Feature/pre commit pyupgrade (#413)

* Add pre-commit hook for pyupgrade.

* Skip exceptions for files that no longer need them.

* Apply modernizations suggested by pyupgrade.

* Apply flake8 changes.

* Show diff if pre-commit fails.

* Update changelog.

.circleci/config.yml

@@ -24,7 +24,7 @@ jobs:
       - run:
           name: Run pre-checks
           command: |
-            pre-commit run --all-files
+            pre-commit run --all-files --show-diff-on-failure
 
   linux-python-38: &linux-template
     docker:

.pre-commit-config.yaml

@@ -7,6 +7,13 @@ repos:
     -   id: trailing-whitespace
         exclude: 'setup.cfg'
     -   id: debug-statements
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v2.7.3
+    hooks:
+    -   id: pyupgrade
+        exclude: '(?:configobj/.*)'
+        args:
+        - --py36-plus
 -   repo: local
     hooks:
     -   id: flake8

.sync-zenodo-metadata.py

@@ -36,7 +36,7 @@ def from_citation_author(cls, **citation):
 
     def as_zenodo_creator(self):
         ret = dict(
-            name='{} {}'.format(self.first_names, self.last_names),
+            name=f'{self.first_names} {self.last_names}',
             affiliation=self.affiliation)
         if self.orcid:
             ret['orcid'] = self.orcid.lstrip('https://orcid.org/')

benchmark.py

@@ -62,7 +62,7 @@
 def size(fn):
     try:
         return os.path.getsize(fn)
-    except (OSError, IOError):
+    except OSError:
         return 0
 
 
@@ -125,7 +125,7 @@ def _make_doc(i, num_keys=1, data_size=0):
     assert num_keys >= 1
     assert data_size >= 0
 
-    doc = {'b_{}'.format(j): _random_str(data_size) for j in range(num_keys - 1)}
+    doc = {f'b_{j}': _random_str(data_size) for j in range(num_keys - 1)}
     doc['a'] = '{}{}'.format(i, _random_str(max(0, data_size - len(str(i)))))
     return doc
 
@@ -162,7 +162,7 @@ def setup_random_project(N, num_keys=1, num_doc_keys=0,
         raise TypeError("N must be an integer!")
 
     with TemporaryDirectory(dir=root) as tmp:
-        project = signac.init_project('benchmark-N={}'.format(N), root=tmp)
+        project = signac.init_project(f'benchmark-N={N}', root=tmp)
         generate_random_data(project, N, num_keys, num_doc_keys, data_size, data_std)
         yield project
 
@@ -182,15 +182,15 @@ def noop(*args, **kwargs):
 
 def benchmark_project(project, keys=None):
     root = project.root_directory()
-    setup = "import signac; project = signac.get_project(root='{}'); ".format(root)
+    setup = f"import signac; project = signac.get_project(root='{root}'); "
     setup += "from itertools import islice, repeat; import random; "
     setup += "from benchmark import noop; "
 
     data = OrderedDict()
 
     def run(key, timer, repeat=3, number=10):
         if keys is None or key in keys:
-            logger.info("Run '{}'...".format(key))
+            logger.info(f"Run '{key}'...")
             data[key] = timer.repeat(repeat=repeat, number=number)
 
     run('determine_len', Timer('len(project)', setup=setup))
@@ -321,7 +321,7 @@ def tr(s):
         'tool,N': "Tool, N",
     }.get(cat, cat)
     if cplx is not None:
-        t += ' O({})'.format(cplx)
+        t += f' O({cplx})'
     return t
 
 
@@ -351,10 +351,10 @@ def main_compare(args):
     repo = git.Repo(search_parent_directories=True)
     rev_this = str(repo.commit(args.rev_this))
     doc_this = read_benchmark(args.filename, {'meta.versions.git.sha1': rev_this})
-    assert len(doc_this), "Can't find results for '{}'.".format(args.rev_this)
+    assert len(doc_this), f"Can't find results for '{args.rev_this}'."
     rev_other = repo.commit(args.rev_other)
     doc_other = read_benchmark(args.filename, {'meta.versions.git.sha1': str(rev_other)})
-    assert len(doc_other), "Can't find results for '{}'.".format(args.rev_other)
+    assert len(doc_other), f"Can't find results for '{args.rev_other}'."
 
     print("Showing runtime {} ({}) / {} ({}):".format(
         args.rev_this, str(rev_this)[:6],

changelog.txt

@@ -14,6 +14,7 @@ Added
 +++++
 
  - Support for h5py version 3 (#411).
+ - Added pyupgrade to pre-commit hooks (#413).
 
 [1.5.0] -- 2020-09-20
 ---------------------

setup.cfg

@@ -12,7 +12,7 @@ python-tag = py3
 
 [flake8]
 max-line-length = 100
-exclude = configobj,passlib,cite.py,conf.py
+exclude = configobj,conf.py
 # Use select to ignore unwanted flake8 plugins
 select = E,F,W
 # Specify errors to ignore by default

setup.py

@@ -23,7 +23,7 @@
     fn_readme = os.path.join(this_path, 'README.md')
     with open(fn_readme) as fh:
         long_description = fh.read()
-except (IOError, OSError):
+except OSError:
     long_description = description
 
 setup(

signac/__main__.py

@@ -132,9 +132,9 @@ def _fmt_bytes(nbytes, suffix='B'):
     """
     for unit in ['', 'Ki', 'Mi', 'Gi', 'Ti', 'Pi', 'Ei', 'Zi']:
         if abs(nbytes) < 1024.0:
-            return "%3.1f %s%s" % (nbytes, unit, suffix)
+            return f"{nbytes:3.1f} {unit}{suffix}"
         nbytes /= 1024.0
-    return "%.1f %s%s" % (nbytes, 'Yi', suffix)
+    return "{:.1f} {}{}".format(nbytes, 'Yi', suffix)
 
 
 def _passlib_available():
@@ -188,7 +188,7 @@ def hashpw(pw):
 
 def _read_index(project, fn_index=None):
     if fn_index is not None:
-        _print_err("Reading index from file '{}'...".format(fn_index))
+        _print_err(f"Reading index from file '{fn_index}'...")
         file_descriptor = open(fn_index)
         return (json.loads(line) for line in file_descriptor)
 
@@ -200,7 +200,7 @@ def _open_job_by_id(project, job_id):
     except KeyError:
         close_matches = difflib.get_close_matches(
             job_id, [jid[:len(job_id)] for jid in project.find_job_ids()])
-        msg = "Did not find job corresponding to id '{}'.".format(job_id)
+        msg = f"Did not find job corresponding to id '{job_id}'."
         if len(close_matches) == 1:
             msg += " Did you mean '{}'?".format(close_matches[0])
         elif len(close_matches) > 1:
@@ -245,7 +245,7 @@ def main_project(args):
     project = get_project()
     if args.access:
         fn = project.create_access_module()
-        _print_err("Created access module '{}'.".format(fn))
+        _print_err(f"Created access module '{fn}'.")
         return
     if args.index:
         for doc in project.index():
@@ -267,7 +267,7 @@ def main_job(args):
     try:
         statepoint = json.loads(sp)
     except ValueError:
-        _print_err("Error while reading statepoint: '{}'".format(sp))
+        _print_err(f"Error while reading statepoint: '{sp}'")
         raise
     job = project.open_job(statepoint)
     if args.create:
@@ -331,9 +331,9 @@ def main_move(args):
             job.move(dst_project)
         except DestinationExistsError:
             _print_err(
-                "Destination already exists: '{}' in '{}'.".format(job, dst_project))
+                f"Destination already exists: '{job}' in '{dst_project}'.")
         else:
-            _print_err("Moved '{}' to '{}'.".format(job, dst_project))
+            _print_err(f"Moved '{job}' to '{dst_project}'.")
 
 
 def main_clone(args):
@@ -345,9 +345,9 @@ def main_clone(args):
             job = _open_job_by_id(project, job_id)
             dst_project.clone(job)
         except DestinationExistsError:
-            _print_err("Destination already exists: '{}' in '{}'.".format(job, dst_project))
+            _print_err(f"Destination already exists: '{job}' in '{dst_project}'.")
         else:
-            _print_err("Cloned '{}' to '{}'.".format(job, dst_project))
+            _print_err(f"Cloned '{job}' to '{dst_project}'.")
 
 
 def main_index(args):
@@ -399,7 +399,7 @@ def format_lines(cat, _id, s):
                 if len(args.doc) != 0:
                     doc = {key: doc[key] for key in args.doc if key in doc}
                 print(format_lines('sp ', job_id, doc))
-    except IOError as error:
+    except OSError as error:
         if error.errno == errno.EPIPE:
             sys.stderr.close()
         else:
@@ -436,7 +436,7 @@ def main_init(args):
         name=args.project_id,
         root=os.getcwd(),
         workspace=args.workspace)
-    _print_err("Initialized project '{}'.".format(project))
+    _print_err(f"Initialized project '{project}'.")
 
 
 def main_schema(args):
@@ -530,13 +530,13 @@ def _sig(st):
             re.compile(args.key)
         except re.error as e:
             raise RuntimeError(
-                "Illegal regular expression '{}': '{}'.".format(args.key, e))
+                f"Illegal regular expression '{args.key}': '{e}'.")
         doc_sync = DocSync.ByKey(lambda key: re.match(args.key, key))
     else:
         doc_sync = DocSync.ByKey()
 
     try:
-        _print_err("Synchronizing '{}' -> '{}'...".format(source, destination))
+        _print_err(f"Synchronizing '{source}' -> '{destination}'...")
         stats = destination.sync(
             other=source,
             strategy=strategy,
@@ -645,11 +645,11 @@ def _main_import_non_interactive(project, origin, args):
                 for src, copy_executor in tqdm(dict(data_mapping).items(), 'Importing'):
                     paths[src] = copy_executor(copytree=shutil.move if args.move else None)
     except DestinationExistsError as error:
-        _print_err("Destination '{}' already exists.".format(error.destination))
+        _print_err(f"Destination '{error.destination}' already exists.")
         if not args.sync:
             _print_err("Consider using '--sync' or '--sync-interactive'!")
     except SyncConflict as error:
-        _print_err("Synchronization failed with error: {}".format(error))
+        _print_err(f"Synchronization failed with error: {error}")
         _print_err("Consider using '--sync-interactive'!")
     else:
         return paths
@@ -700,7 +700,7 @@ def main_export(args):
                 pbar.update(1)
         except _SchemaPathEvaluationError as error:
             raise RuntimeWarning(
-                "An error occurred while evaluating the schema path: {}".format(error))
+                f"An error occurred while evaluating the schema path: {error}")
 
     if paths:
         _print_err("Exported {} job(s).".format(len(paths)))
@@ -716,7 +716,7 @@ def main_update_cache(args):
     if n is None:
         _print_err("Cache is up to date.")
     else:
-        _print_err("Updated cache (size={}).".format(n))
+        _print_err(f"Updated cache (size={n}).")
 
 
 # UNCOMMENT THE FOLLOWING BLOCK WHEN THE FIRST MIGRATION IS INTRODUCED.
@@ -791,7 +791,7 @@ def main_config_show(args):
             mode = ' global '
         else:
             mode = ''
-        _print_err("Did not find a{}configuration file.".format(mode))
+        _print_err(f"Did not find a{mode}configuration file.")
         return
     for key in args.key:
         for kt in key.split('.'):
@@ -832,9 +832,9 @@ def main_config_verify(args):
         else:
             mode = ''
         raise RuntimeWarning(
-            "Did not find a{}configuration file.".format(mode))
+            f"Did not find a{mode}configuration file.")
     if cfg.filename is not None:
-        _print_err("Verifcation of config file '{}'.".format(cfg.filename))
+        _print_err(f"Verifcation of config file '{cfg.filename}'.")
     verify_config(cfg)
 
 
@@ -875,7 +875,7 @@ def main_config_set(args):
         sec = sec.setdefault(key, dict())
     try:
         sec[keys[-1]] = args.value
-        _print_err("Updated value '{}'='{}'.".format(args.key, args.value))
+        _print_err(f"Updated value '{args.key}'='{args.value}'.")
     except TypeError:
         raise KeyError(args.key)
     _print_err("Writing configuration to '{}'.".format(
@@ -922,7 +922,7 @@ def hostcfg():
 
     if args.test:
         if hostcfg():
-            _print_err("Trying to connect to host '{}'...".format(args.hostname))
+            _print_err(f"Trying to connect to host '{args.hostname}'...")
             try:
                 client = get_client(hostcfg())
                 client.address
@@ -931,9 +931,9 @@ def hostcfg():
                            "connect to host '{}'.".format(args.hostname))
                 raise
             else:
-                print("Successfully connected to host '{}'.".format(args.hostname))
+                print(f"Successfully connected to host '{args.hostname}'.")
         else:
-            _print_err("Host '{}' is not configured.".format(args.hostname))
+            _print_err(f"Host '{args.hostname}' is not configured.")
         return
 
     if args.remove:
@@ -959,9 +959,9 @@ def hostcfg():
             return
 
     if hostcfg():
-        _print_err("Configuring host '{}'.".format(args.hostname))
+        _print_err(f"Configuring host '{args.hostname}'.")
     else:
-        _print_err("Configuring new host '{}'.".format(args.hostname))
+        _print_err(f"Configuring new host '{args.hostname}'.")
 
     def hide_password(k, v):
         """Hide all fields containing sensitive information."""
@@ -973,7 +973,7 @@ def update_hostcfg(** update):
         for k, v in update.items():
             if v is None:
                 if k in hostcfg():
-                    logging.info("Deleting key {}".format(k))
+                    logging.info(f"Deleting key {k}")
                     del cfg['hosts'][args.hostname][k]
                     store = True
             elif k not in hostcfg() or v != hostcfg()[k]:
@@ -1025,7 +1025,7 @@ def requires_username():
             new_pw = args.password
         update_hostcfg(password=new_pw, password_config=None)
 
-    _print_err("Configured host '{}':".format(args.hostname))
+    _print_err(f"Configured host '{args.hostname}':")
     print("[hosts]")
     for line in config.Config({args.hostname: hostcfg()}).write():
         print(_hide_password(line))
@@ -1105,7 +1105,7 @@ def write_history_file():
                     python_version=sys.version,
                     signac_version=__version__,
                     project_id=project.id,
-                    job_banner='\nJob:\t\t{job._id}'.format(job=job) if job is not None else '',
+                    job_banner=f'\nJob:\t\t{job._id}' if job is not None else '',
                     root_path=project.root_directory(),
                     workspace_path=project.workspace(),
                     size=len(project)))
@@ -1873,12 +1873,12 @@ def main():
             raise
         sys.exit(1)
     except RuntimeWarning as warning:
-        _print_err("Warning: {}".format(warning))
+        _print_err(f"Warning: {warning}")
         if args.debug:
             raise
         sys.exit(1)
     except Exception as error:
-        _print_err('Error: {}'.format(error))
+        _print_err(f'Error: {error}')
         if args.debug:
             raise
         sys.exit(1)

signac/cite.py

@@ -16,7 +16,9 @@
 """
 
 
-ARXIV_REFERENCE = "Carl S. Adorf, Paul M. Dodd, and Sharon C. Glotzer. signac - A Simple Data Management Framework. 2016. arXiv:1611.03543 [cs.DB]"
+ARXIV_REFERENCE = ("Carl S. Adorf, Paul M. Dodd, and Sharon C. Glotzer. "
+                   "signac - A Simple Data Management Framework. 2016. "
+                   "arXiv:1611.03543 [cs.DB]")
 
 
 def bibtex(file=None):