diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
index 0195d281..8a8c709c 100644
--- a/.github/workflows/ruff.yml
+++ b/.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 .
\ No newline at end of file
+          ruff format --check .
diff --git a/babs/base.py b/babs/base.py
index 0f6ed038..5124b190 100644
--- a/babs/base.py
+++ b/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."""
diff --git a/babs/bootstrap.py b/babs/bootstrap.py
index 8f4102da..06550268 100644
--- a/babs/bootstrap.py
+++ b/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), (
diff --git a/babs/check_setup.py b/babs/check_setup.py
index 0249fb78..1b33924e 100644
--- a/babs/check_setup.py
+++ b/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,'
diff --git a/babs/cli.py b/babs/cli.py
index b9697b95..37f54e2a 100644
--- a/babs/cli.py
+++ b/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():
diff --git a/babs/container.py b/babs/container.py
index 8eebfc76..76b6211d 100644
--- a/babs/container.py
+++ b/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):
diff --git a/babs/input_dataset.py b/babs/input_dataset.py
index 45aba31d..1c9867b8 100644
--- a/babs/input_dataset.py
+++ b/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'
diff --git a/babs/interaction.py b/babs/interaction.py
index 5dc98131..6f6ddc3b 100644
--- a/babs/interaction.py
+++ b/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'
diff --git a/babs/merge.py b/babs/merge.py
index 9b41e7d3..b9c2506c 100644
--- a/babs/merge.py
+++ b/babs/merge.py
@@ -46,6 +46,7 @@ def robust_rm_dir(path, max_retries=3, retry_delay=1):
                     cwd=path,
                     stdout=subprocess.DEVNULL,
                     stderr=subprocess.DEVNULL,
+                    check=False,
                 )
             dlapi.remove(path=path, dataset=path, reckless='availability')
             # datalad remove might not remove everything, check if path still exists
@@ -121,7 +122,7 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
         merge_ds_path = op.join(self.project_root, 'merge_ds')
 
         if op.exists(merge_ds_path):
-            raise Exception(
+            raise RuntimeError(
                 "Folder 'merge_ds' already exists. `babs merge` won't proceed."
                 " If you're sure you want to rerun `babs merge`,"
                 ' please remove this folder before you rerun `babs merge`.'
@@ -165,8 +166,8 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             ['git', 'remote', 'show', 'origin'],
             cwd=merge_ds_path,
             stdout=subprocess.PIPE,
+            check=True,
         )
-        proc_git_remote_show_origin.check_returncode()
         msg = proc_git_remote_show_origin.stdout.decode('utf-8')
         # e.g., '... HEAD branch: master\n....': search between 'HEAD branch: ' and '\n':
         temp = re.search('HEAD branch: ' + '(.+?)' + '\n', msg)
@@ -174,7 +175,7 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             default_branch_name = temp.group(1)  # what's between those two keywords
             # another way: `default_branch_name = msg.split("HEAD branch: ")[1].split("\n")[0]`
         else:
-            raise Exception('There is no HEAD branch in output RIA!')
+            raise RuntimeError('There is no HEAD branch in output RIA!')
         print("Git default branch's name of output RIA is: '" + default_branch_name + "'")
 
         # get current git commit SHASUM before merging as a reference:
@@ -195,7 +196,7 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
 
         # check if there is any valid job (with results):
         if len(list_branches_with_results) == 0:  # empty:
-            raise Exception(
+            raise RuntimeError(
                 'There is no job branch in output RIA that has results yet,'
                 ' i.e., there is no successfully finished job yet.'
                 ' Please run `babs submit` first.'
@@ -242,7 +243,7 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
         # ^^ e.g., [['1', '7', '0'], ['6', '2'], ['5', '6']]
 
         # iterate across chunks:
-        for i_chunk in range(0, num_chunks):
+        for i_chunk in range(num_chunks):
             print(
                 'Merging chunk #'
                 + str(i_chunk + 1)
@@ -261,7 +262,9 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             # Prepend 'origin/' to each branch name
             remote_branches = ['origin/' + branch for branch in joined_by_space.split(' ')]
             cmd = ['git', 'merge', '-m', commit_msg] + remote_branches
-            proc_git_merge = subprocess.run(cmd, cwd=merge_ds_path, capture_output=True, text=True)
+            proc_git_merge = subprocess.run(
+                cmd, cwd=merge_ds_path, capture_output=True, text=True, check=False
+            )
             if proc_git_merge.returncode != 0:
                 print(f'Git merge failed with error:\n{proc_git_merge.stderr}')
                 proc_git_merge.check_returncode()
@@ -269,7 +272,7 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
 
         # Push merging actions back to output RIA:
         if trial_run:
-            print('')  # new empty line
+            print()  # new empty line
             warnings.warn(
                 '`--trial-run` was requested, not to push merging actions to output RIA.',
                 stacklevel=2,
@@ -279,8 +282,9 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
 
         print('\nPushing merging actions to output RIA...')
         # `git push`:
-        proc_git_push = subprocess.run(['git', 'push'], cwd=merge_ds_path, stdout=subprocess.PIPE)
-        proc_git_push.check_returncode()
+        proc_git_push = subprocess.run(
+            ['git', 'push'], cwd=merge_ds_path, stdout=subprocess.PIPE, check=True
+        )
         print(proc_git_push.stdout.decode('utf-8'))
 
         # Get file availability information: which is very important!
@@ -293,8 +297,8 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             ['git', 'annex', 'fsck', '--fast', '-f', 'output-storage'],
             cwd=merge_ds_path,
             stdout=subprocess.PIPE,
+            check=True,
         )
-        proc_git_annex_fsck.check_returncode()
         # if printing the returned msg,
         #   will be a long list of "fsck xxx.zip (fixing location log) ok"
         #   or "fsck xxx.zip ok"
@@ -315,8 +319,8 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             ['git', 'annex', 'find', '--not', '--in', 'output-storage'],
             cwd=merge_ds_path,
             stdout=subprocess.PIPE,
+            check=True,
         )
-        proc_git_annex_find_missing.check_returncode()
         msg = proc_git_annex_find_missing.stdout.decode('utf-8')
         # `msg` should be empty:
         if msg != '':  # if not empty:
@@ -324,7 +328,7 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             with open(fn_list_content_missing, 'w') as f:
                 f.write(msg)
                 f.write('\n')
-            raise Exception(
+            raise RuntimeError(
                 'Unable to find file content for some file(s).'
                 " The information has been saved to this text file: '"
                 + fn_list_content_missing
@@ -338,8 +342,8 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             ['git', 'annex', 'dead', 'here'],
             cwd=merge_ds_path,
             stdout=subprocess.PIPE,
+            check=True,
         )
-        proc_git_annex_dead_here.check_returncode()
         print(proc_git_annex_dead_here.stdout.decode('utf-8'))
 
         # Final `datalad push` to output RIA:
@@ -351,8 +355,8 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
             ['datalad', 'push', '--data', 'nothing'],
             cwd=merge_ds_path,
             stdout=subprocess.PIPE,
+            check=True,
         )
-        proc_datalad_push.check_returncode()
         print(proc_datalad_push.stdout.decode('utf-8'))
 
         # Done:
@@ -375,6 +379,6 @@ def babs_merge(self, chunk_size=1000, trial_run=False):
                 ['git', 'branch', '--delete'] + chunk,
                 cwd=self.output_ria_data_dir,
                 stdout=subprocess.PIPE,
+                check=True,
             )
-            proc_git_branch_delete.check_returncode()
             print(proc_git_branch_delete.stdout.decode('utf-8'))
diff --git a/babs/scheduler.py b/babs/scheduler.py
index f0097d0d..a44881bd 100644
--- a/babs/scheduler.py
+++ b/babs/scheduler.py
@@ -42,7 +42,7 @@ def run_squeue(queue, job_id: int) -> str:
         f'-j{job_id}',
     ]
 
-    result = subprocess.run(cmd, capture_output=True, text=True)
+    result = subprocess.run(cmd, capture_output=True, text=True, check=False)
 
     if result.returncode == 1 and 'Invalid job id specified' in result.stderr:
         return ''
@@ -130,6 +130,7 @@ def squeue_to_pandas(job_id=None) -> pd.DataFrame:
         commandlist,
         capture_output=True,
         text=True,
+        check=False,
     )
 
     # Check if command failed
@@ -160,7 +161,7 @@ def squeue_to_pandas(job_id=None) -> pd.DataFrame:
             skipinitialspace=True,
         )
     except Exception as e:
-        raise RuntimeError(f'Failed to parse squeue output: {str(e)}\nOutput was: {result.stdout}')
+        raise RuntimeError(f'Failed to parse squeue output: {e!s}\nOutput was: {result.stdout}')
 
     # separate job_id into job_id and task_id
     df['task_id'] = df['job_id'].str.split('_').str[1].astype(int)
@@ -205,6 +206,7 @@ def sbatch_get_job_id(sbatch_cmd_list, working_dir):
         cwd=working_dir,
         capture_output=True,
         text=True,
+        check=False,
     )
     if proc_cmd.returncode != 0:
         raise RuntimeError(f'Failed to submit array job: {proc_cmd.stderr}')
@@ -257,7 +259,7 @@ def submit_array(analysis_path, queue, maxarray):
     if queue == 'slurm':
         job_id = sbatch_get_job_id(cmd.split(), analysis_path)
     else:
-        raise Exception('Invalid job scheduler system type `queue`: ' + queue)
+        raise ValueError('Invalid job scheduler system type `queue`: ' + queue)
 
     return job_id
 
@@ -302,7 +304,7 @@ def submit_one_test_job(analysis_path, queue):
     if queue == 'slurm':
         job_id = sbatch_get_job_id(cmd.split(), analysis_path)
     else:
-        raise Exception('Invalid job scheduler system type `queue`: ' + queue)
+        raise ValueError('Invalid job scheduler system type `queue`: ' + queue)
     print(f'Test job has been submitted (job ID: {job_id}).')
 
     return job_id
diff --git a/babs/system.py b/babs/system.py
index 92a363b4..9ece0736 100644
--- a/babs/system.py
+++ b/babs/system.py
@@ -63,7 +63,7 @@ def get_dict(self):
 
         # sanity check:
         if self.type not in dict:
-            raise Exception(
+            raise ValueError(
                 "There is no key called '"
                 + self.type
                 + "' in"
diff --git a/babs/template_test_job.py b/babs/template_test_job.py
index 87b8a93e..c2959cd1 100644
--- a/babs/template_test_job.py
+++ b/babs/template_test_job.py
@@ -34,52 +34,47 @@ def main():
     fn_yaml = op.join(args.path_check_setup, 'check_env.yaml')
     if op.exists(fn_yaml):
         os.remove(fn_yaml)  # remove it
-    yaml_file = open(fn_yaml, 'w')
+    with open(fn_yaml, 'w') as yaml_file:
+        # Initialize the dict:
+        config = {}
 
-    # Initialize the dict:
-    config = {}
+        # If the path of ephemeral compute workspace is writable:
+        flag_writable = os.access(args.path_workspace, os.W_OK)
+        config['workspace_writable'] = flag_writable
+        # change to the version that `read_yaml()` from babs/utils.py can read:
+        if flag_writable:  # True
+            str_writable = 'true'
+        else:
+            str_writable = 'false'
+        yaml_file.write('workspace_writable: ' + str_writable + '\n')
 
-    # If the path of ephemeral compute workspace is writable:
-    flag_writable = os.access(args.path_workspace, os.W_OK)
-    config['workspace_writable'] = flag_writable
-    # change to the version that `read_yaml()` from babs/utils.py can read:
-    if flag_writable:  # True
-        str_writable = 'true'
-    else:
-        str_writable = 'false'
-    yaml_file.write('workspace_writable: ' + str_writable + '\n')
+        # Which python in current env:
+        # assume the python is installed; otherwise this script cannot be run:
+        config['which_python'] = sys.executable
+        yaml_file.write("which_python: '" + sys.executable + "'\n")
 
-    # Which python in current env:
-    # assume the python is installed; otherwise this script cannot be run:
-    config['which_python'] = sys.executable
-    yaml_file.write("which_python: '" + sys.executable + "'\n")
+        # Check each dependent packages' versions:
+        config['version'] = {}
+        yaml_file.write('version:\n')
+        # What packages' versions to check:
+        what_versions = {
+            'datalad': 'datalad --version',
+            'git': 'git --version',
+            'git-annex': 'git-annex version',
+            'datalad_containers': 'datalad containers-add --version',
+        }
+        for key, the_command in what_versions.items():
+            try:
+                proc = subprocess.run(the_command.split(' '), stdout=subprocess.PIPE, check=True)
+                if key == 'git-annex':
+                    temp = proc.stdout.decode('utf-8').split('\n')[0]
+                    config['version'][key] = temp
+                else:
+                    config['version'][key] = proc.stdout.decode('utf-8').replace('\n', '')
+            except Exception:
+                config['version'][key] = 'not_installed'
 
-    # Check each dependent packages' versions:
-    config['version'] = {}
-    yaml_file.write('version:\n')
-    # What packages' versions to check:
-    what_versions = {
-        'datalad': 'datalad --version',
-        'git': 'git --version',
-        'git-annex': 'git-annex version',
-        'datalad_containers': 'datalad containers-add --version',
-    }
-    for key in what_versions:
-        the_command = what_versions[key]
-        try:
-            proc = subprocess.run(the_command.split(' '), stdout=subprocess.PIPE)
-            proc.check_returncode()
-            if key == 'git-annex':
-                temp = proc.stdout.decode('utf-8').split('\n')[0]
-                config['version'][key] = temp
-            else:
-                config['version'][key] = proc.stdout.decode('utf-8').replace('\n', '')
-        except Exception:
-            config['version'][key] = 'not_installed'
-
-        yaml_file.write('  ' + key + ": '" + config['version'][key] + "'\n")
-
-    yaml_file.close()
+            yaml_file.write('  ' + key + ": '" + config['version'][key] + "'\n")
 
 
 if __name__ == '__main__':
diff --git a/babs/utils.py b/babs/utils.py
index 06fb7a6f..f3f47b66 100644
--- a/babs/utils.py
+++ b/babs/utils.py
@@ -118,10 +118,9 @@ def read_yaml(fn, use_filelock=False):
         lock = FileLock(lock_path)
 
         try:
-            with lock.acquire(timeout=5):  # lock the file, i.e., lock job status df
-                with open(fn) as f:
-                    config = yaml.safe_load(f)
-                    # ^^ dict is a dict; elements can be accessed by `dict["key"]["sub-key"]`
+            with lock.acquire(timeout=5), open(fn) as f:
+                config = yaml.safe_load(f)
+                # ^^ dict is a dict; elements can be accessed by `dict["key"]["sub-key"]`
         except Timeout:  # after waiting for time defined in `timeout`:
             # if another instance also uses locks, and is currently running,
             #   there will be a timeout error
@@ -208,7 +207,7 @@ def app_output_settings_from_config(config):
 
     # Sanity check: this section should exist:
     if 'zip_foldernames' not in config:
-        raise Exception(
+        raise ValueError(
             'The `container_config` does not contain'
             ' the section `zip_foldernames`. Please add this section!'
         )
@@ -231,21 +230,23 @@ def app_output_settings_from_config(config):
         )
 
     # Only raise an exception if both are defined and they don't match
-    if None not in (deprecated_create_output_dir_for_single_zip, create_output_dir_for_single_zip):
-        if not deprecated_create_output_dir_for_single_zip == create_output_dir_for_single_zip:
-            raise ValueError(
-                'The `all_results_in_one_zip` and the deprecated placeholder'
-                "'" + PLACEHOLDER_MK_SUB_OUTPUT_FOLDER_DEPRECATED + "' do not match."
-            )
+    if (
+        None not in (deprecated_create_output_dir_for_single_zip, create_output_dir_for_single_zip)
+        and deprecated_create_output_dir_for_single_zip != create_output_dir_for_single_zip
+    ):
+        raise ValueError(
+            'The `all_results_in_one_zip` and the deprecated placeholder'
+            "'" + PLACEHOLDER_MK_SUB_OUTPUT_FOLDER_DEPRECATED + "' do not match."
+        )
 
     # Make sure it's not empty after we popped the deprecated key
     if not config['zip_foldernames']:
-        raise Exception('No output folder name provided in `zip_foldernames` section.')
+        raise ValueError('No output folder name provided in `zip_foldernames` section.')
 
     # Get the dict of foldernames + version number:
     if create_output_dir_for_single_zip:
-        if not len(config['zip_foldernames']) == 1:
-            raise Exception(
+        if len(config['zip_foldernames']) != 1:
+            raise ValueError(
                 'You ask BABS to create more than one output folder,'
                 ' but BABS can only create one output folder.'
                 " Please only keep one of them in 'zip_foldernames' section."
@@ -290,10 +291,9 @@ def print_versions_from_yaml(fn_yaml):
     config = read_yaml(fn_yaml)
     print('Below is the information of designated environment and temporary workspace:\n')
     # print the yaml file:
-    f = open(fn_yaml)
-    file_contents = f.read()
+    with open(fn_yaml) as f:
+        file_contents = f.read()
     print(file_contents)
-    f.close()
 
     # Check if everything is as satisfied:
     if config['workspace_writable']:  # bool; if writable:
@@ -338,9 +338,8 @@ def get_git_show_ref_shasum(branch_name, the_path):
     """
 
     proc_git_show_ref = subprocess.run(
-        ['git', 'show-ref', branch_name], cwd=the_path, stdout=subprocess.PIPE
+        ['git', 'show-ref', branch_name], cwd=the_path, stdout=subprocess.PIPE, check=True
     )
-    proc_git_show_ref.check_returncode()
     msg = proc_git_show_ref.stdout.decode('utf-8')
     # `msg.split()`:    # split by space and '\n'
     #   e.g. for default branch (main or master):
@@ -370,6 +369,7 @@ def get_results_branches(ria_directory):
         cwd=ria_directory,
         capture_output=True,
         text=True,
+        check=True,
     )
 
     # Filter to just branches starting with 'job-'
@@ -406,8 +406,8 @@ def get_results_branches_from_clone(clone_path):
         cwd=clone_path,
         capture_output=True,
         text=True,
+        check=True,
     )
-    out.check_returncode()
     branches = []
     for line in (out.stdout or '').strip().splitlines():
         line = line.strip()
@@ -441,6 +441,7 @@ def get_results_branches_from_ria(ria_data_dir, timeout=30):
         capture_output=True,
         text=True,
         timeout=timeout,
+        check=False,
     )
     if out.returncode != 0:
         return []
@@ -528,7 +529,11 @@ def get_repo_hash(repo_path):
         the hash of the current commit
     """
     proc_hash = subprocess.run(
-        ['git', 'rev-parse', 'HEAD'], cwd=repo_path, capture_output=True, text=True
+        ['git', 'rev-parse', 'HEAD'],
+        cwd=repo_path,
+        capture_output=True,
+        text=True,
+        check=False,
     )
     if proc_hash.returncode != 0:
         raise ValueError(
@@ -658,34 +663,34 @@ def validate_sub_ses_processing_inclusion(processing_inclusion_file, processing_
         try:
             initial_inclu_df = pd.read_csv(processing_inclusion_file)
         except Exception as e:
-            raise Exception(f'Error reading `{processing_inclusion_file}`:\n{e}')
+            raise ValueError(f'Error reading `{processing_inclusion_file}`:\n{e}')
 
     # Sanity check: there are expected column(s):
     if 'sub_id' not in initial_inclu_df.columns:
-        raise Exception(
+        raise ValueError(
             f'Error reading `{processing_inclusion_file}`: '
             f"There is no 'sub_id' column in the CSV file!"
         )
 
     if processing_level == 'session' and 'ses_id' not in initial_inclu_df.columns:
-        raise Exception(
+        raise ValueError(
             "There is no 'ses_id' column in `processing_inclusion_file`! "
             'It is expected as user requested to process data on a session-wise basis.'
         )
 
     # Sanity check: no repeated sub (or sessions):
-    if processing_level == 'subject':
+    if processing_level == 'subject' and initial_inclu_df['sub_id'].duplicated().any():
         # there should only be one occurrence per sub:
-        if initial_inclu_df['sub_id'].duplicated().any():
-            raise Exception("There are repeated 'sub_id' in `processing_inclusion_file`!")
-
-    elif processing_level == 'session':
+        raise ValueError("There are repeated 'sub_id' in `processing_inclusion_file`!")
+    elif (
+        processing_level == 'session'
+        and initial_inclu_df.duplicated(subset=['sub_id', 'ses_id']).any()
+    ):
         # there should not be repeated combinations of `sub_id` and `ses_id`:
-        if initial_inclu_df.duplicated(subset=['sub_id', 'ses_id']).any():
-            raise Exception(
-                "There are repeated combinations of 'sub_id' and 'ses_id' in "
-                f'`{processing_inclusion_file}`!'
-            )
+        raise ValueError(
+            "There are repeated combinations of 'sub_id' and 'ses_id' in "
+            f'`{processing_inclusion_file}`!'
+        )
     # Sort the initial included sub/ses list:
     sorting_indices = ['sub_id'] if processing_level == 'subject' else ['sub_id', 'ses_id']
     initial_inclu_df = initial_inclu_df.sort_values(by=sorting_indices).reset_index(drop=True)
diff --git a/design/status-without-pandas.md b/design/status-without-pandas.md
index 4ac63b39..0626424a 100644
--- a/design/status-without-pandas.md
+++ b/design/status-without-pandas.md
@@ -99,14 +99,15 @@ total_running, total_failed.
 
 ```python
 class SchedulerState(Enum):
-    NOT_SUBMITTED = "NOT_SUBMITTED"
-    PENDING = "PD"
-    RUNNING = "R"
-    COMPLETING = "CG"
-    CONFIGURING = "CF"
-    DONE = "DONE"           # left scheduler, exit code unknown
+    NOT_SUBMITTED = 'NOT_SUBMITTED'
+    PENDING = 'PD'
+    RUNNING = 'R'
+    COMPLETING = 'CG'
+    CONFIGURING = 'CF'
+    DONE = 'DONE'  # left scheduler, exit code unknown
     # future: COMPLETED, FAILED, CANCELLED, TIMEOUT (from sacct)
 
+
 @dataclass
 class JobStatus:
     sub_id: str
@@ -124,8 +125,7 @@ class JobStatus:
 
     @property
     def is_failed(self) -> bool:
-        return (self.scheduler_state == SchedulerState.DONE
-                and not self.has_results)
+        return self.scheduler_state == SchedulerState.DONE and not self.has_results
 
     @property
     def submitted(self) -> bool:
diff --git a/pyproject.toml b/pyproject.toml
index 51a59da3..bde710fc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,7 +46,7 @@ doc = [
     "sphinx_design",            # for adding in-line badges etc
     "sphinx_rtd_theme",         # needed by readthedocs
 ]
-dev = ["ruff ~= 0.4.3", "pre-commit"]
+dev = ["ruff == 0.16.0", "pre-commit"]
 tests = [
     "coverage",
     "pytest",
diff --git a/tests/conftest.py b/tests/conftest.py
index 4c4cfd6d..af752d5d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -27,6 +27,7 @@ def _setup_before_all_tests():
         ['sacctmgr', '-i', 'modify', 'user', 'root', 'set', 'MaxJobs=200'],
         capture_output=True,
         text=True,
+        check=False,
     )
     if result.returncode != 0:
         raise RuntimeError(
@@ -54,7 +55,7 @@ def simbids_apptainer_image():
     Get the path of the simbids-raw-mri apptainer image.
     """
     if not op.exists(f'/singularity_images/simbids_{SIMBIDS_VERSION}.sif'):
-        raise Exception(f'simbids_{SIMBIDS_VERSION}.sif not found!')
+        raise FileNotFoundError(f'simbids_{SIMBIDS_VERSION}.sif not found!')
     return f'/singularity_images/simbids_{SIMBIDS_VERSION}.sif'
 
 
@@ -91,7 +92,7 @@ def get_simbids_raw_bids_data(simbids_apptainer_image_path, bids_dir, session_ty
         'ds004146_configs.yaml' if session_type == 'multi-session' else 'ds005237_configs.yaml'
     )
 
-    proc = subprocess.run(
+    subprocess.run(
         [
             'apptainer',
             'exec',
@@ -103,8 +104,8 @@ def get_simbids_raw_bids_data(simbids_apptainer_image_path, bids_dir, session_ty
             simbids_yaml,
         ],
         stdout=subprocess.PIPE,
+        check=True,
     )
-    proc.check_returncode()
     # Initialize datalad in the bids_dir, forcing it to accept original files
     ds_path = str(bids_dir.absolute() / 'simbids')
     assert op.exists(ds_path)
@@ -160,8 +161,7 @@ def run_simbids_app_simulation(
     ]
     if extra_args:
         args.extend(extra_args)
-    proc = subprocess.run(args, stdout=subprocess.PIPE)
-    proc.check_returncode()
+    subprocess.run(args, stdout=subprocess.PIPE, check=True)
     return app_output_dir
 
 
@@ -362,6 +362,7 @@ def gather_slurm_job_diagnostics(
             capture_output=True,
             text=True,
             timeout=10,
+            check=False,
         )
         lines.append(f'sacct stdout:\n{out.stdout or "(none)"}')
         if out.stderr:
diff --git a/tests/test_babs_workflow.py b/tests/test_babs_workflow.py
index 4e2707a9..d965aa30 100644
--- a/tests/test_babs_workflow.py
+++ b/tests/test_babs_workflow.py
@@ -82,16 +82,20 @@ def test_babs_init_raw_bids(
 
     # Test error when project root already exists
     project_root.mkdir(parents=True, exist_ok=True)
-    with mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=babs_init_opts):
-        with pytest.raises(FileExistsError, match=r'already exists'):
-            _enter_init()
+    with (
+        mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=babs_init_opts),
+        pytest.raises(FileExistsError, match=r'already exists'),
+    ):
+        _enter_init()
 
     # Test error when parent directory doesn't exist
     non_existent_parent = project_base / 'non_existent' / 'my_babs_project'
     babs_init_opts.project_root = non_existent_parent
-    with mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=babs_init_opts):
-        with pytest.raises(ValueError, match=r'parent folder.*does not exist'):
-            _enter_init()
+    with (
+        mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=babs_init_opts),
+        pytest.raises(ValueError, match=r'parent folder.*does not exist'),
+    ):
+        _enter_init()
 
     # Test error when parent directory doesn't exist
     babs_init_opts.project_root = project_root
@@ -231,19 +235,21 @@ def _get_results_branches_use_merge_ds_when_exists(self):
             return get_results_branches_from_clone(str(merge_ds))
         return _orig_get_results_branches_method(self)
 
-    with mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=babs_merge_opts):
-        with mock.patch.object(
+    with (
+        mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=babs_merge_opts),
+        mock.patch.object(
             babs_base.BABS, '_get_results_branches', _get_results_branches_use_merge_ds_when_exists
-        ):
-            try:
-                _enter_merge()
-            except ValueError as e:
-                if 'no successfully finished job' in str(e).lower():
-                    diag = gather_slurm_job_diagnostics(
-                        project_root, log_glob='sim.*', max_logs=None, tail_lines=None
-                    )
-                    raise ValueError(f'{e}\nJob accounting (sacct):\n{diag}') from e
-                raise
+        ),
+    ):
+        try:
+            _enter_merge()
+        except ValueError as e:
+            if 'no successfully finished job' in str(e).lower():
+                diag = gather_slurm_job_diagnostics(
+                    project_root, log_glob='sim.*', max_logs=None, tail_lines=None
+                )
+                raise ValueError(f'{e}\nJob accounting (sacct):\n{diag}') from e
+            raise
 
 
 def test_init_forwards_shared_group(tmp_path):
@@ -261,9 +267,11 @@ def test_init_forwards_shared_group(tmp_path):
         shared_group='my-lab-group',
         no_ignore=[],
     )
-    with mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=options):
-        with mock.patch('babs.BABSBootstrap') as mock_bootstrap_cls:
-            _enter_init()
+    with (
+        mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=options),
+        mock.patch('babs.BABSBootstrap') as mock_bootstrap_cls,
+    ):
+        _enter_init()
 
     mock_bootstrap_cls.assert_called_once_with(
         options.project_root,
@@ -296,9 +304,11 @@ def test_init_forwards_no_ignore(tmp_path):
         shared_group=None,
         no_ignore=['logs'],
     )
-    with mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=options):
-        with mock.patch('babs.BABSBootstrap') as mock_bootstrap_cls:
-            _enter_init()
+    with (
+        mock.patch.object(argparse.ArgumentParser, 'parse_args', return_value=options),
+        mock.patch('babs.BABSBootstrap') as mock_bootstrap_cls,
+    ):
+        _enter_init()
 
     mock_bootstrap_cls.assert_called_once_with(
         options.project_root,
@@ -468,6 +478,7 @@ def test_datalad_save_with_filtering(babs_project_sessionlevel_babsobject):
         cwd=babs_project_sessionlevel_babsobject.analysis_path,
         capture_output=True,
         text=True,
+        check=True,
     )
 
     assert test_file1.name in result.stdout
diff --git a/tests/test_base.py b/tests/test_base.py
index 14f20bc1..53d67ffb 100644
--- a/tests/test_base.py
+++ b/tests/test_base.py
@@ -68,7 +68,7 @@ def test_validate_pipeline_config(babs_project_sessionlevel):
 
     # Test invalid configs
     babs_proj.pipeline = {'not': 'a list'}
-    with pytest.raises(ValueError, match='Pipeline configuration must be a list'):
+    with pytest.raises(TypeError, match='Pipeline configuration must be a list'):
         babs_proj._validate_pipeline_config()
 
     babs_proj.pipeline = []
@@ -76,7 +76,7 @@ def test_validate_pipeline_config(babs_project_sessionlevel):
         babs_proj._validate_pipeline_config()
 
     babs_proj.pipeline = ['not a dict']
-    with pytest.raises(ValueError, match='Pipeline step 0 must be a dictionary'):
+    with pytest.raises(TypeError, match='Pipeline step 0 must be a dictionary'):
         babs_proj._validate_pipeline_config()
 
     babs_proj.pipeline = [{'missing': 'container_name'}]
@@ -483,7 +483,7 @@ def test_shared_group_inits_analysis_and_rias(
         ['git', 'config', '--global', '--get-all', 'safe.directory'],
         stdout=subprocess.PIPE,
         text=True,
-        check=False,
+        check=True,
     ).stdout.splitlines()
     assert str(Path(babs_bootstrap.analysis_path).resolve()) in safe_dirs
     assert str(output_ria_dir.resolve()) in safe_dirs
diff --git a/tests/test_check_setup.py b/tests/test_check_setup.py
index 30267846..a4ffbe34 100644
--- a/tests/test_check_setup.py
+++ b/tests/test_check_setup.py
@@ -149,7 +149,7 @@ def mock_request_status(*args, **kwargs):
 
     sys.stdout.write('DEBUG: All captured printed messages:\n')
     for i, msg in enumerate(printed_messages):
-        sys.stdout.write(f'  {i}: {repr(msg)}\n')
+        sys.stdout.write(f'  {i}: {msg!r}\n')
     sys.stdout.flush()
 
     # Check expected messages and behavior
diff --git a/tests/test_generate_bidsapp_runscript.py b/tests/test_generate_bidsapp_runscript.py
index 19a34402..f8adee23 100644
--- a/tests/test_generate_bidsapp_runscript.py
+++ b/tests/test_generate_bidsapp_runscript.py
@@ -117,7 +117,7 @@ def test_generate_bidsapp_runscript(input_datasets, config_file, processing_leve
     config_path = NOTEBOOKS_DIR / config_file
     container_name = config_file.split('_')[1]
     config = read_yaml(config_path)
-    dict_zip_foldernames, bids_app_output_dir = app_output_settings_from_config(config)
+    _dict_zip_foldernames, bids_app_output_dir = app_output_settings_from_config(config)
     script_content = generate_bidsapp_runscript(
         input_datasets,
         processing_level,
@@ -156,7 +156,9 @@ def run_shellcheck(script_path):
 
     try:
         # Run shellcheck on the temporary file
-        result = subprocess.run(['shellcheck', script_path], capture_output=True, text=True)
+        result = subprocess.run(
+            ['shellcheck', script_path], capture_output=True, text=True, check=False
+        )
         return result.returncode == 0, result.stdout
     except subprocess.CalledProcessError as e:
         return False, e.output
diff --git a/tests/test_generate_submit_script.py b/tests/test_generate_submit_script.py
index 79ff5144..cf8034aa 100644
--- a/tests/test_generate_submit_script.py
+++ b/tests/test_generate_submit_script.py
@@ -138,7 +138,9 @@ def run_shellcheck(script_path):
 
     try:
         # Run shellcheck on the temporary file
-        result = subprocess.run(['shellcheck', script_path], capture_output=True, text=True)
+        result = subprocess.run(
+            ['shellcheck', script_path], capture_output=True, text=True, check=False
+        )
         return result.returncode == 0, result.stdout
     except subprocess.CalledProcessError as e:
         return False, e.output
@@ -300,7 +302,9 @@ def test_find_single_zip_handles_regex_metachars_in_name(name, processing_level,
     )
     # the template defines the finder AND calls it, echoing the located zip path
     script = f'set -e\nsubid=sub-01\nsesid=ses-1\n{finder}\n'
-    result = subprocess.run(['bash', '-c', script], cwd=tmp_path, capture_output=True, text=True)
+    result = subprocess.run(
+        ['bash', '-c', script], cwd=tmp_path, capture_output=True, text=True, check=False
+    )
 
     assert result.returncode == 0, result.stderr
     assert zipname in result.stdout, f'zip not located:\nOUT:{result.stdout}\nERR:{result.stderr}'
diff --git a/tests/test_interaction.py b/tests/test_interaction.py
index ff2f83ea..8955394c 100644
--- a/tests/test_interaction.py
+++ b/tests/test_interaction.py
@@ -111,7 +111,7 @@ def test_babs_status_configures_shared_group_runtime(babs_project_subjectlevel,
         lambda: called.append(True),
     )
     # Stub downstream work; this test verifies guard invocation only.
-    monkeypatch.setattr(babs_proj, '_update_results_status', lambda: {})
+    monkeypatch.setattr(babs_proj, '_update_results_status', dict)
     monkeypatch.setattr('babs.interaction.report_job_status', lambda *_args, **_kwargs: None)
 
     babs_proj.babs_status()
@@ -453,9 +453,7 @@ def _make_statuses(submitted, has_results):
     statuses = {}
     for i, (sub, res) in enumerate(zip(submitted, has_results, strict=True)):
         sub_id = f'sub-{i + 1:02d}'
-        if sub and not res:
-            state = SchedulerState.DONE
-        elif sub:
+        if sub:
             state = SchedulerState.DONE
         else:
             state = SchedulerState.NOT_SUBMITTED
diff --git a/tests/test_merge.py b/tests/test_merge.py
index b7841a8e..52da1eca 100644
--- a/tests/test_merge.py
+++ b/tests/test_merge.py
@@ -16,7 +16,7 @@
 def test_merge_no_branches(babs_project_sessionlevel, monkeypatch):
     """Test babs_merge when no branches have results."""
     babs_proj = BABSMerge(babs_project_sessionlevel)
-    monkeypatch.setattr(babs_proj, '_get_results_branches', lambda: [])
+    monkeypatch.setattr(babs_proj, '_get_results_branches', list)
 
     with pytest.raises(ValueError, match='There is no successfully finished job yet'):
         babs_proj.babs_merge()
@@ -28,16 +28,27 @@ def test_merge_all_branches_no_results(babs_project_sessionlevel, tmp_path, monk
 
     merge_ds_path = tmp_path / 'merge_ds'
     merge_ds_path.mkdir()
-    subprocess.run(['git', 'init'], cwd=merge_ds_path, capture_output=True)
-    subprocess.run(['git', 'config', 'user.name', 'Test'], cwd=merge_ds_path, capture_output=True)
+    subprocess.run(['git', 'init'], cwd=merge_ds_path, capture_output=True, check=True)
+    subprocess.run(
+        ['git', 'config', 'user.name', 'Test'],
+        cwd=merge_ds_path,
+        capture_output=True,
+        check=True,
+    )
     subprocess.run(
         ['git', 'config', 'user.email', 'test@test.com'],
         cwd=merge_ds_path,
         capture_output=True,
+        check=True,
     )
     (merge_ds_path / 'test.txt').write_text('test')
-    subprocess.run(['git', 'add', 'test.txt'], cwd=merge_ds_path, capture_output=True)
-    subprocess.run(['git', 'commit', '-m', 'Initial'], cwd=merge_ds_path, capture_output=True)
+    subprocess.run(['git', 'add', 'test.txt'], cwd=merge_ds_path, capture_output=True, check=True)
+    subprocess.run(
+        ['git', 'commit', '-m', 'Initial'],
+        cwd=merge_ds_path,
+        capture_output=True,
+        check=True,
+    )
 
     default_branch = 'main'
     try:
@@ -45,6 +56,7 @@ def test_merge_all_branches_no_results(babs_project_sessionlevel, tmp_path, monk
             ['git', 'checkout', '-b', default_branch],
             cwd=merge_ds_path,
             capture_output=True,
+            check=True,
         )
     except Exception:
         default_branch = 'master'
@@ -73,7 +85,7 @@ def mock_remote_show(cmd, **kwargs):
             result.returncode = 0
             result.stdout = f'HEAD branch: {default_branch}\n'.encode()
             return result
-        return subprocess.run(cmd, **kwargs)
+        return subprocess.run(cmd, check=kwargs.pop('check', False), **kwargs)
 
     monkeypatch.setattr('babs.merge.subprocess.run', mock_remote_show)
 
@@ -128,7 +140,7 @@ def test_rm_dir_datalad_fail(tmp_path, monkeypatch):
 
     # Mock datalad.remove to raise an exception
     def mock_remove(path=None, dataset=None, **kwargs):
-        raise Exception('datalad remove failed')
+        raise RuntimeError('datalad remove failed')
 
     monkeypatch.setattr(dlapi, 'remove', mock_remove)
 
@@ -283,7 +295,6 @@ def set_analysis_id():
     def mock_clone(source, path):
         # Create the directory so subsequent git commands can run
         os.makedirs(path, exist_ok=True)
-        return None
 
     monkeypatch.setattr(dlapi, 'clone', mock_clone)
 
@@ -293,7 +304,7 @@ def mock_remote_show(cmd, **kwargs):
             result.returncode = 0
             result.stdout = b'No HEAD branch found\n'  # No HEAD branch
             return result
-        return subprocess.run(cmd, **kwargs)
+        return subprocess.run(cmd, check=kwargs.pop('check', False), **kwargs)
 
     monkeypatch.setattr('babs.merge.subprocess.run', mock_remote_show)
 
diff --git a/tests/test_slurm.py b/tests/test_slurm.py
index b448c17a..493ab5fa 100644
--- a/tests/test_slurm.py
+++ b/tests/test_slurm.py
@@ -124,7 +124,7 @@ def test_array_job_submission(
     test_dir = tmp_path_factory.mktemp('test_array_job')
 
     # Submit array job with 3 tasks
-    working_directory, job_id = submit_array_job(test_dir, array_size=3)
+    _working_directory, job_id = submit_array_job(test_dir, array_size=3)
 
     # Wait a moment for job to be registered
     import time
diff --git a/tests/test_template_job.py b/tests/test_template_job.py
index a72b4cf4..05efb99f 100644
--- a/tests/test_template_job.py
+++ b/tests/test_template_job.py
@@ -35,6 +35,7 @@ def test_template_job_execution():
             capture_output=True,
             text=True,
             env={**os.environ, 'RUNNING_PYTEST': '1'},  # Mark as running in test
+            check=False,
         )
 
         # Check that execution was successful
diff --git a/tests/test_utils.py b/tests/test_utils.py
index a986c8b6..4f0b0390 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -102,18 +102,31 @@ def create_git_repo(tmp_path):
     repo_path.mkdir()
 
     # Initialize the git repo
-    subprocess.run(['git', 'init'], cwd=repo_path, capture_output=True)
+    subprocess.run(['git', 'init'], cwd=repo_path, capture_output=True, check=True)
 
     # Configure git user name and email (required for commits)
-    subprocess.run(['git', 'config', 'user.name', 'Test User'], cwd=repo_path, capture_output=True)
     subprocess.run(
-        ['git', 'config', 'user.email', 'test@example.com'], cwd=repo_path, capture_output=True
+        ['git', 'config', 'user.name', 'Test User'],
+        cwd=repo_path,
+        capture_output=True,
+        check=True,
+    )
+    subprocess.run(
+        ['git', 'config', 'user.email', 'test@example.com'],
+        cwd=repo_path,
+        capture_output=True,
+        check=True,
     )
 
     # Create a test file and commit it
     (repo_path / 'test_file.txt').write_text('Test content')
-    subprocess.run(['git', 'add', 'test_file.txt'], cwd=repo_path, capture_output=True)
-    subprocess.run(['git', 'commit', '-m', 'Initial commit'], cwd=repo_path, capture_output=True)
+    subprocess.run(['git', 'add', 'test_file.txt'], cwd=repo_path, capture_output=True, check=True)
+    subprocess.run(
+        ['git', 'commit', '-m', 'Initial commit'],
+        cwd=repo_path,
+        capture_output=True,
+        check=True,
+    )
 
     return repo_path
 
@@ -128,7 +141,11 @@ def test_get_repo_hash(tmp_path):
 
     # Get the hash directly with git
     expected_hash = subprocess.run(
-        ['git', 'rev-parse', 'HEAD'], cwd=repo_path, capture_output=True, text=True
+        ['git', 'rev-parse', 'HEAD'],
+        cwd=repo_path,
+        capture_output=True,
+        text=True,
+        check=True,
     ).stdout.strip()
 
     # They should match
@@ -149,7 +166,11 @@ def test_git_show_ref_shasum(tmp_path):
 
     # Get the current branch name
     branch_name = subprocess.run(
-        ['git', 'branch', '--show-current'], cwd=repo_path, capture_output=True, text=True
+        ['git', 'branch', '--show-current'],
+        cwd=repo_path,
+        capture_output=True,
+        text=True,
+        check=True,
     ).stdout.strip()
 
     # Get the ref with our function
@@ -185,6 +206,7 @@ def test_get_results_branches_from_clone(tmp_path):
         cwd=str(tmp_path),
         capture_output=True,
         text=True,
+        check=True,
     )
 
 
@@ -407,20 +429,36 @@ def test_repo_hashes_mismatch(tmp_path):
 
     for repo_path in [repo1_path, repo2_path]:
         repo_path.mkdir()
-        subprocess.run(['git', 'init'], cwd=repo_path, capture_output=True)
-        subprocess.run(['git', 'config', 'user.name', 'Test'], cwd=repo_path, capture_output=True)
+        subprocess.run(['git', 'init'], cwd=repo_path, capture_output=True, check=True)
+        subprocess.run(
+            ['git', 'config', 'user.name', 'Test'],
+            cwd=repo_path,
+            capture_output=True,
+            check=True,
+        )
         subprocess.run(
             ['git', 'config', 'user.email', 'test@test.com'],
             cwd=repo_path,
             capture_output=True,
+            check=True,
         )
         (repo_path / 'file.txt').write_text('content')
-        subprocess.run(['git', 'add', 'file.txt'], cwd=repo_path, capture_output=True)
-        subprocess.run(['git', 'commit', '-m', 'Initial'], cwd=repo_path, capture_output=True)
+        subprocess.run(['git', 'add', 'file.txt'], cwd=repo_path, capture_output=True, check=True)
+        subprocess.run(
+            ['git', 'commit', '-m', 'Initial'],
+            cwd=repo_path,
+            capture_output=True,
+            check=True,
+        )
 
     (repo2_path / 'file2.txt').write_text('content2')
-    subprocess.run(['git', 'add', 'file2.txt'], cwd=repo2_path, capture_output=True)
-    subprocess.run(['git', 'commit', '-m', 'Second'], cwd=repo2_path, capture_output=True)
+    subprocess.run(['git', 'add', 'file2.txt'], cwd=repo2_path, capture_output=True, check=True)
+    subprocess.run(
+        ['git', 'commit', '-m', 'Second'],
+        cwd=repo2_path,
+        capture_output=True,
+        check=True,
+    )
 
     with pytest.raises(ValueError, match='does not match'):
         compare_repo_commit_hashes(
diff --git a/tox.ini b/tox.ini
index 7430a60f..fa8cde72 100644
--- a/tox.ini
+++ b/tox.ini
@@ -49,7 +49,7 @@ commands =
 description = Check our style guide
 labels = check
 deps =
-  ruff
+  ruff == 0.16.0
 skip_install = true
 commands =
   ruff check --diff
@@ -59,7 +59,7 @@ commands =
 description = Auto-apply style guide to the extent possible
 labels = pre-release
 deps =
-  ruff
+  ruff == 0.16.0
 skip_install = true
 commands =
   ruff check --fix
@@ -99,4 +99,4 @@ deps =
   twine
 skip_install = true
 commands =
-  python -m twine upload dist/*
\ No newline at end of file
+  python -m twine upload dist/*