pi-thon 3.14 fixes by mimakaev · Pull Request #75 · open2c/polychrom

mimakaev · 2025-10-26T20:28:09Z

Description

This PR contains fixes for the python 3.14 switching from fork to forkserver multiprocessing method, addresses some deprecation warnings, and reformats things with black.

Changed CI to include 3.14 and two latest versions of MacOS
black and isort on the codebase
Switched contactmaps to be compatible with spawn and forkserver multiprocessing (latest default in 3.14)
removed confusing test for an old starting conformation generator
Addressed all flake8 issues and some valid VSCode warnings such as possibly unbound variables

PR Checklist

[] apply "black" to the whole codebase (black .)
[] apply isort to the codebase (isort .)
[] fun flake8 and try to resolve all the issues (work in progress!)

Copilot

Pull Request Overview

This PR updates the polychrom codebase for Python 3.14 compatibility, focusing on multiprocessing method changes (fork → forkserver), addressing deprecation warnings, and applying code formatting with black/isort.

Key Changes:

Updated CI/CD to test against Python 3.14 and recent macOS versions
Refactored contactmaps module for spawn/forkserver multiprocessing compatibility (lambda functions → named functions)
Fixed NumPy deprecation (np.in1d → np.isin) and improved type checking patterns
Applied consistent code formatting across the codebase

Reviewed Changes

Copilot reviewed 24 out of 25 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
`.github/workflows/pythonapp.yml`	Added Python 3.14 and macOS testing matrix
`polychrom/contactmaps.py`	Refactored for multiprocessing compatibility: moved lambdas to module-level functions, added default function parameters
`tests/test_contactmaps.py`	Replaced lambda with named `load_function` for spawn/forkserver compatibility; added module-level test data
`polychrom/forces.py`	Updated cylindrical_confinement logic and type hints; contains a bug with bottom=0 handling
`polychrom/forcekits.py`	Added explicit error for unsupported nonbonded forces (potential breaking change)
`tests/test_polymer_analyses.py`	Fixed NumPy deprecation: `np.in1d` → `np.isin`
`tests/test_io.py`	Updated to use new `load_URI` API instead of deprecated `fetch_block`
`polychrom/polymer_analyses.py`	Added TYPE_CHECKING pattern for better Cython import handling
`polychrom/param_units.py`	Reformatted docstrings with black (r""" prefix)
`polychrom/hdf5_format.py`	Changed `type()` to `isinstance()` for better practices
`polychrom/legacy/forces.py`	Reordered imports and changed to `isinstance()`
Various files	Import reordering (isort), spacing fixes, removed extra blank lines (black formatting)
`tests/test_configurations.py`	Removed entire test file for old starting conformation generator
Examples	Import reordering and formatting improvements

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Copilot · 2025-11-11T16:59:27Z

polychrom/forces.py

+    bottom = 0 if bottom is True else bottom

-    if bottom is not None:
+    if bottom:


The logic change here introduces a bug. When bottom=0 is passed, the condition if bottom: (line 734) will evaluate to False because 0 is falsy in Python, causing the code to use the wrong branch.

The original code correctly used if bottom is not None: which would handle bottom=0 properly. The fix should be:

bottom = 0 if bottom is True else bottom if bottom is not None: # ... existing code for bottom confinement

Suggested change

if bottom:

if bottom is not None:

Copilot · 2025-11-11T16:59:28Z

polychrom/forcekits.py

+            else:
+                raise ValueError("Nonbonded force {} does not support exceptions or exclusions.".format(nb_force.name))


This change alters the behavior when except_bonds=True and the nonbonded force doesn't support exceptions or exclusions. Previously, the code would silently continue without adding exceptions. Now it raises a ValueError.

While this is likely an improvement (making the error explicit rather than silent), it could break existing code that relies on the previous behavior. Consider documenting this breaking change or verifying that all nonbonded forces in use support either exceptions or exclusions.

Copilot · 2025-11-11T16:59:28Z

polychrom/legacy/polymerutils.py

@@ -1 +1 @@
-from polychrom.polymerutils import *  # noqa: F403
+from polychrom.polymerutils import *  # noqa: F403


Import pollutes the enclosing namespace, as the imported module polychrom.polymerutils does not define 'all'.

Suggested change

from polychrom.polymerutils import * # noqa: F403

# TODO: Replace the following line with explicit imports of only the required names.

# For example: from polychrom.polymerutils import foo, bar

# from polychrom.polymerutils import * # noqa: F403

Copilot · 2025-11-11T16:59:28Z

examples/loopExtrusion/directionalModel/showContactmap.py

-from mirnylib.numutils import zoomArray
-from openmmlib import polymerutils

+import matplotlib


Import of 'matplotlib' is not used.

Suggested change

import matplotlib

Copilot · 2025-11-11T16:59:29Z

examples/loopExtrusion/directionalModel/showContactmap.py

-from mirnylib.numutils import completeIC, coarsegrain
+from mirnylib.h5dict import h5dict
+from mirnylib.numutils import coarsegrain, completeIC, zoomArray
+from mirnylib.plotting import nicePlot


Import of 'nicePlot' is not used.

Suggested change

from mirnylib.plotting import nicePlot

Copilot · 2025-11-11T16:59:29Z

polychrom/simulation.py

 import warnings
 from collections.abc import Iterable
-from typing import Optional, Dict
+from typing import Dict, Optional


Import of 'Dict' is not used.
Import of 'Optional' is not used.

Suggested change

from typing import Dict, Optional

mimakaev · 2025-11-11T17:25:38Z

unused imports and other things will be addressed in a next PR

mimakaev added 6 commits October 26, 2025 11:54

contactmaps 3.14 compatible; black/isort

b7f3c69

contactmaps multiprocessing friendly

a164043

legacy code README

8735dc3

merge setup.py

bc6a082

black, isort, flake8 issues and some vscode type checks

d58fa72

CI update

f040d98

mimakaev requested a review from Copilot November 11, 2025 16:56

Copilot started reviewing on behalf of mimakaev November 11, 2025 16:56 View session

Copilot finished reviewing on behalf of mimakaev November 11, 2025 16:58

Copilot AI reviewed Nov 11, 2025

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PR template and bugfix

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pi-thon 3.14 fixes#75

pi-thon 3.14 fixes#75
mimakaev wants to merge 7 commits intomasterfrom
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mimakaev commented Oct 26, 2025 •

edited

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		else:
		raise ValueError("Nonbonded force {} does not support exceptions or exclusions.".format(nb_force.name))

		@@ -1 +1 @@
		from polychrom.polymerutils import * # noqa: F403 No newline at end of file
		from polychrom.polymerutils import * # noqa: F403

-from polychrom.polymerutils import *  # noqa: F403
+# TODO: Replace the following line with explicit imports of only the required names.
+# For example: from polychrom.polymerutils import foo, bar
+# from polychrom.polymerutils import *  # noqa: F403

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mimakaev commented Oct 26, 2025 •

edited

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