Add openmm 8 beta to testing matrix

Description
This PR adds the openmm 8 beta to our testing matrix.
Motivation and context
We want to make sure the new beta doesn't break anything!
How has this been tested?
Tested right here :)
Change log
I don't think we need one, but if we want one
Added openmm 8 beta to testing matrix

Looks like we have a mix of failure modes, some of which are related to the changes in the openff toolkit. It does look like we are getting some NaNs, I will work on fixing some of the other errors first to reduce the noise.

@mikemhenry As far as I can see, we shouldn't be pulling openff-toolkit>=0.11 with perses conda-forge packages.

Oh I see, this is actually a problem in the dependencies of  openmmforcefields=0.11.2, which is the one that is being pulled and that one probably needs a more recent version of openff-units. Should we open an issue about this in the openmmforcefields repo?

As far as I can see, the problem of having the wrong openff-units version only appears when we build the environment with openmm=7.6, I don't know why this pulls the wrong version. Do we want to keep supporting this version of openmm?

I'm fine with dropping openmm 7.6, we are not using it and it will trim our matrix down/make debugging easier
We added functionality in openff-units to make the toolkit more backwards compatible, but the edge case is you need the newer version of that package to use the older version of the toolkit in a backwards compatible way. I will try pulling in a newer version of openff-units and see if that helps to fix things. If not, this will be the time to make perses work with the new toolkit.

So everything is okay on openmm 7.7, on nightly we have the charge failure, and on beta we have charge failure + some NaNs it looks like

Wow, how did that bug not get caught before?

Oh and let's allow codecov to fail again, it's been flakey for a few different repos I manage

I realized that the other failing tests, namely the test_cli.py::test_dummy_cli_with_override, test_relative.py::test_RESTCapableHybridTopologyFactory_energies, test_relative_point_mutation_setup.py::test_PointMutationExecutor_endstate_validation, are all failing exclusively if we use the CPU platform. That is, if I use CUDA platform they run fine, locally. We would need to try to further dig into these.

Differences in the test for nonbonded forces are as follows:
CPU platform:
Nonbondeds -- og: -52.1291542657432, hybrid: 69.5571606313417

CUDA platform:
Nonbondeds -- og: -50.75874077259308, hybrid: -50.758743334235376

That is really weird, do you see the same difference with openmm 7.7?

Another check is what the reference platform says, it is normally slow but I think for just evaluating forces it isn't bad for a small system, and it will tell us which is correct... What script are you using that generates that output @ijpulidos

@mikemhenry @zhang-ivy These results come from our own perses tests output. We don't see the same behavior with OpenMM 7.7 since tests are passing for that configuration. However, there are two things to be addressed here, one is the differences in the energies for nonbondeds (the test itself) and another is the differences between platforms (this is not covered by the tests).
So, the results for OpenMM 7.7 in different platforms are as follows (for test_relative.py::test_RESTCapableHybridTopologyFactory_energies)
CPU Platform:
Nonbondeds -- og: -50.85930587590415, hybrid: -50.859318121238914

CUDA Platform:
Nonbondeds -- og: -50.75468720638197, hybrid: -50.75468719701384

So, as expected not only the test passes but it gives consistent results between platforms for OpenMM 7.7.0

I think the difference across platforms is expected because I think PME is computed differently on CPU than it is on GPU -- right @jchodera?

If the tests are passing for 7.7 and not for 8 beta, we should loop Peter in to help us determine what's changed in openmm

If the tests are passing for 7.7 and not for 8 beta, we should loop Peter in to help us determine what's changed in openmm

Yes, I agree, but we probably would like to figure out a simple script that reproduces the problem using only openmm. @zhang-ivy  Do you think it is worth trying to extract the relevant parts from test_relative.py::test_RESTCapableHybridTopologyFactory_energies to achieve that?

Oh actually I just realized that the CPU tests that you are running use ala dipeptide in vacuum, so there shouldn't be a problem with PME

Is the assertion error being thrown here? https://github.com/choderalab/perses/blob/a95bf8d8c0be3b1a5cc5ff57a68365912fc086ff/perses/tests/test_relative.py#L1051

@zhang-ivy We should probably just use this simpler test to extract the relevant code here https://github.com/choderalab/perses/blob/a95bf8d8c0be3b1a5cc5ff57a68365912fc086ff/perses/tests/test_relative_point_mutation_setup.py#L32 which fails the assertion in https://github.com/choderalab/perses/blob/a95bf8d8c0be3b1a5cc5ff57a68365912fc086ff/perses/app/relative_point_mutation_setup.py#L471

Do you think it is worth trying to extract the relevant parts from test_relative.py::test_RESTCapableHybridTopologyFactory_energies to achieve that?

I'm not sure its going to be possible to extract out parts of the code such that it only relies on openmm since the whole point of the test is that it checks whether the old system energy matches the hybrid system energy at lambda = 0 and that the new system energy matches the hybrid system energy at lambda = 1

I tried to create a stripped down, reproducible example of the energy validation issue that we are seeing on CPU and am seeing strange behaviors related to importing from perses.app.relative_point_mutation_setup import PointMutationExecutor.
When I run the attached script (test.py) without importing from perses.app.relative_point_mutation_setup import PointMutationExecutor:
# CPU platform
-10.396224412218231 kJ/mol
conducting subsequent work with the following platform: CPU
{'CustomBondForce': 0.4843042375448105, 'CustomAngleForce': 7.903113289767519, 'CustomTorsionForce': 26.631596091842702, 'CustomNonbondedForce_electrostatics': -134.40419159130172, 'CustomNonbondedForce_sterics': 4.716823990818269, 'CustomBondForce_exceptions': 90.50042600262788, 'NonbondedForce_reciprocal': 0.0, 'NonbondedForce_sterics': 0.0}

# Reference platform
-10.396223075365185 kJ/mol
conducting subsequent work with the following platform: Reference
{'CustomBondForce': 0.4843042375448105, 'CustomAngleForce': 7.903113289767519, 'CustomTorsionForce': 26.631596091842702, 'CustomNonbondedForce_electrostatics': -134.4041878467019, 'CustomNonbondedForce_sterics': 4.716820782173288, 'CustomBondForce_exceptions': 90.50042600262788, 'NonbondedForce_reciprocal': 0.0, 'NonbondedForce_sterics': 0.0}

When I run the attached script (test.py) with importing from perses.app.relative_point_mutation_setup import PointMutationExecutor:
# CPU platform
324.8533636004771 kJ/mol
conducting subsequent work with the following platform: CPU
{'CustomBondForce': 0.4843042375448105, 'CustomAngleForce': 7.903113289767519, 'CustomTorsionForce': 26.631596091842702, 'CustomNonbondedForce_electrostatics': 0.0, 'CustomNonbondedForce_sterics': 4.716823990818269, 'CustomBondForce_exceptions': 90.50042600262788, 'NonbondedForce_reciprocal': 0.0, 'NonbondedForce_sterics': 0.0}

# Reference platform
-10.396223075365185 kJ/mol
conducting subsequent work with the following platform: Reference
{'CustomBondForce': 0.4843042375448105, 'CustomAngleForce': 7.903113289767519, 'CustomTorsionForce': 26.631596091842702, 'CustomNonbondedForce_electrostatics': -134.4041878467019, 'CustomNonbondedForce_sterics': 4.716820782173288, 'CustomBondForce_exceptions': 90.50042600262788, 'NonbondedForce_reciprocal': 0.0, 'NonbondedForce_sterics': 0.0}

For some reason, when we include the PointMutationExecutor import, the CustomNonbondedForce_electrostatics energy is zero on CPU. @ijpulidos Could you debug this further and try to figure out what's causing this?
debug_energy_validation_failure.zip

@zhang-ivy Thanks so much for the streamlined testing example. I'll take a look into this!

The problem seems to have been solved with the changes in the conda-forge/label/openmm_dev openmm8.0.0dev2 package.
Now the question is what actual package do we want to test against, since this PR uses the openmm_rc label instead of the openmm_dev (which I think has to be manually built).
We need a reliable way of building and testing against OpenMM release candidates, since these issues are all not reproducible in different OS (As far as I could tell the problem was apparently only for linux and not macos, which might point towards build issues for specific platforms).

I can't reproduce the above error even with 8.0.0beta.  After uncommenting the import, I get this output:
-10.396224412218231 kJ/mol
conducting subsequent work with the following platform: CPU
{'CustomBondForce': 0.4843042375448105, 'CustomAngleForce': 7.903113289767519, 'CustomTorsionForce': 26.631596091842702, 'CustomNonbondedForce_electrostatics': -134.40419159130172, 'CustomNonbondedForce_sterics': 4.716823990818268, 'CustomBondForce_exceptions': 90.50042600262788, 'NonbondedForce_reciprocal': 0.0, 'NonbondedForce_sterics': 0.0}
-10.396223075365185 kJ/mol
conducting subsequent work with the following platform: Reference
{'CustomBondForce': 0.4843042375448105, 'CustomAngleForce': 7.903113289767519, 'CustomTorsionForce': 26.631596091842702, 'CustomNonbondedForce_electrostatics': -134.4041878467019, 'CustomNonbondedForce_sterics': 4.716820782173288, 'CustomBondForce_exceptions': 90.50042600262788, 'NonbondedForce_reciprocal': 0.0, 'NonbondedForce_sterics': 0.0}

This is on Ubuntu 20.04.

It seems unlikely.  Subnormals are a really esoteric part of the floating point spec.  Nothing in OpenMM should depend on how they're treated.

From the dev sync, we want to be testing with the openmm8.0.0dev2 packages (under the openmm_dev label, instead of the openmm_rc).

I can't reproduce the above error even with 8.0.0beta. After uncommenting the import, I get this output:

@peastman can you please share the spec file for your environment? That can be obtained by running conda list --explicit > spec-file.txt. I'm still getting weird results and I would like to check if it's something with the builds/versions of the packages in the environment. Thanks!

I just created a new environment with these commands.
mamba env create mmh/openmm-8-beta-linux
conda activate openmm-8-beta-linux
mamba install -c conda-forge perses cudatoolkit=11.6

The test works correctly.  Here is the environment.

environment
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda
https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda
https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda
https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/cudatoolkit-11.6.0-hecad31d_11.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/expat-2.5.0-h27087fc_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/fftw-3.3.10-nompi_hf0379b8_106.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h166bdaf_2.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_8.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.14-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h14c3975_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.2.4-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.3-h9c3ff4c_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h516909a_1000.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ninja-1.11.0-h924138e_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/ocl-icd-2.3.1-h7f98852_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_1.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/packmol-20.010-h86c2bf4_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/sleef-3.5.1-h28343ad_2.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/snappy-1.1.9-hbd366e4_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h14c3975_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.0.10-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.9-h14c3975_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h14c3975_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h14c3975_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h14c3975_1007.tar.bz2
https://repo.anaconda.com/pkgs/main/linux-64/xz-5.2.8-h5eee18b_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/cudnn-<IP_ADDRESS>-hed8a83a_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libbrotlidec-1.0.9-h166bdaf_8.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libbrotlienc-1.0.9-h166bdaf_8.tar.bz2
https://repo.anaconda.com/pkgs/main/linux-64/libedit-3.1.20210910-h7f8727e_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libllvm11-11.1.0-he0ac6c6_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hff17c54_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libprotobuf-3.20.2-h6239696_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libxcb-1.13-h7f98852_1004.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libxml2-2.10.3-h7463322_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/libzip-1.9.2-hc929e4a_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/nccl-<IP_ADDRESS>-h0800d71_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ocl-icd-system-1.0.0-1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/pcre2-10.40-hc3806b6_0.tar.bz2
https://repo.anaconda.com/pkgs/main/linux-64/readline-8.2-h5eee18b_0.conda
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/xorg-libsm-1.2.3-hd9c2040_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-h6239696_4.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/blosc-1.21.2-hafa529b_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/boost-cpp-1.74.0-h75c5d50_8.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/brotli-bin-1.0.9-h166bdaf_8.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/freetype-2.12.1-hca18f0e_1.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/gdbm-1.18-h0a1914f_2.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/hdf4-4.2.15-h9772cbc_5.tar.bz2
https://repo.anaconda.com/pkgs/main/linux-64/intel-openmp-2022.1.0-h9e868ea_3769.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/krb5-1.19.3-h08a2579_0.tar.bz2
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https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/cftime-1.6.2-py310hde88566_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/contourpy-1.0.6-py310hbf28c38_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/h5py-3.7.0-nompi_py310h416281c_102.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/mpiplus-v0.0.1-pyhd8ed1ab_1003.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/numba-0.56.4-py310ha5257ce_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/numexpr-2.7.3-py310hb5077e9_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/openff-units-0.2.0-pyh1a96a4e_0.tar.bz2
https://conda.anaconda.org/conda-forge/label/openmm_rc/linux-64/openmm-8.0.0beta-py310h2996cf7_2.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/pandas-1.5.2-py310h769672d_0.conda
https://conda.anaconda.org/conda-forge/linux-64/pytorch-1.11.0-cuda112py310h51fe464_202.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/scipy-1.9.3-py310hdfbd76f_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.13-pyhd8ed1ab_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/distributed-2022.12.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/matplotlib-base-3.6.2-py310h8d5ebf3_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/netcdf4-1.6.2-nompi_py310h55e1e36_100.tar.bz2
https://conda.anaconda.org/conda-forge/label/openmm-torch_rc/linux-64/openmm-torch-1.0beta-cuda112py310hcc28b43_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/parmed-3.4.3-py310hd8f1fbe_3.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/patsy-0.5.3-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/pdbfixer-1.8.1-pyh6c4a22f_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/pymbar-3.1.1-py310hde88566_2.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/pytables-3.7.0-py310hb60b9b2_3.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/scikit-learn-1.1.3-py310h0c3af53_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/ambertools-22.0-py310h206695f_3.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/dask-2022.12.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/dask-jobqueue-0.8.1-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/mdtraj-1.9.7-py310h902c554_4.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/rdkit-2022.09.1-py310h10c98a6_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/seaborn-base-0.12.1-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/sphinx-5.3.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/statsmodels-0.13.5-py310hde88566_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/torchani-2.2.2-cuda112py310h73d5bcf_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/nnpops-0.2-cuda112py310h85a0d14_4.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/numpydoc-1.5.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/openff-toolkit-base-0.10.6-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/label/openmm_rc/noarch/openmm-ml-1.0beta-pyh79ba5db_2.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/openmmtools-0.21.5-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/seaborn-0.12.1-hd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/linux-64/arsenic-0.2.1-py310hff52083_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/openff-toolkit-0.10.6-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/openmoltools-0.8.8-pyhd8ed1ab_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/openmmforcefields-0.11.2-pyhd8ed1ab_1.tar.bz2
https://conda.anaconda.org/t/pe-3157b61b-91a8-43f3-b9ad-6db630ebbb91/conda-forge/noarch/perses-0.10.1-pyha21a80b_1.tar.bz2

As far as I can tell, the error is triggered if we build an environment with conda (which is what we use in CI), instead of mamba. Creating the environment with mamba doesn't really trigger the issue. I don't really know why this is the case, though. Using a different package manager/solver shouldn't change the behavior or OpenMM.
The explicit environment that shows the issue is as follows

environment
```
# This file may be used to create an environment using:
# $ conda create --name  --file
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda
https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/nomkl-1.0-h5ca1d4c_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda
https://conda.anaconda.org/conda-forge/noarch/tzdata-2022f-h191b570_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.8-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2
https://conda.anaconda.org/jaimergp/label/unsupported-cudatoolkit-shim/linux-64/cudatoolkit-11.2.2-hf4e28a0_8.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hf0379b8_105.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gstreamer-orc-0.4.33-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h166bdaf_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lame-3.100-h166bdaf_1003.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.0.9-h166bdaf_8.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libdb-6.2.32-h9c3ff4c_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.14-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libogg-1.3.4-h7f98852_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libopus-1.3.1-h7f98852_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.6-h9c3ff4c_1008.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libudev1-252-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.2.4-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.3-h9c3ff4c_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h516909a_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.30.2-h27087fc_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/nspr-4.32-h9c3ff4c_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ocl-icd-2.3.1-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1s-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/packmol-20.010-h86c2bf4_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.9-hbd366e4_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.0.10-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.9-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h7f98852_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-16_linux64_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.0.9-h166bdaf_8.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.0.9-h166bdaf_8.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libcap-2.66-ha37c62d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h9b69904_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libflac-1.4.2-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgpg-error-1.45-hc0c96e0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libllvm11-11.1.0-he0ac6c6_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hdcd2b5c_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda
https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-haa6b8db_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libvorbis-1.3.7-h9c3ff4c_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h7f98852_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.10.3-h7463322_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libzip-1.9.2-hc869a4a_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mysql-common-8.0.31-haf5c9bc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ocl-icd-system-1.0.0-1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.40-hc3806b6_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-2_h7f98852_perl5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/readline-8.1.2-h0f457ee_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.3-hd9c2040_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-h6239696_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.1-h83bc5f7_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.74.0-h75c5d50_8.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.0.9-h166bdaf_8.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-hca18f0e_1.conda
https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h9772cbc_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.19.3-h3790be6_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-16_linux64_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-1.10.1-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libglib-2.74.1-h606061b_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libllvm15-15.0.5-h63197d8_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libsndfile-1.1.0-h27087fc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.4.0-h55922b4_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxkbcommon-1.0.3-he3ba5ed_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxslt-1.1.37-h873f0b0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.0.31-h28c427c_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/python-3.10.8-h257c98d_0_cpython.conda
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https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.6.2-py310hff52083_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/openff-toolkit-0.10.6-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/s3transfer-0.6.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/sphinx-5.3.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/boto3-1.26.17-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.5.0-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/openmmforcefields-0.11.2-pyhd8ed1ab_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cloudpathlib-s3-0.9.0-py310hff52083_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/openmoltools-0.8.8-pyhd8ed1ab_1.tar.bz2

So are you saying with the same explicit environment file (which means no solving, just downloading), using conda triggers the issue, but using mamba does not?

So are you saying with the same explicit environment file (which means no solving, just downloading), using conda triggers the issue, but using mamba does not?

There's no direct way to test this because as far as I can tell using specific labels to install openmm doesn't really work with mamba. What I mean is comparing creating the environment with mamba as follows (as per Peter's instructions)
mamba env create mmh/openmm-8-beta-linux
conda activate openmm-8-beta-linux
mamba install -c conda-forge perses cudatoolkit=11.6

(Doesn't show the issue)
Compared to installing/creating it with openmm
conda env create -n perses-openmm-8-beta-conda -f devtools/conda-envs/test_env.yaml
conda activate openmm-8-beta-conda
conda install -c conda-forge/label/openmm_rc openmm
conda install -c conda-forge -c openeye perses openeye-toolkits

(shows the issue)

Can you run conda list for each of those environments, then look at the diff to see what is different?

What is the difference in the resulting environments?
Also conda env create mmh/openmm-8-beta-linux Should work as well.

Can you run conda list for each of those environments, then look at the diff to see what is different?

Yes, I did that, tried the different builds and versions for openmm or openff or similar, but the issue was still showing for those that could be solved (sometimes the environment couldn't be solved). Another difference is that the environment shared by @peastman uses mkl, whereas we don't use it in our CI environment, so that changes a lot of things starting from the lower level BLAS implementations (that's probably why the environment cannot be easily solved when going from one to the other).

What is the difference in the resulting environments?
Also conda env create mmh/openmm-8-beta-linux Should work as well.

Could this be used to create our CI environment? Because my main objective here is testing the CI workflow, rather than local tests on my workstation or on lilac.


Close #129 - Bump cats-effect 3 to 3.5.3

Close #129 - Bump cats-effect 3 to 3.5.3

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (d23b32a) 84.21% compared to head (87e4449) 84.21%.
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #131   +/-   ##
=======================================
  Coverage   84.21%   84.21%
=======================================
  Files          18       18
  Lines         361      361
  Branches        4        4
=======================================
  Hits          304      304
  Misses         57       57


huntr - Remote Code Execution Fix

https://app.huntr.dev/users/mufeedvh has fixed a security vulnerability (Remote Code Execution) :hammer:. mufeedvh has been awarded $25 for fixing the vulnerability through the huntr bug bounty program :dollar:. Think you could fix a vulnerability like this? Get involved at https://huntr.dev/!Q | AVersion Affected | ALLBug Fix | YESOriginal Pull Request | https://github.com/418sec/node-pdf-image/pull/1

@onkis @mooz @toddself - any updates on this?

I am generally against console.log calls in libraries -- it can cause issues with CI systems and being that this library doesn't log ever, very unexpected.
I would suggest rather than rejecting this, you should strip them out from the command and run with the characters stripped out.
Additionally, this needs tests to prove that it doesn't interfere with legitimate uses of this libary.

@toddself - thanks for the feedback! I have passed this feedback on to the original contributor (@mufeedvh) - they will comment shortly. Thanks! 👍
@toddself - in the meantime, there is some helpful information in the original merge request that is of value (https://github.com/418sec/node-pdf-image/pull/1).

@JamieSlome i'm confused that this was fixed somewhere on a fork first? ¯_(ツ)_/¯
Yeah, there is a remote code execution issue here, but the risk is pretty low I feel -- you'd have to be passing in non-sanitized input from a remote source to invoke this.  If the OP would update their PR with the requested changes I'd be happy to merge it, although I do not have publish permissions on npm for this package.

@toddself - it was fixed through the huntr bug bounty platform. We request users to fork "our fork" to then do quality checks on the submitted security fixes.
We can await comments and updates from the original contributor and go from there! 🍰


Adopter foster dashboard update the liked pets design

🔗 Issue

(https://github.com/rubyforgood/pet-rescue/issues/899)
✍ Description
This PR updates the UI for displaying liked pets on the adopter's dashboard. The changes involve using the existing AvatarComponent to render the pet's image and name. Additionally, the heart icon has been copied over from the existing card component, maintaining the Turbo Stream functionality, so that users can like or unlike pets directly from the dashboard by clicking the heart icon.
🔗 Issue

📷 Screenshots/Demos
https://github.com/user-attachments/assets/2c678763-339d-45bf-8776-fb7be140fe54

899

@ErinClaudio looks good! I have thought about the implementation. It looks like you're modifying the AvatarComponent to accommodate Pets, and in this particular use case, it also needs to accept likes so you can add the LikeButtonComponent. However, in doing this, we are taking a concept that handled user avatars, and now expanded it to handle Pets and Likes. It feels like these should be handled separately, because user avatars have nothing to do with Likes, if you get me?
I would instead create a new PetAvatarComponent that we can also accept a like argument on. These two concepts make sense to relate with each other. It will simplify the logic in the component as well, so we don't need to have conditionals to find the correct image paths. What do you think about that?

@kasugaijin
Thank you for the review. Just to clarify, I should remove the pet and like-related logic from avatar_component.rb, create a new PetAvatarComponent to handle that logic, and then update any downstream code accordingly?

@kasugaijin Thank you for the review. Just to clarify, I should remove the pet and like-related logic from avatar_component.rb, create a new PetAvatarComponent to handle that logic, and then update any downstream code accordingly?

Yes I think that will be a bit cleaner

@kasugaijin


gstnvtracker fails to dlopen libnvvpi.so.0

Describe the bug
This simple gstreamer (+deepstream) pipeline:
gst-launch-1.0 videotestsrc is-live=true ! "video/x-raw,width=1280,height=720,framerate=30/1" ! \
nvvideoconvert ! "video/x-raw(memory:NVMM), format=NV12" ! \
m.sink_0 nvstreammux name=m width=1280 height=720 batch-size=1 ! \
nvtracker ll-lib-file=/opt/nvidia/deepstream/deepstream-5.0/lib/libnvds_nvdcf.so ! \
nvegltransform ! nveglglessink sync=false

fails with the following error:
gstnvtracker: Loading low-level lib at /opt/nvidia/deepstream/deepstream-5.0/lib/libnvds_nvdcf.so
gstnvtracker: Failed to open low-level lib at /opt/nvidia/deepstream/deepstream-5.0/lib/libnvds_nvdcf.so
 dlopen error: libnvvpi.so.0: cannot open shared object file: No such file or directory
gstnvtracker: Failed to initilaize low level lib.

In order to fix this I had to do:
locate libnvvpi.so.0 # /opt/nvidia/deepstream/deepstream-5.0/lib/libnvvpi.so.0.3.0
ln -s /opt/nvidia/deepstream/deepstream-5.0/lib/libnvvpi.so.0.3.0 /opt/nvidia/deepstream/deepstream-5.0/lib/libnvvpi.so.0

My understanding is that this soft link should already be there.
To Reproduce
Steps to reproduce the behavior:

Build meta-tegra tag 'f5fc11f941cda7778a49f5e6808966d6c7da9e0b' with MACHINE based on 'jetson-agx-xavier-devkit'

My understanding is that this soft link should already be there.

It's not in the deepstream-5.0 deb package, so the recipe would have to be updated to add it.  I'm not sure how this works in stock L4T - the postinstall script in the deb appears to be calling on ldconfig, which might resolve the problem, too.  I'd be a bit concerned about doing the same here, if any of the shared libraries bundled into DS-5 have SONAMEs that conflict with other packages.

Eventually, we should try to update the Deepstream recipe to 5.1, which was introduced with Jetpack 4.5.1. Maybe the changed the dlopen path, or the deb package was updated.


Lack of activity

Noticed a severe lack of activity on an otherwise incredibly interesting project that I was following religiously, please resume hack.

This project made me think about reversing tools in the IPython notebook (your use of Photoshop to view the firmware in the first video I saw was really cool!), so I started hacking up some ways to view binary files with the coming IPython widgets framework in bitjet.

I recently came across this document for an older model drive and thought you might find it useful as it not only includes the internal componant diagram but also the commands that can be issued to the various chips. https://www.scribd.com/doc/257892001/SH-B123L-Product-Specifications

I had a quick look to see what one of these drives costs now. Unfortunately (but unsurprisingly) it seems that the product is discontinued, so it's not such a cheap piece of equipment any more :( If you can find one they seem to generally be over $200 USD. A little hard to justify. Although the prospect of starting over on a new drive is hardly inviting either!

Another interested party here. Would this work with AB and BB versions?

Does anyone know a similar project for the TS-L632H (SN-S082H) drive?


Create API paths under org name

Creates the user-specified API paths under the org name. This is because we share an API Gateway and the paths from different org's can overlap. For production uses, user usually specifies a hostname for the API's.

This change is

@berndtj can you reapprove when you get a chance? Had to fix a minor issue.


fix: not authorizing if no password specified

A number of the requests (such as Subscribing to Bluetooth advertisements) require the ConnectRequest to be sent, and if it's not sent the socket is closed by the esphome device. The ConnectRequest is never sent if the device doesn't have an API password.
Making the ConnectRequest without a password is totally valid and stops the socket being forcibly closed by the esphome device.

yep, looks right.
Thank you.
How do you implement with Bluetooth?

I'm testing out how to get Bluetooth to work currently; will submit PRs as I figure out how to make features work - but I'm using typescript so am also making a typescript type definition for this project.


add connections for airflow test

Scope

add json file containing airflow connections
add airflow connections add command to entrypoint.sh
cleanup deprecated warning
update README for latest config

@jayamanikharyono I've updated the readme to run v2.3 after this pr is merged, could you please tag and release?

This is a new release v2.3
Since you are adding plugins and connections, is that any way to print out those plugins and connections listed to the PR comment? @pindge

This is a new release v2.3 Since you are adding plugins and connections, is that any way to print out those plugins and connections listed to the PR comment? @pindge

yes I can do that, I'll raise another pr


Add --no-confirm Flag to influxd setup

The setup command provides a great way to configure an organisation, user, and bucket; but there's no way to skip the confirmation question.

Oh, it's there! --force / -f
Oops


Does settings a readTimeout to 0 still protect us against CVE-2024-28869?

Welcome!

[X] Yes, I've searched similar issues on GitHub and didn't find any.
[X] Yes, I've searched similar issues on the Traefik community forum and didn't find any.

What did you do?
I do not see whether setting a readTimeout to 0 in the documentation still protect us against the DoS vulnerability (CVE-2024-28869).
What did you see instead?
If setting the readTimeout to 0 does not protect us against this vulnerability, even with >2.11.2, it would be useful to have a warning in the docs that it may render the traefik instance vulnerable when setting to 0.
What version of Traefik are you using?

N/A
If applicable, please paste the log output in DEBUG level
N/A

Hello @gabfv and thanks for your interest in Traefik,
Setting the readTimeout value to 0, disables the timeout which makes Traefik vulnerable to CVE-2024-28869

Is that also true for TCP? The CVE doesn't mention it.
Asking since a have a rsync server here which fails randomly since the last traefik update.

Looks like the restic rest server has the same issue now...

@lazka The fix for CVE-2024-28869 has been to set a non-default value (60s) for the readTimeout option, also applied during the first bytes read operations in Traefik to manage layer 4 routing. So yes, Traefik won't block indefinitely for the first bytes (e.g.: client hello).

Thanks. I was referring to the initial question, if setting it to 0 for TCP makes it a DoS vector.


Maximum amount of segmented cells bounded from segmentation output file format (16-bit unsigned integer TIFF images)

Hi,
I am running the following command:
steinbock segment deepcell --minmax
On a big image, it works fine and segments the image quite well. However, after the segmentation reaches the 65536 cells, it assigns to all the remaining cells the same number(id). Is there any way to circumvent that? For example get as output  a 32-but TIFF file?

Hi @asom
Have a look at #132 for how to change the mask bit encoding. @Milad4849 could you please document this somewhere visible? Let's leave this issue open until it's in the docs.

Thanks @nilseling for your quick response!
Trying to replicate it, running 0.16.1 version, I encounter continiously the same error:
[0m could not open ****my_folder***/STEINBOCK_MASK_DTYPE=uint32: failed to retrieve path for ****my_folder***/STEINBOCK_MASK_DTYPE=uint32: lstat ****my_folder***/STEINBOCK_MASK_DTYPE=uint32: no such file or directory
Somehow recognizes the "STEINBOCK_MASK_DTYPE"  as folder extension.
The command I am running is the following:
singularity run -e STEINBOCK_MASK_DTYPE=uint32 -B /sc:/sc docker://ghcr.io/bodenmillergroup/steinbock:0.16.1 segment deepcell --img img --minmax --panel panel.csv -o masks
I would be more than grateful, if you could give me some further insights.

Since you're using Singularity, you'll need to specify the STEINBOCK_MASK_DTYPE environment variable with --env:
singularity run --env STEINBOCK_MASK_DTYPE=uint32 -B /sc:/sc docker://ghcr.io/bodenmillergroup/steinbock:0.16.1 segment deepcell --img img --minmax --panel panel.csv -o masks

Note that this will only work with Singularity 3.6 or newer.


[Windows] Update wrt-packagemgt-windows-tests to meet the pyunit requ…

…irements
Impacted tests(approved): new 0, update 5, delete 0
Unit test platform: Crosswalk Project for Windows 19.48.495.0
Unit test result summary: pass 5, fail 0, block 0
BUG=https://crosswalk-project.org/jira/browse/XWALK-6569

launch browser should be manual， or don't use popen to fork a browser

merge it first, need to test togother with testkit-lite


Include certificate used by a router in the Traefik API response

Welcome!

[X] Yes, I've searched similar issues on GitHub and didn't find any.
[X] Yes, I've searched similar issues on the Traefik community forum and didn't find any.

What did you expect to see?
I want to be able to know which certificate is used by which router. Therefore, it would be good to return the subject or CN of the used certificate for each router in the /api/http/routers response (and probably also the other API endpoints for router objects, like for TCP and UDP routers).
My actual use-case is to setup a monitoring for the configured routers and their certificate validity and to see whether there are any unused certificates.

Hello @Programie,
Thanks for your interest in Traefik!

I want to be able to know which certificate is used by which router

Unfortunately, this is not be possible. Certificates are not tied to routers, they are chosen at connection level.
Whenever a new TLS connection comes in, the SNI (server name indication), provided in the client hello, is used to find the matching certificate in the store.
We are closing this issue a question accordingly but feel free to ask to reopen if you think we missed something.


Epic: Developers have access to guidance & tools that supports them in building cross-platform packages

We need to make it easier to multi-target across operating systems and architectures, which also includes better support for RID-based multi-targeting.
User Stories

[ ] As a package author, I can use #if to perform version checks dotnet/sdk#14540
[x] Completion should support preprocessor symbols https://github.com/dotnet/roslyn/issues/49694
[ ] Package authors can multi-target between runtime identifiers (RID) #5699
[ ] Package authors can validate that their multi-targeted packages are well-formed #5700
[ ] Package authors can validate that they didn't accidentally make an API breaking change #5701
[ ] Package authors have guidance for building multi-targeted packages #5702
[ ] Package authors have guidance for building packages that deploy native code #5703
[ ] As a developer, I get compile time diagnostics for unsupported APIs https://github.com/dotnet/runtime/issues/47228
[ ] As a package consumer, I can replace a package in my graph with a different ID and version https://github.com/dotnet/core/issues/5864

Bulk closing .NET 6 epics and user stories. If you think this issue was closed in error, please reopen the issue and update it accordingly.


Help offer

This project seems a bit abandoned at the moment. There are several pull requests unattended, the CI tests are failing and links to resources are broken.
Can I contribute in any way to move things forward?

friendly ping @svenfuchs

Help would definitely be very much appreciated as life, kids etc.. is getting in the way of me making any kind of significant contribution for the moment.
Mr @svenfuchs is the only one able to add maintainers though...

friendly ping @svenfuchs

Hey all,
I talked to @svenfuchs about helping out on i18n yesterday over Twitter. He's given me write access to the repo and I can manage the issues and PRs.
No word on yet if I get some gem write access too, but it's a start.
I'll be going through the issues and PRs whenever I get a spare moment, so please let me know if there's any issues you want special attention on by tagging me in them.
Also, if you want to help with triaging the issues and PRs then that would be appreciated too. Just leave a comment on it and tag me, and I can take it from there.
Let's work together on maintaining this wonderful gem!
Thanks everyone! :heart:

@Chipairon and @sandstrom,
I am disappointed that in the 12 days since I posted this, you have not provided any assistance with the maintenance of this project.
I could really do with the assistance and it'd be great if you could find some time to help out.
Thanks!

@radar I don't have any write access, so there isn't that much opportunity for me to help.

You can at least help by triaging issues by leaving comments on them. Let me deal with the things which require write access.

On 14 Nov. 2016, at 23:05, sandstrom<EMAIL_ADDRESS>wrote:
@radar I don't have any write access, so there isn't that much opportunity for me to help.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or mute the thread.


alt attribute is not allowed on the source element

Check these before submitting new pull requests

[x] I read the guidelines for contributing linked above

[x] PHP-only files follow our coding style; in order to do that use php-cs-fixer - http://cs.sensiolabs.org/ - as follows:
php-cs-fixer --config-file==<webroot>/.php_cs fix <filename>

If all the above conditions are met, feel free to delete this whole message and to submit your pull request, and... Thank you, your help is really appreciated!

alt attribute is not allowed on the source element

Seems there is already a pull request for this #3572


use union instead of |

Proposed changes
This should fix ci errors
Checklist
Put an x in the boxes that apply.

[ ] I have read the CONTRIBUTING document
[ ] I have run pre-commit run --all-files to format my code / installed pre-commit prior to committing changes
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] I have updated the necessary documentation (if needed)

@awni this should resolve the errors in CI


Fix \yii\rest\CreateAction::run()

Use Yii::createObject() to import configuration added by service locator.
Use response/request defined in parent controller

Q
A

Is bugfix?
✔

New feature?
❌

Breaks BC?
❌

Tests pass?
✔

Fixed issues

When you create instance native by new, you ignore predefined configuration.
class \app\models\Foo extends \yii\db\ActiveRecord
{
      public $bar = 0;
}

\Yii::$container->set('\app\models\Foo', ['bar' => 1]);

echo (new \app\models\Foo())->bar; // 0
echo \Yii::createObject('\app\models\Foo')->bar; // 1

Why should Active Record instances be configurable via DI container? These aren't meant for it, they aren't services/components.

@samdark nope

@WinterSilence how's that connected?

@samdark that's fields fills by config

I also don't understand the connection and I don't think AR should be done like that.


fix(web): 更新品牌主色

更新主色从#9B0000到#94070A

Codecov Report
Base: 64.57% // Head: 64.57% // No change to project coverage :thumbsup:

Coverage data is based on head (ac3b6cf) compared to base (778ec94).
Patch has no changes to coverable lines.

Additional details and impacted files
@@           Coverage Diff           @@
##           master     #344   +/-   ##
=======================================
  Coverage   64.57%   64.57%
=======================================
  Files         101      101
  Lines        2837     2837
  Branches      353      353
=======================================
  Hits         1832     1832
  Misses        959      959
  Partials       46       46

Impacted Files
Coverage Δ

apps/auth/src/auth/loginHtml.ts
53.33% <ø> (ø)

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

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Don't export 'origin'

It's ubiquitous and will conflict with e.g. UnicodePlots.
Examples already qualify the use as WebSockets.origin anyway.

Incorporated in PR #121 and release v1.1.0. Closing.


Invalid http

I tried using this to discover sonos devices, and received no responses. When i enabled debug logging, I saw this:
Received Invalid HTTP: HTTP/1.1 200 OK
CACHE-CONTROL: max-age = 3600
EXT:
LOCATION: http://<IP_ADDRESS>:1400/xml/group_description.xml
SERVER: Linux UPnP/1.0 Sonos/42.2-51240 (ZPS13)
ST: urn:smartspeaker-audio:service:SpeakerGroup:1
USN: uuid:RINCON_7828CA18303A01400::urn:smartspeaker-audio:service:SpeakerGroup:1
BOOTID.UPNP.ORG: 24
CONFIGID.UPNP.ORG: 1

I'm guessing that it's tripping up on the empty EXT header? If that is the case, is there any workaround either by recovering from an error like this and patching it, or having the parser drop invalid headers? I noticed that the http parser is not directly part of this lib, so I would understand if there's no local solution.

I modified the code to include the parse error in the response and see this:
DEBUG:ssdp::message::ssdp     : Received Invalid HTTP: end of stream before headers finished HTTP/1.1 200 OK

Merged PR, assuming that fixed this. Thanks!


Fixed mask_correlated_samples to return masks

Thanks for spotting this one, essential part of the model. I overlooked it when refactoring the code.


Improve cross-game support for Skyline

Move away from the "stubbing" model and instead move to lazy once-run initialization for services needed by skyline (todo: move to using std::once_flag and std::call_once)

This allows avoiding initializing things early in boot and instead only initialize them as they're needed, while still not risking double-initialization.

Set logging to not flush until after the logger is initialized, allowing us to put off initializing the socket API for longer
Remove eiffel due to stagnation and its increase in difficulty when building (requiring unused submodules to build)
Fix the hardcoded romfs path and instead allow the game to select its own path when it initializes romfs.
Hook the overload for nn::socket::Initialize, ensuring games don't slip through the cracks on socket initialization
Self-initialize nn::ro at the last second if the game hasn't already

A test build is available for download here.
This work has been done in collaboration with @Raytwo and has been tested by myself, him, and @blu-dev across 3 games (pokemon, smash ultimate, spelunky 2), 2 of which previously did not work before.

For Rust mods they need to be built with this commit or newer to work on games that don't have the pthread weak alias of __pthread_mutex_lock or else they'll crash on log https://github.com/ultimate-research/skyline-rs/commit/89e7e43db3cee3fd4486cbcc4eaf2f12b2c9d760

Download has been updated ^


⚠ Turnos 24x7 has degraded performance

In b739ed3, Turnos 24x7 (https://reservas-dev.alternativasinteligentes.com/) experienced degraded performance:

HTTP code: 200
Response time: 1036 ms

Resolved: Turnos 24x7 performance has improved in 9bd6e14.


Feature/secret concealer backend

This adds Conceal to repo and team secret models. This will be used to conceal secrets within the build logs. Next step is to actually conceal the secrets according to this value.
@bradrydzewski @vaijab

@donny-dont sounds like an interesting feature, but I am trying to understand when, as a user, I would want certain secrets to be concealed but not others? From my perspective, all secrets are secrets and should be concealed.
Wouldn't it make more sense to have a flag option per repo instead?

@vaijab well for one there's precedence in Travis where you can either conceal or not conceal a secret.
But for me why this is really important is secrets can also be used for global configuration. Internally we used PLUGIN_PARAMS heavily in Drone 0.4 so global secrets allow me to emulate that behavior in 0.5. As an example I have NPM_REGISTRY as a secret for plugins/npm not because I want to hide it but because it allows me to simplify the configuration for the end user. They don't have to set the registry at all in their YAML.

As an example I have NPM_REGISTRY as a secret

Yes, we use team/global secrets to set kubernetes API URLs, etc.

What I'm saying is there's no reason to conceal the NPM_REGISTRY value. But the NPM_PASSWORD well that should be concealed.

Additionally, secrets frequently come in pairs, one a secret, one not so much. Example, USERNAME / PASSWORD, if USERNAME is drone it's concealed and that's awkward. ;-)

LGTM


[WFCORE-3353] Use the runtime name to look up the logging configurati…

…on service instead of the deployment name.
https://issues.jboss.org/browse/WFCORE-3353

Searching for "FAILURE!" on the build log for the failed windows CI job shows it happened in the new DeploymentResourceTestCase.
I didn't review the tests, but +1 to the functional part of the PR.

Ah yeah. Windows seems to be getting a lot pickier with locking files. I didn't test it on Windows so I'll give it a test and make sure to safely delete the files. Probably not a bit deal if it doesn't delete the file.

Full integration - Windows Build 4513 outcome was FAILURE using a merge of 25e4d7e95e3a3dbb772425123569168bdee99e10
Summary: Execution timeout (new); tests passed: 4020, ignored: 93 Build time: 02:30:29

retest this please, changes on the last run did not seem to be picked up.

Full integration - Windows Build 4516 outcome was FAILURE using a merge of 25e4d7e95e3a3dbb772425123569168bdee99e10
Summary: Execution timeout; tests passed: 4150, ignored: 95 Build time: 02:30:25


UISwitch and UISegmentedControl implementations.

UISwitch and UISegmentedControl implementations. Some other minor fixes. (mouseHovered event also implemented as it's needed for my application, but should be useful in general in Mac applications, and doesn't affect the way UIKit works)

make sure to check out the @seatme/Chameleon branch. we have a significant enhancements over BigZaphod's branch now (taking code from several branches and bringing it together) and includes some iOS 5 features.

Thanks, zbowling. Looks a lot more active too. I'll see if I can open a pull request into that repo/fork then. (Not sure how to go do it. I'll have to git update to that repo first I guess.)

Yeah you can do an integration/feature branch locally, do a 'git remote
add' to the our repo, pull the master from there into your local branch,
then handle and merge issues, then commit into your branch locally, push
the branch to github and send a pull request to us of the feature branch.
Zac
Sent from my next generation secret iPhone I'm not supposed to talk about.
On Nov 30, 2011, at 6:50 PM, Raf <
<EMAIL_ADDRESS>wrote:
Thanks, zbowling. Looks a lot more active too. I'll see if I can open a
pull request into that repo/fork then. (Not sure how to go do it. I'll have
to git update to that repo first I guess.)

Reply to this email directly or view it on GitHub:
https://github.com/BigZaphod/Chameleon/pull/75#issuecomment-2970146