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Migrate to latest and fix code issues #5

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Migrate to latest and fix code issues #5

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patzm
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@patzm patzm commented May 8, 2024

overall fixes #4 when removing the version constraints

  • now works with latest and greatest. Removing those constraints should work:

    amn_release/environment_amn.yml

    Lines 6 to 8 in 10db2a6

    - python=3.7
    - tensorflow=2.6
    - numpy=1.20.3
    • fixed imports
    • added scikeras as an additional dependency to get the wrappers that were migrated there
    • most notably, now works with TensorFlow 2.16, numpy 1.26.4, scipy 1.13.0
  • fixed the signature of Loss_Vin: parameter isn't used, looks like debug code. Also removed passing it from other places.
  • fixed minor pythonic issue in Tutorial.ipynb (string comparison with == instead of is)
full `pip freeze` 
absl-py==2.1.0
annotated-types==0.6.0
anyio==4.3.0
appdirs==1.4.4
appnope==0.1.4
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
arrow==1.3.0
asttokens==2.4.1
astunparse==1.6.3
async-lru==2.0.4
attrs==23.2.0
Babel==2.15.0
beautifulsoup4==4.12.3
black==24.4.2
bleach==6.1.0
certifi==2024.2.2
cffi==1.16.0
charset-normalizer==3.3.2
click==8.1.7
cobra==0.29.0
comm==0.2.2
contourpy==1.2.1
cycler==0.12.1
debugpy==1.8.1
decorator==5.1.1
defusedxml==0.7.1
depinfo==2.2.0
diskcache==5.6.3
exceptiongroup==1.2.1
executing==2.0.1
fastjsonschema==2.19.1
flatbuffers==24.3.25
fonttools==4.51.0
fqdn==1.5.1
future==1.0.0
gast==0.5.4
google-pasta==0.2.0
grpcio==1.63.0
h11==0.14.0
h5py==3.11.0
httpcore==1.0.5
httpx==0.27.0
idna==3.7
importlib_resources==6.4.0
ipykernel==6.29.4
ipython==8.24.0
ipywidgets==8.1.2
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==2.4
jsonschema==4.22.0
jsonschema-specifications==2023.12.1
jupyter==1.0.0
jupyter-console==6.6.3
jupyter-events==0.10.0
jupyter-lsp==2.2.5
jupyter_client==8.6.1
jupyter_core==5.7.2
jupyter_server==2.14.0
jupyter_server_terminals==0.5.3
jupyterlab==4.1.8
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.1
jupyterlab_widgets==3.0.10
keras==3.3.3
kiwisolver==1.4.5
libclang==18.1.1
Markdown==3.6
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.8.4
matplotlib-inline==0.1.7
mdurl==0.1.2
mistune==3.0.2
ml-dtypes==0.3.2
mpmath==1.3.0
mypy-extensions==1.0.0
namex==0.0.8
nbclient==0.10.0
nbconvert==7.16.4
nbformat==5.10.4
nest-asyncio==1.6.0
notebook==7.1.3
notebook_shim==0.2.4
numpy==1.26.4
opt-einsum==3.3.0
optlang==1.8.1
optree==0.11.0
overrides==7.7.0
packaging==24.0
pandas==2.2.2
pandocfilters==1.5.1
parso==0.8.4
pathspec==0.12.1
pexpect==4.9.0
pillow==10.3.0
platformdirs==4.2.1
prometheus_client==0.20.0
prompt-toolkit==3.0.43
protobuf==4.25.3
psutil==5.9.8
ptyprocess==0.7.0
pure-eval==0.2.2
pycparser==2.22
pydantic==2.7.1
pydantic_core==2.18.2
pyDOE2==1.3.0
Pygments==2.18.0
pyparsing==3.1.2
pyreadline==2.1
python-dateutil==2.9.0.post0
python-json-logger==2.0.7
python-libsbml==5.20.2
pytz==2024.1
PyYAML==6.0.1
pyzmq==26.0.3
qtconsole==5.5.2
QtPy==2.4.1
referencing==0.35.1
requests==2.31.0
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rich==13.7.1
rpds-py==0.18.1
ruamel.yaml==0.18.6
ruamel.yaml.clib==0.2.8
scikeras==0.13.0
scikit-learn==1.4.2
scipy==1.13.0
seaborn==0.13.2
Send2Trash==1.8.3
silence_tensorflow==1.2.1
six==1.16.0
sniffio==1.3.1
soupsieve==2.5
stack-data==0.6.3
support_developer==1.0.5
swiglpk==5.0.10
sympy==1.12
tensorboard==2.16.2
tensorboard-data-server==0.7.2
tensorflow==2.16.1
tensorflow-io-gcs-filesystem==0.37.0
termcolor==2.4.0
terminado==0.18.1
threadpoolctl==3.5.0
tinycss2==1.3.0
tomli==2.0.1
tornado==6.4
traitlets==5.14.3
types-python-dateutil==2.9.0.20240316
typing_extensions==4.11.0
tzdata==2024.1
uri-template==1.3.0
urllib3==2.2.1
wcwidth==0.2.13
webcolors==1.13
webencodings==0.5.1
websocket-client==1.8.0
Werkzeug==3.0.3
widgetsnbextension==4.0.10
wrapt==1.16.0

@hites77
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hites77 commented May 11, 2024

@patzm Thanks
After installing latest version and updating to your changes, i still encounter few issues. While running the codes of the tutorial notebook, there were section of the codes that gives out the error, can you please check what might be the possible cause for that. I am attaching a text file with code section along with the error it gives.
errors.txt

patzm
patzm commented May 13, 2024
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ModuleNotFoundError: No module named 'keras.api._v2'

did you start with a fresh environment? Which Keras version are you running? Compare to the frozen versions I included in the fold comment of the PR.

Not sure about the other errors. But maybe we can clarify those points before.

Tutorial.ipynb
Comment on lines -614 to -616
"if model.model_type is 'MM_QP':\n",
"if model.model_type == 'MM_QP':\n",
" Ypred, Stats = MM_QP(model, verbose=True)\n",
"if model.model_type is 'MM_LP':\n",
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if model.model_type is 'MM_QP':
    Ypred, Stats = MM_QP(model, verbose=True)
if model.model_type is 'MM_LP':
    Ypred, Stats = MM_LP(model, verbose=True)

this warning should be gone after the changes I introduced here. Are you sure you had this branch pulled and were running Tutorial.ipynb?

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local install fail
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@patzm @hites77