diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index 74f47548..c0f807fd 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -43,43 +43,26 @@ runs:
     - run: |
         conda --version
         conda env list
-      shell: bash {0}
+      shell: bash -l {0}
 
     - name: Python info
-      shell: bash -e {0}
+      shell: bash -l {0}
       run: |
         which python3
         python3 --version
 
-    - name: Activate deeprank2 environment on Linux
-      shell: bash -el {0}
-      env:
-        CMAKE_INSTALL_PREFIX: .local
-      if: runner.os == 'Linux'
-      run: |
-        conda activate deeprank2
-        # # Install deeprank2 conda dependencies
-        # ## sbl channel
-        # conda install dssp>=4.2.2.1 -c sbl
-        # ## bioconda channel
-        # conda install msms>=2.6.1 markov_clustering>=0.0.6 -c bioconda
-        # ## pytorch and pyg channels
-        # ### Installing for CPU only on the CI
-        # conda install pytorch=2.1.1 torchvision>=0.16.1 torchaudio>=2.1.1 cpuonly>=2.0 -c pytorch
-        # conda install pyg>=2.4.0 pytorch-scatter>=2.1.2 pytorch-sparse>=0.6.18 pytorch-cluster>=1.6.3 pytorch-spline-conv>=1.2.2 -c pyg
-        # ## conda-forge channel
-        # conda install tables>=3.8.0 numpy>=1.21.5 scipy>=1.11.2 h5py>=3.6.0 networkx>=2.6.3 matplotlib>=3.5.1 scikit-learn>=1.0.2 chart-studio>=1.1.0 biopython>=1.81 python-louvain>=0.16 tqdm>=4.63.0 freesasa>=2.1.0 tensorboard>=0.9.0 protobuf>=3.20.1 ruff>=0.1.13 dill>=0.3.8 -c conda-forge
-
     - name: Install the GitHub repository version of the package
-      shell: bash -el {0}
+      shell: bash -l {0}
       if: ${{ inputs.pkg-installation-type == 'repository' }}
       run: |
         conda activate deeprank2
         pip install .'[${{ inputs.extras-require }}]'
-    - name: Install the latest released version of the package
-      shell: bash {0}
+
+    - name: Install the latest released PyPI version of the package
+      shell: bash -l {0}
       if: ${{ inputs.pkg-installation-type == 'latest' }}
       run: |
+        conda activate deeprank2
         pip install pytest
         rm -r deeprank2
         pip install deeprank2
diff --git a/.github/workflows/build-repo.yml b/.github/workflows/build-repo.yml
index b3b1cf3e..7af4cc7a 100644
--- a/.github/workflows/build-repo.yml
+++ b/.github/workflows/build-repo.yml
@@ -54,9 +54,7 @@ jobs:
           pkg-installation-type: "repository"
 
       - name: Run unit tests
-        run: |
-          conda activate deeprank2
-          pytest -v
+        run: pytest -v
 
       - name: Verify that we can build the package
         run: python3 -m build
diff --git a/pyproject.toml b/pyproject.toml
index e65c3981..49df56d2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,26 +34,6 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
 ]
-dependencies = [
-    # "tables >= 3.8.0",
-    # "numpy >= 1.21.5",
-    # "scipy >= 1.11.2",
-    # "h5py >= 3.6.0",
-    # "networkx >= 2.6.3",
-    # "matplotlib >= 3.5.1",
-    # "pdb2sql >= 0.5.1",
-    # "scikit-learn >= 1.0.2",
-    # "chart-studio >= 1.1.0",
-    # "biopython >= 1.81",
-    # "python-louvain >= 0.16",
-    # "markov-clustering >= 0.0.6.dev0",
-    # "tqdm >= 4.63.0",
-    # "freesasa >= 2.1.0",
-    # "tensorboard >= 0.9.0",
-    # "protobuf >= 3.20.1",
-    # "ruff >= 0.1.13",
-    # "dill",
-]
 
 [project.optional-dependencies]
 # development dependency groups