0.22.0

docs/.gitignore

@@ -0,0 +1,2 @@
+autodoc_build/
+

docs/changelog.md

@@ -1,5 +1,16 @@
 # Changelog
 
+## [0.22.0] -- (2019-06-06)
+### 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.
+
+
 ## [0.21.0] -- (2019-05-02)
 
 ### Added
@@ -12,7 +23,7 @@
 - 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 simly `name`.
+- On `Sample`, reference to `sample_name` is deprecated in favor of simply `name`.
 
 ## [0.20.0] -- (2019-04-17)
 ### Added
@@ -26,11 +37,11 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 
 ## [0.19.0] -- (2019-01-16)
 ### New  
-- Added ``activate_subproject`` method to ``Project``.
+- 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``.  
+- `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`.  
 
 ## [0.18.2] -- (2018-07-23)
 ### Fixed
@@ -39,12 +50,12 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 ## [0.18.1] -- (2018-06-29)
 ### Fixed
 - Fixed a bug that would cause sample attributes to lose order.
-- Fixed a bug that caused an install error with newer ``numexpr`` versions.
+- 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.
+- 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.
 
 ## [0.17.2] -- (2018-04-03)
 ## Fixed
@@ -57,10 +68,10 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 
 ## [0.9.0] -- (2017-12-21)
 ### New
-- Separation completed, ``peppy`` package is now standalone
-- ``looper`` can now rely on ``peppy``
+- Separation completed, `peppy` package is now standalone
+- `looper` can now rely on `peppy`
 ### Changed
-- ``merge_table`` renamed to ``sample_subannotation``
+- `merge_table` renamed to `sample_subannotation`
 - setup changed for compatibility with PyPI
 
 ## [0.8.1] -- (2017-11-16)
@@ -74,11 +85,11 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 ## [0.7.1] -- (2017-11-15)
 ### Fixed
 - No longer falsely display that there's a submission failure.
-- Allow non-string values to be unquoted in the ``pipeline_args`` section.
+- Allow non-string values to be unquoted in the `pipeline_args` section.
 
 ## [0.7.0] -- (2017-11-15)
 ### New
-- Add ``--lump`` and ``--lumpn`` options
+- Add `--lump` and `--lumpn` options
 - Catch submission errors from cluster resource managers
 - Implied columns can now be derived  
 - Now protocols can be specified on the command-line `--include-protocols`  
@@ -95,18 +106,18 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 ### New
 - Add support for implied_column section of the project config file
 - Add support for Python 3
-- Merges pipeline interface and protocol mappings. This means we now allow direct pointers to ``pipeline_interface.yaml`` files, increasing flexibility, so this relaxes the specified folder structure that was previously used for ``pipelines_dir`` (with ``config`` subfolder).
+- Merges pipeline interface and protocol mappings. This means we now allow direct pointers to `pipeline_interface.yaml` files, increasing flexibility, so this relaxes the specified folder structure that was previously used for `pipelines_dir` (with `config` subfolder).
 - Allow URLs as paths to sample sheets.
 - Allow tsv format for sample sheets.
 - Checks that the path to a pipeline actually exists before writing the submission script. 
 ### Changed
 - Changed LOOPERENV environment variable to PEPENV, generalizing it to generic models
-- Changed name of ``pipelines_dir`` to ``pipeline_interfaces`` (but maintained backwards compatibility for now).
-- Changed name of ``run`` column to ``toggle``, since ``run`` can also refer to a sequencing run.
+- Changed name of `pipelines_dir` to `pipeline_interfaces` (but maintained backwards compatibility for now).
+- Changed name of `run` column to `toggle`, since `run` can also refer to a sequencing run.
 - Relaxes many constraints (like resources sections, pipelines_dir columns), making project configuration files useful outside looper. This moves us closer to dividing models from looper, and improves flexibility.
 - Various small bug fixes and dev improvements.
 - Require `setuptools` for installation, and `pandas 0.20.2`. If `numexpr` is installed, version `2.6.2` is required.
-- Allows tilde in ``pipeline_interfaces``
+- Allows tilde in `pipeline_interfaces`
 
 ## [0.5.0] -- (2017-03-01)
 ### New
@@ -124,12 +135,12 @@ Additionally, the attribute value matching is more strict now -- requires perfec
 ## [0.4.0] -- (2017-01-12)
 ### New
 - New command-line interface (CLI) based on sub-commands
-- New subcommand (``looper summarize``) replacing the ``summarizePipelineStats.R`` script
-- New subcommand (``looper check``) replacing the ``flagCheck.sh`` script
-- New command (``looper destroy``) to remove all output of a project
-- New command (``looper clean``) to remove intermediate files of a project flagged for deletion
+- New subcommand (`looper summarize`) replacing the `summarizePipelineStats.R` script
+- New subcommand (`looper check`) replacing the `flagCheck.sh` script
+- New command (`looper destroy`) to remove all output of a project
+- New command (`looper clean`) to remove intermediate files of a project flagged for deletion
 - Support for portable and pipeline-independent allocation of computing resources with Looperenv.
 ### Changed
-- Removed requirement to have ``pipelines`` repository installed in order to extend base Sample objects
+- Removed requirement to have `pipelines` repository installed in order to extend base Sample objects
 - Maintenance of sample attributes as provided by user by means of reading them in as strings (to be improved further
 - Improved serialization of Sample objects

peppy/__init__.py

@@ -9,12 +9,12 @@
 
 from ._version import __version__
 from .const import *
-from .exceptions import PeppyError
+from .exceptions import *
 from .project import Project, ProjectContext
 from .sample import Sample, Subsample
 from .snake_project import *
 from .utils import fetch_samples, grab_project_data, CommandChecker
-#from logmuse import setup_logger
+#from logmuse import init_logger
 
 _EXPORT_FROM_UTILS = [fetch_samples.__name__, grab_project_data.__name__,
                       CommandChecker.__name__]
@@ -31,4 +31,4 @@
 #_LOGGER = logging.getLogger(__name__)
 #if not logging.getLogger().handlers:
 #    _LOGGER.addHandler(logging.NullHandler())
-#_LOGGER = setup_logger(name="peppy", level=LOGGING_LEVEL)
+#_LOGGER = init_logger(name="peppy", level=LOGGING_LEVEL)

peppy/_version.py

@@ -1,2 +1 @@
-__version__ = "0.21.0"
-
+__version__ = "0.22.0"

peppy/const.py

@@ -8,19 +8,24 @@
 
 # Project-related
 NAME_TABLE_ATTR = "sample_table"
+CONSTANTS_DECLARATION = "constant_attributes"
 DATA_SOURCES_SECTION = "data_sources"
 DERIVATIONS_DECLARATION = "derived_attributes"
 IMPLICATIONS_DECLARATION = "implied_attributes"
 METADATA_KEY = "metadata"
 OUTDIR_KEY = "output_dir"
 SAMPLE_INDEPENDENT_PROJECT_SECTIONS = \
-        [METADATA_KEY, DERIVATIONS_DECLARATION, IMPLICATIONS_DECLARATION, "trackhubs"]
+        [METADATA_KEY, DERIVATIONS_DECLARATION, IMPLICATIONS_DECLARATION,
+         "trackhubs"]
 SUBPROJECTS_SECTION = "subprojects"
 PIPE_ARGS_SECTION = "pipeline_args"
+SUBMISSION_FOLDER_KEY = "submission_subdir"
+RESULTS_FOLDER_KEY = "results_subdir"
 PROJECT_CONSTANTS = [
-    "DATA_SOURCES_SECTION", "DERIVATIONS_DECLARATION",
+    "CONSTANTS_DECLARATION", "DATA_SOURCES_SECTION", "DERIVATIONS_DECLARATION",
     "IMPLICATIONS_DECLARATION", "METADATA_KEY", "NAME_TABLE_ATTR", "OUTDIR_KEY",
-    "PIPE_ARGS_SECTION", "SAMPLE_INDEPENDENT_PROJECT_SECTIONS",
+    "PIPE_ARGS_SECTION", "RESULTS_FOLDER_KEY",
+    "SAMPLE_INDEPENDENT_PROJECT_SECTIONS", "SUBMISSION_FOLDER_KEY",
     "SUBPROJECTS_SECTION"]
 SNAKEMAKE_SAMPLE_COL = "sample"
 

peppy/exceptions.py

@@ -2,6 +2,11 @@
 
 from abc import ABCMeta
 
+__author__ = "Vince Reuter"
+__email__ = "[email protected]"
+
+__all__ = ["IllegalStateException", "PeppyError"]
+
 
 class PeppyError(Exception):
     """ Base error type for peppy custom errors. """
@@ -10,3 +15,8 @@ class PeppyError(Exception):
 
     def __init__(self, msg):
         super(PeppyError, self).__init__(msg)
+
+
+class IllegalStateException(PeppyError):
+    """ Occurrence of some illogical/prohibited state within an object. """
+    pass