IMO this is simply more of #206, and I've already demonstrated the problem there. But it's been a month and no one has re-opened, so I'm opening this more specific issue to address the problem.

Here's an example dev-requirements.txt from the plumbum project:

pytest
pytest-cov
pytest-mock
idna<2.8 ; python_version < '2.7'
pycparser<2.18 ; python_version < '2.7'
paramiko<2.4 ; python_version < '2.7'
paramiko ; python_version >= '2.7'
setuptools
wheel ; python_version >= '2.7'
psutil

pip-sync dev-requirements.txt

Identical output whether in a Python 3.7.4 or 2.7.16 env:

Incompatible requirements found: paramiko (from -r dev-requirements.txt (line 7)) and paramiko<2.4 (from -r dev-requirements.txt (line 6))

No packages end up installed aside from pip-tools and its deps.

Environment Versions

1. Arch Linux
2. Python version: 3.7.4
3. pip version: 19.2.3
4. pip-tools version: 4.1.0

Steps to replicate

echo "paramiko==2.4.0 ; python_version < '2.7'" > mark.txt
echo "paramiko==2.6.0 ; python_version >= '2.7'" >> mark.txt
pip-sync mark.txt

Note that this works:

pip install --no-deps -r mark.txt

Expected result

pip-sync should ignore non-matching requirements when environment markers are present.

Actual result

pip-sync checks for conflicts as if it wants to install requirements for all platforms.

Further notes

mv mark.txt mark.in
pip-compile --no-header mark.in

asn1crypto==1.0.1         # via cryptography
bcrypt==3.1.7             # via paramiko
cffi==1.12.3              # via bcrypt, cryptography, pynacl
cryptography==2.7         # via paramiko
paramiko==2.6.0 ; python_version >= "2.7"
pycparser==2.19           # via cffi
pynacl==1.3.0             # via paramiko
six==1.12.0               # via bcrypt, cryptography, pynacl

Currently, compiling such an in-file will only include the compile-time platform's matching reqs. This hides the issue under discussion, and arguably means it's not a bug. But I believe it is generally desired for pip-sync to honor environment markers, as evidenced by the contents of #206 (closed, but not solved), #600 (merged), #459 (replaced), #460 (merged), #518 (open 2yrs), #563 (open 2yrs), #585 (open 2yrs), #896 (open), etc.

This is probably even more relevant for working with a single python version across different platforms.