Define named directory structure using placeholders
Project description
pathtree
Named path hierarchies
The goal of this package is to make it easier to both define and understand folder structures in your scripts and pipelines. I find it difficult to visualize file structure when looking at a series of os.path.join
commands scattered throughout a script, so instead, you define all of the paths up top, and fill in the placeholders later.
Install
pip install path-tree
Tutorial
Quick start
import pathtree
paths = pathtree.paths('./logs', {
'{log_id}': {
'model.h5': 'model',
'model_spec.pkl': 'model_spec',
'plots': {
'epoch_{i_epoch:04d}': {
'{plot_name}.png': 'plot',
'': 'plot_dir'
}
}
}
})
...
paths.update(log_id=12345)
...
plt.imwrite(paths.plot.format(i_epoch=5, plot_name='f1_score'))
# writes to ./logs/12345/plots/epoch_0005/f1_score.png
The old way - makes my brain sad
Usually, you end up defining paths doing something like this (unless I'm doing something weird/dumb - lmk !!). And often, these end up scattered throughout your project and getting a high level picture of your path hierarchy is difficult.
base_log_dir = './blah/logs'
run_dir = os.path.join(base_log_dir, log_id)
resources_dir = os.path.join(run_dir, 'resources')
...
model_file = os.path.join(run_dir, 'model.h5')
model_spec = os.path.join(run_dir, 'model_spec.pkl')
...
pump_file = os.path.join(resources_dir, 'pump.pkl')
...
plot_dir = os.path.join(run_dir, 'plots', 'epoch_{i_epoch:04d}')
plot_file = os.path.join(plot_dir, '{plot_name}.png')
The new way ! *brain smiles*
Instead, you can define your path hierarchy all in one place and give each tree node a name.
import os
import pathtree
# define the entire directory structure
# the tree keys represent folder names.
# the final non-dict key represents the name for
# that directory node.
#
# e.g.: {folder1: {folder2: name}}
# paths.name => folder1/folder2
#
# Notice the blank key under "plots". This takes advantage
# of the fact that os.path.join('plots', '') == 'plots'.
# So the name assigned to the blank string is naming the
# directory
base_paths = pathtree.paths('./logs', {
'{log_id}': {
'model.h5': 'model',
'model_spec.pkl': 'model_spec',
'plots': {
'epoch_{i_epoch:04d}': {
'{plot_name}.png': 'plot',
'': 'plot_dir'
}
}
}
})
# specify the log_id
paths = base_paths.specify(log_id=12345)
Conversion to string
You can access the paths using the name defined in the tree:
assert str(paths.model_spec) == './logs/12345/model_spec.pkl'
A Paths
object (as defined above) is really just a dictionary of name => pathtree.Path
objects. This is a wrapper around string format pattern and a data dictionary.
To convert a Path
to a string, there are a few ways to get what you want.
For fully specified strings (meaning that str.format will run without a KeyError), all three of these methods return the same thing: a fully formatted string.
assert paths.model.format() == './logs/12345/model.h5'
assert paths.model.partial_format() == './logs/12345/model.h5'
assert paths.model.maybe_format() == './logs/12345/model.h5'
For an underspecified string (missing data keys), the return values are different:
# str.format is missing a key and will throw an exception
try:
paths.plot.format(plot_name='f1_score')
assert False
except KeyError: # missing i_epoch
assert True
# str.format is missing a key so the missing key will be left in
assert (paths.plot.partial_format(plot_name='f1_score') ==
'./logs/12345/plots/epoch_{i_epoch:04d}/f1_score.png')
# str.format is missing a key so it will keep it as a Path object
# with the updated key `plot_name`.
# this retains the ability to use data updating functionality.
assert isinstance(
paths.plot.maybe_format(plot_name='f1_score'), pathtree.Path)
Paths are castable to string which is the same as partial_format
. You can also access the unformatted path using Path().path
.
assert str(paths.plot) == paths.plot.partial_format()
assert paths.plot.path == the_unformatted_plot_path
pathtree.Path
subclasses os.PathLike
, meaning that os.path functions know how to convert it to a path automatically.
assert isinstance(paths.model, os.PathLike)
assert os.path.join(paths.model) == paths.model.format()
assert os.path.isfile(paths.model)
Updating format data
You can add path specificity at various points along the way. This is helpful when you need to reference subdirectories based on some loops or similar pattern. You can do that in a couple ways:
# across the entire directory object
# update in place
paths.update(log_id=12345)
# or create a copy
paths2 = paths.specify(log_id=23456)
assert paths.data['log_id'] == 12345 and paths2.data['log_id'] = 23456
# reverse specify - remove a data key
paths2 = paths2.unspecify('log_id')
assert 'log_id' not in paths2.data
# or for a single path
# in place
plot_file = paths.plot
plot_file.update(plot_name='f1_score')
# create a copy
plot_file = paths.plot.specify(plot_name='f1_score')
assert 'plot_name' not in paths.data
assert plot_file.data['plot_name'] == 'f1_score'
# reverse specify - remove a data key
plot_file = plot_file.unspecify('plot_name')
assert 'plot_name' not in plot_file.data
Additional Features
You can automatically do glob searching. Any missing fields will be filled with a glob wildcard (asterisk). Note that this would fail using plain string format because the leading zero formatter (:04d
) will throw an error if you try to insert '*'
(because it's a string).
plot_file = paths.plot.specify(plot_name='f1_score')
assert (plot_file.partial_format() ==
'./logs/12345/plots/epoch_{i_epoch:04d}/f1_score.png')
assert (plot_file.glob_pattern ==
'./logs/12345/plots/epoch_*/f1_score.png')
assert (plot_file.glob() ==
glob.glob('./logs/12345/plots/epoch_*/f1_score.png'))
You can also sometimes parse out data from a formatted string. Be warned, it may not always work correctly because sometimes the parsing is ambiguous. See https://github.com/r1chardj0n3s/parse#potential-gotchas
plot_file = paths.plot.specify(root='some/logs')
assert (plot_file.partial_format() ==
'some/logs/12345/plots/epoch_{i_epoch:04d}/{plot_name}.png')
expected = {
'root': 'some/logs'
'log_id': '12345',
'i_epoch': '0002',
'plot_name': 'f1_score.png',
}
plot_data = plot_file.parse('./logs/12345/plots/0002/f1_score.png')
assert set(plot_data.items()) == set(expected.items())
Usage Example
Here's a screenshot from one of the projects I'm using pathtree in and I really like how it simplifies defining the structure of your project files. I'm able to take a bunch of h5 files, parse out the path components, and translate them to their corresponding audio and jams file in another directory all while keeping a single point of truth for my file structure in the path definition. :)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.