improve conda install in gh action

.github/workflows/main.yml

@@ -20,19 +20,17 @@ jobs:
         python-version: ['3.8', '3.9', '3.10']
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v2
-    # Setting up miniconda
+    - uses: actions/checkout@v3
+    # Install requirements with miniconda
     - uses: conda-incubator/setup-miniconda@v2
       with:
-        condarc-file: .condarc.yml
-        activate-environment: test
         python-version: ${{ matrix.python-version }}
-    # Install the dependencies
-    - name: Set up test environment
-      shell: bash -l {0}
+        channels: conda-forge,bioconda,defaults
+        environment-file: ppanggolin_env.yaml
+        activate-environment: ppanggolin
+    - name: Install ppanggolin
       run: |
-        conda install -y --file requirements.txt 
-        pip install .[test]
+        pip install .
     # Check that it is installed and displays help without error
     - name: Check that PPanGGOLiN is installed
       shell: bash -l {0}

ppanggolin_env.yaml

@@ -0,0 +1,23 @@
+name: ppanggolin
+channels:
+  - bioconda
+  - defaults
+  - conda-forge
+dependencies:
+  - tqdm>=4.64
+  - pytables>=3.7
+  - pyrodigal>=3.0.1
+  - networkx>=3.0
+  - dataclasses>=0.8
+  - scipy>=1.10.0
+  - plotly>=4.14.3
+  - gmpy2>=2.1.2
+  - pandas>=2.0
+  - colorlover>=0.3
+  - numpy>=1.24
+  - bokeh>=3.1
+  # Tool that are not in python 
+  - infernal>=1.1.4
+  - aragorn>=1.2.41
+  - mmseqs2>=13.45111
+  - mafft>=7.505