Merge pull request #36 from metagenlab/unit-tests

Optimized unit tests

.github/workflows/unit-tests.yml

@@ -49,19 +49,25 @@ jobs:
       - name: Setup apptainer
         uses: eWaterCycle/[email protected]
 
-      - name: Setup MeSS environment
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Setup pip
+        uses: actions/setup-python@v5
         with:
-          miniforge-version: latest
-          activate-environment: mess
           python-version: ${{ matrix.python-version }}
-          auto-update-conda: true
+          cache: "pip" # caching pip dependencies
+          cache-dependency-path: setup.py
 
       - name: Install MeSS and pytest-cov
         run: |
-          pip install -e .
+          pip install -e . 
           pip install pytest coverage
 
+      - name: Cache apptainer containers
+        uses: actions/cache@v3
+        with:
+          path: .snakemake/apptainer # Cache the Apptainer containers directory
+          key: ${{ runner.os }}-apptainer-${{ hashFiles('mess/workflow/envs/containers.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-apptainer-
       - name: Run tests on ${{ matrix.os }} for python ${{ matrix.python-version }}
         run: |
           coverage run -m pytest

mess/test_data/minimal_test.tsv

@@ -1,3 +1,3 @@
 taxon	nb	cov_sim	sample
-staphylococcus_aureus	1	0.1	sample1
-1290	1	0.1	sample2
+candidatus_carsonella	1	0.1	sample1
+336810	1	0.1	sample2

mess/test_data/simulate_test.tsv

@@ -1,3 +1,3 @@
 fasta	tax_id	cov_sim	sample
-GCF_000418345.1	1280	0.1	sample1
-GCF_003812505.1	1290	0.1	sample2
+GCF_000287275.1	1202538	0.1	sample1
+GCF_001447915.1	336810	0.1	sample2

mess/workflow/rules/preflight/functions.smk

@@ -42,7 +42,7 @@ def list_reads(wildcards):
             bam=["bam", "bam.bai"],
         )
         reads = reads + bams_ef
-        
+
     return reads