Release 0.11.0 (#357)

* Merge changelog from 0.10.1.

* Update changelog number and date for 0.11.0.

* Update Zenodo.

* ngpu without nranks no longer uses MPI in version 0.11.0.

* Remove --cmd argument.

* Minor formatting changes.

* Bump up to version 0.11.0.

* Remove unused import.

* Update pre-commit config to skip setup.cfg.

* Update zenodo script.

* Remove deprecated code path ``project.py script --cmd``

* Fix ...Fixed. 🤔

Co-authored-by: Brandon Butler <[email protected]>

Author: bdice

.pre-commit-config.yaml

@@ -3,7 +3,9 @@ repos:
     rev: ''
     hooks:
     -   id: end-of-file-fixer
+        exclude: 'setup.cfg'
     -   id: trailing-whitespace
+        exclude: 'setup.cfg'
     -   id: debug-statements
 -   repo: local
     hooks:

.sync-zenodo-metadata.py

@@ -13,6 +13,7 @@
 [2] https://citation-file-format.github.io/1.0.3/specifications/#/person-objects
 """
 from dataclasses import dataclass
+from typing import Optional
 
 import click
 import json
@@ -24,7 +25,7 @@ class Contributor:
     last_names: str
     first_names: str
     affiliation: str
-    orcid: str = None
+    orcid: Optional[str] = None
 
     @classmethod
     def from_citation_author(cls, **citation):
@@ -41,11 +42,6 @@ def as_zenodo_creator(self):
             ret['orcid'] = self.orcid.lstrip('https://orcid.org/')
         return ret
 
-    def as_zenodo_contributor(self):
-        ret = self.as_zenodo_creator()
-        ret['type'] = 'Other'
-        return ret
-
 
 @click.command()
 @click.pass_context
@@ -70,7 +66,7 @@ def sync(ctx, in_place=False, check=True):
         zenodo = json.loads(file.read())
         zenodo_updated = zenodo.copy()
         zenodo_updated['creators'] = [a.as_zenodo_creator() for a in authors]
-        zenodo_updated['contributors'] = [c.as_zenodo_contributor()
+        zenodo_updated['contributors'] = [c.as_zenodo_creator()
                                           for c in contributors if c not in authors]
         for key in ('version', 'keywords'):
             zenodo_updated[key] = citation[key]

.zenodo.json

@@ -3,110 +3,96 @@
         {
             "affiliation": "University of Michigan",
             "name": "Benjamin Swerdlow",
-            "orcid": "0000-0001-6240-1430",
-            "type": "Other"
+            "orcid": "0000-0001-6240-1430"
         },
         {
             "affiliation": "University of Michigan",
-            "name": "Joshua A. Anderson",
-            "type": "Other"
+            "name": "Joshua A. Anderson"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Jens Glaser",
-            "orcid": "0000-0003-1852-3849",
-            "type": "Other"
+            "orcid": "0000-0003-1852-3849"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Timothy C. Moore",
-            "orcid": "0000-0002-5709-7259",
-            "type": "Other"
+            "orcid": "0000-0002-5709-7259"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Rose Cersonsky",
-            "orcid": "0000-0003-4515-3441",
-            "type": "Other"
+            "orcid": "0000-0003-4515-3441"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Yuan Zhou",
-            "orcid": "0000-0002-6727-0836",
-            "type": "Other"
+            "orcid": "0000-0002-6727-0836"
         },
         {
             "affiliation": "Vanderbilt University",
             "name": "Matthew  W. Thompson",
-            "orcid": "0000-0002-1460-3983",
-            "type": "Other"
+            "orcid": "0000-0002-1460-3983"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Shannon Moran",
-            "orcid": "0000-0002-3579-3149",
-            "type": "Other"
+            "orcid": "0000-0002-3579-3149"
         },
         {
             "affiliation": "University of Michigan",
-            "name": "Yannah Melle",
-            "type": "Other"
+            "name": "Yannah Melle"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Pengji Zhou",
-            "orcid": "0000-0002-1409-9633",
-            "type": "Other"
+            "orcid": "0000-0002-1409-9633"
         },
         {
             "affiliation": "Vanderbilt University",
             "name": "Justin Gilmer",
-            "orcid": "0000-0002-6915-5591",
-            "type": "Other"
+            "orcid": "0000-0002-6915-5591"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Alyssa Travitz",
-            "orcid": "0000-0001-5953-8807",
-            "type": "Other"
+            "orcid": "0000-0001-5953-8807"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Corwin Kerr",
-            "orcid": "0000-0003-0776-2596",
-            "type": "Other"
+            "orcid": "0000-0003-0776-2596"
         },
         {
             "affiliation": "University of Michigan",
             "name": "Tobias Dwyer",
-            "orcid": "0000-0001-6443-7744",
-            "type": "Other"
+            "orcid": "0000-0001-6443-7744"
         },
         {
             "affiliation": "National Institute of Technology, Hamirpur",
-            "name": "Vishav Sharma",
-            "type": "Other"
+            "name": "Vishav Sharma"
         },
         {
             "affiliation": "Indian Institute of Technology Roorkee",
-            "name": "Hardik Ojha",
-            "type": "Other"
+            "name": "Hardik Ojha"
         },
         {
             "affiliation": "Birla Institute of Technology and Science, Pilani - Goa Campus",
-            "name": "Yash Bhardwaj",
-            "type": "Other"
+            "name": "Yash Bhardwaj"
         },
         {
             "affiliation": "",
             "name": "Jacob Dice",
-            "orcid": "0000-0002-9479-1661",
-            "type": "Other"
+            "orcid": "0000-0002-9479-1661"
         },
         {
             "affiliation": "Indian Institute of Technology, Gandhinagar",
-            "name": "Abhavya Chandra",
-            "type": "Other"
+            "name": "Abhavya Chandra"
+        },
+        {
+            "affiliation": "University of Minnesota",
+            "name": "Ramanish Singh",
+            "orcid": "0000-0002-7908-060X"
         }
     ],
     "creators": [
@@ -161,5 +147,5 @@
     },
     "title": "signac-flow",
     "upload_type": "software",
-    "version": "0.10.0"
+    "version": "0.11.0"
 }

CITATION.cff

@@ -2,7 +2,7 @@
 ---
 cff-version: "1.0.3"
 title: signac-flow
-version: 0.10.0
+version: 0.11.0
 abstract: |
     The signac-flow tool provides the basic components to set up simple to complex workflows for projects as part of the signac framework. That includes the definition of data pipelines, execution of data space operations and the submission of operations to high-performance super computers.
 authors:

changelog.txt

@@ -5,14 +5,15 @@ Changelog
 The **signac-flow** package follows `semantic versioning <https://semver.org/>`_.
 The numbers in brackets denote the related GitHub issue and/or pull request.
 
-next
-====
+Version 0.11
+============
 
-next
-----
+[0.11.0] -- 2020-10-09
+----------------------
 
 Added
 +++++
+
 - Added classes ``_Directives`` and ``_Directive`` that serve as a smart mapping for directives specified by the environment or user (#265, #283).
 - Added support for `pre-commit hooks <https://pre-commit.com/>`__ (#333).
 - Add environment profile for University of Minnesota, Minnesota Supercomputing Institute, Mangi supercomputer (#353).
@@ -26,6 +27,7 @@ Changed
 
 Fixed
 +++++
+
 - Serial execution on Summit correctly counts total node requirements (#342).
 - Fixed performance regression in job submission in large workspaces (#354).
 
@@ -38,6 +40,14 @@ Removed
 Version 0.10
 ============
 
+[0.10.1] -- 2020-08-20
+----------------------
+
+Fixed
++++++
+
+- Fix issue with the submission of bundled operations on cluster environments that do not allow slashes ('/') in cluster scheduler job names (#343).
+
 [0.10.0] -- 2020-06-27
 ----------------------
 
@@ -69,6 +79,7 @@ Changed
 
 Fixed
 +++++
+
 - Ensure that label names are used when displaying status (#263).
 - Fix node counting for large resource sets on Summit (#294).
 
@@ -128,7 +139,7 @@ Added
 - Enable option to always show the full traceback with ``show_traceback = on`` within the ``[flow]`` section of the signac configuration (#61, #144).
 - Add full launcher support for job submission on XSEDE Stampede2 for large parallel single processor jobs (#85, #91).
 
-Fixes
+Fixed
 +++++
 
 - Both the ``nranks`` and ``omp_num_threads`` directives properly support callables (#118).
@@ -170,12 +181,12 @@ Added
 - Add function to automatically print all varying state point parameters in the detailed status view triggered by providing option `-p/--parameters` without arguments (#19, #87).
 - Add clear environment notification when submitting job scripts (#43, #88).
 
-Fixes
+Fixed
 +++++
 
 - Fix issue where the scheduler status of job-operations would not be properly updated for *ineligible* operations (#96).
 
-Fixes (compute environments)
+Fixed (compute environments)
 ++++++++++++++++++++++++++++
 
 - Fix issue with the TORQUE scheduler that occured when there was no job scheduled at all on the system (for any user) (#92, #93).
@@ -195,7 +206,7 @@ Added
 - Add legend explaining the scheduler-related symbols to the detailed status view (#68).
 - Allow the specification of the number of tasks per resource set and additional jsrun arguments for Summit scripts.
 
-Fixes (general)
+Fixed (general)
 +++++++++++++++
 
 - Fixes issue where callable cmd-directives were not evaluated (#47).
@@ -205,7 +216,7 @@ Fixes (general)
 - Fixes issue where using the buffered mode would lead to confusing error messages when condition-functions would raise an AttributeError exception.
 - Fixes issue with erroneous unused-directive-keys-warning.
 
-Fixes (compute environments)
+Fixed (compute environments)
 ++++++++++++++++++++++++++++
 
 - Fixes issues with the Summit environment resource set calculation for parallel operations under specific conditions (#63).

doc/conf.py

@@ -73,9 +73,9 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = '0.10.0'
+version = '0.11.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.10.0'
+release = '0.11.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

flow/environment.py

@@ -16,7 +16,6 @@
 import importlib
 from collections import OrderedDict
 import importlib.machinery
-import warnings
 
 from signac.common import config
 
@@ -227,10 +226,6 @@ def _get_mpi_prefix(cls, operation, parallel):
         """
         if operation.directives.get('nranks'):
             return '{} -n {} '.format(cls.mpi_cmd, operation.directives['nranks'])
-        elif operation.directives.get('ngpu', 0) > 1:
-            warnings.warn("Setting ngpu directive without nranks will no longer use MPI "
-                          "in version 0.11.", DeprecationWarning)
-            return '{} -n {}'.format(cls.mpi_cmd, operation.directives['ngpu'])
         else:
             return ''