added conda environment

.github/workflows/main.yml

@@ -10,20 +10,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: "3.10"
-    - name: Install dependencies
+        micromamba-version: '1.5.6-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yaml
+        init-shell: >-
+          bash
+        cache-environment: true
+        post-cleanup: 'all'
+    - name: Install additional dependencies
       run: |
-        sudo apt-get update
-        sudo apt-get install -y libcurl4-openssl-dev
-        python -m pip install --upgrade pip
-        sudo apt-get install -y r-base
-        sudo apt-get install graphviz libgraphviz-dev pkg-config
-        pip install pytest-cov flake8 decoupler omnipath requests rpy2 pathos pyocclient
-        pip install git+https://github.com/saezlab/corneto.git@dev networkx pygraphviz picos .
+        pip install git+https://github.com/saezlab/corneto.git@dev .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

environment.yaml

@@ -0,0 +1,31 @@
+name: networkcommons
+channels:
+  - bioconda
+  - r
+  - conda-forge
+  - defaults
+dependencies:
+  - bioconductor-deseq2=1.42.0
+  - graphviz=2.50.0
+  - python=3.10.14
+  - python-graphviz=0.20.3
+  - r-base=4.3.1
+  - setuptools=69.5.1
+  - pip:
+      - cvxpy==1.4.3
+      - decoupler==1.6.0
+      - flake8==7.0.0
+      - gurobipy==11.0.1      
+      - networkx==3.3
+      - omnipath==1.0.8
+      - pathos==0.3.2
+      - picos==2.4.17
+      - pyocclient==0.6
+      - pytest==8.2.0
+      - pytest-cov==5.0.0
+      - requests==2.31.0
+      - rpy2==3.5.16
+      - ruamel-yaml==0.18.6
+      - ruamel-yaml-clib==0.2.8
+      - scipy==1.11.4
+      - urllib3==2.2.1