Skip to content

Adds more helpful error messages, always runs file registration for isolation #318

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
miguelgondu merged 2 commits into from
Sep 28, 2025
Merged

Adds more helpful error messages, always runs file registration for isolation #318

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
25c6520
Adds a helpful error when conda env creation fails
miguelgondu Sep 26, 2025
e3e18ee
Runs registration always, mitigating stale config.rc file issues
miguelgondu Sep 26, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 14 additions & 0 deletions examples/minimal_isolation_example.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
import numpy as np

from poli.repository import EhrlichHoloBlackBox

f = EhrlichHoloBlackBox(
sequence_length=10,
motif_length=3,
n_motifs=2,
)

print(f.alphabet)
print(f)
print(f(np.array(["ACGTACGTAA", "ACGTACGTAC"])))
print(f)
45 changes: 16 additions & 29 deletions src/poli/core/util/isolation/instancing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,11 @@ def __create_conda_env(environment_file: Path, quiet: bool = False):
if not quiet:
print(f"poli 🧪: {env_name} already exists.")
else:
raise e
raise RuntimeError(
"Failed to create the underlying conda environment."
" Try to create the environment manually by running:\n"
f"conda env create -f {environment_file}\n"
) from e


def __register_isolated_function_from_repository(
Expand Down Expand Up @@ -212,31 +216,15 @@ def register_isolated_function(name: str, quiet: bool = False):
If True, we squelch the messages giving feedback about the creation process.
By default, it is False.
"""
config = load_config()
if name not in config:
# Register problem

# Two cases:
# (i) some of the isolated functions are not alongside
# their black boxes and problem factories, but are rather inside
# the core of poli. For now, the only case is tdc, but more may
# come in the future.
#
# (ii) the isolated function is in the repository, living alongside
# the black box and the problem factory.
if name == "tdc__isolated":
logging.debug(
"poli 🧪: Registered the isolated function from the repository."
)
__register_isolated_function_from_core(name, quiet=quiet)
config = load_config()
else:
logging.debug(
"poli 🧪: Registered the isolated function from the repository."
)
__register_isolated_function_from_repository(name, quiet=quiet)
# Refresh the config
config = load_config()
if name == "tdc__isolated":
logging.debug("poli 🧪: Registered the isolated function from core.")
__register_isolated_function_from_core(name, quiet=quiet)
_ = load_config()
else:
logging.debug("poli 🧪: Registered the isolated function from the repository.")
__register_isolated_function_from_repository(name, quiet=quiet)
# Refresh the config
_ = load_config()


def __create_function_as_isolated_process(
Expand All @@ -262,6 +250,8 @@ def __create_function_as_isolated_process(
**kwargs_for_factory : dict, optional
Additional keyword arguments for the factory.
"""
register_isolated_function(name=name, quiet=quiet)

config = load_config()
if name not in config:
raise ValueError(
Expand Down Expand Up @@ -319,9 +309,6 @@ def instance_function_as_isolated_process(
"https://machinelearninglifescience.github.io/poli-docs/."
)

# Register the problem if it hasn't been registered.
register_isolated_function(name=name, quiet=quiet)

f = __create_function_as_isolated_process(
name=name,
quiet=quiet,
Expand Down