Merge remote-tracking branch 'origin/master' into additional_deprecat…

…ions

changelog.txt

@@ -20,6 +20,7 @@ Changed
 +++++++
 
  - Schema migration is now performed on directories rather than signac projects and supports a wider range of schemas (#654).
+ - Deprecated features now use ``FutureWarning`` instead of ``DeprecationWarning``, which is hidden by default (#687, #691).
 
 Deprecated
 ++++++++++
@@ -31,6 +32,11 @@ Deprecated
  - ``signac.cite`` module is deprecated (#611, #592).
  - ``config.get_config`` method is deprecated (#675).
 
+Changed
++++++++
+
+ - Project names have a default in anticipation of removing names entirely. Project names will be removed in signac 2.0.
+
 Fixed
 +++++
 

contributors.yaml

@@ -107,4 +107,8 @@ contributors:
     family-names: Dave
     given-names: Shantanu
     affiliation: "Jodhpur Institute of Engineering and Technology"
+  -
+    family-names: Mahapatra
+    given-names: Onkar
+    affiliation: "Cluster Innovation Centre, New Delhi"
 ...

requirements/requirements-benchmark.txt

@@ -1,6 +1,6 @@
-click==8.0.3
+click==8.0.4
 gitdb2==4.0.2
-GitPython==3.1.26
-numpy==1.22.1
-pandas==1.4.0; implementation_name=='cpython' --no-binary :none:
+GitPython==3.1.27
+numpy==1.22.2
+pandas==1.4.1; implementation_name=='cpython' --no-binary :none:
 psutil==5.9.0

requirements/requirements-test-optional.txt

@@ -1,8 +1,8 @@
 h5py==3.6.0; implementation_name=='cpython'
-numpy==1.22.1
-pandas==1.4.0; implementation_name=='cpython'
+numpy==1.22.2
+pandas==1.4.1; implementation_name=='cpython'
 pymongo==4.0.1; implementation_name=='cpython'
-redis==4.1.2
-ruamel.yaml==0.17.20
+redis==4.1.4
+ruamel.yaml==0.17.21
 tables==3.7.0; implementation_name=='cpython'
 zarr==2.10.3; platform_system!='Windows'

requirements/requirements-test.txt

@@ -1,3 +1,3 @@
-coverage==6.3
-pytest==6.2.5
+coverage==6.3.2
+pytest==7.0.1
 pytest-cov==3.0.0

signac/__main__.py

@@ -1093,10 +1093,7 @@ def main_shell(args):
     except LookupError:
         print("signac", __version__)
         print("No project within this directory.")
-        print(
-            "If you want to initialize a project, execute `$ signac init <project-name>`, "
-            "where <project-name> can be freely chosen."
-        )
+        print("If you want to initialize a project, execute `$ signac init`.")
     else:
         _jobs = find_with_filter(args)
 
@@ -1201,7 +1198,10 @@ def main():
 
     parser_init = subparsers.add_parser("init")
     parser_init.add_argument(
-        "project_id", type=str, help="Initialize a project with the given project id."
+        "project_id",
+        nargs="?",
+        type=str,
+        help="Initialize a project with the given project id.",
     )
     parser_init.add_argument(
         "-w",

signac/contrib/project.py

@@ -83,6 +83,9 @@ def get_indexes(root):
     "information."
 )
 
+# Temporary default for project names until they are removed entirely in signac 2.0
+_DEFAULT_PROJECT_NAME = None
+
 
 class JobSearchIndex:
     """Search for specific jobs with filters.
@@ -170,7 +173,7 @@ def find_job_ids(self, filter=None, doc_filter=None):
             if doc_filter:
                 filter.update(doc_filter)
         elif doc_filter:
-            warnings.warn(DOC_FILTER_WARNING, DeprecationWarning)
+            warnings.warn(DOC_FILTER_WARNING, FutureWarning)
             filter = doc_filter
         return self._collection._find(filter)
 
@@ -917,7 +920,7 @@ def detect_schema(self, exclude_const=False, subset=None, index=None):
         if index is None:
             index = self.index(include_job_document=False)
         else:
-            warnings.warn(INDEX_DEPRECATION_WARNING, DeprecationWarning)
+            warnings.warn(INDEX_DEPRECATION_WARNING, FutureWarning)
         if subset is not None:
             subset = {str(s) for s in subset}
             index = [doc for doc in index if doc["_id"] in subset]
@@ -1031,15 +1034,15 @@ def _find_job_ids(self, filter=None, doc_filter=None, index=None):
         if index is None:
             filter = dict(parse_filter(_add_prefix("sp.", filter)))
             if doc_filter:
-                warnings.warn(DOC_FILTER_WARNING, DeprecationWarning)
+                warnings.warn(DOC_FILTER_WARNING, FutureWarning)
                 filter.update(parse_filter(_add_prefix("doc.", doc_filter)))
                 index = self.index(include_job_document=True)
             elif "doc" in _root_keys(filter):
                 index = self.index(include_job_document=True)
             else:
                 index = self._sp_index()
         else:
-            warnings.warn(INDEX_DEPRECATION_WARNING, DeprecationWarning)
+            warnings.warn(INDEX_DEPRECATION_WARNING, FutureWarning)
 
         return Collection(index, _trust=True)._find(filter)
 
@@ -1079,7 +1082,7 @@ def find_jobs(self, filter=None, doc_filter=None):
         """
         filter = dict(parse_filter(_add_prefix("sp.", filter)))
         if doc_filter:
-            warnings.warn(DOC_FILTER_WARNING, DeprecationWarning)
+            warnings.warn(DOC_FILTER_WARNING, FutureWarning)
             filter.update(parse_filter(_add_prefix("doc.", doc_filter)))
         return JobsCursor(self, filter)
 
@@ -1521,7 +1524,7 @@ def create_linked_view(self, prefix=None, job_ids=None, index=None, path=None):
 
         """
         if index is not None:
-            warnings.warn(INDEX_DEPRECATION_WARNING, DeprecationWarning)
+            warnings.warn(INDEX_DEPRECATION_WARNING, FutureWarning)
         from .linked_view import create_linked_view
 
         return create_linked_view(self, prefix, job_ids, index, path)
@@ -1922,7 +1925,7 @@ def repair(self, fn_statepoints=None, index=None, job_ids=None):
         if index is not None:
             for doc in index:
                 self._sp_cache[doc["signac_id"]] = doc["sp"]
-            warnings.warn(INDEX_DEPRECATION_WARNING, DeprecationWarning)
+            warnings.warn(INDEX_DEPRECATION_WARNING, FutureWarning)
         corrupted = []
         for job_id in job_ids:
             try:
@@ -2226,7 +2229,7 @@ def create_access_module(self, filename=None, main=True, master=None):
         """
         if master is not None:
             warnings.warn(
-                "The parameter master has been renamed to main.", DeprecationWarning
+                "The parameter master has been renamed to main.", FutureWarning
             )
             main = master
 
@@ -2282,8 +2285,8 @@ def temporary_project(self, name=None, dir=None):
             yield tmp_project
 
     @classmethod
-    def init_project(cls, name, root=None, workspace=None, make_dir=True):
-        """Initialize a project with the given name.
+    def init_project(cls, name=None, root=None, workspace=None, make_dir=True):
+        """Initialize a project.
 
         It is safe to call this function multiple times with the same
         arguments. However, a `RuntimeError` is raised if an existing project
@@ -2294,15 +2297,15 @@ def init_project(cls, name, root=None, workspace=None, make_dir=True):
 
         Parameters
         ----------
-        name : str
-            The name of the project to initialize.
-        root : str
+        name : str, optional
+            The name of the project to initialize (Default value = None).
+        root : str, optional
             The root directory for the project.
             Defaults to the current working directory.
-        workspace : str
+        workspace : str, optional
             The workspace directory for the project.
             Defaults to a subdirectory ``workspace`` in the project root.
-        make_dir : bool
+        make_dir : bool, optional
             Create the project root directory if it does not exist yet
             (Default value = True).
 
@@ -2320,6 +2323,16 @@ def init_project(cls, name, root=None, workspace=None, make_dir=True):
         """
         if root is None:
             root = os.getcwd()
+
+        if name is not None:
+            warnings.warn(
+                "Project names are deprecated and will be removed in signac 2.0 in favor of using "
+                "the project root directory to identify projects. The name argument to "
+                "init_project should be removed.",
+                FutureWarning,
+            )
+        else:
+            name = _DEFAULT_PROJECT_NAME
         try:
             project = cls.get_project(root=root, search=False)
         except LookupError:
@@ -3033,24 +3046,24 @@ def _repr_html_(self):
         return repr(self) + self._repr_html_jobs()
 
 
-def init_project(name, root=None, workspace=None, make_dir=True):
-    """Initialize a project with the given name.
+def init_project(name=None, root=None, workspace=None, make_dir=True):
+    """Initialize a project.
 
     It is safe to call this function multiple times with the same arguments.
     However, a `RuntimeError` is raised if an existing project configuration
     would conflict with the provided initialization parameters.
 
     Parameters
     ----------
-    name : str
+    name : str, optional
         The name of the project to initialize.
-    root : str
+    root : str, optional
         The root directory for the project.
         Defaults to the current working directory.
-    workspace : str
+    workspace : str, optional
         The workspace directory for the project.
         Defaults to a subdirectory ``workspace`` in the project root.
-    make_dir : bool
+    make_dir : bool, optional
         Create the project root directory, if it does not exist yet (Default
         value = True).
 

signac/diff.py

@@ -30,7 +30,7 @@ def diff_jobs(*jobs):
     Examples
     --------
     >>> import signac
-    >>> project = signac.init_project('project_name')
+    >>> project = signac.init_project()
     >>> job1 = project.open_job({'constant': 42, 'diff1': 0, 'diff2': 1}).init()
     >>> job2 = project.open_job({'constant': 42, 'diff1': 1, 'diff2': 1}).init()
     >>> job3 = project.open_job({'constant': 42, 'diff1': 2, 'diff2': 2}).init()