Skip to content
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

refactor(collate): deprecationwarning for collate #462

Merged
merged 3 commits into from
Nov 6, 2024
Merged

refactor(collate): deprecationwarning for collate #462

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
95c5673
refactor(collate): deprecationwarning for collate
d33bs Oct 18, 2024
2c4ffd9
Update pycytominer/cyto_utils/collate.py
d33bs Nov 6, 2024
3cb971c
linting
d33bs Nov 6, 2024
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
11 changes: 11 additions & 0 deletions pycytominer/cyto_utils/collate.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import subprocess
import sys
import sqlite3
import warnings


def run_check_errors(cmd):
Expand Down Expand Up @@ -81,6 +82,16 @@ def collate(
"""
)

# show a warning about collate deprecation
warnings.warn(
(
"pycytominer.cyto_utils.collate is deprecated and will be removed in future versions of Pycytominer. "
"Please consider using CellProfiler's ExportToDatabase module to create single-cell "
"profile SQLite files or CytoTable to create similar Parquet file output."
d33bs marked this conversation as resolved.
Show resolved Hide resolved
),
DeprecationWarning,
)

# Set up directories (these need to be abspaths to keep from confusing makedirs later)
input_dir = pathlib.Path(f"{base_directory}/analysis/{batch}/{plate}/{csv_dir}")
backend_dir = pathlib.Path(f"{base_directory}/backend/{batch}/{plate}")
Expand Down
3 changes: 3 additions & 0 deletions pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,9 @@ lint.per-file-ignores."tests/*" = [ "S101" ]

[tool.pytest.ini_options]
testpaths = "tests"
filterwarnings = [
"ignore::DeprecationWarning:pycytominer.*",
]

[tool.mypy]
exclude = [
Expand Down