Added PR tests

.github/workflows/linting_and_testing.yml

@@ -39,8 +39,8 @@ jobs:
 
       - name: Remove all micromamba installations
         run: |
-          rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null
-          touch /home/user/.bash_profile
+          rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null
+          touch $HOME/.bash_profile
 
       - name: setup-micromamba
         uses: mamba-org/[email protected]

.github/workflows/pr-tests.yml

@@ -0,0 +1,87 @@
+name: PR Tests
+
+# Trigger the workflow on pull request events
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  pr_test:
+    strategy:
+      matrix:
+        os: [self-hosted]
+        python-version: ["3.10"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+
+      - run: echo "Repository -> ${{ github.repository }}"
+      - run: echo "Branch -> ${{ github.ref }}"
+      - run: echo "Trigger event -> ${{ github.event_name }}"
+      - run: echo "Runner OS -> ${{ runner.os }}"
+
+      - name: List files in the repository
+        run: |
+          ls ${{ github.workspace }}
+
+      - name: Remove all micromamba installations
+        run: |
+          rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null
+          touch $HOME/.bash_profile
+
+      - name: setup-micromamba
+        uses: mamba-org/[email protected]
+        with:
+          generate-run-shell: true
+          micromamba-version: '2.0.2-2'
+          post-cleanup: 'all'
+          init-shell: bash
+          environment-file: .github/env.yaml
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pytest
+            pytest-cov
+            pytest-html
+            flake8
+            pip
+
+      - name: List installed package versions
+        shell: bash -l {0}
+        run: micromamba list
+
+      - name: Checkout biobb_common
+        uses: actions/checkout@v4
+        with:
+          repository: bioexcel/biobb_common
+          path: './biobb_common'
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          # Ignoring docker and singularity tests
+          export PYTHONPATH=.:./biobb_common:$PYTHONPATH
+
+          # Create directory for tests reports
+          mkdir -p ./reports/junit
+
+          # Production one
+          pytest biobb_vs/test/unitests/ --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py
+
+      # Notify user about test results
+      - name: Comment on PR
+        if: always() # This ensures the step runs even if tests fail
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const { payload, repo } = context; // Access GitHub context
+            const prNumber = payload.pull_request.number;
+            const jobStatus = '${{ job.status }}'; // Get job status (success/failure)
+            const testStatus = jobStatus === 'success' ? '✅ Tests Passed!' : '❌ Tests Failed.';
+            
+            await github.rest.issues.createComment({
+              owner: repo.owner,
+              repo: repo.repo,
+              issue_number: prNumber,
+              body: `**Test Results for PR #${prNumber}**\n\n${testStatus}`
+            });

biobb_vs/fpocket/fpocket_filter.py

@@ -131,8 +131,7 @@ def score_matcher(self, score):
 
     def druggability_score_matcher(self, druggability_score):
         return (
-            lambda d: d["druggability_score"] > druggability_score[0]
-            and d["druggability_score"] <= druggability_score[1]
+            lambda d: d["druggability_score"] > druggability_score[0] and d["druggability_score"] <= druggability_score[1]
         )
 
     def volume_matcher(self, volume):

biobb_vs/utils/bindingsite.py

@@ -184,14 +184,12 @@ def launch(self) -> int:
         structPDB_seq = get_pdb_sequence(structPDB)
         if len(structPDB_seq) == 0:
             fu.log(
-                self.__class__.__name__
-                + ": Cannot extract AA sequence from the input PDB structure %s. Wrong format?"
+                self.__class__.__name__ + ": Cannot extract AA sequence from the input PDB structure %s. Wrong format?"
                 % self.io_dict["in"]["input_pdb_path"],
                 self.out_log,
             )
             raise SystemExit(
-                self.__class__.__name__
-                + ": Cannot extract AA sequence from the input PDB structure %s. Wrong format?"
+                self.__class__.__name__ + ": Cannot extract AA sequence from the input PDB structure %s. Wrong format?"
                 % self.io_dict["in"]["input_pdb_path"]
             )
         else:
@@ -336,14 +334,12 @@ def launch(self) -> int:
 
             if len(cluster_atoms) == 0:
                 fu.log(
-                    self.__class__.__name__
-                    + ": Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member."
+                    self.__class__.__name__ + ": Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member."
                     % (cluster_name, structure_name),
                     self.out_log,
                 )
                 raise SystemExit(
-                    self.__class__.__name__
-                    + ": Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member."
+                    self.__class__.__name__ + ": Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member."
                     % (cluster_name, structure_name)
                 )
             else:

biobb_vs/utils/box_residues.py

@@ -168,17 +168,15 @@ def launch(self) -> int:
 
         if len(selection_res_list) == 0:
             fu.log(
-                self.__class__.__name__
-                + ": Cannot match any of the residues listed in [%s] into %s"
+                self.__class__.__name__ + ": Cannot match any of the residues listed in [%s] into %s"
                 % (
                     ", ".join(str(v) for v in self.resid_list),
                     self.io_dict["in"]["input_pdb_path"],
                 ),
                 self.out_log,
             )
             raise SystemExit(
-                self.__class__.__name__
-                + ": Cannot match any of the residues listed in [%s] into %s"
+                self.__class__.__name__ + ": Cannot match any of the residues listed in [%s] into %s"
                 % (
                     ", ".join(str(v) for v in self.resid_list),
                     self.io_dict["in"]["input_pdb_path"],
@@ -206,8 +204,7 @@ def launch(self) -> int:
 
         # compute box center
         selection_box_center = (
-            sum(atom.coord for res in selection_res_list for atom in res.get_atoms())
-            / selection_atoms_num
+            sum(atom.coord for res in selection_res_list for atom in res.get_atoms()) / selection_atoms_num
         )
         fu.log(
             "Binding site center (Angstroms): %10.3f%10.3f%10.3f"

biobb_vs/utils/common.py

@@ -31,14 +31,12 @@ def check_input_path(path, argument, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_file(file_extension[1:], argument):
         fu.log(
-            classname
-            + ": Format %s in %s file is not compatible"
+            classname + ": Format %s in %s file is not compatible"
             % (file_extension[1:], argument),
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in %s file is not compatible"
+            classname + ": Format %s in %s file is not compatible"
             % (file_extension[1:], argument)
         )
     return path
@@ -54,14 +52,12 @@ def check_output_path(path, argument, optional, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_file(file_extension[1:], argument):
         fu.log(
-            classname
-            + ": Format %s in  %s file is not compatible"
+            classname + ": Format %s in  %s file is not compatible"
             % (file_extension[1:], argument),
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in  %s file is not compatible"
+            classname + ": Format %s in  %s file is not compatible"
             % (file_extension[1:], argument)
         )
     return path

biobb_vs/utils/extract_model_pdbqt.py

@@ -135,14 +135,12 @@ def launch(self) -> int:
 
         if self.model not in models:
             fu.log(
-                self.__class__.__name__
-                + ": Selected model %d not found in %s structure."
+                self.__class__.__name__ + ": Selected model %d not found in %s structure."
                 % (self.model, self.io_dict["in"]["input_pdbqt_path"]),
                 self.out_log,
             )
             raise SystemExit(
-                self.__class__.__name__
-                + ": Selected model %d not found in %s structure."
+                self.__class__.__name__ + ": Selected model %d not found in %s structure."
                 % (self.model, self.io_dict["in"]["input_pdbqt_path"])
             )
 

biobb_vs/vina/common.py

@@ -15,14 +15,12 @@ def check_input_path(path, argument, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_file(file_extension[1:], argument):
         fu.log(
-            classname
-            + ": Format %s in %s file is not compatible"
+            classname + ": Format %s in %s file is not compatible"
             % (file_extension[1:], argument),
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in %s file is not compatible"
+            classname + ": Format %s in %s file is not compatible"
             % (file_extension[1:], argument)
         )
     return path
@@ -38,14 +36,12 @@ def check_output_path(path, argument, optional, out_log, classname):
     file_extension = PurePath(path).suffix
     if not is_valid_file(file_extension[1:], argument):
         fu.log(
-            classname
-            + ": Format %s in  %s file is not compatible"
+            classname + ": Format %s in  %s file is not compatible"
             % (file_extension[1:], argument),
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in  %s file is not compatible"
+            classname + ": Format %s in  %s file is not compatible"
             % (file_extension[1:], argument)
         )
     return path