Merge pull request #13 from cokelaer/main

Fixing CI, requirements-->tools, add env.yml

Author: cokelaer

.github/workflows/apptainer.yml

@@ -55,5 +55,5 @@ jobs:
 
     - name: testing
       run: |
-        sequana_nanomerge --input-directory test/data/barcoded --samplesheet test/data/samplesheet.csv --input-pattern "barcode*/*fastq.gz" --summary test/data/sequence_summary.txt --use-apptainer && cd nanomerge && sh nanomerge.sh
+        sequana_nanomerge --input-directory test/data/barcoded --sample-sheet test/data/samplesheet.csv --input-pattern "barcode*/*fastq.gz" --summary test/data/sequence_summary.txt --use-apptainer && cd nanomerge && sh nanomerge.sh
 

.github/workflows/main.yml

@@ -6,6 +6,7 @@ on:
     branches:
       - main
       - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
   schedule:
@@ -30,33 +31,33 @@ jobs:
     - name: checkout git repo
       uses: actions/checkout@v2
 
-    - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+    - name: conda/mamba
+      uses: mamba-org/provision-with-micromamba@main
       with:
-        python-version: ${{ matrix.python }}
+          environment-file: environment.yml
+          extra-specs: |
+            python=${{ matrix.python }}
 
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
 
-    - name: Install dependencies
+    - name: install package itself
+      shell: bash -l {0}
       run: |
-        pip install pycoQC
-        pip install .[testing]
+        pip install .
 
-    - name: install package itself
+    - name: Install dependencies
+      shell: bash -l {0}
       run: |
-         pip install .
+        pip install coveralls pytest-cov pytest pytest-xdist
 
     - name: testing
+      shell: bash -l {0}
       run: |
-        pytest --cov-report term --cov=sequana_pipelines.nanomerge
+        pytest -v --cov-report term-missing --cov=sequana_pipelines.nanomerge
+
     - name: coveralls
+      shell: bash -l {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github
       env:
-          GITHUB_TOKEN:  ${{ github.token }} 
-
-
+          GITHUB_TOKEN: ${{ github.token }}

environment.yml

@@ -0,0 +1,13 @@
+name: nanomerge
+
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - pycoQC
+  - pip:
+    - sequana
+
+