Merge develop with faster tests (#199)

* Use caching for tests

---------

Co-authored-by: alsmith <asmith151@outlook.com>

.github/workflows/test_pipelines.yml

@@ -3,17 +3,13 @@ name: Python package
 on: [push]
 
 jobs:
-  Test:
-    if: github.event_name == 'pull_request' || github.event_name == 'push'
   Test:
     if: github.event_name == 'pull_request' || github.event_name == 'push'
     runs-on: ubuntu-latest
     strategy:
       matrix:
         test: ["config", "design", "pipeline"]
         assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"]
-        test: ["config", "design", "pipeline"]
-        assay: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"]
 
     steps:
       - uses: actions/checkout@v3
@@ -28,7 +24,6 @@ jobs:
           key: ${{ runner.os }}-env-${{ hashFiles('**/testing.yml') }}
           restore-keys: |
             ${{ runner.os }}-env-
-
       - name: Setup conda
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -41,7 +36,6 @@ jobs:
         shell: pwsh
         run: |
           pip install .
-
       - name: Cache singularity
         if: matrix.test == 'pipeline'
         id: cache-singularity
@@ -51,7 +45,6 @@ jobs:
           key: ${{ runner.os }}-singularity-${{ hashFiles('tmp/*') }}
           restore-keys: |
             ${{ runner.os }}-singularity-
-
       - uses: eWaterCycle/setup-apptainer@v2
         if: matrix.test == 'pipeline'
         with:
@@ -63,7 +56,6 @@ jobs:
         run: |
           apptainer remote add --no-login SylabsCloud cloud.sylabs.io
           apptainer remote use SylabsCloud
-
       - name: Pull singularity images
         if: matrix.test == 'pipeline' && steps.cache-singularity.outputs.cache-hit != 'true'
         shell: bash
@@ -77,10 +69,9 @@ jobs:
           elif [[ "${{ matrix.assay }}" == "rna-rx" ]]; then
             apptainer pull --force library://asmith151/seqnado/seqnado_report:latest
           fi
-
       - name: Test ${{ matrix.test }} ${{ matrix.assay }}
         shell: pwsh
         env:
           TMPDIR: /tmp
         run: |
-          pytest tests/test_pipelines.py::test_${{ matrix.test }}[${{ matrix.assay }}] -vv -s --cores 4
+          pytest tests/test_pipelines.py::test_${{ matrix.test }}[${{ matrix.assay }}] -vv -s --cores 4