Bump signac from 1.8.0 to 2.0.0 in /.github/workflows

[dependabot]

Bumps signac from 1.8.0 to 2.0.0.

Release notes

Sourced from signac's releases.

2.0.0

[2.0.0] -- 2023-03-30

Added

• Official support for Python 3.11 (#875).
• H5Store related errors are now included in the public API (#775).
• Users can now access the project to which a job belongs with the Job.project attribute (#808).

Changed

• Functions raising AssertionError now raise RuntimeError (#612).
• State points and documents require keys to be of type str (#719).
• The keyword _id of the Job constructor has been renamed to id_ (#681).
• The signac schema to use version 2. This update involves a number of changes:
  • The project configuration is now stored at .signac/config instead of signac.rc or .signacrc (#678).
  • Schema versions are now identified by simple integers rather than semantic versioning style versions (#688).
  • Projects no longer have names and are identified solely by their root directories. This change also affects a number of public APIs where names are including, most prominently signac.init_project and Project.init_project. Projects can now be constructed with just a root directory rather than a preloaded config (#677, #684, #706).
  • Project workspaces are no longer configurable, but are instead always defined as a subdirectory of the Project's root directory called workspace (#714).
• Rather than searching upwards until the root, load_config will only load configuration files in the specified directory, which is assumed to be a project directory, as well as the user's home directory (#711).
• Changed the root parameter to path in the signac.get_project and signac.init_project functions and corresponding Project methods (#757, #758).
• The prefix argument to $ signac view is now optional and can be provided with -p/--prefix (#653, #774).
• Tests are run with xfail_strict = True (#850).
• Detection of an invalid config will raise an error rather than a debug log (#855).
• The package namespace has been flattened so that most functionality is directly available in the signac namespace (#756, #868).
• The calc_id function has been moved from the hashing module to the job module (#873).
• Tests are run with all warnings treated as errors (#871).
• The contents of the syncutil module have been moved into sync (#869).
• The project now leverages a fully pyproject.toml-driven build (#878).

Removed

• The pre-SyncedCollection synchronized dictionary classes, including SyncedDict, SyncedAttrDict, and JSONDict (#577).
• The old custom JSON encoder and dumps wrapper (#577).
• The MPIPool and the filesystems.py module (#575).
• The following Project methods: get_id, build_job_search_index, build_job_statepoint_index, find_job_ids, reset_statepoint, update_statepoint, create_access_module, index, dump_statepoints, get_statepoint, read_statepoints, write_statepoints, groupbydoc, root_directory, num_jobs (#574, #593, #599, #601, #752).
• The following Job methods: get_id, workspace, ws, reset_statepoint (#578, #752).
• The syncutil.copytree method (#581).
• All Crawlers, including RegexFileCrawler, MainCrawler, MasterCrawler, SignacProjectCrawler, and BaseCrawler, in addition to all associated functionality in indexing.py (#580).
• The cite.py module (#594).
• The following types of exceptions: AuthenticationError, ExportError`, FetchError, PermissionsError`` (#595, #596).
• All MongoDB database functionality, including the db subpackage, the connection, crypt, and host submodules in the common subpackage, and all associated configuration information (#576, #596).
• The JobSearchIndex class (#587).
• The ability to pass indexes to various Project methods (#599).
• The following JobsCursor methods: groupbydoc, next (#601, #604).
• The Project.config property is no longer mutable. Use the command line $ signac config to modify configuration (#608, #246, #244).
• The config module and all its functions, all of which have been made private (#674, #753, #789, #847, #877).
• Project subclasses can no longer define a Job subclass to use (#588, #693).
• The Collection class (#664, #667, #683).

... (truncated)

Changelog

Sourced from signac's changelog.

[2.0.0] -- 2023-03-30

Added +++++

• Official support for Python 3.11 (#875).
• H5Store related errors are now included in the public API (#775).
• Users can now access the project to which a job belongs with the Job.project attribute (#808).

Changed +++++++

• Functions raising AssertionError now raise RuntimeError (#612).
• State points and documents require keys to be of type str (#719).
• The keyword _id of the Job constructor has been renamed to id_ (#681).
• The signac schema to use version 2. This update involves a number of changes:
  • The project configuration is now stored at .signac/config instead of signac.rc or .signacrc (#678).
  • Schema versions are now identified by simple integers rather than semantic versioning style versions (#688).
  • Projects no longer have names and are identified solely by their root directories. This change also affects a number of public APIs where names are including, most prominently signac.init_project and Project.init_project. Projects can now be constructed with just a root directory rather than a preloaded config (#677, #684, #706).
  • Project workspaces are no longer configurable, but are instead always defined as a subdirectory of the Project's root directory called workspace (#714).
• Rather than searching upwards until the root, load_config will only load configuration files in the specified directory, which is assumed to be a project directory, as well as the user's home directory (#711).
• Changed the root parameter to path in the signac.get_project and signac.init_project functions and corresponding Project methods (#757, #758).
• The prefix argument to $ signac view is now optional and can be provided with -p/--prefix (#653, #774).
• Tests are run with xfail_strict = True (#850).
• Detection of an invalid config will raise an error rather than a debug log (#855).
• The package namespace has been flattened so that most functionality is directly available in the signac namespace (#756, #868).
• The calc_id function has been moved from the hashing module to the job module (#873).
• Tests are run with all warnings treated as errors (#871).
• The contents of the syncutil module have been moved into sync (#869).
• The project now leverages a fully pyproject.toml-driven build (#878).

Removed +++++++

• The pre-SyncedCollection synchronized dictionary classes, including SyncedDict, SyncedAttrDict, and JSONDict (#577).
• The old custom JSON encoder and dumps wrapper (#577).
• The MPIPool and the filesystems.py module (#575).
• The following Project methods: get_id, build_job_search_index, build_job_statepoint_index, find_job_ids, reset_statepoint, update_statepoint, create_access_module, index, dump_statepoints, get_statepoint, read_statepoints, write_statepoints, groupbydoc, root_directory, num_jobs (#574, #593, #599, #601, #752).
• The following Job methods: get_id, workspace, ws, reset_statepoint (#578, #752).
• The syncutil.copytree method (#581).
• All Crawlers, including RegexFileCrawler, MainCrawler, MasterCrawler, SignacProjectCrawler, and BaseCrawler, in addition to all associated functionality in indexing.py (#580).
• The cite.py module (#594).
• The following types of exceptions: AuthenticationError, ExportError`, FetchError, PermissionsError`` (#595, #596).
• All MongoDB database functionality, including the db subpackage, the connection, crypt, and host submodules in the common subpackage, and all associated configuration information (#576, #596).
• The JobSearchIndex class (#587).
• The ability to pass indexes to various Project methods (#599).
• The following JobsCursor methods: groupbydoc, next (#601, #604).
• The Project.config property is no longer mutable. Use the command line $ signac config to modify configuration (#608, #246, #244).
• The config module and all its functions, all of which have been made private (#674, #753, #789, #847, #877).

... (truncated)

Commits

• 6599893 Release/2.0.0 (#911)
• 2b6519d Remove Zenodo. (#903)
• 6f61a54 Use main. (#906)
• 92cbb72 Bump coverage from 7.2.1 to 7.2.2 (#908)
• 0309704 Bump redis from 4.5.3 to 4.5.4 (#909)
• 52c9318 Bump pytest from 7.2.1 to 7.2.2 (#910)
• 96c409b Bump pytest-xdist from 3.2.0 to 3.2.1 (#907)
• 6002df3 Warn if old schema on init_project() (#905)
• 03b957e Bump redis from 4.5.1 to 4.5.3 in /requirements (#904)
• e8a7885 Pre-release 2.0.0 (#902)
• Additional commits viewable in compare view

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[joaander]

As discussed offline, let's update trunk-major to work with signac 2.0. I will merge trunk-major into trunk with the HOOMD-blue v4.0.0 release coming in the next few weeks.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[tommy-waltmann]

will be addressed on #50

[dependabot]

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If you change your mind, just re-open this PR and I'll resolve any conflicts on it.