Dependency & Environment Conflicts

Environment bugs come from mismatched Python versions, divergent lockfiles, shadowed packages on PYTHONPATH, and editable installs pointing at the wrong checkout. Symptoms are import errors, ABI crashes, and tests that pass locally but fail in CI.

Recipe

Quick-reference recipe card - copy-paste ready.

python3 --version          # expect 3.14.0 in prod-aligned envs
which python3
uv sync                    # install from uv.lock
uv run pytest
python -c "import mypkg; print(mypkg.__file__)"

When to reach for this:

ModuleNotFoundError for a package you "just installed"
ImportError: DLL load failed / incompatible binary wheels
CI fails while laptop passes (or vice versa)
Two projects need conflicting versions of the same library

Working Example

# diagnose.sh - run from repo root
set -euo pipefail
 
echo "=== Python ==="
python3 --version
which python3
 
echo "=== Virtual env ==="
echo "${VIRTUAL_ENV:-not activated}"
 
echo "=== Lockfile install ==="
uv sync --frozen
 
echo "=== Package location ==="
uv run python -c "import orders; print(orders.__file__)"
 
echo "=== Installed dists (top) ==="
uv pip list | head -20
 
echo "=== pip check ==="
uv pip check

# pyproject.toml - pin runtime and isolate groups
[project]
name = "orders"
requires-python = ">=3.14"
dependencies = ["fastapi>=0.115", "pydantic>=2"]
 
[dependency-groups]
dev = ["pytest>=8", "ruff>=0.9"]
 
[tool.uv]
dev-dependencies = ["pytest>=8", "ruff>=0.9"]

# verify_imports.py - CI smoke
import importlib
import sys
 
REQUIRED = ("fastapi", "pydantic", "orders")
 
def main() -> None:
    print("executable:", sys.executable)
    print("version:", sys.version.replace("\n", " "))
    for name in REQUIRED:
        mod = importlib.import_module(name)
        print(f"{name} -> {getattr(mod, '__file__', mod)}")
 
if __name__ == "__main__":
    main()

What this demonstrates:

Version and path printed before debugging imports
uv sync --frozen fails if lockfile out of date with pyproject.toml
requires-python documents supported interpreter floor
Smoke import script catches wrong package on path early

Deep Dive

How It Works

Virtual environments isolate site-packages per project
Lockfiles pin transitive versions; loose pip install does not
Binary wheels tie to Python ABI tags (cp314 vs cp313)
Editable installs (-e .) symlink source; wrong cwd means wrong code

Conflict Checklist

Signal	Likely cause	Fix
Old package despite upgrade	wrong venv active	`deactivate`; activate `.venv`
Two versions in `pip list`	system + user site	pure venv; `pip install --force-reinstall`
`cpython-312` wheel on 3.14	wrong wheel	regen lock on target Python
Import from unexpected path	PYTHONPATH shadow	remove; fix packaging
Poetry + uv mixed	two lock tools	standardize on uv 0.6+

Python Notes

# reproduce CI locally with container
docker run --rm -v "$PWD:/app" -w /app python:3.14.0-bookworm \
  bash -lc "pip install uv && uv sync --frozen && uv run pytest"

Gotchas

Global pip install - pollutes base Python; breaks other projects. Fix: venv per project; never install app deps globally.
Committed .venv - platform-specific binaries in git. Fix: gitignore; document uv sync in README.
Optional extras not installed in CI - pip install . without [ml] extra missing torch. Fix: document extras; CI installs needed groups.
Different cwd in IDE test runner - imports local shadow module json.py. Fix: rename shadows; src layout.
Stale editable install after rename - old package name cached. Fix: reinstall editable; clear *.egg-link.
Conda + pip mixing - broken numpy/openssl ABIs. Fix: one tool per env; conda OR uv/pip stack.

Alternatives

Alternative	Use When	Don't Use When
`uv` lock + sync	fast reproducible envs	org mandates poetry only (bridge carefully)
`pip-tools` compile	existing pip-tools shops	greenfield without constraint
Docker-only dev	strict prod parity	fast laptop iteration needed
`tox`/`nox` matrices	multi-version libraries	single-version microservices

FAQs

Why does uv sync fix "works on my machine"?

Everyone installs the same resolved graph from uv.lock on the same Python ABI. Drift shows up as lock mismatch instead of mystery imports.

Should CI use --frozen?

Yes in release pipelines. Fails when pyproject.toml changes without updating the lockfile, preventing silent upgrades.

How do I debug wrong module path?

python -c "import m; print(m.__file__)" and compare to expected site-packages or src/ editable path.

Can two projects share one venv?

Avoid it. Conflicting pins and import shadowing return. One venv per repo or use uv workspace with explicit members.

What if PyTorch CUDA wheels differ by machine?

Document optional extra indexes in README. CI CPU-only jobs install CPU index; GPU machines install platform-specific extra.

How do I pin Python 3.14 in Docker?

Use python:3.14.0-bookworm (or slim) and match requires-python in pyproject.toml.

Does ruff need the same venv?

Run ruff 0.9+ via uv run ruff so rules and auto-fixes see installed third-party stubs consistently.

How do I fix pip check failures?

uv pip check reports incompatible pins. Regenerate lock from a clean venv; remove manual pip install overrides in Dockerfile.

What about system Python on macOS?

Use python3 from .venv after uv venv. Homebrew/system Pythons are fine as base interpreters, not as install targets.

How do optional dependency groups help?

Keep heavy ML stacks optional ([project.optional-dependencies]) so API services do not install PyTorch in every image.

Can I delete uv.lock and regenerate?

Yes when upgrading major versions deliberately. Commit the new lock and run full CI matrix afterward.

How do IDE and CLI conflicts happen?

IDE points at different interpreter than terminal. Set workspace interpreter to .venv/bin/python explicitly.

Configuration & Settings - env vars vs packages
src Layout & Package Structure - install before test
Circular Import Scenarios - import errors that look like missing deps
Codebase Audit Checklist - lockfile and audit items
Debugging Tools - inspect sys.path in pdb

Stack versions: This page was written for Python 3.14.0 (stable 3.14, maintenance 3.13), FastAPI 0.115+, Django 5.2, Flask 3.1, Pydantic 2, PyTorch 2.6+, pandas 2.2+, Polars 1.x, ruff 0.9+, and uv 0.6+.

Dependency & Environment Conflicts

Recipe

Quick-reference recipe card - copy-paste ready.

python3 --version          # expect 3.14.0 in prod-aligned envs
which python3
uv sync                    # install from uv.lock
uv run pytest
python -c "import mypkg; print(mypkg.__file__)"

When to reach for this:

ModuleNotFoundError for a package you "just installed"
ImportError: DLL load failed / incompatible binary wheels
CI fails while laptop passes (or vice versa)
Two projects need conflicting versions of the same library

Working Example

# diagnose.sh - run from repo root
set -euo pipefail
 
echo "=== Python ==="
python3 --version
which python3
 
echo "=== Virtual env ==="
echo "${VIRTUAL_ENV:-not activated}"
 
echo "=== Lockfile install ==="
uv sync --frozen
 
echo "=== Package location ==="
uv run python -c "import orders; print(orders.__file__)"
 
echo "=== Installed dists (top) ==="
uv pip list | head -20
 
echo "=== pip check ==="
uv pip check

# pyproject.toml - pin runtime and isolate groups
[project]
name = "orders"
requires-python = ">=3.14"
dependencies = ["fastapi>=0.115", "pydantic>=2"]
 
[dependency-groups]
dev = ["pytest>=8", "ruff>=0.9"]
 
[tool.uv]
dev-dependencies = ["pytest>=8", "ruff>=0.9"]

# verify_imports.py - CI smoke
import importlib
import sys
 
REQUIRED = ("fastapi", "pydantic", "orders")
 
def main() -> None:
    print("executable:", sys.executable)
    print("version:", sys.version.replace("\n", " "))
    for name in REQUIRED:
        mod = importlib.import_module(name)
        print(f"{name} -> {getattr(mod, '__file__', mod)}")
 
if __name__ == "__main__":
    main()

What this demonstrates:

Version and path printed before debugging imports
uv sync --frozen fails if lockfile out of date with pyproject.toml
requires-python documents supported interpreter floor
Smoke import script catches wrong package on path early

Deep Dive

How It Works

Virtual environments isolate site-packages per project
Lockfiles pin transitive versions; loose pip install does not
Binary wheels tie to Python ABI tags (cp314 vs cp313)
Editable installs (-e .) symlink source; wrong cwd means wrong code

Conflict Checklist

Signal	Likely cause	Fix
Old package despite upgrade	wrong venv active	`deactivate`; activate `.venv`
Two versions in `pip list`	system + user site	pure venv; `pip install --force-reinstall`
`cpython-312` wheel on 3.14	wrong wheel	regen lock on target Python
Import from unexpected path	PYTHONPATH shadow	remove; fix packaging
Poetry + uv mixed	two lock tools	standardize on uv 0.6+

Python Notes

# reproduce CI locally with container
docker run --rm -v "$PWD:/app" -w /app python:3.14.0-bookworm \
  bash -lc "pip install uv && uv sync --frozen && uv run pytest"

Gotchas

Global pip install - pollutes base Python; breaks other projects. Fix: venv per project; never install app deps globally.
Committed .venv - platform-specific binaries in git. Fix: gitignore; document uv sync in README.
Optional extras not installed in CI - pip install . without [ml] extra missing torch. Fix: document extras; CI installs needed groups.
Different cwd in IDE test runner - imports local shadow module json.py. Fix: rename shadows; src layout.
Stale editable install after rename - old package name cached. Fix: reinstall editable; clear *.egg-link.
Conda + pip mixing - broken numpy/openssl ABIs. Fix: one tool per env; conda OR uv/pip stack.

Alternatives

Alternative	Use When	Don't Use When
`uv` lock + sync	fast reproducible envs	org mandates poetry only (bridge carefully)
`pip-tools` compile	existing pip-tools shops	greenfield without constraint
Docker-only dev	strict prod parity	fast laptop iteration needed
`tox`/`nox` matrices	multi-version libraries	single-version microservices

FAQs

Why does uv sync fix "works on my machine"?

Everyone installs the same resolved graph from uv.lock on the same Python ABI. Drift shows up as lock mismatch instead of mystery imports.

Should CI use --frozen?

Yes in release pipelines. Fails when pyproject.toml changes without updating the lockfile, preventing silent upgrades.

How do I debug wrong module path?

python -c "import m; print(m.__file__)" and compare to expected site-packages or src/ editable path.

Can two projects share one venv?

Avoid it. Conflicting pins and import shadowing return. One venv per repo or use uv workspace with explicit members.

What if PyTorch CUDA wheels differ by machine?

Document optional extra indexes in README. CI CPU-only jobs install CPU index; GPU machines install platform-specific extra.

How do I pin Python 3.14 in Docker?

Use python:3.14.0-bookworm (or slim) and match requires-python in pyproject.toml.

Does ruff need the same venv?

Run ruff 0.9+ via uv run ruff so rules and auto-fixes see installed third-party stubs consistently.

How do I fix pip check failures?

uv pip check reports incompatible pins. Regenerate lock from a clean venv; remove manual pip install overrides in Dockerfile.

What about system Python on macOS?

Use python3 from .venv after uv venv. Homebrew/system Pythons are fine as base interpreters, not as install targets.

How do optional dependency groups help?

Keep heavy ML stacks optional ([project.optional-dependencies]) so API services do not install PyTorch in every image.

Can I delete uv.lock and regenerate?

Yes when upgrading major versions deliberately. Commit the new lock and run full CI matrix afterward.

How do IDE and CLI conflicts happen?

IDE points at different interpreter than terminal. Set workspace interpreter to .venv/bin/python explicitly.

Configuration & Settings - env vars vs packages
src Layout & Package Structure - install before test
Circular Import Scenarios - import errors that look like missing deps
Codebase Audit Checklist - lockfile and audit items
Debugging Tools - inspect sys.path in pdb

Stack versions: This page was written for Python 3.14.0 (stable 3.14, maintenance 3.13), FastAPI 0.115+, Django 5.2, Flask 3.1, Pydantic 2, PyTorch 2.6+, pandas 2.2+, Polars 1.x, ruff 0.9+, and uv 0.6+.

Dependency & Environment Conflicts

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Dependency & Environment Conflicts