Signac

Added

- Support for h5py version 3 (411).
- Added pyupgrade to pre-commit hooks (413).
- Code is formatted with ``black`` and ``isort`` pre-commit hooks (415).
- Added macOS to CircleCI testing pipeline (281, 414).
- Official support for Python 3.9 (417).

Changed

- Optimized internal function ``_mkdir_p`` (421).
- Optimized performance of job initialization (422).
- Optimized performance of buffer storage (428).
- Optimized performance of creating/loading synced data structures (429).

Added

- Type annotations are validated during continuous integration (313).
- Added ``_repr_html_`` method in ``ProjectSchema`` class (314, 324).
- Allow grouping by variables that are not present in all jobs in the project in ``JobsCursor.groupby`` (321, 323).
- Added parameters ``usecols`` and ``flatten`` to allow selection of columns and flattening of nested data when converting signac data into a pandas DataFrame (327, 330).
- Added support for [pre-commit hooks](https://pre-commit.com/) (#355, 358).
- Expanded CLI documentation (187, 359, 377).

Changed

- Docstrings are now written in [numpydoc style](https://numpydoc.readthedocs.io/en/latest/format.html).

Fixed

- Fix the ``signac config verify`` command (previously broken) (301, 302).
- Warnings now appear when raised by the ``signac`` CLI (317, 308).
- Fix dots in synchronization error messages (375, 376).

Deprecated

- Deprecate the ``create_access_modules`` method in ``Project``, to be removed in 2.0 (303, 308).
- The ``MainCrawler`` class has replaced the ``MasterCrawler`` class. Both classes are deprecated (342).

Removed

- Dropped support for Python 3.5 (340). The signac project will follow the [NEP 29 deprecation policy](https://numpy.org/neps/nep-0029-deprecation_policy.html) going forward.
- Removed dependency on ``pytest-subtests`` (379).

Added

- Added Windows to platforms tested with continuous integration (264, 266).
- Add command line option `-m/--merge` for `signac sync` (280, 230).

Changed

- Workspace directory is created when `Project` is initialized (267, 271).
- Changed testing framework from `unittest` to `pytest` (212, 275).
- Refactored internal use of deprecated `get_statepoint` function (227, 282).

Fixed

- Fixed issues on Windows with `H5Store`, project import/export, and operations that move files (264, 266).
- Calling `items` or `values` on `_SyncedDict` objects does not mutate nested dictionaries (234, 269).
- Fixed issue with `project.data` access from separate instances of `H5StoreManager` (274, 278).
- Fixed error when launching `signac shell` if permissions are denied for `.signac_shell_history` (279).

Removed

- Removed vendored `tqdm` module and replaced it with a requirement (289).
- Removed support for `rapidjson` as an alternative JSON library (285, 287).
- Removed tuple of keys implementation of nested dictionaries (272, 296).

Added

- Official support for Python 3.8 (258).
- Add properties `Project.id` and `Job.id` (250).
- Add `signac.diff_jobs` function to compare two or more state points (248, 247).
- Add function to initialize a sample data space for testing purposes (215).
- Add schema version to ensure compatibility and enable migrations in future package versions (165, 253).

Changed

- Implemented `Project.__contains__` check in constant time (231).

Fixed

- Attempting to create a linked view for a Project on Windows now raises an informative error message (214, 236).
- Project configuration is initialized using ConfigObj, allowing the configuration to include commas and special characters (251, 252).

Deprecated

- Deprecate the ``get_id`` method in ``Project`` and ``Job`` classes in favor of the ``id`` property, to be removed in 2.0 (250).
- In-memory modification of the project configuration, to be removed in 2.0 (246).

Removed

- Dropped support for Python 2.7 (232).

Added

- Keep signac shell command history on a per-project basis (134, 194).
- Add ``read_json()`` and ``to_json()`` methods to ``Collection`` class (104, 200).

Fixed

- Fix issue where shallow copies of instances of ``Job`` would behave incorrectly (153, 207).
- Fix issue causing a failure of the automatic conversion of valid key types (168, 205).
- Improve the "dots in keys" error message to make it easier to fix related issues (170, 205).
- Update the ``__repr__`` and ``__repr_html__`` implementations of the ``Project``, ``Job``, and ``JobsCursor`` classes (193).
- Reduce the logging verbosity about a missing default host key in the configuration (201).
- Fix issue with incorrect detection of dict-like files managed with the ``DictManager`` class (e.g. ``job.stores``) (203).
- Fix issue with generating views from the command line for projects with only one job (208, 211).
- Fix issue with heterogeneous types in state point values that are lists (209, 210).

Added

- Add command line options ``--sp`` and ``--doc`` for ``signac find`` that allow users to display key-value pairs of the state point and document in combination with the job id (97, 146).
- Improve the representation (return value of `repr()`) of instances of ``H5Group`` and ``SyncedAttrDict``.

Fixed

- Fix: Searches for whole numbers will match all numerically matching integers regardless of whether they are stored as decimals or whole numbers (169).
- Fix: Passing an instance of dict to `H5Store.setdefault()` will return an instance of `H5Group` instead of a dict (180).
- Fix error with storing numpy arrays and scalars in a synced dictionary (e.g. `job.statepoint`, `job.document`) (184).
- Fix issue with ``ResourceWarning`` originating from unclosed instance of ``Collection`` (186).
- Fix issue with using the ``get_project()`` function with a relative path and ``search=False`` (191).

Removed

- Support for Python version 3.4 (no longer tested).