[INFRA] Try mamba

.github/vercel/0_setup.sh

@@ -4,26 +4,15 @@
 # SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-set -euxo pipefail
+set -euo pipefail
 
-WORK_DIR=`pwd`
-CACHE_DIR="${WORK_DIR}/node_modules" # The node_modules directory is always cached.
+FILE="Miniforge3-$(uname)-$(uname -m).sh"
+curl -LsO "https://github.com/conda-forge/miniforge/releases/latest/download/${FILE}"
+chmod +x ${FILE}
+./${FILE} -b
+rm -rf ${FILE}
 
-mkdir -p ${CACHE_DIR}/miniconda3
-curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o ${CACHE_DIR}/miniconda3/miniconda.sh
-chmod +x ${CACHE_DIR}/miniconda3/miniconda.sh
-${CACHE_DIR}/miniconda3/miniconda.sh -b -u -p ${CACHE_DIR}/miniconda3
-rm -rf ${CACHE_DIR}/miniconda3/miniconda.sh
-
-${CACHE_DIR}/miniconda3/bin/conda init bash
-
-set +x
 source ~/.bashrc
-set -x
-
-conda config --add channels defaults
-conda config --add channels bioconda
-conda config --add channels conda-forge
-conda config --set channel_priority strict
 
-conda install --quiet --yes snakemake zstd wget mamba
+mamba config --set default_threads 4
+mamba install --quiet --yes snakemake -c bioconda

.github/vercel/1_build.sh

@@ -4,16 +4,12 @@
 # SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: BSD-3-Clause
 
-set -euxo pipefail
+set -euo pipefail
 
-set +x
 source ~/.bashrc
-conda activate
-set -x
+mamba activate
 
-export WORK_DIR=`pwd`
+mkdir -p results
+zstd --decompress .github/data/data.tar.zst -c | tar xf - -C results
 
-mkdir -p ${WORK_DIR}/results
-zstd --decompress ${WORK_DIR}/.github/data/data.tar.zst -c | tar xf - -C ${WORK_DIR}/results
-
-snakemake --use-conda --cores 2
+snakemake --use-conda --conda-frontend mamba --cores 4

.github/workflows/lint.yml

@@ -16,7 +16,7 @@ defaults:
 
 jobs:
   auto-lint:
-    name: Formatting
+    name: Formatting and Style
     runs-on: ubuntu-22.04
     timeout-minutes: 15
     outputs:
@@ -38,6 +38,7 @@ jobs:
           channel-priority: strict
           environment-file: workflow/envs/lint.yml
           miniforge-version: latest
+          use-mamba: true
 
       - name: Run isort
         run: isort .
@@ -65,29 +66,13 @@ jobs:
           author_email: [email protected]
           message: '[MISC] automatic linting'
 
-  lint:
-    needs: auto-lint
-    if: needs.auto-lint.outputs.has_changes == 'false'
-    name: Style Guide
-    runs-on: ubuntu-22.04
-    timeout-minutes: 15
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          repository: ${{ github.event.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.ref }}
-
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: lint
-          auto-activate-base: false
-          auto-update-conda: false
-          channel-priority: strict
-          environment-file: workflow/envs/lint.yml
-          miniforge-version: latest
+      # Wait for new commit to start new workflow run such that this run is cancelled.
+      # Useful for auto-merge on success of all workflows.
+      - name: Wait
+        if: needs.auto-lint.outputs.has_changes == 'true'
+        run: sleep 60
 
+      # Otherwise, continue.
       - name: Run pylint
+        if: needs.auto-lint.outputs.has_changes == 'false'
         run: pylint .
-

.github/workflows/pages.yml

@@ -35,14 +35,15 @@ jobs:
           channel-priority: strict
           environment-file: workflow/envs/snakemake.yml
           miniforge-version: latest
+          use-mamba: true
 
       - name: Extract data
         run: |
           mkdir -p ${{ github.workspace }}/results
           tar xf ${{ github.workspace }}/.github/data/data.tar.zst -C ${{ github.workspace }}/results
 
       - name: Run snakemake
-        run: snakemake --use-conda --cores 2
+        run: snakemake --use-conda --conda-frontend mamba --cores 2
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3

.github/workflows/test.yml

@@ -32,11 +32,12 @@ jobs:
           channel-priority: strict
           environment-file: workflow/envs/snakemake.yml
           miniforge-version: latest
+          use-mamba: true
 
       - name: Extract data
         run: |
           mkdir -p ${{ github.workspace }}/results
           tar xf ${{ github.workspace }}/.github/data/data.tar.zst -C ${{ github.workspace }}/results
 
       - name: Run snakemake
-        run: snakemake --use-conda --cores 2
+        run: snakemake --use-conda --conda-frontend mamba --cores 2

workflow/envs/bokeh.yml

@@ -1,6 +1,5 @@
 name: bokeh
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - bokeh=3.4.1

workflow/envs/lint.yml

@@ -1,7 +1,6 @@
 name: lint
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - black=24.4.0
   - isort=5.13.2

workflow/envs/r.yml

@@ -1,7 +1,6 @@
 name: r
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - r-base=4.3.3
   - r-here

workflow/envs/raptor.yml

@@ -1,6 +1,5 @@
 name: raptor
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - bioconda::raptor

workflow/envs/snakemake.yml

@@ -1,6 +1,5 @@
 name: snakemake
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - bioconda::snakemake=8.10.7