Merge branch 'master' into feature/optimize-job-hash-eq

.circleci/config.yml

@@ -43,7 +43,6 @@ jobs:
           paths:
             - ".pre-commit-cache"
 
-
   linux-python-39: &linux-template
     docker:
       - image: circleci/python:3.9

benchmark.py

@@ -203,8 +203,8 @@ def run(key, timer, repeat=3, number=10):
     run(
         "select_by_id",
         Timer(
-            stmt="project.open_job(id=jobid)",
-            setup=setup + "jobid = random.choice(list(islice(project, 100))).get_id()",
+            stmt="project.open_job(id=job_id)",
+            setup=setup + "job_id = random.choice(list(islice(project, 100))).get_id()",
         ),
     )
 

signac/__main__.py

@@ -315,7 +315,7 @@ def main_remove(args):
     for job_id in args.job_id:
         job = _open_job_by_id(project, job_id)
         if args.interactive and not query_yes_no(
-            "Are you sure you want to {action} job with id '{job._id}'?".format(
+            "Are you sure you want to {action} job with id '{job.id}'?".format(
                 action="clear" if args.clear else "remove", job=job
             ),
             default="no",
@@ -400,10 +400,12 @@ def format_lines(cat, _id, s):
             job = project.open_job(id=job_id)
 
             if args.sp is not None:
-                sp = job.statepoint()
+                statepoint = job.statepoint()
                 if len(args.sp) != 0:
-                    sp = {key: sp[key] for key in args.sp if key in sp}
-                print(format_lines("sp ", job_id, sp))
+                    statepoint = {
+                        key: statepoint[key] for key in args.sp if key in statepoint
+                    }
+                print(format_lines("sp ", job_id, statepoint))
 
             if args.doc is not None:
                 doc = job.document()
@@ -428,9 +430,9 @@ def main_diff(args):
 
     diff = diff_jobs(*jobs)
 
-    for jobid, sp in diff.items():
-        print(jobid)
-        pprint(sp)
+    for job_id, statepoint in diff.items():
+        print(job_id)
+        pprint(statepoint)
 
 
 def main_view(args):
@@ -1166,7 +1168,7 @@ def write_history_file():
                     python_version=sys.version,
                     signac_version=__version__,
                     project_id=project.id,
-                    job_banner=f"\nJob:\t\t{job._id}" 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),

signac/contrib/import_export.py

@@ -62,7 +62,7 @@ def _make_schema_based_path_function(jobs, exclude_keys=None, delimiter_nested="
         # signature of the path function below.
         return lambda job, sep=None: ""
 
-    index = [{"_id": job._id, "statepoint": job.sp()} for job in jobs]
+    index = [{"_id": job.id, "statepoint": job.statepoint()} for job in jobs]
     jsi = _build_job_statepoint_index(exclude_const=True, index=index)
     sp_index = OrderedDict(jsi)
 
@@ -100,9 +100,9 @@ def path(job, sep=None):
         """
         try:
             if sep:
-                return os.path.normpath(sep.join(paths[job._id]))
+                return os.path.normpath(sep.join(paths[job.id]))
             else:
-                return os.path.normpath(os.path.join(*paths[job._id]))
+                return os.path.normpath(os.path.join(*paths[job.id]))
         except KeyError:
             raise RuntimeError(
                 "Unable to determine path for job '{}'.\nThis is usually caused by a "
@@ -126,11 +126,9 @@ def format_field(self, value, format_spec):
         ----------
         value :
             The value to be formatted.
-
         format_spec :
             The format specification.
 
-
         Returns
         -------
         str
@@ -220,7 +218,7 @@ def path_function(job):
             """
             try:
                 try:
-                    ret = path.format(job=job, **job.sp)
+                    ret = path.format(job=job, **job.statepoint)
                 except TypeError as error:
                     if (
                         str(error)
@@ -605,11 +603,13 @@ def parse_path(path):
         """
         match = re.match(schema_regex, os.path.normpath(path))
         if match:
-            sp = match.groupdict()
+            statepoint = match.groupdict()
             for key in types:
-                if key in sp:
-                    sp[key] = types[key](sp[key])
-            return _dotted_dict_to_nested_dicts(sp, delimiter_nested=_DOT_MAGIC_WORD)
+                if key in statepoint:
+                    statepoint[key] = types[key](statepoint[key])
+            return _dotted_dict_to_nested_dicts(
+                statepoint, delimiter_nested=_DOT_MAGIC_WORD
+            )
 
     return parse_path
 

signac/contrib/job.py

@@ -215,18 +215,18 @@ def reset_statepoint(self, new_statepoint):
         self._cwd = []
         logger.info(f"Moved '{self}' -> '{dst}'.")
 
-    def _reset_sp(self, new_sp=None):
+    def _reset_sp(self, new_statepoint=None):
         """Check for new state point requested to assign this job.
 
         Parameters
         ----------
-        new_sp : dict
+        new_statepoint : dict
             The job's new state point (Default value = None).
 
         """
-        if new_sp is None:
-            new_sp = self.statepoint()
-        self.reset_statepoint(new_sp)
+        if new_statepoint is None:
+            new_statepoint = self.statepoint()
+        self.reset_statepoint(new_statepoint)
 
     def update_statepoint(self, update, overwrite=False):
         """Update the state point of this job.
@@ -290,16 +290,16 @@ def statepoint(self):
         return self._statepoint
 
     @statepoint.setter
-    def statepoint(self, new_sp):
+    def statepoint(self, new_statepoint):
         """Assign a new state point to this job.
 
         Parameters
         ----------
-        new_sp : dict
+        new_statepoint : dict
             The new state point to be assigned.
 
         """
-        self._reset_sp(new_sp)
+        self._reset_sp(new_statepoint)
 
     @property
     def sp(self):
@@ -493,9 +493,9 @@ def _check_manifest(self):
         fn_manifest = os.path.join(self._wd, self.FN_MANIFEST)
         try:
             with open(fn_manifest, "rb") as file:
-                assert calc_id(json.loads(file.read().decode())) == self._id
+                assert calc_id(json.loads(file.read().decode())) == self.id
         except (AssertionError, ValueError):
-            raise JobsCorruptedError([self._id])
+            raise JobsCorruptedError([self.id])
 
     def init(self, force=False):
         """Initialize the job's workspace directory.
@@ -523,7 +523,7 @@ def init(self, force=False):
             self._init(force=force)
         except Exception:
             logger.error(
-                f"State point manifest file of job '{self._id}' appears to be corrupted."
+                f"State point manifest file of job '{self.id}' appears to be corrupted."
             )
             raise
         return self
@@ -619,7 +619,7 @@ def move(self, project):
         self.__dict__.update(dst.__dict__)
 
     def sync(self, other, strategy=None, exclude=None, doc_sync=None, **kwargs):
-        """Perform a one-way synchronization of this job with the other job.
+        r"""Perform a one-way synchronization of this job with the other job.
 
         By default, this method will synchronize all files and document data with
         the other job to this job until a synchronization conflict occurs. There
@@ -652,11 +652,9 @@ def sync(self, other, strategy=None, exclude=None, doc_sync=None, **kwargs):
             no keys will be synchronized upon conflict.
         dry_run :
             If True, do not actually perform the synchronization.
-        kwargs :
+        \*\*kwargs :
             Extra keyword arguments will be forward to the :meth:`~signac.sync.sync_jobs`
             function which actually excutes the synchronization operation.
-        **kwargs :
-
 
         Raises
         ------
@@ -748,6 +746,6 @@ def __deepcopy__(self, memo):
         cls = self.__class__
         result = cls.__new__(cls)
         memo[id(self)] = result
-        for k, v in self.__dict__.items():
-            setattr(result, k, deepcopy(v, memo))
+        for key, value in self.__dict__.items():
+            setattr(result, key, deepcopy(value, memo))
         return result

signac/contrib/linked_view.py

@@ -62,11 +62,11 @@ def create_linked_view(project, prefix=None, job_ids=None, index=None, path=None
 
     if index is None:
         if job_ids is None:
-            index = [{"_id": job._id, "statepoint": job.sp()} for job in project]
+            index = [{"_id": job.id, "statepoint": job.statepoint()} for job in project]
             jobs = list(project)
         else:
             index = [
-                {"_id": job_id, "statepoint": project.open_job(id=job_id).sp()}
+                {"_id": job_id, "statepoint": project.open_job(id=job_id).statepoint()}
                 for job_id in job_ids
             ]
             jobs = list(project.open_job(id=job_id) for job_id in job_ids)