disable jax if PYMBAR_DISABLE_JAX is set #569
Merged
+73
−2
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ijpulidos
reviewed
Oct 15, 2025
ijpulidos
reviewed
Oct 15, 2025
ijpulidos
reviewed
Oct 15, 2025
pymbar/tests/test_mbar_solvers.py
Outdated
| def test_env_values(self, monkeypatch, env_value, expected): | ||
| """Test various environment variable values.""" | ||
| monkeypatch.setenv("PYMBAR_DISABLE_JAX", env_value) | ||
| assert _setup_jax_accleration() is expected |
There was a problem hiding this comment.
Do we want to specify an error message in case the assertion fails? Something like "received X but expected Y"?
There was a problem hiding this comment.
pytest will do that for us
ijpulidos
requested changes
Oct 15, 2025
Co-authored-by: Iván Pulido <[email protected]>
Co-authored-by: Iván Pulido <[email protected]>
…x-at-runtime-option' into feat/add-disable-jax-at-runtime-option
|
#509 is how we will fix this long term, but this should work for now. |
atravitz
reviewed
Oct 15, 2025
atravitz
reviewed
Oct 15, 2025
pymbar/tests/test_mbar_solvers.py
Outdated
| ("yes", True), | ||
| ("YES", True), | ||
| ("YeS", True), | ||
| ("0", True), |
There was a problem hiding this comment.
I would expect 0=False and 1=True, no?
There was a problem hiding this comment.
duh! I was thinking about 0 being the "good" exit code and that was "true" to be BUT as soon as you mention that, it is the opposite of the convention
Co-authored-by: Alyssa Travitz <[email protected]>
ijpulidos
approved these changes
Oct 16, 2025
README.md
Outdated
|
|
||
| However, many packages released on conda-forge specify `pymbar` as a dependency, making it impossible to install the non-jax accelerated of PyMbar. | ||
| In `pymbar >= 4.2.0` JAX acceleration can be controlled with the environmental variable `PYMBAR_DISABLE_JAX`. | ||
| Setting `PYMBAR_DISABLE_JAX` to a truth-y value (`TRUE`, `YES`, `0`) will disable JAX acceleration even if the `jax` package is installed. |
There was a problem hiding this comment.
I guess we mean here 1 instead of 0 as a truth-y value?
…x-at-runtime-option' into feat/add-disable-jax-at-runtime-option
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This will let a user disable jax at runtime. A larger refactor is needed to test this since at import time the
PYMBAR_DISABLE_JAXvariable is checked, so even if monkey patched the module has already been imported. This also means that once pymbar has been imported, settingPYMBAR_DISABLE_JAXwill do nothing.TODO: add docs