Pin ruff 0.16.0

.github/workflows/ruff.yml

@@ -15,8 +15,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install ruff
+          pip install ruff==0.16.0
       - name: Run Ruff
         run: |
           ruff check .
-          ruff format --check .
+          ruff format --check .

babs/base.py

@@ -133,7 +133,7 @@ def __init__(self, project_root, container_config=None):
                 with open(root_config_path) as f:
                     cfg = yaml.safe_load(f) or {}
         if not isinstance(cfg, dict):
-            raise ValueError(
+            raise TypeError(
                 f'container_config_yaml must be a YAML mapping (key: value pairs), '
                 f'got {type(cfg).__name__}'
             )
@@ -223,11 +223,13 @@ def _validate_pipeline_config(self) -> None:
 
         Raises
         ------
+        TypeError
+            If the pipeline or one of its steps has an invalid type.
         ValueError
-            If the pipeline configuration is invalid.
+            If the pipeline configuration is otherwise invalid.
         """
         if not isinstance(self.pipeline, list):
-            raise ValueError('Pipeline configuration must be a list of steps')
+            raise TypeError('Pipeline configuration must be a list of steps')
 
         if len(self.pipeline) == 0:
             raise ValueError('Pipeline configuration cannot be empty')
@@ -236,7 +238,7 @@ def _validate_pipeline_config(self) -> None:
 
         for i, step in enumerate(self.pipeline):
             if not isinstance(step, dict):
-                raise ValueError(f'Pipeline step {i} must be a dictionary')
+                raise TypeError(f'Pipeline step {i} must be a dictionary')
 
             required_fields = ['container_name']
             for field in required_fields:
@@ -356,8 +358,8 @@ def wtf_key_info(self, flag_output_ria_only=False) -> None:
                 'output',
             ],
             stdout=subprocess.PIPE,
+            check=True,
         )
-        proc_output_ria_data_dir.check_returncode()
         self.output_ria_data_dir = urlparse(
             proc_output_ria_data_dir.stdout.decode('utf-8')
         ).path.strip()
@@ -376,9 +378,9 @@ def wtf_key_info(self, flag_output_ria_only=False) -> None:
                 ['datalad', '-f', "'{infos[dataset][id]}'", 'wtf', '-S', 'dataset'],
                 cwd=self.analysis_path,
                 stdout=subprocess.PIPE,
+                check=True,
             )
             # datalad -f '{infos[dataset][id]}' wtf -S dataset
-            proc_analysis_dataset_id.check_returncode()
             self.analysis_dataset_id = (
                 proc_analysis_dataset_id.stdout.decode('utf-8').strip().lstrip("'").rstrip("'")
             )
@@ -474,6 +476,7 @@ def ensure_shared_group_git_safe_directories(self) -> None:
             ['git', 'config', '--global', '--get-all', 'safe.directory'],
             capture_output=True,
             text=True,
+            check=False,
         )
         existing = (
             {line.strip() for line in proc_existing.stdout.splitlines() if line.strip()}
@@ -488,6 +491,7 @@ def ensure_shared_group_git_safe_directories(self) -> None:
                 ['git', 'config', '--global', '--add', 'safe.directory', repo_path],
                 capture_output=True,
                 text=True,
+                check=True,
             )
             existing.add(repo_path)
 
@@ -533,8 +537,7 @@ def datalad_save(
             # Create a temporary .gitignore file to exclude specified files
             gitignore_path = op.join(self.analysis_path, '.gitignore')
             with open(gitignore_path, 'w') as f:
-                for file in filter_files:
-                    f.write(f'{file}\n')
+                f.writelines(f'{file}\n' for file in filter_files)
 
             try:
                 statuses = self.analysis_datalad_handle.save(path=path, message=message)
@@ -552,7 +555,7 @@ def datalad_save(
         if not saved_status.issubset({'ok', 'notneeded'}):
             # exists element in `saved_status` that is not "ok" or "notneeded"
             # ^^ "notneeded": nothing to save
-            raise Exception('`datalad save` failed!')
+            raise RuntimeError('`datalad save` failed!')
 
     def _get_results_branches(self) -> list[str]:
         """Get the results branch names from the output RIA in a list."""

babs/bootstrap.py

@@ -150,29 +150,26 @@ def babs_bootstrap(
         # if exists already, remove it:
         if op.exists(gitignore_path):
             os.remove(gitignore_path)
-        gitignore_file = open(gitignore_path, 'a')  # open in append mode
-
-        # not to track input/output RIA stores:
-        gitignore_file.write('\n' + op.basename(self.input_ria_path))
-        gitignore_file.write('\n' + op.basename(self.output_ria_path))
-        # not to track `logs` folder:
-        if 'logs' not in (no_ignore or []):
-            gitignore_file.write('\nlogs')
-        # not to track `.*_datalad_lock`:
-        gitignore_file.write('\n.*_datalad_lock')
-        # not to track lock file:
-        gitignore_file.write('\n' + 'code/babs_proj_config.yaml.lock')
-        # not to track `job_status.csv`:
-        gitignore_file.write('\n' + 'code/job_status.csv')
-        gitignore_file.write('\n' + 'code/job_status.csv.lock')
-        gitignore_file.write('\n' + 'code/job_submit.csv')
-        gitignore_file.write('\n' + 'code/job_submit.csv.lock')
-        # not to track files generated by `babs check-setup`:
-        gitignore_file.write('\n' + 'code/check_setup/test_job_info.yaml')
-        gitignore_file.write('\n' + 'code/check_setup/check_env.yaml')
-        gitignore_file.write('\n')
-
-        gitignore_file.close()
+        with open(gitignore_path, 'a') as gitignore_file:  # open in append mode
+            # not to track input/output RIA stores:
+            gitignore_file.write('\n' + op.basename(self.input_ria_path))
+            gitignore_file.write('\n' + op.basename(self.output_ria_path))
+            # not to track `logs` folder:
+            if 'logs' not in (no_ignore or []):
+                gitignore_file.write('\nlogs')
+            # not to track `.*_datalad_lock`:
+            gitignore_file.write('\n.*_datalad_lock')
+            # not to track lock file:
+            gitignore_file.write('\n' + 'code/babs_proj_config.yaml.lock')
+            # not to track `job_status.csv`:
+            gitignore_file.write('\n' + 'code/job_status.csv')
+            gitignore_file.write('\n' + 'code/job_status.csv.lock')
+            gitignore_file.write('\n' + 'code/job_submit.csv')
+            gitignore_file.write('\n' + 'code/job_submit.csv.lock')
+            # not to track files generated by `babs check-setup`:
+            gitignore_file.write('\n' + 'code/check_setup/test_job_info.yaml')
+            gitignore_file.write('\n' + 'code/check_setup/check_env.yaml')
+            gitignore_file.write('\n')
         self.datalad_save(path='.gitignore', message='Save .gitignore file')
 
         # Create `babs_proj_config.yaml` file: ----------------------
@@ -246,13 +243,12 @@ def babs_bootstrap(
             commit_message = f"Register input data dataset '{dataset_name}' as a subdataset"
             git_cmd = ['git', 'commit', '--amend', '-m', commit_message]
 
-            result = subprocess.run(
+            subprocess.run(
                 git_cmd,
                 cwd=self.analysis_path,
                 stdout=subprocess.PIPE,
                 check=True,
             )
-            result.check_returncode()
 
         # Perform checks on the inputs:
         self.input_datasets.validate_input_contents()
@@ -636,12 +632,12 @@ def clean_up(self):
 
                 # `git annex dead here`:
                 print('\nRunning `git annex dead here`...')
-                proc_git_annex_dead = subprocess.run(
+                subprocess.run(
                     ['git', 'annex', 'dead', 'here'],
                     cwd=self.analysis_path,
                     stdout=subprocess.PIPE,
+                    check=True,
                 )
-                proc_git_annex_dead.check_returncode()
 
                 # Update input and output RIA:
                 print('\nUpdating input and output RIA if created...')
@@ -654,10 +650,7 @@ def clean_up(self):
 
             # Now we can delete this project folder:
             print('\nDeleting created BABS project folder...')
-            proc_rm_project_folder = subprocess.run(
-                ['rm', '-rf', self.project_root], stdout=subprocess.PIPE
-            )
-            proc_rm_project_folder.check_returncode()
+            subprocess.run(['rm', '-rf', self.project_root], stdout=subprocess.PIPE, check=True)
 
         # confirm the BABS project has been removed:
         assert not op.exists(self.project_root), (

babs/check_setup.py

@@ -67,7 +67,7 @@ def babs_check_setup(self, submit_a_test_job):
         }
 
         # statuses should be all "clean", without anything else e.g., "modified":
-        if not analysis_statuses == {'clean'}:
+        if analysis_statuses != {'clean'}:
             problem_statuses = [
                 status
                 for status in self.analysis_datalad_handle.status(eval_subdataset_state='commit')
@@ -177,9 +177,8 @@ def babs_check_setup(self, submit_a_test_job):
                     + " in 'analysis/code' folder in this BABS project!"
                 )
             # check if bash files are executable:
-            if op.splitext(temp_fn)[1] == '.sh':  # extension is '.sh':
-                if not os.access(temp_fn, os.X_OK):
-                    raise PermissionError('This code file should be executable: ' + temp_fn)
+            if op.splitext(temp_fn)[1] == '.sh' and not os.access(temp_fn, os.X_OK):
+                raise PermissionError('This code file should be executable: ' + temp_fn)
         print(CHECK_MARK + ' All good!')
 
         # Check input and output RIA: ----------------------
@@ -209,7 +208,7 @@ def babs_check_setup(self, submit_a_test_job):
         analysis_siblings = self.analysis_datalad_handle.siblings(action='query')
         has_sibling_input = False
         has_sibling_output = False
-        for i_sibling in range(0, len(analysis_siblings)):
+        for i_sibling in range(len(analysis_siblings)):
             the_sibling = analysis_siblings[i_sibling]
             if the_sibling['name'] == 'output':  # output ria:
                 has_sibling_output = True
@@ -299,7 +298,7 @@ def _submit_test_job(self):
                     new_job_status = request_all_job_status(self.queue, job_id)
 
                 if not job_status.shape[0] == 1:
-                    raise Exception(
+                    raise RuntimeError(
                         f'Expected 1 job for {step_container_name}, got {job_status.shape[0]}'
                     )
 
@@ -320,14 +319,14 @@ def _submit_test_job(self):
                 if op.exists(fn_check_env_yaml):
                     flag_writable, flag_all_installed = print_versions_from_yaml(fn_check_env_yaml)
                     if not flag_writable:
-                        raise Exception(
+                        raise RuntimeError(
                             f'The designated workspace is not writable for {step_container_name}!'
                             ' Please change it in the YAML file'
                             ' used in `babs init --container-config`,'
                             ' then rerun `babs init` with updated YAML file.'
                         )
                     if not flag_all_installed:
-                        raise Exception(
+                        raise RuntimeError(
                             f'Some required package(s) were not installed for '
                             f'{step_container_name} in the designated environment!'
                             ' Please install them in the designated environment,'
@@ -349,7 +348,7 @@ def _submit_test_job(self):
                 new_job_status = request_all_job_status(self.queue, job_id)
 
             if not job_status.shape[0] == 1:
-                raise Exception(f'Expected 1 job, got {job_status.shape[0]}')
+                raise RuntimeError(f'Expected 1 job, got {job_status.shape[0]}')
 
             test_info = job_status.iloc[0].to_dict()
 
@@ -366,7 +365,7 @@ def _submit_test_job(self):
             fn_check_env_yaml = op.join(self.analysis_path, 'code/check_setup', 'check_env.yaml')
             flag_writable, flag_all_installed = print_versions_from_yaml(fn_check_env_yaml)
             if not flag_writable:
-                raise Exception(
+                raise RuntimeError(
                     'The designated workspace is not writable!'
                     ' Please change it in the YAML file'
                     ' used in `babs init --container-config`,'
@@ -375,7 +374,7 @@ def _submit_test_job(self):
                 # NOTE: ^^ currently this is not aligned with YAML file sections;
                 # this will make more sense after adding section of workspace path in YAML file
             if not flag_all_installed:
-                raise Exception(
+                raise RuntimeError(
                     'Some required package(s) were not installed'
                     ' in the designated environment!'
                     ' Please install them in the designated environment,'

babs/cli.py

@@ -229,14 +229,14 @@ def babs_init_main(
             shared_group=shared_group,
             no_ignore=no_ignore,
         )
-    except Exception as exc:
+    except Exception:
         print('\n`babs init` failed! Below is the error message:')
         if not keep_if_failed:
             print('\nCleaning up created BABS project...')
             babs_proj.clean_up()
         else:
             print('\n`--keep-if-failed` is requested, so not to clean up created BABS project.')
-        raise exc
+        raise
 
 
 def _parse_check_setup():

babs/container.py

@@ -227,9 +227,11 @@ def generate_bash_test_job(self, folder_check_setup, system, shared_group_mode=F
         os.chmod(fn_call_test_job, 0o770 if shared_group_mode else 0o700)
 
         # Copy the template file into the check_setup folder
-        with resources.files('babs').joinpath('template_test_job.py').open('rb') as src:
-            with open(fn_test_job, 'wb') as dst:
-                dst.write(src.read())
+        with (
+            resources.files('babs').joinpath('template_test_job.py').open('rb') as src,
+            open(fn_test_job, 'wb') as dst,
+        ):
+            dst.write(src.read())
         os.chmod(fn_test_job, 0o770 if shared_group_mode else 0o700)
 
     def generate_job_submit_template(self, yaml_path, babs, system, test=False):

babs/input_dataset.py

@@ -104,7 +104,7 @@ def is_up_to_date(self):
         origin_ds = dlapi.Dataset(self.origin_url)
         origin_sha = origin_ds.repo.get_hexsha()
 
-        if not babs_sha == origin_sha:
+        if babs_sha != origin_sha:
             print(f'Input dataset {self.name} is not up to date.')
             print(f'BABS SHA: {babs_sha}')
             print(f'Origin SHA: {origin_sha}')
@@ -287,7 +287,7 @@ def as_dict(self):
 def validate_zipped_input_contents(
     dataset_abs_path, root_dir_name, processing_level, included_subjects_df=None
 ):
-    """ """
+    """Validate the contents of a zipped input dataset."""
     zip_pattern = (
         f'sub-*_ses-*_{root_dir_name}*.zip'
         if processing_level == 'session'

babs/interaction.py

@@ -92,7 +92,7 @@ def babs_submit(self, count=None, submit_df=None, skip_failed=False, skip_runnin
             )
             if non_cg_states.any():
                 if not skip_running_jobs:
-                    raise Exception(
+                    raise RuntimeError(
                         'There are still jobs running. '
                         'Please wait for them to finish or cancel them. '
                         'Current running jobs:\n'