Integration tests!

[Yoshanuikabundi]

Let's add an integration test suite to BespokeFit.

BespokeFit has good unit-test coverage, but much of its behavior is non-local. The 0.2.0 release was broken because of a bug in ForceBalance which was not detected by unit tests. The goal of this test suite should be to provide a place to test for non-local interactions in the codebase, to catch bugs before they are released, and to ensure that deployed versions of BespokeFit are still working.

The integration test suite should test at least the following behavior:

• BespokeFit can complete a torsion optimization of a simple, drug-like molecule (aspirin? one of the molecules we report in the paper?) using XTB (and otherwise the default settings) without raising an error and with reasonable output torsions.
• BespokeFit can complete a torsion optimization of ethane, hydrogen peroxide, or a similarly simple molecule with the default settings (using Psi4, and except for necessary changes to torsion_smirks) without raising an error.
• A failure in ForceBalance leading to a traceback in optimise.err is correctly reported (Better track ForceBalance Failures #217, Optimization failed with openff-bespokefit 0.1.1 (ForceBalance 1.9.4) #216, Support OpenFF Toolkit v0.11+ #198 (comment))
• (more to add later)

This integration suite should not be run in PRs (it'll be too slow), but it should be executed:

• Before releases
• Immediately after releases (with the deployed environment)
• After a PR is merged (or a commit is made to main)
• If it hasn't been run in the last week (to catch any changes released upstream)

This integration suite should pull in dependencies from Conda as much as possible to match the recipe for the next release.

This integration suite should NOT be derived from the documentation - while code in the documentation should be tested, that is not the purpose of this suite. The documentation should be free to change without considering the impact on test coverage, and it should be possible to add to the test suite without having to invent new documentation.

[jthorton]

Just adding some notes on running the current integration test locally.
Created a bespokefit-0.1.3 environment on mac using the command
mamba create --name bespokefit-1-3 openff-bespokefit=0.1.3 openff-toolkit xtb-python

Conda list output

# packages in environment at /Users/joshua/mambaforge/envs/bespokefit-1-3:
#
# Name                    Version                   Build  Channel
amberlite                 22.0                     pypi_0    pypi
ambertools                22.2            py310h6a0e7a1_0    conda-forge
amberutils                21.0                     pypi_0    pypi
amqp                      5.1.1              pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argcomplete               2.1.1              pyhd8ed1ab_0    conda-forge
arpack                    3.7.0                hefb7bc6_2    conda-forge
arrow-cpp                 11.0.0          h694c41f_12_cpu    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
aws-c-auth                0.6.26               h3d80c0d_0    conda-forge
aws-c-cal                 0.5.21               hf54dd2f_2    conda-forge
aws-c-common              0.8.14               hb7f2c08_0    conda-forge
aws-c-compression         0.2.16               h99c63db_5    conda-forge
aws-c-event-stream        0.2.20               h0ae4c0f_4    conda-forge
aws-c-http                0.7.5                hcdd7835_5    conda-forge
aws-c-io                  0.13.19              had634fe_1    conda-forge
aws-c-mqtt                0.8.6               h7399336_11    conda-forge
aws-c-s3                  0.2.7                h12b47ae_0    conda-forge
aws-c-sdkutils            0.1.8                h99c63db_0    conda-forge
aws-checksums             0.1.14               h99c63db_5    conda-forge
aws-crt-cpp               0.19.8              h79318f4_11    conda-forge
aws-sdk-cpp               1.10.57              h0d082ec_8    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
basis_set_exchange        0.9                pyhd8ed1ab_0    conda-forge
billiard                  3.6.4.0         py310h90acd4f_3    conda-forge
blosc                     1.21.2               hebb52c4_0    conda-forge
boost                     1.78.0          py310h3e792ce_4    conda-forge
boost-cpp                 1.78.0               h8b082ac_1    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0           py310h90acd4f_1005    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h904041c_1014    conda-forge
celery                    5.2.7              pyhd8ed1ab_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310ha78151a_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
chemper                   1.0.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           py310h2ec42d9_1    conda-forge
click-didyoumean          0.3.0              pyhd8ed1ab_0    conda-forge
click-option-group        0.5.3              pyhd8ed1ab_1    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
click-repl                0.2.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7           py310ha23aa8a_0    conda-forge
cryptography              39.0.2          py310hdd0c95c_0    conda-forge
curl                      7.88.1               h6df9250_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.33         py310h7a76584_0    conda-forge
debugpy                   1.6.6           py310h7a76584_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hf0c8a7f_0    conda-forge
fastapi                   0.86.0             pyhd8ed1ab_0    conda-forge
fftw                      3.3.10          nompi_h4fa670e_106    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.2          py310h90acd4f_0    conda-forge
forcebalance              1.9.3           py310h3e792ce_2    conda-forge
freetype                  2.12.1               h3f81eb7_1    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
geometric                 1.0                pyhd8ed1ab_1    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
gflags                    2.2.2             hb1e8313_1004    conda-forge
glog                      0.6.0                h8ac2a54_0    conda-forge
greenlet                  2.0.2           py310h7a76584_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
h5py                      3.8.0           nompi_py310h1de854f_101    conda-forge
hdf4                      4.2.15               h9804679_6    conda-forge
hdf5                      1.14.0          nompi_hbf0aa07_103    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  0.16.3             pyhd8ed1ab_0    conda-forge
httpx                     0.23.3             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib_metadata        6.0.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.21.2             pyh736e0ef_0    conda-forge
ipython                   8.11.0             pyhd1c38e8_0    conda-forge
ipywidgets                8.0.4              pyhd8ed1ab_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.0.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0           py310h2ec42d9_0    conda-forge
jupyterlab_widgets        3.0.5              pyhd8ed1ab_0    conda-forge
khronos-opencl-icd-loader 2022.09.30           hb7f2c08_2    conda-forge
kiwisolver                1.4.4           py310ha23aa8a_1    conda-forge
kombu                     5.2.4           py310h2ec42d9_2    conda-forge
krb5                      1.20.1               h049b76e_0    conda-forge
lcms2                     2.15                 h2dcdeff_1    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libabseil                 20230125.0      cxx17_hf0c8a7f_1    conda-forge
libaec                    1.0.6                hf0c8a7f_1    conda-forge
libarrow                  11.0.0          h547aefa_12_cpu    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libcrc32c                 1.1.2                he49afe7_0    conda-forge
libcurl                   7.88.1               h6df9250_0    conda-forge
libcxx                    15.0.7               h71dddab_0    conda-forge
libdeflate                1.17                 hac1461d_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libevent                  2.1.10               h7d65743_4    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           11_3_0_h97931a8_31    conda-forge
libgfortran5              12.2.0              he409387_31    conda-forge
libglib                   2.74.1               h4c723e1_1    conda-forge
libgoogle-cloud           2.8.0                h176059f_1    conda-forge
libgrpc                   1.52.1               h5bc3d57_1    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
libjpeg-turbo             2.1.5.1              hb7f2c08_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libnetcdf                 4.9.1           nompi_hb6dca1b_103    conda-forge
libnghttp2                1.52.0               he2ab024_0    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libprotobuf               3.21.12              hbc0c0cd_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.40.0               ha978bb4_0    conda-forge
libssh2                   1.10.0               h47af595_3    conda-forge
libthrift                 0.18.1               h16802d8_0    conda-forge
libtiff                   4.5.0                hd920806_5    conda-forge
libutf8proc               2.8.0                hb7f2c08_0    conda-forge
libwebp-base              1.3.0                hb7f2c08_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.10.3               hb9e07b5_0    conda-forge
libxslt                   1.1.37               h5d22bc9_0    conda-forge
libzip                    1.9.2                h6db710c_1    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               15.0.7               h61d9ccf_0    conda-forge
lxml                      4.9.2           py310h0b20c97_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.2           py310h90acd4f_0    conda-forge
matplotlib-base           3.7.1           py310he725631_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mctc-lib                  0.3.1                h5f0aba5_0    conda-forge
mdtraj                    1.9.7           py310h1b5c016_4    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
msgpack-python            1.0.5           py310ha23aa8a_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.0           nompi_hf174cb6_104    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
nglview                   3.0.3              pyh8a188c0_0    conda-forge
numexpr                   2.8.3           py310hecf8f37_1    conda-forge
numpy                     1.24.2          py310h788a5b3_0    conda-forge
ocl_icd_wrapper_apple     1.0.0                hbcb3906_0    conda-forge
openff-bespokefit         0.1.3              pyhd8ed1ab_3    conda-forge
openff-forcefields        2023.02.1          pyh1a96a4e_0    conda-forge
openff-fragmenter-base    0.1.2              pyhd8ed1ab_1    conda-forge
openff-qcsubmit           0.3.2              pyhd8ed1ab_0    conda-forge
openff-toolkit            0.10.7             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.10.7             pyhd8ed1ab_0    conda-forge
openff-utilities          0.1.8              pyh1a96a4e_0    conda-forge
openjpeg                  2.5.0                h13ac156_2    conda-forge
openmm                    8.0.0           py310haad9867_0_khronos    conda-forge
openssl                   3.1.0                hfd90126_0    conda-forge
orc                       1.8.3                ha9d861c_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h508aa58_0    conda-forge
packmol-memgen            1.2.3rc0                 pypi_0    pypi
pandas                    1.5.3           py310hecf8f37_0    conda-forge
parmed                    3.4.3           py310h7a76584_3    conda-forge
parquet-cpp               1.5.1                         1    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                h1c4e4bc_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          2_h0d85af4_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0           py310h6b2f720_2    conda-forge
pint                      0.20.1             pyhd8ed1ab_0    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.1.1              pyhd8ed1ab_0    conda-forge
plotly                    5.13.1             pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.4           py310h90acd4f_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pyarrow                   11.0.0          py310h435aefc_12_cpu    conda-forge
pycairo                   1.23.0          py310h8cdeff8_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.6          py310h90acd4f_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pymbar                    3.1.1           py310h936d966_2    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py310h90acd4f_0    conda-forge
pysocks                   1.7.1           py310h2ec42d9_5    conda-forge
pytables                  3.7.0           py310he6142c8_4    conda-forge
python                    3.10.9          he7542f4_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0             py310h90acd4f_5    conda-forge
pyzmq                     25.0.1          py310hf615a82_0    conda-forge
qcelemental               0.25.1             pyhd8ed1ab_1    conda-forge
qcengine                  0.26.0             pyhd8ed1ab_0    conda-forge
qcportal                  0.15.8             pyhd8ed1ab_0    conda-forge
rdkit                     2022.09.5       py310h5286a41_0    conda-forge
re2                       2023.02.02           hf0c8a7f_0    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
redis-py                  4.5.1              pyhd8ed1ab_0    conda-forge
redis-server              7.0.9                hc68d04a_0    conda-forge
regex                     2022.10.31      py310h90acd4f_0    conda-forge
reportlab                 3.6.12          py310hc0d9dca_2    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
rfc3986                   1.5.0              pyhd8ed1ab_0    conda-forge
rich                      13.3.2             pyhd8ed1ab_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.10.1          py310h240c617_0    conda-forge
setuptools                67.6.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.10               h225ccf5_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
sqlalchemy                2.0.6           py310h90acd4f_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
starlette                 0.20.4             pyhd8ed1ab_1    conda-forge
tenacity                  8.2.2              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tornado                   6.2             py310h90acd4f_1    conda-forge
torsiondrive              1.1.0              pyhd8ed1ab_0    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
unicodedata2              15.0.0          py310h90acd4f_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
uvicorn                   0.21.1          py310h2ec42d9_0    conda-forge
vine                      5.0.0              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.5              pyhd8ed1ab_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.0.10               h0d85af4_0    conda-forge
xorg-libsm                1.2.3             h0d85af4_1000    conda-forge
xorg-libx11               1.8.4                hb7f2c08_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                hb7f2c08_2    conda-forge
xorg-libxt                1.2.1                h0d85af4_2    conda-forge
xorg-xextproto            7.3.0             hb7f2c08_1003    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xtb                       6.5.1                h5bf119a_1    conda-forge
xtb-python                22.1            py310h90acd4f_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hfd90126_4    conda-forge
zstd                      1.5.2                hbc0c0cd_6    conda-forge

run the test using

openff-bespoke executor run --smiles                 'CC'               \
                                      --workflow               'default'          \
                                      --default-qc-spec        xtb gfn2xtb none   \
                                      --target-torsion         '[C:1]-[C:2]' --directory bespokefit-1-3 --qc-compute-n-cores 1

The test works with the following output

3. running the fitting pipeline                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                             
[✓] fragmentation successful
[✓] qc-generation successful
[✓] optimization successful

Looking at the bottom of the forcebalance output I notice it runs 2 iterations (0 and 1) and completes in ~11 seconds as expected.

I then created the test environment locally the no_openeye.yaml file.

Conda list output no-openeye

# packages in environment at /Users/joshua/mambaforge/envs/bespokefit-no-openeye:
#
# Name                    Version                   Build  Channel
amberlite                 22.0                     pypi_0    pypi
ambertools                22.2            py310h6a0e7a1_0    conda-forge
amberutils                21.0                     pypi_0    pypi
amqp                      5.1.1              pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argcomplete               2.1.1              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h90acd4f_3    conda-forge
arpack                    3.7.0                hefb7bc6_2    conda-forge
arrow-cpp                 11.0.0          h694c41f_12_cpu    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
aws-c-auth                0.6.26               h3d80c0d_0    conda-forge
aws-c-cal                 0.5.21               hf54dd2f_2    conda-forge
aws-c-common              0.8.14               hb7f2c08_0    conda-forge
aws-c-compression         0.2.16               h99c63db_5    conda-forge
aws-c-event-stream        0.2.20               h0ae4c0f_4    conda-forge
aws-c-http                0.7.5                hcdd7835_5    conda-forge
aws-c-io                  0.13.19              had634fe_1    conda-forge
aws-c-mqtt                0.8.6               h7399336_11    conda-forge
aws-c-s3                  0.2.7                h12b47ae_0    conda-forge
aws-c-sdkutils            0.1.8                h99c63db_0    conda-forge
aws-checksums             0.1.14               h99c63db_5    conda-forge
aws-crt-cpp               0.19.8              h79318f4_11    conda-forge
aws-sdk-cpp               1.10.57              h0d082ec_8    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
basis_set_exchange        0.9                pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.2             pyha770c72_0    conda-forge
billiard                  3.6.4.0         py310h90acd4f_3    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.2               hebb52c4_0    conda-forge
boost                     1.78.0          py310h3e792ce_4    conda-forge
boost-cpp                 1.78.0               h8b082ac_1    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0           py310h90acd4f_1005    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h904041c_1014    conda-forge
celery                    5.2.7              pyhd8ed1ab_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310ha78151a_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
chemper                   1.0.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           py310h2ec42d9_1    conda-forge
click-didyoumean          0.3.0              pyhd8ed1ab_0    conda-forge
click-option-group        0.5.3              pyhd8ed1ab_1    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
click-repl                0.2.0              pyhd8ed1ab_0    conda-forge
codecov                   2.1.12             pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7           py310ha23aa8a_0    conda-forge
coverage                  7.2.2           py310h90acd4f_0    conda-forge
cryptography              39.0.2          py310hdd0c95c_0    conda-forge
curl                      7.88.1               h6df9250_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.33         py310h7a76584_0    conda-forge
debugpy                   1.6.6           py310h7a76584_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hf0c8a7f_0    conda-forge
fastapi                   0.86.0             pyhd8ed1ab_0    conda-forge
fftw                      3.3.10          nompi_h4fa670e_106    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.2          py310h90acd4f_0    conda-forge
forcebalance              1.9.5                    pypi_0    pypi
freetype                  2.12.1               h3f81eb7_1    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
geometric                 0.9.7.2                    py_0    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
gflags                    2.2.2             hb1e8313_1004    conda-forge
glog                      0.6.0                h8ac2a54_0    conda-forge
greenlet                  2.0.2           py310h7a76584_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
h5py                      3.8.0           nompi_py310h1de854f_101    conda-forge
hdf4                      4.2.15               h9804679_6    conda-forge
hdf5                      1.14.0          nompi_hbf0aa07_103    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  0.16.3             pyhd8ed1ab_0    conda-forge
httpx                     0.23.3             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib_metadata        6.0.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.21.2             pyh736e0ef_0    conda-forge
ipython                   8.11.0             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.7.3              pyhd8ed1ab_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.0.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0           py310h2ec42d9_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.4.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.2              pyhd8ed1ab_0    conda-forge
khronos-opencl-icd-loader 2022.09.30           hb7f2c08_2    conda-forge
kiwisolver                1.4.4           py310ha23aa8a_1    conda-forge
kombu                     5.2.4           py310h2ec42d9_2    conda-forge
krb5                      1.20.1               h049b76e_0    conda-forge
lcms2                     2.15                 h2dcdeff_1    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libabseil                 20230125.0      cxx17_hf0c8a7f_1    conda-forge
libaec                    1.0.6                hf0c8a7f_1    conda-forge
libarrow                  11.0.0          h547aefa_12_cpu    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libcrc32c                 1.1.2                he49afe7_0    conda-forge
libcurl                   7.88.1               h6df9250_0    conda-forge
libcxx                    15.0.7               h71dddab_0    conda-forge
libdeflate                1.17                 hac1461d_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libevent                  2.1.10               h7d65743_4    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           11_3_0_h97931a8_31    conda-forge
libgfortran5              12.2.0              he409387_31    conda-forge
libglib                   2.74.1               h4c723e1_1    conda-forge
libgoogle-cloud           2.8.0                h176059f_1    conda-forge
libgrpc                   1.52.1               h5bc3d57_1    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
libjpeg-turbo             2.1.5.1              hb7f2c08_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libnetcdf                 4.9.1           nompi_hb6dca1b_103    conda-forge
libnghttp2                1.52.0               he2ab024_0    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libprotobuf               3.21.12              hbc0c0cd_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.40.0               ha978bb4_0    conda-forge
libssh2                   1.10.0               h47af595_3    conda-forge
libthrift                 0.18.1               h16802d8_0    conda-forge
libtiff                   4.5.0                hd920806_5    conda-forge
libutf8proc               2.8.0                hb7f2c08_0    conda-forge
libwebp-base              1.3.0                hb7f2c08_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.10.3               hb9e07b5_0    conda-forge
libxslt                   1.1.37               h5d22bc9_0    conda-forge
libzip                    1.9.2                h6db710c_1    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               15.0.7               h61d9ccf_0    conda-forge
lxml                      4.9.2           py310h0b20c97_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.2           py310h90acd4f_0    conda-forge
matplotlib-base           3.7.1           py310he725631_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mctc-lib                  0.3.1                h5f0aba5_0    conda-forge
mdtraj                    1.9.7           py310h1b5c016_4    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
msgpack-python            1.0.5           py310ha23aa8a_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclassic                 0.5.3              pyhb4ecaf3_3    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.0           nompi_hf174cb6_104    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
nglview                   3.0.3              pyh8a188c0_0    conda-forge
notebook                  6.5.3              pyha770c72_0    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.3           py310hecf8f37_1    conda-forge
numpy                     1.24.2          py310h788a5b3_0    conda-forge
ocl_icd_wrapper_apple     1.0.0                hbcb3906_0    conda-forge
openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge
openff-bespokefit         0.2.0+7.g1b87638           dev_0    <develop>
openff-forcefields        2023.02.1          pyh1a96a4e_0    conda-forge
openff-fragmenter-base    0.2.0              pyhd8ed1ab_0    conda-forge
openff-interchange        0.2.3              pyhd8ed1ab_1    conda-forge
openff-interchange-base   0.2.3              pyhd8ed1ab_1    conda-forge
openff-qcsubmit           0.4.1              pyhd8ed1ab_0    conda-forge
openff-toolkit            0.12.1             pyhd8ed1ab_1    conda-forge
openff-toolkit-base       0.12.1             pyhd8ed1ab_1    conda-forge
openff-units              0.2.0              pyh1a96a4e_0    conda-forge
openff-utilities          0.1.8              pyh1a96a4e_0    conda-forge
openjpeg                  2.5.0                h13ac156_2    conda-forge
openmm                    8.0.0           py310haad9867_0_khronos    conda-forge
openssl                   3.1.0                hfd90126_0    conda-forge
orc                       1.8.3                ha9d861c_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h508aa58_0    conda-forge
packmol-memgen            1.2.3rc0                 pypi_0    pypi
pandas                    1.5.3           py310hecf8f37_0    conda-forge
pandoc                    3.1.1                h9d075a6_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panedr                    0.7.1              pyhd8ed1ab_0    conda-forge
parmed                    3.4.3           py310h7a76584_3    conda-forge
parquet-cpp               1.5.1                         1    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pbr                       5.11.1             pyhd8ed1ab_0    conda-forge
pcre2                     10.40                h1c4e4bc_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          2_h0d85af4_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0           py310h6b2f720_2    conda-forge
pint                      0.20.1             pyhd8ed1ab_0    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.1.1              pyhd8ed1ab_0    conda-forge
plotly                    5.13.1             pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0           py310h2ec42d9_4    conda-forge
pooch                     1.7.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.4           py310h90acd4f_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pyarrow                   11.0.0          py310h435aefc_12_cpu    conda-forge
pycairo                   1.23.0          py310h8cdeff8_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.6          py310h90acd4f_0    conda-forge
pyedr                     0.7.1              pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pymbar                    3.1.1           py310h936d966_2    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py310h90acd4f_0    conda-forge
pysocks                   1.7.1           py310h2ec42d9_5    conda-forge
pytables                  3.7.0           py310he6142c8_4    conda-forge
pytest                    7.2.2              pyhd8ed1ab_0    conda-forge
pytest-asyncio            0.20.3             pyhd8ed1ab_0    conda-forge
pytest-celery             0.0.0a1            pyh9f0ad1d_1    conda-forge
pytest-cov                4.0.0              pyhd8ed1ab_0    conda-forge
python                    3.10.9          he7542f4_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0             py310h90acd4f_5    conda-forge
pyzmq                     25.0.1          py310hf615a82_0    conda-forge
qcelemental               0.25.1             pyhd8ed1ab_1    conda-forge
qcengine                  0.26.0             pyhd8ed1ab_0    conda-forge
qcportal                  0.15.8             pyhd8ed1ab_0    conda-forge
rdkit                     2022.09.5       py310h5286a41_0    conda-forge
re2                       2023.02.02           hf0c8a7f_0    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
redis-py                  4.5.1              pyhd8ed1ab_0    conda-forge
redis-server              7.0.9                hc68d04a_0    conda-forge
regex                     2022.10.31      py310h90acd4f_0    conda-forge
reportlab                 3.6.12          py310hc0d9dca_2    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
requests-mock             1.10.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986                   1.5.0              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.3.2             pyhd8ed1ab_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.10.1          py310h240c617_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                67.6.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.10               h225ccf5_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlalchemy                2.0.6           py310h90acd4f_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
starlette                 0.20.4             pyhd8ed1ab_1    conda-forge
tenacity                  8.2.2              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h90acd4f_1    conda-forge
torsiondrive              1.1.0              pyhd8ed1ab_0    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
unicodedata2              15.0.0          py310h90acd4f_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
uvicorn                   0.21.1          py310h2ec42d9_0    conda-forge
vine                      5.0.0              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.1              pyha770c72_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.0.10               h0d85af4_0    conda-forge
xorg-libsm                1.2.3             h0d85af4_1000    conda-forge
xorg-libx11               1.8.4                hb7f2c08_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                hb7f2c08_2    conda-forge
xorg-libxt                1.2.1                h0d85af4_2    conda-forge
xorg-xextproto            7.3.0             hb7f2c08_1003    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xtb                       6.5.1                h5bf119a_1    conda-forge
xtb-python                22.1            py310h90acd4f_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hfd90126_4    conda-forge
zstd                      1.5.2                hbc0c0cd_6    conda-forge

I ran the same command as above and changed bespokefit to run the optimisation in a local folder and not clean it up, the test fails so reproduces the CI. I noticed that this also runs 2 iterations but takes almost 60 seconds.