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update readme and environment
This commit is contained in:
Hannes Signer
parent
d5d836bd98
commit
05bbb87562
22
README.md
22
README.md
@ -1,5 +1,23 @@
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# Training of AI Surrogate Models
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- run `git lfs pull` to get the data from the large file storage
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- create conda environment with `conda env create -f environment.yml`
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This notebook contains the current experiments for training AI models that attempt to predict the chemistry component of POET.
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The repository is structured as follows:
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```
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└── dataset
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└── Barite_50_Data_training.h5
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└── barite_50_4_corner.h5
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└── doc
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└── results
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└── src
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└── POET_Training.ipynb
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└── convert_data.jl
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└── optuna_runs.py
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└── preprocessing.py
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```
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The datasets in `datasets` must first be pulled via `git lfs pull` to get the data from the large file storage.
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A conda environment can then be set up with the packages contained in environment.yml with `conda env create -f environment.yml`
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The `preprocessing.py` file defines all the necessary steps for preprocessing as well as the keras models used. The actual training and additional explanations then take place in `POET_Training.ipynb`.
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248
environment.yaml
Normal file
248
environment.yaml
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name: training
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channels:
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- conda-forge
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- defaults
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dependencies:
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- _libgcc_mutex=0.1=main
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- _openmp_mutex=5.1=1_gnu
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- absl-py=2.1.0=py311h06a4308_0
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- alembic=1.13.3=py311h06a4308_0
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- anyio=4.6.2=py311h06a4308_0
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- argon2-cffi=21.3.0=pyhd3eb1b0_0
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- argon2-cffi-bindings=21.2.0=py311h5eee18b_1
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- asttokens=2.0.5=pyhd3eb1b0_0
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- astunparse=1.6.3=py_0
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- async-lru=2.0.4=py311h06a4308_0
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- attrs=24.3.0=py311h06a4308_0
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- babel=2.11.0=py311h06a4308_0
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- beautifulsoup4=4.12.3=py311h06a4308_0
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- blas=1.0=mkl
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- bleach=6.2.0=py311h06a4308_0
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- bottleneck=1.4.2=py311hf4808d0_0
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- brotli=1.0.9=h5eee18b_9
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- brotli-bin=1.0.9=h5eee18b_9
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- brotli-python=1.0.9=py311h6a678d5_9
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- bzip2=1.0.8=h5eee18b_6
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- c-ares=1.19.1=h5eee18b_0
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- ca-certificates=2024.12.31=h06a4308_0
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- certifi=2025.1.31=py311h06a4308_0
|
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- cffi=1.17.1=py311h1fdaa30_1
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- charset-normalizer=3.3.2=pyhd3eb1b0_0
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- colorlog=5.0.1=py311h06a4308_1
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- comm=0.2.1=py311h06a4308_0
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- contourpy=1.3.1=py311hdb19cb5_0
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- cycler=0.11.0=pyhd3eb1b0_0
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- cyrus-sasl=2.1.28=h52b45da_1
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- dbus=1.13.18=hb2f20db_0
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- debugpy=1.8.11=py311h6a678d5_0
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- decorator=5.1.1=pyhd3eb1b0_0
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- defusedxml=0.7.1=pyhd3eb1b0_0
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- executing=0.8.3=pyhd3eb1b0_0
|
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- expat=2.6.4=h6a678d5_0
|
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- flatbuffers=24.3.25=h6a678d5_0
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- fontconfig=2.14.1=h55d465d_3
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- fonttools=4.51.0=py311h5eee18b_0
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- freetype=2.12.1=h4a9f257_0
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- gast=0.5.3=pyhd3eb1b0_0
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- giflib=5.2.2=h5eee18b_0
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- glib=2.78.4=h6a678d5_0
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- glib-tools=2.78.4=h6a678d5_0
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- google-pasta=0.2.0=pyhd3eb1b0_0
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- greenlet=3.1.1=py311h6a678d5_0
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- grpcio=1.62.2=py311h6a678d5_0
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- gst-plugins-base=1.14.1=h6a678d5_1
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- gstreamer=1.14.1=h5eee18b_1
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- h11=0.14.0=py311h06a4308_0
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- h5py=3.12.1=py311hc0802c4_0
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- hdf5=1.12.1=h2b7332f_3
|
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- httpcore=1.0.2=py311h06a4308_0
|
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- httpx=0.27.0=py311h06a4308_0
|
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- icu=73.1=h6a678d5_0
|
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- idna=3.7=py311h06a4308_0
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- imbalanced-learn=0.12.3=py311h06a4308_1
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- intel-openmp=2023.1.0=hdb19cb5_46306
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- ipykernel=6.29.5=py311h06a4308_0
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- ipython=8.30.0=py311h06a4308_0
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- ipywidgets=8.1.5=py311h06a4308_0
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- jedi=0.19.2=py311h06a4308_0
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- jinja2=3.1.4=py311h06a4308_1
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- joblib=1.4.2=py311h06a4308_0
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- jpeg=9e=h5eee18b_3
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- json5=0.9.25=py311h06a4308_0
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- jsonschema=4.23.0=py311h06a4308_0
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- jsonschema-specifications=2023.7.1=py311h06a4308_0
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- jupyter=1.0.0=py311h06a4308_9
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- jupyter-lsp=2.2.0=py311h06a4308_0
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- jupyter_client=8.6.0=py311h06a4308_0
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- jupyter_console=6.6.3=py311h06a4308_0
|
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- jupyter_core=5.7.2=py311h06a4308_0
|
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- jupyter_events=0.10.0=py311h06a4308_0
|
||||
- jupyter_server=2.14.1=py311h06a4308_0
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- jupyter_server_terminals=0.4.4=py311h06a4308_1
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- jupyterlab=4.2.5=py311h06a4308_0
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- jupyterlab_pygments=0.1.2=py_0
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- jupyterlab_server=2.27.3=py311h06a4308_0
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- jupyterlab_widgets=3.0.13=py311h06a4308_0
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- keras=3.6.0=py311h06a4308_0
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- kiwisolver=1.4.4=py311h6a678d5_0
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- krb5=1.20.1=h143b758_1
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- lcms2=2.16=hb9589c4_0
|
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- ld_impl_linux-64=2.40=h12ee557_0
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- lerc=4.0.0=h6a678d5_0
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- libabseil=20240116.2=cxx17_h6a678d5_0
|
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- libbrotlicommon=1.0.9=h5eee18b_9
|
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- libbrotlidec=1.0.9=h5eee18b_9
|
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- libbrotlienc=1.0.9=h5eee18b_9
|
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- libclang=14.0.6=default_hc6dbbc7_2
|
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- libclang13=14.0.6=default_he11475f_2
|
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- libcups=2.4.2=h2d74bed_1
|
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- libcurl=8.11.1=hc9e6f67_0
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- libdeflate=1.22=h5eee18b_0
|
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- libedit=3.1.20230828=h5eee18b_0
|
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- libev=4.33=h7f8727e_1
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- libffi=3.4.4=h6a678d5_1
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- libgcc-ng=11.2.0=h1234567_1
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- libgfortran-ng=11.2.0=h00389a5_1
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- libgfortran5=11.2.0=h1234567_1
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- libglib=2.78.4=hdc74915_0
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- libgomp=11.2.0=h1234567_1
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- libgrpc=1.62.2=h2d74bed_0
|
||||
- libiconv=1.16=h5eee18b_3
|
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- libllvm14=14.0.6=hecde1de_4
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- libnghttp2=1.57.0=h2d74bed_0
|
||||
- libpng=1.6.39=h5eee18b_0
|
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- libpq=17.2=hdbd6064_0
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- libprotobuf=4.25.3=he621ea3_0
|
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- libsodium=1.0.18=h7b6447c_0
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- libssh2=1.11.1=h251f7ec_0
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- libstdcxx-ng=11.2.0=h1234567_1
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- libtiff=4.5.1=hffd6297_1
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- libuuid=1.41.5=h5eee18b_0
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- libwebp-base=1.3.2=h5eee18b_1
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- libxcb=1.15=h7f8727e_0
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- libxkbcommon=1.0.1=h097e994_2
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- libxml2=2.13.5=hfdd30dd_0
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- lz4-c=1.9.4=h6a678d5_1
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- mako=1.2.3=py311h06a4308_0
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- markdown=3.4.1=py311h06a4308_0
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- markdown-it-py=2.2.0=py311h06a4308_1
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- markupsafe=2.1.3=py311h5eee18b_1
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- matplotlib=3.10.0=py311h06a4308_0
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- matplotlib-base=3.10.0=py311hbfdbfaf_0
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- matplotlib-inline=0.1.6=py311h06a4308_0
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- mdurl=0.1.0=py311h06a4308_0
|
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- mistune=2.0.4=py311h06a4308_0
|
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- mkl=2023.1.0=h213fc3f_46344
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- mkl-service=2.4.0=py311h5eee18b_2
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- mkl_fft=1.3.11=py311h5eee18b_0
|
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- mkl_random=1.2.8=py311ha02d727_0
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- ml_dtypes=0.4.0=py311ha02d727_0
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- mysql=8.4.0=h29a9f33_1
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- namex=0.0.7=py311h06a4308_0
|
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- nbclient=0.8.0=py311h06a4308_0
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- nbconvert=7.16.4=py311h06a4308_0
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- nbformat=5.10.4=py311h06a4308_0
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- ncurses=6.4=h6a678d5_0
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- nest-asyncio=1.6.0=py311h06a4308_0
|
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- notebook=7.2.2=py311h06a4308_1
|
||||
- notebook-shim=0.2.3=py311h06a4308_0
|
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- numexpr=2.10.1=py311h3c60e43_0
|
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- numpy=1.26.4=py311h08b1b3b_0
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- numpy-base=1.26.4=py311hf175353_0
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- openjpeg=2.5.2=he7f1fd0_0
|
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- openldap=2.6.4=h42fbc30_0
|
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- openssl=3.0.15=h5eee18b_0
|
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- opt_einsum=3.3.0=pyhd3eb1b0_1
|
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- optree=0.12.1=py311hdb19cb5_0
|
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- optuna=4.2.1=pyhd8ed1ab_0
|
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- overrides=7.4.0=py311h06a4308_0
|
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- packaging=24.2=py311h06a4308_0
|
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- pandas=2.2.3=py311h6a678d5_0
|
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- pandocfilters=1.5.0=pyhd3eb1b0_0
|
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- parso=0.8.4=py311h06a4308_0
|
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- pcre2=10.42=hebb0a14_1
|
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- pexpect=4.8.0=pyhd3eb1b0_3
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- pillow=11.0.0=py311hcea889d_1
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- pip=24.2=py311h06a4308_0
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- platformdirs=3.10.0=py311h06a4308_0
|
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- ply=3.11=py311h06a4308_0
|
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- prometheus_client=0.21.0=py311h06a4308_0
|
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- prompt-toolkit=3.0.43=py311h06a4308_0
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- prompt_toolkit=3.0.43=hd3eb1b0_0
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- protobuf=4.25.3=py311he36ed58_1
|
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- psutil=5.9.0=py311h5eee18b_1
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- ptyprocess=0.7.0=pyhd3eb1b0_2
|
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- pure_eval=0.2.2=pyhd3eb1b0_0
|
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- pycparser=2.21=pyhd3eb1b0_0
|
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- pygments=2.15.1=py311h06a4308_1
|
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- pyparsing=3.2.0=py311h06a4308_0
|
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- pyqt=5.15.10=py311h6a678d5_0
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- pyqt5-sip=12.13.0=py311h5eee18b_0
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- pysocks=1.7.1=py311h06a4308_0
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- python=3.11.11=he870216_0
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- python-dateutil=2.9.0post0=py311h06a4308_2
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- python-fastjsonschema=2.20.0=py311h06a4308_0
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- python-flatbuffers=24.3.25=py311h06a4308_0
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- python-json-logger=3.2.1=py311h06a4308_0
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- python-tzdata=2023.3=pyhd3eb1b0_0
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- pytz=2024.1=py311h06a4308_0
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- pyyaml=6.0.2=py311h5eee18b_0
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- pyzmq=26.2.0=py311h6a678d5_0
|
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- qt-main=5.15.2=hb6262e9_11
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- qtconsole=5.6.0=py311h06a4308_0
|
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- qtpy=2.4.1=py311h06a4308_0
|
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- re2=2022.04.01=h295c915_0
|
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- readline=8.2=h5eee18b_0
|
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- referencing=0.30.2=py311h06a4308_0
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- requests=2.32.3=py311h06a4308_1
|
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- rfc3339-validator=0.1.4=py311h06a4308_0
|
||||
- rfc3986-validator=0.1.1=py311h06a4308_0
|
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- rich=13.9.4=py311h06a4308_0
|
||||
- rpds-py=0.22.3=py311h4aa5aa6_0
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- scipy=1.14.1=py311h08b1b3b_0
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- seaborn=0.13.2=py311h06a4308_1
|
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|
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|
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|
||||
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|
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
- tzdata=2024b=h04d1e81_0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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- zlib=1.2.13=h5eee18b_1
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- zstd=1.5.6=hc292b87_0
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- pip:
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- smogn==0.1.2
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prefix: /home/signer/bin/miniconda3/envs/training
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162
environment.yml
162
environment.yml
@ -1,162 +0,0 @@
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name: ai
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channels:
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- conda-forge
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- defaults
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||||
- https://repo.anaconda.com/pkgs/main
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- https://repo.anaconda.com/pkgs/r
|
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dependencies:
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- absl-py=2.1.0=py311hca03da5_0
|
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- appnope=0.1.4=pyhd8ed1ab_1
|
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- asttokens=3.0.0=pyhd8ed1ab_1
|
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- astunparse=1.6.3=py_0
|
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- blas=1.0=openblas
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- bottleneck=1.4.2=py311hb9f6ed7_0
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- brotli=1.0.9=h80987f9_9
|
||||
- brotli-bin=1.0.9=h80987f9_9
|
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- brotli-python=1.0.9=py311h313beb8_9
|
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- bzip2=1.0.8=h80987f9_6
|
||||
- c-ares=1.34.4=h5505292_0
|
||||
- ca-certificates=2024.12.31=hca03da5_0
|
||||
- cached-property=1.5.2=py_0
|
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- certifi=2024.12.14=py311hca03da5_0
|
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- charset-normalizer=3.3.2=pyhd3eb1b0_0
|
||||
- comm=0.2.2=pyhd8ed1ab_1
|
||||
- contourpy=1.3.1=py311h48ca7d4_0
|
||||
- cycler=0.11.0=pyhd3eb1b0_0
|
||||
- debugpy=1.8.11=py311h155a34a_0
|
||||
- decorator=5.1.1=pyhd8ed1ab_1
|
||||
- exceptiongroup=1.2.2=pyhd8ed1ab_1
|
||||
- executing=2.1.0=pyhd8ed1ab_1
|
||||
- flatbuffers=24.3.25=h313beb8_0
|
||||
- fonttools=4.51.0=py311h80987f9_0
|
||||
- freetype=2.12.1=hadb7bae_2
|
||||
- gast=0.5.3=pyhd3eb1b0_0
|
||||
- giflib=5.2.2=h80987f9_0
|
||||
- google-pasta=0.2.0=pyhd3eb1b0_0
|
||||
- grpcio=1.65.5=py311hc367efa_0
|
||||
- h5py=3.12.1=nompi_py311h5dd25b7_103
|
||||
- hdf5=1.14.4=nompi_ha698983_105
|
||||
- icu=75.1=hfee45f7_0
|
||||
- idna=3.7=py311hca03da5_0
|
||||
- importlib-metadata=8.5.0=pyha770c72_1
|
||||
- ipykernel=6.29.5=pyh57ce528_0
|
||||
- ipython=8.31.0=pyh707e725_0
|
||||
- jedi=0.19.2=pyhd8ed1ab_1
|
||||
- joblib=1.4.2=py311hca03da5_0
|
||||
- jupyter_client=8.6.3=pyhd8ed1ab_1
|
||||
- jupyter_core=5.7.2=pyh31011fe_1
|
||||
- keras=3.8.0=pyh753f3f9_0
|
||||
- kiwisolver=1.4.4=py311h313beb8_0
|
||||
- krb5=1.21.3=hf3e1bf2_0
|
||||
- lcms2=2.16=ha0e7c42_0
|
||||
- lerc=4.0.0=h313beb8_0
|
||||
- libabseil=20240722.0=cxx17_h07bc746_4
|
||||
- libaec=1.1.3=h313beb8_0
|
||||
- libbrotlicommon=1.0.9=h80987f9_9
|
||||
- libbrotlidec=1.0.9=h80987f9_9
|
||||
- libbrotlienc=1.0.9=h80987f9_9
|
||||
- libcurl=8.11.1=h73640d1_0
|
||||
- libcxx=19.1.6=ha82da77_1
|
||||
- libdeflate=1.23=hec38601_0
|
||||
- libedit=3.1.20230828=h80987f9_0
|
||||
- libev=4.33=h1a28f6b_1
|
||||
- libexpat=2.6.4=h286801f_0
|
||||
- libffi=3.4.4=hca03da5_1
|
||||
- libgfortran=5.0.0=13_2_0_hd922786_3
|
||||
- libgfortran5=13.2.0=hf226fd6_3
|
||||
- libgrpc=1.65.5=h3d9cf25_0
|
||||
- libjpeg-turbo=3.0.3=h80987f9_0
|
||||
- liblzma=5.6.3=h39f12f2_1
|
||||
- libnghttp2=1.64.0=h6d7220d_0
|
||||
- libopenblas=0.3.21=h269037a_0
|
||||
- libpng=1.6.45=h3783ad8_0
|
||||
- libprotobuf=5.27.5=h53f8970_2
|
||||
- libre2-11=2024.07.02=h07bc746_2
|
||||
- libsodium=1.0.20=h99b78c6_0
|
||||
- libsqlite=3.47.2=h3f77e49_0
|
||||
- libssh2=1.11.1=h9cc3647_0
|
||||
- libtiff=4.7.0=h551f018_3
|
||||
- libwebp-base=1.5.0=h2471fea_0
|
||||
- libxcb=1.17.0=hdb1d25a_0
|
||||
- libzlib=1.3.1=h8359307_2
|
||||
- llvm-openmp=14.0.6=hc6e5704_0
|
||||
- lz4-c=1.9.4=h313beb8_1
|
||||
- markdown=3.4.1=py311hca03da5_0
|
||||
- markdown-it-py=2.2.0=py311hca03da5_1
|
||||
- markupsafe=2.1.3=py311h80987f9_1
|
||||
- matplotlib=3.10.0=py311hca03da5_0
|
||||
- matplotlib-base=3.10.0=py311h7ef442a_0
|
||||
- matplotlib-inline=0.1.7=pyhd8ed1ab_1
|
||||
- mdurl=0.1.0=py311hca03da5_0
|
||||
- ml_dtypes=0.4.0=py311h7aedaa7_0
|
||||
- namex=0.0.7=py311hca03da5_0
|
||||
- ncurses=6.5=h5e97a16_2
|
||||
- nest-asyncio=1.6.0=pyhd8ed1ab_1
|
||||
- numexpr=2.10.1=py311h5d9532f_0
|
||||
- numpy=1.26.4=py311he598dae_0
|
||||
- numpy-base=1.26.4=py311hfbfe69c_0
|
||||
- openjpeg=2.5.3=h8a3d83b_0
|
||||
- openssl=3.4.0=h81ee809_1
|
||||
- opt_einsum=3.3.0=pyhd3eb1b0_1
|
||||
- optree=0.12.1=py311h48ca7d4_0
|
||||
- packaging=24.2=py311hca03da5_0
|
||||
- pandas=2.2.3=py311hcf29cfe_0
|
||||
- parso=0.8.4=pyhd8ed1ab_1
|
||||
- pexpect=4.9.0=pyhd8ed1ab_1
|
||||
- pickleshare=0.7.5=pyhd8ed1ab_1004
|
||||
- pillow=11.1.0=py311hb9ba9e9_0
|
||||
- pip=24.2=py311hca03da5_0
|
||||
- platformdirs=4.3.6=pyhd8ed1ab_1
|
||||
- prompt-toolkit=3.0.48=pyha770c72_1
|
||||
- protobuf=5.27.5=py311h3f08180_0
|
||||
- psutil=6.1.1=py311h917b07b_0
|
||||
- pthread-stubs=0.3=h1a28f6b_1
|
||||
- ptyprocess=0.7.0=pyhd8ed1ab_1
|
||||
- pure_eval=0.2.3=pyhd8ed1ab_1
|
||||
- pygments=2.15.1=py311hca03da5_1
|
||||
- pyparsing=3.2.0=py311hca03da5_0
|
||||
- pysocks=1.7.1=py311hca03da5_0
|
||||
- python=3.11.11=hc22306f_1_cpython
|
||||
- python-dateutil=2.9.0.post0=pyhff2d567_1
|
||||
- python-flatbuffers=24.3.25=py311hca03da5_0
|
||||
- python-tzdata=2023.3=pyhd3eb1b0_0
|
||||
- python_abi=3.11=5_cp311
|
||||
- pytz=2024.1=py311hca03da5_0
|
||||
- pyzmq=26.2.0=py311h730b646_3
|
||||
- re2=2024.07.02=h6589ca4_2
|
||||
- readline=8.2=h1a28f6b_0
|
||||
- requests=2.32.3=py311hca03da5_1
|
||||
- rich=13.9.4=py311hca03da5_0
|
||||
- scikit-learn=1.5.2=py311h313beb8_0
|
||||
- scipy=1.14.1=py311hac8794a_0
|
||||
- setuptools=75.1.0=py311hca03da5_0
|
||||
- six=1.16.0=pyhd3eb1b0_1
|
||||
- snappy=1.2.1=h313beb8_0
|
||||
- sqlite=3.47.2=hd7222ec_0
|
||||
- stack_data=0.6.3=pyhd8ed1ab_1
|
||||
- tensorboard=2.17.1=pyhd8ed1ab_0
|
||||
- tensorboard-data-server=0.7.0=py311ha6e5c4f_1
|
||||
- tensorflow=2.17.0=cpu_py311h9d3d1e9_3
|
||||
- tensorflow-base=2.17.0=cpu_py311ha270cad_3
|
||||
- tensorflow-estimator=2.17.0=cpu_py311h935fadc_3
|
||||
- termcolor=2.1.0=py311hca03da5_0
|
||||
- threadpoolctl=3.5.0=py311hb6e6a13_0
|
||||
- tk=8.6.13=h5083fa2_1
|
||||
- tornado=6.4.2=py311h917b07b_0
|
||||
- traitlets=5.14.3=pyhd8ed1ab_1
|
||||
- typing-extensions=4.12.2=py311hca03da5_0
|
||||
- typing_extensions=4.12.2=py311hca03da5_0
|
||||
- tzdata=2024b=h04d1e81_0
|
||||
- unicodedata2=15.1.0=py311h80987f9_1
|
||||
- urllib3=2.2.3=py311hca03da5_0
|
||||
- wcwidth=0.2.13=pyhd8ed1ab_1
|
||||
- werkzeug=3.0.6=py311hca03da5_0
|
||||
- wheel=0.44.0=py311hca03da5_0
|
||||
- wrapt=1.17.0=py311h80987f9_0
|
||||
- xorg-libxau=1.0.12=h5505292_0
|
||||
- xorg-libxdmcp=1.1.5=hd74edd7_0
|
||||
- xz=5.4.6=h80987f9_1
|
||||
- zeromq=4.3.5=hc1bb282_7
|
||||
- zipp=3.21.0=pyhd8ed1ab_1
|
||||
- zlib=1.3.1=h8359307_2
|
||||
- zstd=1.5.6=hb46c0d2_0
|
||||
Loading…
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Reference in New Issue
Block a user