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Gamora: Graph Learning based Symbolic Reasoning for Large-Scale Boolean Networks (DAC'23)
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Correcting meta-information for 'additional node files' keyword. #10

Closed drivanov closed 3 weeks ago

drivanov commented 1 month ago

In April-May 2024, a new version of pandas changed how None values in CSV files are handled. Previously, all None values were interpreted as text strings, but in the new version, they are treated as delimiters.

As a result, after reading the CSV file, the value of self.meta_info['additional node files'] checked in

if self.meta_info['additional node files'] == 'None':
    additional_node_files = []
else:
    additional_node_files = self.meta_info['additional node files'].split(',')

is set to nan instead of None as originally intended, leading to the following crash:

Traceback (most recent call last):
  File "/workspace/examples/Gamora/abc2pyg/gnn_multitask_v2.py", line 745, in <module>
    main()
  File "/workspace/examples/Gamora/abc2pyg/gnn_multitask_v2.py", line 604, in main
    dataset_r = PygNodePropPredDataset(name = design_name + '_root')
  File "/workspace/examples/Gamora/abc2pyg/dataset_prep/dataset_pyg.py", line 75, in __init__
    super(PygNodePropPredDataset, self).__init__(self.root, transform, pre_transform)
  File "/usr/local/lib/python3.10/dist-packages/torch_geometric/data/in_memory_dataset.py", line 81, in __init__
    super().__init__(root, transform, pre_transform, pre_filter, log,
  File "/usr/local/lib/python3.10/dist-packages/torch_geometric/data/dataset.py", line 115, in __init__
    self._process()
  File "/usr/local/lib/python3.10/dist-packages/torch_geometric/data/dataset.py", line 260, in _process
    self.process()
  File "/workspace/examples/Gamora/abc2pyg/dataset_prep/dataset_pyg.py", line 137, in process
    additional_node_files = self.meta_info['additional node files'].split(',')
AttributeError: 'float' object has no attribute 'split'
ycunxi commented 4 weeks ago

Thanks for contributing to the code. Would you please provide a detailed list of your package versions in your environment ? I will merge the exact setup (versions) into this pull request so they will be able to match the new updates. @drivanov

drivanov commented 3 weeks ago

@ycunxi : Here they are. packages.txt

ycunxi commented 3 weeks ago

Tested environment for this commit.

Package                    Version
-------------------------- -----------------------------
absl-py                    2.1.0
accelerate                 1.0.1
aiohappyeyeballs           2.4.2
aiohttp                    3.10.6
aiosignal                  1.3.1
alembic                    1.13.3
annotated-types            0.7.0
anyio                      4.6.2.post1
apex                       0.1
argon2-cffi                23.1.0
argon2-cffi-bindings       21.2.0
arrow                      1.3.0
asciitree                  0.3.3
asttokens                  2.4.1
astunparse                 1.6.3
async-lru                  2.0.4
attrs                      24.2.0
audioread                  3.0.1
babel                      2.16.0
beautifulsoup4             4.12.3
black                      24.10.0
bleach                     6.1.0
blinker                    1.7.0
blis                       0.7.11
cachetools                 5.5.0
calmsize                   0.1.3
catalogue                  2.0.10
catboost                   1.2.7
certifi                    2024.8.30
cffi                       1.17.1
charset-normalizer         3.4.0
click                      8.1.7
cloudpathlib               0.20.0
cloudpickle                3.0.0
cmake                      3.30.5
colorlog                   6.8.2
comm                       0.2.2
confection                 0.1.5
contourpy                  1.3.0
coverage                   7.6.4
cryptography               41.0.7
cuda-python                12.6.0
cudf                       24.8.0
cudf-polars                24.8.0
cugraph                    24.8.0
cugraph-dgl                24.8.0
cugraph-equivariant        24.8.0
cugraph-pyg                24.8.0
cugraph-service-client     24.8.0
cugraph-service-server     24.8.0
cuml                       24.8.0
cupy-cuda12x               13.2.0
cycler                     0.12.1
cymem                      2.0.8
Cython                     3.0.11
dask                       2024.7.1
dask-cuda                  24.8.0
dask-cudf                  24.8.0
dask-expr                  1.1.9
datasets                   3.0.2
dbus-python                1.3.2
debugpy                    1.8.7
decorator                  5.1.1
defusedxml                 0.7.1
dill                       0.3.8
distributed                2024.7.1
distributed-ucxx           0.39.0
distro                     1.9.0
distro-info                1.7+build1
dm-tree                    0.1.8
duckdb                     1.1.2
einops                     0.8.0
entrypoints                0.4
execnet                    2.1.1
executing                  2.1.0
expecttest                 0.2.1
faiss                      1.7.4
faiss                      1.7.4
fasteners                  0.19
fastjsonschema             2.20.0
fastrlock                  0.8.2
filelock                   3.16.1
flash_attn                 2.4.2
fonttools                  4.54.1
fqdn                       1.5.1
frozenlist                 1.4.1
fsspec                     2024.9.0
gast                       0.6.0
graphviz                   0.20.3
greenlet                   3.1.1
grpcio                     1.62.1
h11                        0.14.0
httpcore                   1.0.6
httplib2                   0.20.4
httpx                      0.27.2
huggingface-hub            0.26.2
hypothesis                 5.35.1
idna                       3.10
igraph                     0.11.8
igraph                     0.11.8
imageio                    2.36.0
importlib_metadata         8.5.0
iniconfig                  2.0.0
intel-openmp               2021.4.0
ipykernel                  6.29.5
ipython                    8.29.0
isoduration                20.11.0
isort                      5.13.2
jedi                       0.19.1
Jinja2                     3.1.4
joblib                     1.4.2
json5                      0.9.25
jsonpointer                3.0.0
jsonschema                 4.23.0
jsonschema-specifications  2024.10.1
jupyter_client             8.6.3
jupyter_core               5.7.2
jupyter-events             0.10.0
jupyter-lsp                2.2.5
jupyter_server             2.14.2
jupyter_server_terminals   0.5.3
jupyterlab                 4.2.5
jupyterlab_code_formatter  3.0.2
jupyterlab_pygments        0.3.0
jupyterlab_server          2.27.3
jupyterlab-tensorboard-pro 4.0.0
jupytext                   1.16.4
kiwisolver                 1.4.7
kvikio                     24.8.0
langcodes                  3.4.1
language_data              1.2.0
launchpadlib               1.11.0
lazr.restfulclient         0.14.6
lazr.uri                   1.0.6
lazy_loader                0.4
libkvikio                  24.8.0
librmm                     24.8.0
librosa                    0.10.1
lightgbm                   4.5.0
lightning-thunder          0.2.0.dev0
lightning-thunder          0.2.0.dev0
lightning-utilities        0.11.8
lightning-utilities        0.11.8
lintrunner                 0.12.5
littleutils                0.2.4
llvmlite                   0.42.0
locket                     1.0.0
looseversion               1.3.0
looseversion               1.3.0
Mako                       1.3.6
marisa-trie                1.2.1
Markdown                   3.7
markdown-it-py             3.0.0
MarkupSafe                 2.1.5
matplotlib                 3.9.2
matplotlib-inline          0.1.7
mdit-py-plugins            0.4.2
mdurl                      0.1.2
mistune                    3.0.2
mkl                        2021.1.1
mkl-devel                  2021.1.1
mkl-include                2021.1.1
mlxtend                    0.23.1
mock                       5.1.0
mpmath                     1.3.0
msgpack                    1.1.0
multidict                  6.1.0
multiprocess               0.70.16
murmurhash                 1.0.10
mypy-extensions            1.0.0
nbclient                   0.10.0
nbconvert                  7.16.4
nbformat                   5.10.4
nest-asyncio               1.6.0
networkx                   3.3
ninja                      1.11.1.1
notebook                   7.2.2
notebook_shim              0.2.4
numba                      0.59.1
numcodecs                  0.11.0
numpy                      1.26.4
nvfuser                    0.2.13a0+0d33366
nvfuser                    0.2.13a0+0d33366
nvidia-cudnn-frontend      1.7.0
nvidia-dali-cuda120        1.43.0
nvidia-modelopt            0.17.0
nvidia-nccl-cu12           2.23.4
nvidia-nvimgcodec-cu12     0.3.0.5
nvidia-pyindex             1.0.9
nvtx                       0.2.5
nx-cugraph                 24.8.0
oauthlib                   3.2.2
ogb                        1.3.6
onnx                       1.16.2
opencv                     4.10.0
opt_einsum                 3.4.0
opt_einsum                 3.4.0
optree                     0.13.0
optuna                     4.0.0
optuna-integration         4.0.0
orjson                     3.10.10
outdated                   0.2.2
overrides                  7.7.0
packaging                  23.2
pandas                     2.2.2
pandocfilters              1.5.1
parso                      0.8.4
partd                      1.4.2
pathspec                   0.12.1
pcst_fast                  1.0.10
pexpect                    4.9.0
pillow                     11.0.0
pip                        24.2
platformdirs               4.3.6
plotly                     5.24.1
pluggy                     1.5.0
ply                        3.11
polars                     1.8.2
polygraphy                 0.49.13
pooch                      1.8.2
preshed                    3.0.9
prometheus_client          0.21.0
prompt_toolkit             3.0.48
protobuf                   4.24.4
psutil                     6.0.0
ptyprocess                 0.7.0
PuLP                       2.9.0
pure_eval                  0.2.3
pyarrow                    16.1.0
pybind11                   2.13.6
pybind11_global            2.13.6
pycocotools                2.0+nv0.8.1
pycparser                  2.22
pydantic                   2.9.2
pydantic_core              2.23.4
pyg_lib                    0.4.0
pyg_lib                    0.4.0
Pygments                   2.18.0
PyGObject                  3.48.2
PyJWT                      2.7.0
pylibcugraph               24.8.0
pylibcugraphops            24.8.0
pylibraft                  24.8.0
pylibwholegraph            24.8.0
pynvjitlink                0.3.0
pynvml                     11.4.1
pyparsing                  3.2.0
pytest                     8.1.1
pytest-cov                 5.0.0
pytest-flakefinder         1.1.0
pytest-rerunfailures       14.0
pytest-shard               0.1.2
pytest-xdist               3.6.1
python-apt                 2.7.7+ubuntu3
python-dateutil            2.9.0.post0
python-hostlist            2.0.0
python-json-logger         2.0.7
pytorch_frame              0.2.3
pytorch-memlab             0.3.0
pytorch-triton             3.0.0+72734f086
pytz                       2023.4
PyYAML                     6.0.2
pyzmq                      26.2.0
raft-dask                  24.8.0
rapids-dask-dependency     24.8.0a0
rdflib                     7.1.1
rdkit                      2024.3.5
referencing                0.35.1
regex                      2024.9.11
relbench                   1.1.0
requests                   2.32.3
rfc3339-validator          0.1.4
rfc3986-validator          0.1.1
rich                       13.8.1
rmm                        24.8.0
rpds-py                    0.20.0
safetensors                0.4.5
scikit-image               0.24.0
scikit-learn               1.5.2
scipy                      1.14.1
Send2Trash                 1.8.3
sentence-transformers      3.2.1
sentencepiece              0.2.0
setuptools                 70.3.0
shellingham                1.5.4
six                        1.16.0
smart-open                 7.0.5
sniffio                    1.3.1
sortedcontainers           2.4.0
soundfile                  0.12.1
soupsieve                  2.6
soxr                       0.5.0.post1
spacy                      3.7.5
spacy-legacy               3.0.12
spacy-loggers              1.0.5
SQLAlchemy                 2.0.36
srsly                      2.4.8
stack-data                 0.6.3
swig                       4.1.0
sympy                      1.13.1
tabulate                   0.9.0
tbb                        2021.13.1
tblib                      3.0.0
tenacity                   9.0.0
tensorboard                2.16.2
tensorboard-data-server    0.7.2
tensordict                 0.6.0
tensorrt                   10.6.0
terminado                  0.18.1
texttable                  1.7.0
texttable                  1.7.0
thinc                      8.2.5
threadpoolctl              3.5.0
thriftpy2                  0.4.20
tifffile                   2024.9.20
tinycss2                   1.4.0
tokenizers                 0.20.1
toolz                      0.12.1
torch                      2.6.0a0+df5bbc09d1.nvinternal
torch-geometric            2.7.0
torch_tensorrt             2.5.0a0
torchdata                  0.9.0
torchmetrics               1.5.1
torchprofile               0.0.4
torchvision                0.20.0a0
tornado                    6.2
tqdm                       4.66.5
traitlets                  5.14.3
transformer_engine         1.12.0+80e3e0b
transformers               4.46.0
treelite                   4.3.0
typer                      0.12.5
types-dataclasses          0.6.6
types-python-dateutil      2.9.0.20241003
typing_extensions          4.12.2
tzdata                     2024.2
ucx-py                     0.39.0
ucxx                       0.39.0
ujson                      5.10.0
unattended-upgrades        0.1
uri-template               1.3.0
urllib3                    2.0.7
wadllib                    1.3.6
wasabi                     1.1.3
wcwidth                    0.2.13
weasel                     0.4.1
webcolors                  24.8.0
webencodings               0.5.1
websocket-client           1.8.0
Werkzeug                   3.0.6
wheel                      0.44.0
wrapt                      1.16.0
xdoctest                   1.0.2
xgboost                    2.1.1
xxhash                     3.5.0
yarl                       1.13.0
zarr                       2.18.3
zict                       3.0.0
zipp                       3.20.2