def test_merge(builder):
# This is just a basic test; there's a more thorough test suite in
# test_merge.py.
builder.assign("a", 1)
builder.declare("b")
@builder
def h(a, b):
return a + b
builder2 = bn.FlowBuilder("flow2")
builder2.assign("b", 2)
builder.merge(builder2.build())
assert builder.build().get("h") == 3
builder3 = bn.FlowBuilder("flow3")
builder3.declare("a")
builder3.declare("b")
@builder3 # noqa: F811
def h(a, b):
return a * b
builder.merge(builder3.build(), keep="new")
# Notice: we correctly find the new value for `h`, rather than the cached
# version.
assert builder.build().get("h") == 2
def test_cache_dir_not_set():
old_flow = bn.FlowBuilder('old').build()
new_flow = bn.FlowBuilder('new').build()
for keep in ALL_KEEP_VALUES:
assert old_flow.merging(new_flow, keep=keep)\
.get(CACHE_DIR_ENT) == 'bndata'
def test_cache_dir_set_on_incoming():
old_flow = bn.FlowBuilder("old").build()
new_flow = bn.FlowBuilder("new").build().setting(CACHE_DIR_ENT, "new_dir")
for keep in ALL_KEEP_VALUES:
assert old_flow.merging(new_flow,
keep=keep).get(CACHE_DIR_ENT) == "new_dir"
def test_merge(builder):
# This is just a basic test; there's a more thorough test suite in
# test_merge.py.
builder.assign('a', 1)
builder.declare('b')
@builder
def h(a, b):
return a + b
builder2 = bn.FlowBuilder('flow2')
builder2.assign('b', 2)
builder.merge(builder2.build())
assert builder.build().get('h') == 3
builder3 = bn.FlowBuilder('flow3')
builder3.declare('a')
builder3.declare('b')
@builder3 # noqa: F811
def h(a, b):
return a * b
builder.merge(builder3.build(), keep='new')
# Notice: we correctly find the new value for `h`, rather than the cached
# version.
assert builder.build().get('h') == 2
def test_cache_dir_set_on_incoming():
old_flow = bn.FlowBuilder('old').build()
new_flow = bn.FlowBuilder('new').build()\
.setting(CACHE_DIR_ENT, 'new_dir')
for keep in ALL_KEEP_VALUES:
assert old_flow.merging(new_flow, keep=keep)\
.get(CACHE_DIR_ENT) == 'new_dir'
def test_cache_dir_conflicts():
old_flow = bn.FlowBuilder("old").build().setting(CACHE_DIR_ENT, "old_dir")
new_flow = bn.FlowBuilder("new").build().setting(CACHE_DIR_ENT, "new_dir")
with pytest.raises(AlreadyDefinedEntityError):
old_flow.merging(new_flow, keep="error")
assert old_flow.merging(new_flow,
keep="old").get(CACHE_DIR_ENT) == "old_dir"
assert old_flow.merging(new_flow,
keep="new").get(CACHE_DIR_ENT) == "new_dir"
def test_cache_dir_conflicts():
old_flow = bn.FlowBuilder('old').build()\
.setting(CACHE_DIR_ENT, 'old_dir')
new_flow = bn.FlowBuilder('new').build()\
.setting(CACHE_DIR_ENT, 'new_dir')
with pytest.raises(AlreadyDefinedEntityError):
old_flow.merging(new_flow, keep='error')
assert old_flow.merging(new_flow, keep='old').get(CACHE_DIR_ENT) ==\
'old_dir'
assert old_flow.merging(new_flow, keep='new').get(CACHE_DIR_ENT) ==\
'new_dir'
def builder(parallel_execution_enabled, tmp_path):
builder = bn.FlowBuilder("test")
builder.set("core__persistent_cache__flow_dir",
str(tmp_path / "BNTESTDATA"))
builder.set("core__parallel_execution__enabled",
parallel_execution_enabled)
return builder
def __init__(self, cache_dir, make_counter):
builder = bn.FlowBuilder("test")
builder.set("core__persistent_cache__flow_dir", cache_dir)
builder.assign("x", 2)
builder.assign("y", 3)
builder.assign("z", 4)
xy_counter = make_counter()
@builder
@count_calls(xy_counter)
def xy(x, y):
return x * y
yz_counter = make_counter()
@builder
@count_calls(yz_counter)
def yz(y, z):
return y * z
xy_plus_yz_counter = make_counter()
@builder
@count_calls(xy_plus_yz_counter)
def xy_plus_yz(xy, yz):
return xy + yz
self.flow = builder.build()
self.xy_counter = xy_counter
self.yz_counter = yz_counter
self.xy_plus_yz_counter = xy_plus_yz_counter
def __init__(self, cache_dir):
builder = bn.FlowBuilder('test')
builder.set('core__persistent_cache__flow_dir', cache_dir)
builder.assign('x', 2)
builder.assign('y', 3)
builder.assign('z', 4)
@builder
@count_calls
def xy(x, y):
return x * y
@builder
@count_calls
def yz(y, z):
return y * z
@builder
@count_calls
def xy_plus_yz(xy, yz):
return xy + yz
self.flow = builder.build()
self.xy = xy
self.yz = yz
self.xy_plus_yz = xy_plus_yz
def test_protocol_is_overwritten(builder):
builder.declare("x", protocol=bn.protocol.type(int))
incoming_builder = bn.FlowBuilder("new_name")
incoming_builder.assign("x", "blue", protocol=bn.protocol.type(str))
builder.merge(incoming_builder.build(), keep="new")
with pytest.raises(AssertionError):
builder.set("x", 3)
assert builder.build().get("x") == "blue"
def test_protocol_is_overwritten(builder):
builder.declare('x', protocol=bn.protocol.type(int))
incoming_builder = bn.FlowBuilder('new_name')
incoming_builder.assign('x', 'blue', protocol=bn.protocol.type(str))
builder.merge(incoming_builder.build(), keep='new')
with pytest.raises(AssertionError):
builder.set('x', 3)
assert builder.build().get('x') == 'blue'
def test_merging(preset_flow):
flow = preset_flow
new_flow = bn.FlowBuilder("new_flow").build().assigning("x", 5).assigning("y", 6)
assert flow.get("f", set) == set()
with pytest.raises(AlreadyDefinedEntityError):
assert flow.merging(new_flow)
assert flow.merging(new_flow, keep="old").get("f") == 6
assert flow.merging(new_flow, keep="self").get("f") == 6
assert flow.merging(new_flow, keep="new").get("f") == 11
assert flow.merging(new_flow, keep="arg").get("f") == 11
def test_merging(preset_flow):
flow = preset_flow
new_flow = (bn.FlowBuilder('new_flow').build().assigning('x', 5).assigning(
'y', 6))
assert flow.get('f', set) == set()
with pytest.raises(AlreadyDefinedEntityError):
assert flow.merging(new_flow)
assert flow.merging(new_flow, keep='old').get('f') == 6
assert flow.merging(new_flow, keep='self').get('f') == 6
assert flow.merging(new_flow, keep='new').get('f') == 11
assert flow.merging(new_flow, keep='arg').get('f') == 11
def test_protocols_conflict(builder):
builder.declare("x", protocol=bn.protocol.type(int))
incoming_builder = bn.FlowBuilder("new_name")
incoming_builder.declare("x", protocol=bn.protocol.type(str))
with pytest.raises(AlreadyDefinedEntityError):
builder.merge(incoming_builder.build())
builder.merge(incoming_builder.build(), keep="old")
builder.set("x", 1)
with pytest.raises(AssertionError):
builder.set("x", "blue")
builder.merge(incoming_builder.build(), keep="new")
builder.set("x", "blue")
with pytest.raises(AssertionError):
builder.set("x", 1)
def test_protocols_conflict(builder):
builder.declare('x', protocol=bn.protocol.type(int))
incoming_builder = bn.FlowBuilder('new_name')
incoming_builder.declare('x', protocol=bn.protocol.type(str))
with pytest.raises(AlreadyDefinedEntityError):
builder.merge(incoming_builder.build())
builder.merge(incoming_builder.build(), keep='old')
builder.set('x', 1)
with pytest.raises(AssertionError):
builder.set('x', 'blue')
builder.merge(incoming_builder.build(), keep='new')
builder.set('x', 'blue')
with pytest.raises(AssertionError):
builder.set('x', 1)
def builder(process_executor, process_manager, tmp_path):
builder = bn.FlowBuilder("test")
builder.set("core__persistent_cache__flow_dir",
str(tmp_path / "BNTESTDATA"))
# We can't use builder.set here because that uses ValueProvider which tries to
# tokenize the value by writing / pickling it. We go around that issue by making
# them use FunctionProvider.
@builder
@persist(False)
def core__process_executor():
return process_executor
@builder
@persist(False)
def core__process_manager():
return process_manager
return builder
def __init__(self, cache_dir, make_counter):
lowercase_sum_counter = make_counter()
uppercase_sum_counter = make_counter()
total_sum_counter = make_counter()
builder = bn.FlowBuilder("test")
builder.set("core__persistent_cache__flow_dir", cache_dir)
# It's important that this test uses sets, because we want to check that sets
# are hashed deterministically. (Set iteration is non-deterministic, but it's
# always the same within one Python process, so a simpler test where we just
# run a flow multiple times won't work for this.)
builder.assign("lowercase_chars", set("abcdef"))
builder.assign("uppercase_chars", frozenset("ABCDEF"))
@builder
@bn.version_no_warnings
def lowercase_sum(lowercase_chars):
lowercase_sum_counter.mark()
return sum(ord(char) for char in lowercase_chars)
@builder
@bn.version_no_warnings
def uppercase_sum(uppercase_chars):
uppercase_sum_counter.mark()
return sum(ord(char) for char in uppercase_chars)
@builder
@bn.version_no_warnings
def total_sum(lowercase_sum, uppercase_sum):
total_sum_counter.mark()
return lowercase_sum + uppercase_sum
self.lowercase_sum_counter = lowercase_sum_counter
self.uppercase_sum_counter = uppercase_sum_counter
self.total_sum_counter = total_sum_counter
self.manual_flow = builder.build()
builder.set("core__versioning_mode", "auto")
self.auto_flow = builder.build()
def builder(tmp_path):
builder = bn.FlowBuilder('test')
builder.set('core__persistent_cache__flow_dir',
str(tmp_path / 'BNTESTDATA'))
return builder
import bionic as bn
builder = bn.FlowBuilder("basic_workflow")
builder.assign("x", values=[2, 3])
builder.assign("y", values=[5, 7])
@builder
def x_plus_y(x, y):
return x + y
flow = builder.build()
if __name__ == "__main__":
bn.utils.misc.init_basic_logging()
for _, row in flow.get("x_plus_y", "series").reset_index().iterrows():
print(f"{row['x']} + {row['y']} = {row['x_plus_y']}")
def flow():
"""Create FlowImage fixture for testing"""
builder = bionic.FlowBuilder("hello_world")
builder.assign("greeting", "hello world", doc="a friendly greeting")
return builder.build()
def test_old_name_is_kept_even_on_explicit_rename():
old_flow = bn.FlowBuilder("old").build()
new_flow = bn.FlowBuilder("new").build().setting("core__flow_name", "NEW")
for keep in ALL_KEEP_VALUES:
assert old_flow.merging(new_flow, keep=keep).name == "old"
def test_old_name_is_kept_even_on_explicit_rename():
old_flow = bn.FlowBuilder('old').build()
new_flow = bn.FlowBuilder('new').build().setting('core__flow_name', 'NEW')
for keep in ALL_KEEP_VALUES:
assert old_flow.merging(new_flow, keep=keep).name == 'old'
def test_old_name_is_kept():
old_flow = bn.FlowBuilder('old').build()
new_flow = bn.FlowBuilder('new').build()
for keep in ALL_KEEP_VALUES:
assert old_flow.merging(new_flow, keep=keep).name == 'old'
def merge_tester(builder):
f = builder.build()
tester = MergeTester()
tester.add('Missing', f)
tester.add('Declared', f.declaring('x'))
tester.add('FixedSingle', f.assigning('x', 2))
tester.add('FixedMulti', f.assigning('x', values=[3, 4]))
fb = f.to_builder()
fb.assign('root_x', 3)
@fb
def x(root_x):
return root_x ** 2
tester.add('DerivedSingle', fb.build())
fb = f.to_builder()
fb.assign('x_y', (5, 6))
@fb # noqa: F811
@bn.outputs('x', 'y')
def x(x_y):
return x_y
tester.add('DerivedJoint', fb.build())
tester.add(
'FixedJoint',
f.declaring('x').declaring('y').adding_case('x', 7, 'y', 8))
# This new flow will use the default cache directory, which is bad, because
# it could pick up data from previous test runs. Unfortunately it's tricky
# to set another cache directory on this flow, because it will cause a
# conflict when merging the two flows (even if the two cache directories
# are the same). To work around this, we disable persistence for all
# derived entities in this flow, so the cache shouldn't be used at all.
# Longer-term, we may want a smarter way of merging that either recognizes
# when two values are the same, or handles "infrastructure" entities like
# this differently. Or a way to just run a flow without caching.
f = bn.FlowBuilder('new_flow').build()
tester.add('M', f)
tester.add('D', f.declaring('x'))
tester.add('FS', f.assigning('x', 12))
tester.add('FM', f.assigning('x', values=[13, 14]))
fb = f.to_builder()
fb.assign('root_x', 3)
@fb # noqa: F811
@bn.persist(False)
def x(root_x):
return root_x ** 2
tester.add('DS', fb.build())
fb = f.to_builder()
fb.assign('x_y', (5, 6))
@fb # noqa: F811
@bn.outputs('x', 'y')
@bn.persist(False)
def x(x_y):
return x_y
tester.add('DJ', fb.build())
tester.add(
'FJ',
f.declaring('x').declaring('y').adding_case('x', 17, 'y', 18))
return tester
'''
A toy ML workflow intended to demonstrate basic Bionic features. Trains a
logistic regression model on the UCI ML Breast Cancer Wisconsin (Diagnostic)
dataset.
'''
import re
from sklearn import datasets, model_selection, linear_model, metrics
import pandas as pd
import bionic as bn
# Initialize our builder.
builder = bn.FlowBuilder('ml_workflow')
# Define some basic parameters.
builder.assign('random_seed', 0)
builder.assign('test_split_fraction', 0.3)
builder.assign('hyperparams_dict', {'C': 1})
builder.assign('feature_inclusion_regex', '.*')
# Load the raw data.
@builder
def raw_frame():
dataset = datasets.load_breast_cancer()
df = pd.DataFrame(
data=dataset.data,
columns=dataset.feature_names,
)
def builder(tmp_path):
builder = bn.FlowBuilder("test")
builder.set("core__persistent_cache__flow_dir",
str(tmp_path / "BNTESTDATA"))
return builder
from __future__ import print_function
import bionic as bn
# Initialize the builder object we'll use to construct our flow.
builder = bn.FlowBuilder('hello_world')
# Define new entities "greeting" and "subject" with fixed values.
builder.assign('greeting', 'Hello')
builder.assign('subject', 'world')
# Define a "message" entity, constructed by taking the values of "greeting" and
# "subject" and combining them in a sentence.
# The `@builder` decorator tells Bionic to define a new derived entity; Bionic
# infers the name of the new entity ("message") and the names of its
# dependencies ("greeting" and "subject").
@builder
def message(greeting, subject):
return '{0} {1}!'.format(greeting, subject)
# Assemble the flow object, which is capable of computing any of the entities
# we've defined.
flow = builder.build()
if __name__ == '__main__':
# Use our flow to compute the message "Hello world!"
print(flow.get('message'))
import numpy as np
import pandas as pd
from scipy.stats import multivariate_normal
from sklearn.linear_model import LinearRegression
import bionic as bn
builder = bn.FlowBuilder("intro")
builder.assign("random_seed", 0)
builder.assign("variance", 2)
builder.assign("correlation", 0.5)
builder.assign("n_samples", 1000)
@builder
def my_random_df(random_seed, variance, correlation, n_samples):
data = multivariate_normal(
mean=[0, 0],
cov=[[variance, correlation * variance], [correlation * variance, variance]],
).rvs(size=n_samples, random_state=random_seed)
return pd.DataFrame(columns=["x", "y"], data=data)
@builder
def my_model(my_random_df):
model = LinearRegression()
model.fit(my_random_df[["x"]], my_random_df["y"])
return model
from __future__ import print_function
import pandas as pd
import numpy as np
from sklearn.linear_model import LinearRegression
from scipy.stats import multivariate_normal
import bionic as bn
builder = bn.FlowBuilder('intro')
builder.assign('random_seed', 0)
builder.assign('variance', 2)
builder.assign('correlation', 0.5)
builder.assign('n_samples', 1000)
@builder
def my_random_df(random_seed, variance, correlation, n_samples):
data = multivariate_normal(
mean=[0, 0],
cov=[
[variance, correlation * variance],
[correlation * variance, variance],
],
).rvs(
size=n_samples,
random_state=random_seed,
)
return pd.DataFrame(columns=['x', 'y'], data=data)