Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Do not export unnecessary conda env vars, use conda run #232

Merged
merged 10 commits into from
May 17, 2024
Merged

Do not export unnecessary conda env vars, use conda run #232

Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
de2bcae
Do not export unnecessary conda env vars, add activate command
rly Oct 9, 2023
2f33799
Update utils.py
rly Oct 9, 2023
2fa457b
Update utils.py
rly Oct 9, 2023
db7de93
Update utils.py
rly Oct 9, 2023
4b6cf15
Update utils.py
rly Oct 9, 2023
c4f2cbb
Update utils.py
rly Oct 9, 2023
8d04555
Update utils.py
rly Oct 9, 2023
a880468
Update utils.py
rly Oct 9, 2023
f30138d
Merge branch 'master' into patch-2
rly Nov 10, 2023
d4462c4
Update
rly Nov 10, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 13 additions & 10 deletions mesmerize_core/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,14 +103,7 @@ def make_runfile(

f.write(f"#!/bin/bash\n")

if "CONDA_PREFIX" in os.environ.keys():
f.write(
f'export CONDA_PREFIX={os.environ["CONDA_PREFIX"]}\n'
f'export CONDA_PYTHON_EXE={os.environ["CONDA_PYTHON_EXE"]}\n'
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Are we sure this is no longer necessary?

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I mean the CONDA_PYTHON_EXE

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I believe these env variables will not do anything if the conda environment is not activated and you call the default python below.

f'export CONDA_PREFIX_1={os.environ["CONDA_PREFIX_1"]}\n'
)

elif "VIRTUAL_ENV" in os.environ.keys():
if "VIRTUAL_ENV" in os.environ.keys():
f.write(
f'export PATH={os.environ["PATH"]}\n'
f'export VIRTUAL_ENV={os.environ["VIRTUAL_ENV"]}\n'
Expand All @@ -132,9 +125,17 @@ def make_runfile(
f'export MESMERIZE_N_PROCESSES={os.environ["MESMERIZE_N_PROCESSES"]}\n'
)

f.write(f"export OPENBLAS_NUM_THREADS=1\n" f"export MKL_NUM_THREADS=1\n")
f.write(
f"export OPENBLAS_NUM_THREADS=1\n"
f"export MKL_NUM_THREADS=1\n"
)

f.write(f"python {module_path} {args_str}") # call the script to run
if "CONDA_PREFIX" in os.environ.keys():
# add command to run the python script in the conda environment
# that was active at the time that this shell script was generated
f.write(f'{os.environ["CONDA_EXE"]} run -p {os.environ["CONDA_PREFIX"]} python {module_path} {args_str}')
else:
f.write(f"python {module_path} {args_str}") # call the script to run

else:
with open(sh_file, "w") as f:
Expand All @@ -155,6 +156,8 @@ def make_runfile(
st = os.stat(sh_file)
os.chmod(sh_file, st.st_mode | S_IEXEC)

print(sh_file)

return sh_file


Expand Down
Loading