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molecular-workflow-repository / molflow

Workflow runner for the molecular workflow repository
Apache License 2.0
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Duplicate workflow discovery when running in `~/.molflow/workflows` #2

Closed avirshup closed 7 years ago

avirshup commented 7 years ago

Everything runs normally everywhere else.

[~/.molflow/workflows]$ molflow list
A workflow named 'add_two_to_it' was found via multiple local workflow paths.
Locations found: [[PosixPath('~/.molflow/workflows'), PosixPath('.')], [PosixPath('~/.molflow/workflows'), PosixPath('.')]]
A workflow named 'convert' was found via multiple local workflow paths.
Locations found: [[PosixPath('~/.molflow/workflows'), PosixPath('.')], [PosixPath('~/.molflow/workflows'), PosixPath('.')]]
A workflow named 'count_atoms' was found via multiple local workflow paths.
Locations found: [[PosixPath('~/.molflow/workflows'), PosixPath('.')], [PosixPath('~/.molflow/workflows'), PosixPath('.')]]
A workflow named 'parameterize_small_molecule' was found via multiple local workflow paths.
Locations found: [[PosixPath('~/.molflow/workflows'), PosixPath('.')], [PosixPath('~/.molflow/workflows'), PosixPath('.')]]
Workflow location: Current directory
 - add_two_to_it (v0.1.0): Add 2 to integer, float, or complex number.
 - convert (v0.1.0): Translate a molecule between a variety of file formats, chemical ids, and python objects.
 - count_atoms (v0.0.1): Returns the number of atoms in a molecule.
 - parameterize_small_molecule (v0.0.1): Automatically parameterize a small molecule.
 - add_two_to_it (v0.1.0): Add 2 to integer, float, or complex number.
 - convert (v0.1.0): Translate a molecule between a variety of file formats, chemical ids, and python objects.
 - count_atoms (v0.0.1): Returns the number of atoms in a molecule.
 - parameterize_small_molecule (v0.0.1): Automatically parameterize a small molecule.

Workflow location: Current directory
 - add_two_to_it (v0.1.0): Add 2 to integer, float, or complex number.
 - convert (v0.1.0): Translate a molecule between a variety of file formats, chemical ids, and python objects.
 - count_atoms (v0.0.1): Returns the number of atoms in a molecule.
 - parameterize_small_molecule (v0.0.1): Automatically parameterize a small molecule.
 - add_two_to_it (v0.1.0): Add 2 to integer, float, or complex number.
 - convert (v0.1.0): Translate a molecule between a variety of file formats, chemical ids, and python objects.
 - count_atoms (v0.0.1): Returns the number of atoms in a molecule.
 - parameterize_small_molecule (v0.0.1): Automatically parameterize a small molecule.
joseph-schaeffer commented 7 years ago

This is technically intended, but we should probably do some sort of special case for it. The reason it happens is the default config includes both ./ and ~/.molflow/workflows/ as local repo locations. I can add a check that looks to see if those happen to be the same thing, and if so, only includes one of them.

joseph-schaeffer commented 7 years ago

Or rather, more generally check to make sure we eliminate duplicates from the config local repo paths.

joseph-schaeffer commented 7 years ago

Fixed by PR #4.