Peppy

Changed

- Deprecate `Project` `constants` in favor of `constant_attributes.`
- Improved `Project` text representation for interactive/terminal display (`__repr__`): [Issue 296](https://github.com/pepkit/peppy/issues/296)

Fixed

- Properly use `constant_attributes` if present from subproject. [Issue 292](https://github.com/pepkit/peppy/issues/292)
- Fixed a bug with subproject activation paths
- Revert deprecation of `sample_name` to `name`; so `sample_name` is again approved.

Added

- Support for Snakemake projects (particularly `SnakeProject`)
- Hook for `get_arg_string` on `Project` to omit some pipeline options/arguments from the returned argument string
- `sample_table` and `subsample_table` functions, providing a functional syntax for requesting the respective attribute values from a `Project`
- Hook on `merge_sample` for specifying name of subannotation column that stores name for each sample

Changed

- Improved messaging: ["Unmatched regex-like"](https://github.com/pepkit/peppy/issues/223), ["Missing and/or empty attribute(s)"](https://github.com/pepkit/peppy/issues/282)
- On `Project`, `sheet` is deprecated in favor of `sample_table`.
- On `Project`, `sample_subannotation` is deprecated in favor of `subsample_table`.
- On `Sample`, reference to `sample_name` is deprecated in favor of simply `name`.

Added

- `subsample_table` on a `Project` gives the table of sample subannotation / "units" if applicable.

Changed

- Add `attribute` parameter to `fetch_samples` function to enable more general applicability.
Additionally, the attribute value matching is more strict now -- requires perfect match.
- Remove Python 3.4 support.
- Use `attmap` for implementation of attribute-style access into a key-value collection.
- Deprecate `sample_annotation` and `sample_subannotation` in favor of `sample_table` and `subsample_table`, respectively.

New

- Added `activate_subproject` method to `Project`.

Changed

- `Project` construction no longer requires sample annotations sheet.
- Specification of assembly/ies in project config outside of `implied_attributes` is deprecated.
- `implied_columns` and `derived_columns` are deprecated in favor of `implied_attributes` and `derived_attributes`.

Fixed

- Made requirements more lenient to allow for newer versions of required packages.

Fixed

- Fixed a bug that would cause sample attributes to lose order.
- Fixed a bug that caused an install error with newer `numexpr` versions.

New

- Project names are now inferred with the `infer_name` function, which uses a priority lookup to infer the project name: First, the `name` attribute in the `yaml` file; otherwise, the containing folder unless it is `metadata`, in which case, it's the parent of that folder.
- Add `get_sample` and `get_samples` functions to `Project` objects.
- Add `get_subsamples`and `get_subsample` functions to both `Project` and `Sample` objects.
- Subsamples are now objects that can be retrieved individually by name, with the `subsample_name` as the index column header.