update env yml (#76)

Co-authored-by: Xiang Chen <[email protected]>

Author: xiangchenjhu

blue_env.yml

@@ -1,36 +1,43 @@
 name: blue_env
 channels:
-  - pytorch
   - anaconda
+  - pytorch
   - conda-forge
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=2_gnu
   - _r-mutex=1.0.1=anacondar_1
   - ase=3.22.1=pyhd8ed1ab_1
+  - asttokens=2.4.1=pyhd8ed1ab_0
   - autopep8=2.0.4=pyhd3eb1b0_0
   - binutils_impl_linux-64=2.38=h2a08ee3_1
   - binutils_linux-64=2.38.0=hc2dff05_0
   - blas=1.1=openblas
   - blinker=1.6.3=pyhd8ed1ab_0
+  - bottleneck=1.3.7=py311hf4808d0_0
   - brotli=1.1.0=hd590300_1
   - brotli-bin=1.1.0=hd590300_1
   - brotli-python=1.0.9=py311h6a678d5_7
   - bwidget=1.9.14=ha770c72_1
   - bzip2=1.0.8=h7b6447c_0
   - c-ares=1.19.1=h5eee18b_0
-  - ca-certificates=2023.12.12=h06a4308_0
+  - ca-certificates=2024.3.11=h06a4308_0
   - cairo=1.16.0=hb05425b_5
-  - certifi=2024.2.2=py311h06a4308_0
+  - certifi=2024.6.2=py311h06a4308_0
   - cffi=1.15.1=py311h5eee18b_3
-  - chardet=4.0.0=py311h06a4308_1003
   - click=8.1.7=unix_pyh707e725_0
+  - comm=0.2.2=pyhd8ed1ab_0
   - contourpy=1.1.1=py311h9547e67_1
   - cryptography=41.0.3=py311hdda0065_0
   - cudatoolkit=11.3.1=h2bc3f7f_2
   - curl=8.4.0=hdbd6064_0
   - cycler=0.12.1=pyhd8ed1ab_0
+  - debugpy=1.8.1=py311hb755f60_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - entrypoints=0.4=pyhd8ed1ab_0
+  - exceptiongroup=1.2.0=pyhd8ed1ab_2
+  - executing=2.0.1=pyhd8ed1ab_0
   - expat=2.5.0=h6a678d5_0
   - ffmpeg=4.3=hf484d3e_0
   - flask=3.0.0=pyhd8ed1ab_0
@@ -42,9 +49,12 @@ dependencies:
   - fsspec=2023.10.0=py311h06a4308_0
   - gcc_impl_linux-64=11.2.0=h1234567_1
   - gcc_linux-64=11.2.0=h5c386dc_0
+  - gettext=0.22.5=h59595ed_2
+  - gettext-tools=0.22.5=h59595ed_2
   - gfortran_impl_linux-64=11.2.0=h1234567_1
   - gfortran_linux-64=11.2.0=hc2dff05_0
   - giflib=5.2.1=h0b41bf4_3
+  - git=2.40.1=pl5340h36fbf9e_1
   - glib=2.69.1=he621ea3_2
   - gmp=6.2.1=h295c915_3
   - gmpy2=2.1.2=py311hc9b5ff0_0
@@ -57,16 +67,23 @@ dependencies:
   - icu=73.1=h6a678d5_0
   - idna=3.4=py311h06a4308_0
   - importlib-metadata=6.8.0=pyha770c72_0
+  - iniconfig=1.1.1=pyhd3eb1b0_0
+  - ipykernel=6.29.3=pyhd33586a_0
   - itsdangerous=2.1.2=pyhd8ed1ab_0
+  - jedi=0.19.1=pyhd8ed1ab_0
   - jinja2=3.1.2=py311h06a4308_0
   - jpeg=9e=h166bdaf_1
+  - jupyter_client=7.4.9=pyhd8ed1ab_0
+  - jupyter_core=5.7.2=py311h38be061_0
   - kernel-headers_linux-64=2.6.32=he073ed8_16
   - kiwisolver=1.4.5=py311h9547e67_1
   - krb5=1.20.1=h143b758_1
   - lame=3.100=h7b6447c_0
   - lcms2=2.15=hfd0df8a_0
   - ld_impl_linux-64=2.38=h1181459_1
   - lerc=3.0=h295c915_0
+  - libasprintf=0.22.5=h661eb56_2
+  - libasprintf-devel=0.22.5=h661eb56_2
   - libblas=3.9.0=16_linux64_openblas
   - libboost=1.82.0=h109eef0_2
   - libboost-python=1.82.0=py311h92ebd52_6
@@ -81,6 +98,8 @@ dependencies:
   - libffi=3.4.4=h6a678d5_0
   - libgcc-devel_linux-64=11.2.0=h1234567_1
   - libgcc-ng=13.2.0=h807b86a_2
+  - libgettextpo=0.22.5=h59595ed_2
+  - libgettextpo-devel=0.22.5=h59595ed_2
   - libgfortran=3.0.0=1
   - libgfortran-ng=11.4.0=h69a702a_2
   - libgfortran5=11.4.0=h2c0dd1a_2
@@ -93,6 +112,7 @@ dependencies:
   - libopenblas=0.3.21=h043d6bf_0
   - libpng=1.6.39=h5eee18b_0
   - libprotobuf=3.20.3=he621ea3_0
+  - libsodium=1.0.18=h36c2ea0_1
   - libssh2=1.10.0=hdbd6064_2
   - libstdcxx-devel_linux-64=11.2.0=h1234567_1
   - libstdcxx-ng=13.2.0=h7e041cc_2
@@ -103,52 +123,66 @@ dependencies:
   - libwebp=1.3.2=h11a3e52_0
   - libwebp-base=1.3.2=h5eee18b_0
   - libxcb=1.15=h7f8727e_0
+  - libxcrypt=4.4.36=hd590300_1
   - libxml2=2.10.4=hf1b16e4_1
   - libzlib=1.2.13=hd590300_5
   - lz4-c=1.9.4=h6a678d5_0
   - make=4.3=hd18ef5c_1
   - markupsafe=2.1.3=py311h5eee18b_0
   - matplotlib-base=3.8.0=py311h54ef318_1
+  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
   - mctc-lib=0.3.1=hc3ea6d6_0
   - mpc=1.1.0=h10f8cd9_1
   - mpfr=4.0.2=hb69a4c5_1
   - mpi=1.0=openmpi
   - mpmath=1.3.0=py311h06a4308_0
   - munkres=1.1.4=pyh9f0ad1d_0
   - ncurses=6.4=h6a678d5_0
+  - nest-asyncio=1.6.0=pyhd8ed1ab_0
   - nettle=3.7.3=hbbd107a_1
   - ninja=1.10.2=h06a4308_5
   - ninja-base=1.10.2=hd09550d_5
+  - numexpr=2.8.7=py311h812550d_0
   - numpy-base=1.25.0=py311hbfb1bba_0
   - openblas=0.3.3=ha44fe06_1
   - openh264=2.1.1=h4ff587b_0
   - openjpeg=2.4.0=h3ad879b_0
   - openmpi=4.1.5=h414af15_101
   - openmpi-mpicc=4.1.5=h0b41bf4_101
-  - openssl=3.0.13=h7f8727e_0
+  - openssl=3.0.14=h5eee18b_0
   - packaging=23.2=pyhd8ed1ab_0
-  - pandas=2.1.1=py311h320fe9a_1
+  - pandas=2.1.4=py311ha02d727_0
   - pandoc=2.19.2=ha770c72_0
   - pango=1.50.7=h05da053_0
   - pcre=8.45=h9c3ff4c_0
   - pcre2=10.42=hebb0a14_0
+  - perl=5.32.1=7_hd590300_perl5
+  - pexpect=4.9.0=pyhd8ed1ab_0
+  - pickleshare=0.7.5=py_1003
   - pip=23.3=py311h06a4308_0
   - pixman=0.40.0=h7f8727e_1
+  - platformdirs=4.2.0=pyhd8ed1ab_0
+  - prometheus_client=0.14.1=py311h06a4308_0
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pure_eval=0.2.2=pyhd8ed1ab_0
   - pybind11=2.11.1=py311h9547e67_2
   - pybind11-global=2.11.1=py311h9547e67_2
   - pycairo=1.25.0=py311h8feb60e_1
   - pycodestyle=2.11.1=py311h06a4308_0
   - pycparser=2.21=pyhd3eb1b0_0
+  - pygments=2.17.2=pyhd8ed1ab_0
   - pyopenssl=23.2.0=py311h06a4308_0
   - pyparsing=3.1.1=pyhd8ed1ab_0
   - pysocks=1.7.1=py311h06a4308_0
+  - pytest=7.4.0=py311h06a4308_0
   - python=3.11.5=h955ad1f_0
   - python-dateutil=2.8.2=pyhd8ed1ab_0
   - python-tzdata=2023.3=pyhd8ed1ab_0
   - python_abi=3.11=2_cp311
   - pytorch=2.2.0=cpu_py311h53e38e9_0
   - pytorch-mutex=1.0=cpu
   - pytz=2023.3.post1=pyhd8ed1ab_0
+  - pyzmq=25.1.2=py311h34ded2d_0
   - r-askpass=1.2.0=r43h76d94ec_0
   - r-assertthat=0.2.1=r43hc72bb7e_4
   - r-backports=1.4.1=r43h76d94ec_0
@@ -263,38 +297,89 @@ dependencies:
   - reportlab=4.0.6=py311h459d7ec_0
   - requests=2.31.0=py311h06a4308_0
   - rlpycairo=0.2.0=pyhd8ed1ab_0
+  - ruff=0.3.5=py311hab49468_0
   - setuptools=68.0.0=py311h06a4308_0
   - six=1.16.0=pyh6c4a22f_0
   - sqlalchemy=2.0.22=py311h459d7ec_0
   - sqlite=3.41.2=h5eee18b_0
+  - stack_data=0.6.2=pyhd8ed1ab_0
   - sympy=1.12=py311h06a4308_0
   - sysroot_linux-64=2.12=he073ed8_16
   - tk=8.6.12=h1ccaba5_0
   - tktable=2.10=hb7b940f_3
   - torchaudio=2.2.0=py311_cpu
   - torchvision=0.17.0=py311_cpu
+  - tornado=6.4=py311h459d7ec_0
+  - traitlets=5.14.2=pyhd8ed1ab_0
   - typing-extensions=4.8.0=hd8ed1ab_0
   - typing_extensions=4.8.0=pyha770c72_0
   - tzdata=2023c=h04d1e81_0
+  - wcwidth=0.2.13=pyhd8ed1ab_0
   - werkzeug=3.0.1=pyhd8ed1ab_0
   - wheel=0.41.2=py311h06a4308_0
   - xz=5.4.2=h5eee18b_0
+  - zeromq=4.3.5=h59595ed_1
   - zipp=3.17.0=pyhd8ed1ab_0
   - zlib=1.2.13=hd590300_5
   - zstd=1.5.5=hc292b87_0
   - pip:
+      - aiohttp==3.9.5
+      - aiohttp-cors==0.7.0
       - aiosignal==1.3.1
+      - annotated-types==0.6.0
+      - anyio==4.3.0
+      - astroid==3.2.2
       - attrs==23.2.0
+      - backcall==0.2.0
+      - beautifulsoup4==4.12.3
       - black==24.2.0
+      - bleach==6.1.0
+      - blessed==1.20.0
+      - bs4==0.0.1
+      - cachetools==5.3.3
+      - chardet==5.2.0
       - charset-normalizer==3.3.2
-      - dplutils==0.3.1
-      - filelock==3.12.4
+      - colorama==0.4.6
+      - colorful==0.5.6
+      - coverage==7.5.3
+      - defusedxml==0.7.1
+      - dill==0.3.8
+      - distlib==0.3.8
+      - docopt==0.6.2
+      - docx2txt==0.8
+      - dplutils==0.6.0
+      - dputils==0.3.0
+      - fastjsonschema==2.19.1
+      - filelock==3.13.3
+      - fpdf2==2.7.8
       - frozenlist==1.4.1
+      - google-api-core==2.19.0
+      - google-auth==2.29.0
+      - googleapis-common-protos==1.63.0
+      - gpustat==1.1.1
+      - grpcio==1.63.0
+      - h11==0.14.0
+      - h2==4.1.0
+      - hpack==4.0.0
+      - httpcore==1.0.5
+      - httpx==0.25.2
+      - hyperframe==6.0.1
+      - ipython==8.12.3
+      - isort==5.13.2
       - joblib==1.3.2
       - jsonschema==4.21.1
       - jsonschema-specifications==2023.12.1
+      - jupyter-client==8.6.1
+      - jupyterlab-pygments==0.3.0
+      - lxml==5.2.1
+      - mccabe==0.7.0
+      - mistune==3.0.2
       - msgpack==1.0.8
+      - multidict==6.0.5
       - mypy-extensions==1.0.0
+      - nbclient==0.10.0
+      - nbconvert==7.16.3
+      - nbformat==5.10.3
       - networkx==3.2
       - numpy==1.26.1
       - nvidia-cublas-cu12==12.1.3.1
@@ -306,26 +391,57 @@ dependencies:
       - nvidia-curand-cu12==10.3.2.106
       - nvidia-cusolver-cu12==11.4.5.107
       - nvidia-cusparse-cu12==12.1.0.106
+      - nvidia-ml-py==12.550.52
       - nvidia-nccl-cu12==2.18.1
       - nvidia-nvjitlink-cu12==12.3.52
       - nvidia-nvtx-cu12==12.1.105
+      - opencensus==0.11.4
+      - opencensus-context==0.1.3
+      - pandocfilters==1.5.1
+      - parso==0.8.3
       - pathspec==0.12.1
+      - pdfminer-six==20220524
       - pillow==10.1.0
-      - platformdirs==4.2.0
+      - pipreqs==0.5.0
+      - pluggy==1.4.0
+      - prompt-toolkit==3.0.43
+      - proto-plus==1.23.0
       - protobuf==4.25.3
       - psutil==5.9.6
+      - py-spy==0.3.14
       - pyarrow==15.0.0
+      - pyasn1==0.6.0
+      - pyasn1-modules==0.4.0
+      - pydantic==2.7.1
+      - pydantic-core==2.18.2
+      - pylint==3.2.5
+      - pyproject-api==1.6.1
+      - pytest-cov==5.0.0
+      - python-docx==0.8.11
       - pyyaml==6.0.1
-      - ray==2.9.3
+      - ray==2.34.0
       - rdkit-pypi==2022.9.5
       - referencing==0.33.0
       - rpds-py==0.18.0
+      - rsa==4.9
       - scikit-learn==1.3.2
       - scipy==1.11.3
+      - smart-open==7.0.4
+      - sniffio==1.3.1
+      - soupsieve==2.5
+      - stack-data==0.6.3
       - threadpoolctl==3.2.0
+      - tinycss2==1.2.1
+      - tomlkit==0.13.0
       - torch-geometric==2.4.0
+      - tox==4.14.2
       - tqdm==4.66.1
       - triton==2.1.0
       - urllib3==2.0.7
+      - virtualenv==20.25.1
+      - webencodings==0.5.1
+      - wrapt==1.16.0
       - xtb==22.1
+      - yarg==0.1.9
+      - yarl==1.9.4
 prefix: /home/xchen286/miniconda3/envs/blue_env