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hesther / templatecorr

Hierarchical template correction for chemical reactions
BSD 3-Clause "New" or "Revised" License
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Running the script on test data provided in the repo returns empty csv #7

Closed milicazmarkovic closed 1 month ago

milicazmarkovic commented 1 month ago

Hello!

I tried replicating the results from the paper, but ended up getting an empty csv file as output. I suspect divergence in required packages versions could be causing this, since I have not modified the code at all. Could you specify versions of required packages and python version in environment.yml? Also if you know of any other issues that could cause this to happen, let me know!

hesther commented 1 month ago

I can look into the environment later this week (don't have access to the old environments anymore), but could you meanwhile provide the terminal output of the script? I wonder whether there were e.g. all reactions lost along the pipeline

hesther commented 1 month ago

This is how it should look: Untitled

hesther commented 1 month ago

@milicazmarkovic And this is the exact environment I used just now (just now on my laptop, not back when we wrote the paper), but I am not aware of a package mismatch that could cause the output to be empty. If you send me a list of package versions you used I will try to recreate the error and track down the package that causes this, then we can specify that version in the environment.

# Name                    Version                   Build  Channel
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38hed1de0f_2    conda-forge
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    5.0.0              pyhd8ed1ab_0    conda-forge
boost                     1.74.0           py38hb0f0857_5    conda-forge
boost-cpp                 1.74.0               hdbf7018_7    conda-forge
brotli                    1.0.9                h5eb16cf_7    conda-forge
brotli-bin                1.0.9                h5eb16cf_7    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2022.6.15            h033912b_0    conda-forge
cairo                     1.16.0            h9e0e54b_1010    conda-forge
certifi                   2022.6.15        py38h50d1736_0    conda-forge
cffi                      1.15.0           py38h1a44b6c_0    conda-forge
cli-exit-tools            1.2.3.2                  pypi_0    pypi
click                     8.1.3                    pypi_0    pypi
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dbus                      1.13.6               h811a1a6_3    conda-forge
debugpy                   1.6.0            py38h038c8f4_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.5.1                  pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
enzymemap                 0.0.0+1.geddd0ce.dirty           dev_0    <develop>
executing                 0.8.3              pyhd8ed1ab_0    conda-forge
expat                     2.4.8                h96cf925_0    conda-forge
flit-core                 3.7.1              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                2.14.0               h676cef8_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.33.3           py38h0dd4459_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
greenlet                  1.1.2            py38h038c8f4_2    conda-forge
icu                       69.1                 he49afe7_0    conda-forge
importlib-metadata        4.11.4           py38h50d1736_0    conda-forge
importlib_resources       5.7.1              pyhd8ed1ab_1    conda-forge
ipykernel                 6.13.1           py38h60dac5d_0    conda-forge
ipython                   8.4.0            py38h50d1736_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.7.0              pyhd8ed1ab_0    conda-forge
jedi                      0.18.1           py38h50d1736_1    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h5eb16cf_1    conda-forge
jsonschema                4.6.0              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py38h50d1736_7    conda-forge
jupyter_client            7.3.3              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.3              pyhd8ed1ab_0    conda-forge
jupyter_core              4.10.0           py38h50d1736_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.0              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.2            py38h8b7791e_1    conda-forge
krb5                      1.19.3               hb98e516_0    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
lib-detect-testenv        2.0.2.2                  pypi_0    pypi
libblas                   3.9.0           15_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                h5eb16cf_7    conda-forge
libbrotlidec              1.0.9                h5eb16cf_7    conda-forge
libbrotlienc              1.0.9                h5eb16cf_7    conda-forge
libcblas                  3.9.0           15_osx64_openblas    conda-forge
libclang                  13.0.1          default_he082bbe_0    conda-forge
libcxx                    14.0.4               hc203e6f_0    conda-forge
libdeflate                1.10                 h0d85af4_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libglib                   2.70.2               hf1fb8c0_4    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.9.0           15_osx64_openblas    conda-forge
libllvm13                 13.0.1               h64f94b2_2    conda-forge
libopenblas               0.3.20          openmp_hb3cd9ec_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libpq                     14.3                 h2b7167c_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libtiff                   4.4.0                hfca7e8f_0    conda-forge
libwebp                   1.2.2                h28dabe5_0    conda-forge
libwebp-base              1.2.2                h0d85af4_1    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libzlib                   1.2.12               h6c3fc93_0    conda-forge
llvm-openmp               14.0.4               ha654fa7_0    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
markupsafe                2.1.1            py38hed1de0f_1    conda-forge
matplotlib-base           3.5.2            py38h1b6b9d1_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py38h96a0964_1005    conda-forge
multiprocess              0.70.13                  pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.29               h9525fdc_1    conda-forge
mysql-libs                8.0.29               h8d0e597_1    conda-forge
nbclient                  0.6.4              pyhd8ed1ab_1    conda-forge
nbconvert                 6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          6.5.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge
notebook                  6.4.11             pyha770c72_0    conda-forge
nspr                      4.32                 hcd9eead_1    conda-forge
nss                       3.78                 ha8197d3_0    conda-forge
numpy                     1.22.4           py38h3ad0702_0    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openssl                   3.0.5                hb81d4ab_1    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.2            py38h2b30649_2    conda-forge
pandoc                    2.18                 h694c41f_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.1.1            py38h21af888_1    conda-forge
pip                       22.1.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.29             pyha770c72_0    conda-forge
prompt_toolkit            3.0.29               hd8ed1ab_0    conda-forge
psutil                    5.9.1            py38h0dd4459_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
pycairo                   1.21.0           py38h2e817b2_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.12.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.12.3           py38hca2ab18_4    conda-forge
pyqt5-sip                 4.19.18                  pypi_0    pypi
pyqtchart                 5.12                     pypi_0    pypi
pyqtwebengine             5.12.1                   pypi_0    pypi
pyrsistent                0.18.1           py38hed1de0f_1    conda-forge
python                    3.8.13          h66c20e1_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyzmq                     23.1.0           py38h34ba744_0    conda-forge
qt                        5.12.9               h2a607e2_5    conda-forge
qtconsole                 5.3.1              pyhd8ed1ab_0    conda-forge
qtconsole-base            5.3.1              pyha770c72_0    conda-forge
qtpy                      2.1.0              pyhd8ed1ab_0    conda-forge
rdchiral_cpp              1.1.2            py38he65332d_0    conda-forge
rdkit                     2021.09.5        py38hc2778ef_0    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
reportlab                 3.5.68           py38hf6ac518_1    conda-forge
scipy                     1.9.0            py38hb261484_0    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                62.3.2           py38h50d1736_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge
sqlalchemy                1.4.37           py38h0dd4459_0    conda-forge
sqlite                    3.38.5               hd9f0692_0    conda-forge
stack_data                0.2.0              pyhd8ed1ab_0    conda-forge
statsmodels               0.13.2           py38hc1426ef_0    conda-forge
templatecorr              0+untagged.21.g7095b4b           dev_0    <develop>
terminado                 0.15.0           py38h50d1736_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tornado                   6.1              py38hed1de0f_3    conda-forge
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
traitlets                 5.2.2.post1        pyhd8ed1ab_0    conda-forge
typing-extensions         4.2.0                hd8ed1ab_1    conda-forge
typing_extensions         4.2.0              pyha770c72_1    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
unicodedata2              14.0.0           py38hed1de0f_1    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.0            py38h50d1736_0    conda-forge
wrapt                     1.14.1                   pypi_0    pypi
wrapt-timeout-decorator   1.3.12.2                 pypi_0    pypi
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.8.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               h6c3fc93_0    conda-forge
zstd                      1.5.2                ha9df2e0_1    conda-forge
hesther commented 1 month ago

Another question: which script exactly did you run? correct.py on the uspto_50k.csv?

milicazmarkovic commented 1 month ago

Ok so, I tried multiple versions of rdkit and rdchiral, I haven't touched the rest of the packages. I ran the following command:

python correct.py --path data/uspto_50k --reaction_column rxn_smiles --name template --nproc 20 --data_format csv

And here is the output that I am getting:

` Reading file... Preprocessing reactants... [Parallel(n_jobs=20)]: Using backend LokyBackend with 20 concurrent workers. [Parallel(n_jobs=20)]: Done 10 tasks | elapsed: 11.6s [Parallel(n_jobs=20)]: Done 308 tasks | elapsed: 11.7s [Parallel(n_jobs=20)]: Done 14481 tasks | elapsed: 13.7s [Parallel(n_jobs=20)]: Done 48545 tasks | elapsed: 17.1s [Parallel(n_jobs=20)]: Done 49977 out of 50016 | elapsed: 17.2s remaining: 0.0s [Parallel(n_jobs=20)]: Done 50016 out of 50016 | elapsed: 17.3s finished Extracting templates (Radius 1 with special groups)... 100%|██████████████████████████████████████████████████████████| 50016/50016 [00:03<00:00, 15084.85it/s] Extracting templates (Radius 1 without special groups)... 100%|██████████████████████████████████████████████████████████| 50016/50016 [00:03<00:00, 15408.17it/s] Extracting templates (Radius 0 without special groups)... 100%|██████████████████████████████████████████████████████████| 50016/50016 [00:02<00:00, 17921.67it/s] Hierarchically correcting templates... ...Unique templates in column template_r0 : 0 ...Unique templates in column template_r1 : 0 ...Correcting templates in column template_r1 [Parallel(n_jobs=20)]: Using backend LokyBackend with 20 concurrent workers. ...Unique corrected templates in column template_r1 : 0

...Unique templates in column template_r1 : 0 ...Unique templates in column template : 0 ...Correcting templates in column template [Parallel(n_jobs=20)]: Using backend LokyBackend with 20 concurrent workers. ...Unique corrected templates in column template : 0

Wrote dataframe to data/uspto_50k_corrected.csv`

milicazmarkovic commented 1 month ago

Additionally, I tried running scripts/01 and 02 steps separately, but 02 failed because output of 01 was empty...

Here are my current packages list. I assumed this was an issue with compatibility/dependency because I have not changed the code or got any meaningful errors.

Name Version Build Channel

boost 1.74.0 py38h1e2c3d9_5 conda-forge boost-cpp 1.74.0 h32e41df_4 conda-forge brotli 1.1.0 hb547adb_1 conda-forge brotli-bin 1.1.0 hb547adb_1 conda-forge bzip2 1.0.8 h99b78c6_7 conda-forge ca-certificates 2024.7.4 hf0a4a13_0 conda-forge cairo 1.16.0 h302bd0f_5
certifi 2024.7.4 py38hca03da5_0
chardet 5.2.0 py38h10201cd_1 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.1.1 py38h9afee92_1 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 hebf3989_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 h77eed37_2 conda-forge fontconfig 2.14.2 h82840c6_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.1 py38h3237794_0 conda-forge freetype 2.12.1 hadb7bae_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge gettext 0.21.0 h826f4ad_0
glib 2.78.4 h313beb8_0
glib-tools 2.78.4 h313beb8_0
greenlet 3.0.3 py38hb9fa5a8_0 conda-forge icu 68.1 hc377ac9_0
importlib-resources 6.4.0 pyhd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge kiwisolver 1.4.5 py38h9afee92_1 conda-forge krb5 1.21.3 h237132a_0 conda-forge lcms2 2.16 ha0e7c42_0 conda-forge lerc 4.0.0 h9a09cb3_0 conda-forge libblas 3.9.0 23_osxarm64_openblas conda-forge libbrotlicommon 1.1.0 hb547adb_1 conda-forge libbrotlidec 1.1.0 hb547adb_1 conda-forge libbrotlienc 1.1.0 hb547adb_1 conda-forge libcblas 3.9.0 23_osxarm64_openblas conda-forge libcxx 18.1.8 h5a72898_2 conda-forge libdeflate 1.20 h93a5062_0 conda-forge libedit 3.1.20191231 hc8eb9b7_2 conda-forge libexpat 2.6.2 hebf3989_0 conda-forge libffi 3.4.2 h3422bc3_5 conda-forge libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge libgfortran5 13.2.0 hf226fd6_3 conda-forge libglib 2.78.4 h0a96307_0
libiconv 1.17 h0d3ecfb_2 conda-forge libintl 0.22.5 h8fbad5d_2 conda-forge libjpeg-turbo 3.0.0 hb547adb_1 conda-forge liblapack 3.9.0 23_osxarm64_openblas conda-forge libopenblas 0.3.27 openmp_h517c56d_1 conda-forge libpng 1.6.43 h091b4b1_0 conda-forge libpq 16.3 h7afe498_0 conda-forge libsqlite 3.46.0 hfb93653_0 conda-forge libtiff 4.6.0 h07db509_3 conda-forge libwebp-base 1.4.0 h93a5062_0 conda-forge libxcb 1.15 hf346824_0 conda-forge libxml2 2.9.14 h8c5e841_0
libzlib 1.2.13 hfb2fe0b_6 conda-forge llvm-openmp 18.1.8 hde57baf_0 conda-forge matplotlib-base 3.7.3 py38hef9d0d7_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.5 hb89a1cb_0 conda-forge numpy 1.24.4 py38ha84db1f_0 conda-forge openjpeg 2.5.2 h9f1df11_0 conda-forge openssl 3.3.1 hfb2fe0b_2 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.0.3 py38hefb543e_1 conda-forge pcre2 10.42 hb066dcc_1
pillow 10.3.0 py38h9ef4633_0 conda-forge pip 24.2 pyhd8ed1ab_0 conda-forge pixman 0.43.4 hebf3989_0 conda-forge pthread-stubs 0.4 h27ca646_1001 conda-forge pycairo 1.23.0 py38hc7d53f0_0
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge python 3.8.19 h2469fbe_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.8 4_cp38 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge rdchiral 1.1.0 pypi_0 pypi rdkit 2021.03.1 py38hbcbf861_0 conda-forge readline 8.2 h92ec313_1 conda-forge reportlab 4.2.2 py38h3237794_0 conda-forge rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge setuptools 72.1.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlalchemy 2.0.32 py38h3237794_0 conda-forge templatecorr 0+untagged.21.g7095b4b.dirty dev_0 tk 8.6.13 h5083fa2_1 conda-forge tqdm 4.66.5 pyhd8ed1ab_0 conda-forge typing-extensions 4.12.2 hd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge unicodedata2 15.1.0 py38hb192615_0 conda-forge wheel 0.44.0 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.11 hb547adb_0 conda-forge xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge xz 5.2.6 h57fd34a_0 conda-forge zipp 3.19.2 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hfb2fe0b_6 conda-forge zstd 1.5.6 hb46c0d2_0 conda-forge

Python is 3.8.19 and I don't see any package compatibility issues, but output is invariably empty regardless of input.

hesther commented 1 month ago

@milicazmarkovic Ok so your template extraction does not work (and will not, with whatever input csv you use), you can see in the terminal output that the extraction only takes 3 seconds and yields 0 templates. There is probably an error when rdchiral is called that was erroneously caught by an exception. From your list of packages, it seems like you did not install rdchiral_cpp. This is necessary for the code. The regular rdchiral does not take arguments for the radius or special group. Did you also try this with rdchiral_cpp?

hesther commented 1 month ago

If you want to, you could replace https://github.com/hesther/templatecorr/blob/7095b4b8fecd6ea06f8c603b8e8641518b37d931/templatecorr/extract_templates.py#L41 (Line 41) in extract_templates.py with

except Exception as e:
    print(e)

which will probably tell you that rdchiral does not take the arguments you provided because you installed rdchiral instead of rdchiral_cpp

hesther commented 1 month ago

I will fix this in a PR soon so it gives a meaningful error, thank you very much for finding that bug!

milicazmarkovic commented 1 month ago

I actually attempted running it with rdchiral_cpp first, but got the empty data frame then switched to rdchiral and ended up with the same result, but this is super helpful! I just realized that this has to do with installation of this package -- I have weird issues with some conda packages due to M1 Mac chip... I think I know how to fix this now on my end and that has nothing to do with your code. :)

Thanks for a quick response and confirmation that the code works as intended!

milicazmarkovic commented 1 month ago

I created a small pull request with option to run script using docker, which resolved this issue for me. Hopefully it helps other people with similar problem :)

hesther commented 1 month ago

Thanks! I merged the change with the docker container, as well as added a more meaningful error message when using the wrong rdchiral version. Thanks again for finding this bug!