Add typing to signac.core.json. (#313)

* Add typing to signac.core.json.

* Run mypy in continuous integration.

* Remove unused FileNotFoundError (likely Python 2 legacy compatibility).

* Ignore missing imports in mypy checks.

* Define mypy config.

* Ignore typing in syncutil dircmp_deep.

* Fix error in print statement parentheses.

* Add type ignores.

* Remove unused format argument.

* Ignore errors in custom logging level.

* Run mypy on . instead of just signac package.

* Update changelog.

* Rename style-check to pre-checks.

* Update signac/syncutil.py

Co-Authored-By: Carl Simon Adorf <[email protected]>

* Update signac/syncutil.py

Co-authored-by: Carl Simon Adorf <[email protected]>

.circleci/config.yml

@@ -8,7 +8,7 @@ orbs:
   win: circleci/[email protected]  # Enables Windows executors
 
 jobs:
-  style-check:
+  pre-checks:
     docker:
       - image: circleci/python:3.8
 
@@ -19,18 +19,23 @@ jobs:
       - run:
           name: install-dependencies
           command: |
-            pip install --progress-bar off --user -U flake8==3.7.1 pydocstyle==5.0.2
+            pip install --progress-bar off --user -U flake8==3.7.1 pydocstyle==5.0.2 mypy==0.770
 
       - run:
-          name: style-check-code
+          name: check-style
           command: |
             python -m flake8 --show-source .
 
       - run:
-          name: style-check-doc-strings
+          name: check-docstyle
           command: |
             pydocstyle
 
+      - run:
+          name: check-type-hints
+          command: |
+            mypy .
+
   linux-python-38: &linux-template
     docker:
       - image: circleci/python:3.8
@@ -180,25 +185,25 @@ workflows:
   version: 2
   test:
     jobs:
-      - style-check
+      - pre-checks
       - linux-python-38:
           requires:
-            - style-check
+            - pre-checks
       - linux-python-37:
           requires:
-            - style-check
+            - pre-checks
       - linux-python-36:
           requires:
-            - style-check
+            - pre-checks
       - linux-python-35:
           requires:
-            - style-check
+            - pre-checks
       - linux-pypy-3:
           requires:
             - linux-python-36
       - windows-python-38:
           requires:
-            - style-check
+            - pre-checks
       - check-metadata:
           filters:
             branches:

changelog.txt

@@ -10,6 +10,14 @@ Version 1
 next
 ----
 
+Added
++++++
+
+- Type annotations are validated during continuous integration (#313).
+
+Fixed
++++++
+
 - Fix the ``signac config verify`` command (previously broken) (#301, #302).
 
 [1.4.0] -- 2020-02-28

setup.cfg

@@ -18,6 +18,9 @@ exclude = configobj,passlib,cite.py,conf.py
 match = jsondict.py
 ignore = D105, D107, D203, D213
 
+[mypy]
+ignore_missing_imports = True
+
 [coverage:run]
 source = signac
 omit =

signac/common/errors.py

@@ -22,9 +22,5 @@ class ExportError(Error, RuntimeError):
     pass
 
 
-class FileNotFoundError(Error, FileNotFoundError):
-    pass
-
-
 class FetchError(FileNotFoundError):
     pass

signac/common/host.py

@@ -17,7 +17,7 @@
 
 
 SESSION_PASSWORD_HASH_CACHE = SimpleKeyring()
-SESSION_USERNAME_CACHE = dict()
+SESSION_USERNAME_CACHE = dict()  # type: ignore
 
 """
 THIS MODULE IS DEPRECATED!

signac/contrib/filterparse.py

@@ -56,7 +56,7 @@ def _cast(x):
     "Attempt to interpret x with the correct type."
     try:
         if x in CAST_MAPPING_WARNING:
-            print("Did you mean {}?".format(CAST_MAPPING_WARNING[x], file=sys.stderr))
+            print("Did you mean {}?".format(CAST_MAPPING_WARNING[x]), file=sys.stderr)
         return CAST_MAPPING[x]
     except KeyError:
         try:

signac/contrib/indexing.py

@@ -159,7 +159,7 @@ class RegexFileCrawler(BaseCrawler):
         MyCrawler.define('.*\/a_(?P<a>\d+)\.txt', 'TextFile')
     """
     "Mapping of compiled regex objects and associated formats."
-    definitions = dict()
+    definitions = dict()  # type: ignore
 
     @classmethod
     @deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,

signac/contrib/project.py

@@ -1195,7 +1195,7 @@ def check(self):
         if corrupted:
             logger.error(
                 "At least one job appears to be corrupted. Call Project.repair() "
-                "to try to fix errors.".format(len(corrupted)))
+                "to try to fix errors.")
             raise JobsCorruptedError(corrupted)
 
     def repair(self, fn_statepoints=None, index=None, job_ids=None):

signac/core/h5store.py

@@ -507,8 +507,8 @@ class H5StoreManager(DictManager):
     :param prefix:
         The directory prefix shared by all stores managed by this class.
     """
-    cls = H5Store
-    suffix = '.h5'
+    cls = H5Store  # type: ignore
+    suffix = '.h5'  # type: ignore
 
     @staticmethod
     def _validate_key(key):

signac/core/json.py

@@ -4,6 +4,7 @@
 import logging
 from json import load, loads, JSONEncoder
 from json.decoder import JSONDecodeError
+from typing import Any, Dict, Optional
 
 logger = logging.getLogger(__name__)
 
@@ -21,7 +22,7 @@ class CustomJSONEncoder(JSONEncoder):
     an object that is otherwise not serializable, by calling the object's
     `_as_dict()` method.
     """
-    def default(self, o):
+    def default(self, o: Any) -> Dict[str, Any]:
         if NUMPY:
             if isinstance(o, numpy.number):
                 return o.item()
@@ -35,7 +36,7 @@ def default(self, o):
             return super(CustomJSONEncoder, self).default(o)
 
 
-def dumps(o, sort_keys=False, indent=None):
+def dumps(o: Any, sort_keys: bool = False, indent: Optional[int] = None) -> str:
     return CustomJSONEncoder(sort_keys=sort_keys, indent=indent).encode(o)
 
 

signac/errors.py

@@ -10,7 +10,6 @@
 from .common.errors import ConfigError
 from .common.errors import AuthenticationError
 from .common.errors import ExportError
-from .common.errors import FileNotFoundError
 from .common.errors import FetchError
 
 from .contrib.errors import DestinationExistsError
@@ -67,7 +66,6 @@ class KeyTypeError(TypeError):
     'ConfigError',
     'AuthenticationError',
     'ExportError',
-    'FileNotFoundError',
     'FetchError',
     'DestinationExistsError',
     'JobsCorruptedError',

signac/syncutil.py

@@ -11,14 +11,14 @@
 
 logger = logging.getLogger('sync')
 logging.addLevelName(LEVEL_MORE, 'MORE')
-logging.MORE = LEVEL_MORE
+logging.MORE = LEVEL_MORE  # type: ignore
 
 
 def log_more(msg, *args, **kwargs):
     logger.log(LEVEL_MORE, msg, *args, **kwargs)
 
 
-logger.more = log_more
+logger.more = log_more  # type: ignore
 
 
 def copytree(src, dst, copy_function=shutil.copy2, symlinks=False):
@@ -48,13 +48,14 @@ def copytree(src, dst, copy_function=shutil.copy2, symlinks=False):
 
 
 class dircmp_deep(dircmp):
-
     def phase3(self):  # Find out differences between common files
         xx = filecmp.cmpfiles(self.left, self.right, self.common_files, shallow=False)
         self.same_files, self.diff_files, self.funny_files = xx
 
     methodmap = dict(dircmp.methodmap)
-    methodmap['samefiles'] = methodmap['diff_files'] = phase3
+    # The type check for the following line must be ignored.
+    # See: https://github.com/python/mypy/issues/708
+    methodmap['same_files'] = methodmap['diff_files'] = phase3  # type: ignore
 
 
 class _DocProxy(object):