Add the initial GitHub Action

.github/workflows/build.yml

@@ -0,0 +1,40 @@
+name: Build and test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build-and-test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    outputs:
+      version: ${{ steps.get_version.outputs.version }}
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Docker
+      uses: docker/setup-buildx-action@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install poetry
+        poetry install
+    - name: Test with pytest
+      run: |
+        poetry run pytest
+    - name: Build the package
+      run: |
+        poetry build

.gitignore

@@ -147,3 +147,6 @@ dmypy.json
 tests/data/benchmarks.json
 tests/data/workflow.cwl_output/*
 src/workflomics_benchmarker/to_implement.py
+tests/data/workflow_output/*
+tests/data/workflow_fail_output/*
+tests/data/workflow_fail2_output/*

README.md

@@ -91,7 +91,7 @@ python src/benchmarker/workflomics.py benchmark tests/data/ --singularity
 Run the following command to execute tests:
 
 ```bash
-poetry run pytest -s 
+poetry run pytest 
 ```
 
 This command runs a workflow and benchmarks it, assuming Docker is operational. Results are stored in the `./tests/data` directory.

src/workflomics_benchmarker/cwltool_runner.py

@@ -5,12 +5,14 @@
 from workflomics_benchmarker.cwltool_wrapper import CWLToolWrapper
 from workflomics_benchmarker.loggingwrapper import LoggingWrapper
 
+
 class CWLToolRunner(CWLToolWrapper):
     """
     Class to manage and run CWL (Common Workflow Language) workflows.
     """
-    success_workflows : list = []
-    failed_workflows : list = []
+
+    success_workflows: list = []
+    failed_workflows: list = []
 
     def __init__(self, args):
         """
@@ -37,15 +39,21 @@ def _construct_command(self, workflow_path):
         list
             A list of command segments to execute the workflow.
         """
-        base_command = ['cwltool --on-error continue']
+        base_command = ["cwltool"]
         if self.container == "singularity":
-            base_command.append('--singularity')
+            base_command.append("--singularity")
 
         workflow_name = Path(workflow_path).stem
         output_directory = os.path.join(self.outdir, f"{workflow_name}_output")
         Path(output_directory).mkdir(exist_ok=True)
 
-        return base_command + ['--outdir', output_directory, workflow_path, self.input_yaml_path], output_directory
+        base_command.extend(["--on-error", "continue"])
+
+        return (
+            base_command
+            + ["--outdir", output_directory, workflow_path, self.input_yaml_path],
+            output_directory,
+        )
 
     def _execute_command(self, command, workflow_name):
         """
@@ -63,11 +71,15 @@ def _execute_command(self, command, workflow_name):
         bool
             True if the workflow executed successfully, False otherwise.
         """
-        result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)
+        result = subprocess.run(
+            command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True
+        )
         print(result.stdout)
 
         if result.returncode == 0:
-            LoggingWrapper.info(f"Workflow {workflow_name} finished successfully.", color="green")
+            LoggingWrapper.info(
+                f"Workflow {workflow_name} finished successfully.", color="green"
+            )
             return True
         else:
             LoggingWrapper.error(f"Workflow {workflow_name} failed.", color="red")
@@ -97,4 +109,6 @@ def run_workflows(self):
         for workflow_path in self.workflows:
             self.execute_workflow(workflow_path)
         total_workflows = len(self.success_workflows) + len(self.failed_workflows)
-        LoggingWrapper.info(f"Execution summary: {total_workflows} total, {len(self.success_workflows)} succeeded, {len(self.failed_workflows)} failed.")
+        LoggingWrapper.info(
+            f"Execution summary: {total_workflows} total, {len(self.success_workflows)} succeeded, {len(self.failed_workflows)} failed."
+        )

src/workflomics_benchmarker/cwltool_wrapper.py

@@ -33,7 +33,12 @@ def __init__(self, args):
 
         self.workflows = sorted([str(file) for file in Path(args.workflows).glob('*.cwl')], key=natural_keys)
         self.version = self.check_cwltool()
-        self.input = self.update_input_yaml(self.input_yaml_path)
+        if hasattr(args, 'interactive'):
+            interactive = True
+        else:
+            interactive = False
+
+        self.input = self.update_input_yaml(self.input_yaml_path, interactive)
 
 
     def check_cwltool(self):
@@ -47,24 +52,44 @@ def check_cwltool(self):
             print("cwltool is not installed.")
         return version
 
-    def update_input_yaml(self, input_yaml_path):
-        """Update the input yaml file with the paths to the input files"""
+    def update_input_yaml(self, input_yaml_path:str, interactive: bool) -> dict:
+        """
+        Update the input yaml file with the paths to the input files. 
+        If interactive is set to True, the user will be allowed to edit the paths to the input files.
+
+        Parameters
+        ----------
+        input_yaml_path : str
+            The path to the input yaml file.
+
+        interactive : bool
+            If True, the user will be allowed to edit the paths to the input files.
+
+        Returns
+        -------
+        dict
+            A dictionary containing the input file names.
+        """
         inputs = {}
         with open(input_yaml_path, 'r') as file:
             input_data = yaml.safe_load(file)
 
         for key, value in input_data.items():
             if key.startswith('input'):
-                print(f"The path for {key} is {value['path']}. Do you want to change it? (y/n)")
+                if not interactive:
+                    inputs[key] = {"filename": Path(value['path']).name}
+                    continue
+
+                print(f"The path for {key} is {value['path']}. Would you like to keep this path? ([Y]/n)")
                 answer = input()
-                if answer == 'y':
+                if answer == 'n':
                     new_path = input(f"Enter the path for {key}: ")
                     value['path'] = new_path.strip()
                     inputs[key] = {"filename": Path(value['path']).name}
                 else:
                     inputs[key] = {"filename": Path(value['path']).name}
         with open(input_yaml_path, 'w') as file:
-            documents = yaml.dump(input_data, file)
+            yaml.dump(input_data, file)
         return inputs
 
 

src/workflomics_benchmarker/workflomics.py

@@ -9,6 +9,7 @@
 def add_benchmark_args(parser):
     """Add the arguments for the benchmark command."""
     parser.add_argument('--singularity', action='store_true', help='Use singularity instead of docker.')
+    parser.add_argument('--interactive', action='store_true', help='Allow the user to interact with the library while running, e.g., to edit the paths to the input files before executing the workflows.')
     parser.add_argument('-o','--outdir', help='Path to the output directory to store the results (default: workflows directory).', default= None)
     parser.add_argument('-v', '--verbose', action='store_true', help='Print the output of the cwltool command.')
     parser.add_argument('-i','--input', help='Path to the input yaml file (default: input.yml in the workflows directory).', default= None)
@@ -17,6 +18,7 @@ def add_benchmark_args(parser):
 def add_run_args(parser):
     """Add the arguments for the run command."""
     parser.add_argument('--singularity', action='store_true', help='Use singularity instead of docker.')
+    parser.add_argument('--interactive', action='store_true', help='Allow the user to interact with the library while running, e.g., to edit the paths to the input files before executing the workflows.')
     parser.add_argument('-o','--outdir', help='Path to the output directory to store the results (default: workflows directory).', default= None)
     parser.add_argument('-v', '--verbose', action='store_true', help='Print the output of the cwltool command.')
     parser.add_argument('-i','--input', help='Path to the input yaml file (default: input.yml in the workflows directory).', default= None)