colab.yaml

@@ -3,8 +3,8 @@ name: Test that tutorial runs on latest colab image
 on:
     # push:
     #     branches: [main]
-    pull_request:
-        branches: [main]
+    # pull_request:
+    #     branches: [main]
     schedule:
         - cron: '0 2 3 * *'
 

.github/workflows/workflow_website.yaml

@@ -1,7 +1,7 @@
 name: Build workflow website on public Alzheimer dataset (for protein groups)
 on:
-  pull_request:
-    branches: [main, dev]
+  # pull_request:
+  #   branches: [main, dev]
   release:
       types: [published]
   schedule:
@@ -73,4 +73,4 @@ jobs:
       uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: project/runs/alzheimer_study/_build/
+        publish_dir: project/runs/alzheimer_study/_build/

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.10"
     # You can also specify other tool versions:
     # nodejs: "19"
     # rust: "1.64"
@@ -32,4 +32,4 @@ python:
    - method: pip
      path: .
      extra_requirements:
-      - docs
+      - docs

environment.yml

@@ -9,7 +9,7 @@ channels:
   - plotly
   # - defaults
 dependencies:
-  - python>=3.8,<=3.12
+  - python>=3.9,<=3.12
   - numpy
   - pandas>=1
   - scipy>=1.6