Refactor: Replace wildcard imports with explicit imports in integration test files

[Copilot]

Generic request

• PR name follows the pattern #1234 – issue name
• branch name does not contain '#'
• base branch (master or release/xx) is correct
• PR is linked with the issue
• task status changed to "Code review"
• code follows product standards
• regression tests updated

Optional

• unit-tests written
• documentation updated

Description

Replace from env_indigo import * with explicit named imports across 100 test files under api/tests/integration/tests/.

• AST-based analysis determined which env_indigo names each file actually uses
• Removed redundant imports — stdlib modules (os, sys, threading) already imported directly are not re-imported from env_indigo
• Moved threading to direct import threading in 4 files that previously obtained it through the wildcard

Import style:

# ≤3 names: single line
from env_indigo import Indigo, joinPathPy

# >3 names: parenthesized multi-line
from env_indigo import (
    Indigo,
    IndigoException,
    getIndigoExceptionText,
    joinPathPy,
)

Only files listed in the issue were modified. deco/extract_scaffold.py (not in scope) is unchanged.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Refactor: Wildcard imports should not be used</issue_title>
<issue_description>Problem:
Import only needed names or import the module and then use its members.

Why is this an issue?
Importing every public name from a module using a wildcard (from mymodule import *) is a bad idea because:

• It could lead to conflicts between names defined locally and the ones imported.
• It reduces code readability as developers will have a hard time knowing where names come from.
• It clutters the local namespace, which makes debugging more difficult.

Remember that imported names can change when you update your dependencies. A wildcard import that works today might be broken tomorrow.
Exceptions

No issue will be raised in __init__.py files. Wildcard imports are a common way of populating these modules.

No issue will be raised in modules doing only imports. Local modules are sometimes created as a proxy for third-party modules.

# file: mylibrary/pyplot.py
try:
    from guiqwt.pyplot import *  # Ok
except Exception:
    from matplotlib.pyplot import *  # Ok

Just keep in mind that wildcard imports might still create issues in these cases. It’s always better to import only what you need.

How can I fix it?
There are two ways to avoid a wildcard import:

• Replace it with import mymodule and access module members as mymodule.myfunction. If the module name is too long, alias it to a shorter name. Example: import pandas as pd
• List every imported name. If necessary import statements can be split on multiple lines using parentheses (preferred solution) or backslashes.

Noncompliant code example

from math import *  # Noncompliant
def exp(x):
    pass
print(exp(0))   # "None" will be printed

Compliant solution

import math
def exp(x):
    pass
print(math.exp(0))   # "1.0" will be printed

Or

from math import exp as m_exp
def exp(x):
    pass
print(m_exp(0))   # "1.0" will be printed

NOTE: Resulted code shoul follow clang-format formating.

Problem locations:
api/tests/integration/tests/aam/aam_access.py
api/tests/integration/tests/aam/aam_basic.py
api/tests/integration/tests/aam/aam_hard.py
api/tests/integration/tests/arom/arom_d_orbital.py
api/tests/integration/tests/arom/arom_merge.py
api/tests/integration/tests/arom/basic.py
api/tests/integration/tests/arom/elements.py
api/tests/integration/tests/arom/extended.py
api/tests/integration/tests/arom/partial_arom_cano.py
api/tests/integration/tests/arom/query_dearom.py
api/tests/integration/tests/basic/allenes.py
api/tests/integration/tests/basic/atom_bond_indicies.py
api/tests/integration/tests/basic/attachment_points.py
api/tests/integration/tests/basic/badval_smiles.py
api/tests/integration/tests/basic/basic.py
api/tests/integration/tests/basic/basic_check.py
api/tests/integration/tests/basic/basic_load.py
api/tests/integration/tests/basic/buffer_string_load_iterate.py
api/tests/integration/tests/basic/check_query.py
api/tests/integration/tests/basic/chiral_test.py
api/tests/integration/tests/basic/cis_trans.py
api/tests/integration/tests/basic/components.py
api/tests/integration/tests/basic/create_query.py
api/tests/integration/tests/basic/debug.py
api/tests/integration/tests/basic/exceptions.py
api/tests/integration/tests/basic/fischer_proj.py
api/tests/integration/tests/basic/fold_then_smiles.py
api/tests/integration/tests/basic/fold_unfold.py
api/tests/integration/tests/basic/get_original_format.py
api/tests/integration/tests/basic/hash.py
api/tests/integration/tests/basic/highlighting.py
api/tests/integration/tests/basic/hybridization.py
api/tests/integration/tests/basic/imp_h_test.py
api/tests/integration/tests/basic/imp_h_test_ket.py
api/tests/integration/tests/basic/ketfile_stereo_desc.py
api/tests/integration/tests/basic/leak.py
api/tests/integration/tests/basic/load.py
api/tests/integration/tests/basic/load_dearom_save.py
api/tests/integration/tests/basic/load_structure.py
api/tests/integration/tests/basic/molfile_stereo_desc.py
api/tests/integration/tests/basic/molfile_stereoparity.py
api/tests/integration/tests/basic/multiple_instances.py
api/tests/integration/tests/basic/murcko.py
api/tests/integration/tests/basic/options.py
api/tests/integration/tests/basic/properties.py
api/tests/integration/tests/basic/pseudoatoms.py
api/tests/integration/tests/basic/query_instrumentation.py
api/tests/integration/tests/basic/radicals.py
api/tests/integration/tests/basic/reaction_instrumentation.py
api/tests/integration/tests/basic/reaction_saveload.py
api/tests/integration/tests/basic/rings.py
api/tests/integration/tests/basic/rsite.py
api/tests/integration/tests/basic/savers.py
api/tests/integration/tests/basic/scsr_basic.py
api/tests/integration/tests/basic/scsr_instrumentation.py
api/tests/integration/tests/basic/set_charge.py
api/tests/integration/tests/basic/sssr.py
api/tests/integration/tests/basic/stereo_test.py
api/test...

• Fixes Refactor: Wildcard imports should not be used #3491

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