runtests.sh Installs Links to Current Code Directory #3552
Description
Describe the bug
When runtests.sh is run it tries to build with the compile_cpp function every time some operation is done such as autofixing. This installs links in various places to add the current directory into the Python environment such as in $HOME/.local/lib/python3.8/site-packages (for Python 3.8). This changes files such as the easy-install.pth file in that directory, and adds monai.edd-link, so that the current directory appears in sys.path mysteriously if the user isn't aware of this behaviour. If this is being run from a MONAI checkout then the directory will appear in virtual environments or conda environments even if these have MONAI already installed in them which will confuse the user about which version of the library is being used.
When the script is run there shouldn't be anything installed just by doing checks or autofixing code, so something like -n needs to be added to the setup.py commands in compile_cpp or the uninstall process run at the end of that function as well as the beginning. The invocation of setup.py includes the --user argument which is why the files in $HOME/.local are changed, without it files in the current environment will be changed instead to install links there in the same way. Removing this argument therefore won't solve this problem.
To Reproduce
Steps to reproduce the behavior:
- Go to a MONAI checkout directory
- Run commands './runtests.sh --autofix'
Expected behavior
The state of the environment should be unchanged after the script is run.
Environment
Ensuring you use the relevant python executable, please paste the output of:
================================
Printing MONAI config...
================================
MONAI version: 0.7.0+236.g5efba23f
Numpy version: 1.20.3
Pytorch version: 1.10.0
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 5efba23f47c706703897546d6fa2c2d5b1947abf
Optional dependencies:
Pytorch Ignite version: 0.4.7
Nibabel version: 3.2.1
scikit-image version: 0.18.3
Pillow version: 8.4.0
Tensorboard version: 2.7.0
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: 0.11.1
tqdm version: 4.62.3
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: 5.8.0
pandas version: 1.3.4
einops version: NOT INSTALLED or UNKNOWN VERSION.
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: 1.22.0
For details about installing the optional dependencies, please visit:
https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
================================
Printing system config...
================================
System: Linux
Linux version: Ubuntu 20.04.3 LTS
Platform: Linux-5.4.0-88-generic-x86_64-with-glibc2.17
Processor: x86_64
Machine: x86_64
Python version: 3.8.12
Process name: python
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Open files: []
Num physical CPUs: 6
Num logical CPUs: 12
Num usable CPUs: 12
CPU usage (%): [15.8, 7.5, 53.7, 0.0, 0.0, 41.4, 0.0, 0.0, 26.9, 0.0, 80.4, 0.9]
CPU freq. (MHz): 1772
Load avg. in last 1, 5, 15 mins (%): [19.6, 15.2, 7.2]
Disk usage (%): 76.2
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 31.3
Available memory (GB): 17.1
Used memory (GB): 13.6
================================
Printing GPU config...
================================
Num GPUs: 2
Has CUDA: True
CUDA version: 10.2
cuDNN enabled: True
cuDNN version: 7605
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_61', 'sm_70', 'sm_75', 'compute_37']
GPU 0 Name: NVIDIA TITAN X (Pascal)
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 28
GPU 0 Total memory (GB): 11.9
GPU 0 CUDA capability (maj.min): 6.1
GPU 1 Name: NVIDIA GeForce GTX 980
GPU 1 Is integrated: False
GPU 1 Is multi GPU board: False
GPU 1 Multi processor count: 16
GPU 1 Total memory (GB): 3.9
GPU 1 CUDA capability (maj.min): 5.2