From 7b5d4fef826fe63caa05c94a438267fefccf3069 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 21 Feb 2025 10:18:02 -0800 Subject: [PATCH 1/2] starting to add air gapped data upload docs --- docs/installation.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/installation.rst b/docs/installation.rst index 2d64a410a..73ee2eb7f 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -650,6 +650,16 @@ The output of the script will also be printed to standard out as it is executed. While no sensitive information is extracted, it is good practice to review the output before sending it or posting it to ensure that nothing needs to be redacted. For example, if your python path was ``/data/SECRET_COMPOUND_NAME/python`` then that would show up in ``debug.log``. +Testing on an Air Gapped Network (most HPCs) +-------------------------------------------- + +If you run OpenFE's test suite on an HPC that restricts public internet access, OpenFE's tests that require data that are stored on `Zenodo `_ will be skipped. + +As a workaround, can manually download the data from zenodo, then upload it to the HPC for OpenFE to use: + +.. parsed-literal:: + $ + $ python -c "import pooch; print(pooch.os_cache('openfe'))" Common Errors ------------- From badaefb53904b7a21f2b3f406f1bd09a06675250 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 25 Feb 2025 09:49:41 -0800 Subject: [PATCH 2/2] updating section title --- docs/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 73ee2eb7f..927f9ad31 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -650,8 +650,8 @@ The output of the script will also be printed to standard out as it is executed. While no sensitive information is extracted, it is good practice to review the output before sending it or posting it to ensure that nothing needs to be redacted. For example, if your python path was ``/data/SECRET_COMPOUND_NAME/python`` then that would show up in ``debug.log``. -Testing on an Air Gapped Network (most HPCs) --------------------------------------------- +Testing on Systems Without Internet Access +------------------------------------------ If you run OpenFE's test suite on an HPC that restricts public internet access, OpenFE's tests that require data that are stored on `Zenodo `_ will be skipped.