Update requirements.yml

hvgazula commented 3 years ago

@zkokaja Can you please update the environment file as well to reflect any new modules you may be using as part of the last 2 PRs? Thanks.

zkokaja commented 2 years ago

Let's all put our latest environment here so we can agree on one environment for all

miahong commented 2 years ago

@hvgazula it seems I cannot upload yml file here, so just emailed you the file I used laterly. let me know if you have more questions.

hvgazula commented 2 years ago

Here's mine hg-reqs.txt

@miahong You can make a text file and then 'drag-and-drop' here.

hvgazula commented 2 years ago

FYI, the command I used is as follows: conda env export > hg-reqs.txt

VeritasJoker commented 2 years ago

Mine is the exact same as the yaml file in 247-main.

On Wed, Apr 20, 2022 at 2:36 PM H Gazula @.***> wrote:

FYI, the command I used is as follows: conda env export > hg-reqs.txt

— Reply to this email directly, view it on GitHub https://github.com/hassonlab/247-main/issues/15#issuecomment-1104319831, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHZU6UQQD7ELE52PK3VL67TVGBFDBANCNFSM5AWAMXUQ . You are receiving this because you were assigned.Message ID: @.***>

hvgazula commented 2 years ago

Mine is the exact same as the yaml file in 247-main. Best, Ken … On Wed, Apr 20, 2022 at 2:36 PM H Gazula @.> wrote: FYI, the command I used is as follows: conda env export > hg-reqs.txt — Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHZU6UQQD7ELE52PK3VL67TVGBFDBANCNFSM5AWAMXUQ . You are receiving this because you were assigned.Message ID: @.>

Are you sure yours is that simple? Why not just run the command and put your file there so i makes it easy for comparison? :)

VeritasJoker commented 2 years ago

Ah my bad, I thought you meant the original yaml file. Here is my hg-reqs.txt hq-reqs.txt

zkokaja commented 2 years ago

Here's mine! zz-reqs.txt

hvgazula commented 2 years ago

@miahong Can you too please post your reks file here using the command above (in this chain)? I am about to diff and merge all our requirements.

miahong commented 2 years ago

name: 247-main channels:

pytorch
conda-forge
defaults dependencies:
_libgcc_mutex=0.1=conda_forge
_openmp_mutex=4.5=1_llvm
abseil-cpp=20210324.2=h9c3ff4c_0
absl-py=0.15.0=pyhd8ed1ab_0
aiohttp=3.8.1=py38h497a2fe_0
aiosignal=1.2.0=pyhd8ed1ab_0
alsa-lib=1.2.3=h516909a_0
anyio=3.5.0=py38h578d9bd_0
argon2-cffi=21.3.0=pyhd8ed1ab_0
argon2-cffi-bindings=21.2.0=py38h497a2fe_1
astroid=2.7.3=py38h578d9bd_0
asttokens=2.0.5=pyhd8ed1ab_0
astunparse=1.6.3=pyhd8ed1ab_0
async-timeout=4.0.2=pyhd8ed1ab_0
attrs=21.4.0=pyhd8ed1ab_0
autopep8=1.5.6=pyhd8ed1ab_0
babel=2.9.1=pyh44b312d_0
backcall=0.2.0=pyh9f0ad1d_0
backports=1.0=py_2
backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
beautifulsoup4=4.10.0=pyha770c72_0
blas=2.113=mkl
blas-devel=3.9.0=13_linux64_mkl
bleach=4.1.0=pyhd8ed1ab_0
blinker=1.4=py_1
brotli=1.0.9=h7f98852_6
brotli-bin=1.0.9=h7f98852_6
brotlipy=0.7.0=py38h497a2fe_1003
bzip2=1.0.8=h7f98852_4
c-ares=1.18.1=h7f98852_0
ca-certificates=2021.10.8=ha878542_0
cached-property=1.5.2=hd8ed1ab_1
cached_property=1.5.2=pyha770c72_1
cachetools=4.2.4=pyhd8ed1ab_0
certifi=2021.10.8=py38h578d9bd_2
cffi=1.15.0=py38h3931269_0
charset-normalizer=2.0.12=pyhd8ed1ab_0
click=8.1.1=py38h578d9bd_1
colorama=0.4.4=pyh9f0ad1d_0
cryptography=36.0.2=py38h2b5fc30_0
cudatoolkit=10.2.89=h8f6ccaa_10
cudnn=7.6.5.32=h01f27c4_1
cycler=0.11.0=pyhd8ed1ab_0
dataclasses=0.8=pyhc8e2a94_3
dbus=1.13.6=h5008d03_3
debugpy=1.5.1=py38h709712a_0
decorator=5.1.1=pyhd8ed1ab_0
defusedxml=0.7.1=pyhd8ed1ab_0
entrypoints=0.4=pyhd8ed1ab_0
executing=0.8.3=pyhd8ed1ab_0
expat=2.4.8=h27087fc_0
filelock=3.6.0=pyhd8ed1ab_0
flake8=3.8.4=py_0
flit-core=3.7.1=pyhd8ed1ab_0
font-ttf-dejavu-sans-mono=2.37=hab24e00_0
font-ttf-inconsolata=3.000=h77eed37_0
font-ttf-source-code-pro=2.038=h77eed37_0
font-ttf-ubuntu=0.83=hab24e00_0
fontconfig=2.13.96=h8e229c2_2
fonts-conda-ecosystem=1=0
fonts-conda-forge=1=0
fonttools=4.31.2=py38h0a891b7_0
freetype=2.10.4=h0708190_1
frozenlist=1.3.0=py38h497a2fe_0
future=0.18.2=py38h578d9bd_4
gast=0.4.0=pyh9f0ad1d_0
gensim=3.8.3=py38h950e882_2
gettext=0.19.8.1=h73d1719_1008
giflib=5.2.1=h36c2ea0_2
google-auth=1.35.0=pyh6c4a22f_0
google-auth-oauthlib=0.4.6=pyhd8ed1ab_0
google-pasta=0.2.0=pyh8c360ce_0
grpc-cpp=1.41.1=h75e9d12_2
grpcio=1.41.1=py38hdd6454d_1
gst-plugins-base=1.20.1=hcf0ee16_1
gstreamer=1.20.1=hd4edc92_1
h5py=3.1.0=nompi_py38hafa665b_100
hdf5=1.10.6=nompi_h6a2412b_1114
huggingface_hub=0.4.0=pyhd8ed1ab_0
icu=69.1=h9c3ff4c_0
idna=3.3=pyhd8ed1ab_0
importlib-metadata=4.11.3=py38h578d9bd_1
importlib_metadata=4.11.3=hd8ed1ab_1
importlib_resources=5.6.0=pyhd8ed1ab_0
ipykernel=6.11.0=py38h7f3c49e_0
ipython=8.2.0=py38h578d9bd_0
ipython_genutils=0.2.0=py_1
isort=5.10.1=pyhd8ed1ab_0
jbig=2.1=h7f98852_2003
jedi=0.17.2=py38h578d9bd_2
jinja2=3.1.1=pyhd8ed1ab_0
joblib=1.1.0=pyhd8ed1ab_0
jpeg=9e=h7f98852_0
json5=0.9.5=pyh9f0ad1d_0
jsonschema=4.4.0=pyhd8ed1ab_0
jupyter_client=7.2.1=pyhd8ed1ab_0
jupyter_core=4.9.2=py38h578d9bd_0
jupyter_server=1.16.0=pyhd8ed1ab_1
jupyterlab=3.3.2=pyhd8ed1ab_0
jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
jupyterlab_server=2.12.0=pyhd8ed1ab_0
keras=2.6.0=pyhd8ed1ab_1
keras-preprocessing=1.1.2=pyhd8ed1ab_0
keyutils=1.6.1=h166bdaf_0
kiwisolver=1.4.2=py38h43d8883_0
krb5=1.19.3=h3790be6_0
lazy-object-proxy=1.7.1=py38h497a2fe_0
lcms2=2.12=hddcbb42_0
ld_impl_linux-64=2.36.1=hea4e1c9_2
lerc=3.0=h9c3ff4c_0
libblas=3.9.0=13_linux64_mkl
libbrotlicommon=1.0.9=h7f98852_6
libbrotlidec=1.0.9=h7f98852_6
libbrotlienc=1.0.9=h7f98852_6
libcblas=3.9.0=13_linux64_mkl
libclang=13.0.1=default_hc23dcda_0
libcurl=7.82.0=h7bff187_0
libdeflate=1.10=h7f98852_0
libedit=3.1.20191231=he28a2e2_2
libev=4.33=h516909a_1
libevent=2.1.10=h9b69904_4
libffi=3.4.2=h7f98852_5
libgcc-ng=11.2.0=h1d223b6_14
libgfortran-ng=11.2.0=h69a702a_14
libgfortran5=11.2.0=h5c6108e_14
libglib=2.70.2=h174f98d_4
libiconv=1.16=h516909a_0
liblapack=3.9.0=13_linux64_mkl
liblapacke=3.9.0=13_linux64_mkl
libllvm11=11.1.0=hf817b99_3
libllvm13=13.0.1=hf817b99_2
libnghttp2=1.47.0=h727a467_0
libnsl=2.0.0=h7f98852_0
libogg=1.3.4=h7f98852_1
libopus=1.3.1=h7f98852_1
libpng=1.6.37=h21135ba_2
libpq=14.2=hd57d9b9_0
libprotobuf=3.18.1=h780b84a_0
libsodium=1.0.18=h36c2ea0_1
libssh2=1.10.0=ha56f1ee_2
libstdcxx-ng=11.2.0=he4da1e4_14
libtiff=4.3.0=h542a066_3
libuuid=2.32.1=h7f98852_1000
libuv=1.43.0=h7f98852_0
libvorbis=1.3.7=h9c3ff4c_0
libwebp=1.2.2=h3452ae3_0
libwebp-base=1.2.2=h7f98852_1
libxcb=1.13=h7f98852_1004
libxkbcommon=1.0.3=he3ba5ed_0
libxml2=2.9.12=h885dcf4_1
libzlib=1.2.11=h166bdaf_1014
llvm-openmp=13.0.1=he0ac6c6_1
llvmlite=0.38.0=py38h4630a5e_0
lz4-c=1.9.3=h9c3ff4c_1
markdown=3.3.6=pyhd8ed1ab_0
markupsafe=2.1.1=py38h0a891b7_1
matplotlib=3.5.1=py38h578d9bd_0
matplotlib-base=3.5.1=py38hf4fb855_0
matplotlib-inline=0.1.3=pyhd8ed1ab_0
mccabe=0.6.1=py_1
mistune=0.8.4=py38h497a2fe_1005
mkl=2022.0.1=h8d4b97c_803
mkl-devel=2022.0.1=ha770c72_804
mkl-include=2022.0.1=h8d4b97c_803
multidict=6.0.2=py38h497a2fe_0
munkres=1.1.4=pyh9f0ad1d_0
mysql-common=8.0.28=haf5c9bc_2
mysql-libs=8.0.28=h28c427c_2
nbclassic=0.3.7=pyhd8ed1ab_0
nbclient=0.5.13=pyhd8ed1ab_0
nbconvert=6.4.5=pyhd8ed1ab_1
nbconvert-core=6.4.5=pyhd8ed1ab_1
nbconvert-pandoc=6.4.5=pyhd8ed1ab_1
nbformat=5.2.0=pyhd8ed1ab_0
nccl=2.12.7.1=h1a5f58c_0
ncurses=6.3=h9c3ff4c_0
nest-asyncio=1.5.4=pyhd8ed1ab_0
nltk=3.6.7=pyhd8ed1ab_0
notebook=6.4.10=pyha770c72_0
notebook-shim=0.1.0=pyhd8ed1ab_0
nspr=4.32=h9c3ff4c_1
nss=3.76=h2350873_0
numba=0.55.1=py38h4bf6c61_0
numexpr=2.8.0=mkl_py38h008d376_1
numpy=1.19.5=py38h9894fe3_2
oauthlib=3.2.0=pyhd8ed1ab_0
openjpeg=2.4.0=hb52868f_1
openssl=1.1.1n=h166bdaf_0
opt_einsum=3.3.0=pyhd8ed1ab_1
packaging=21.3=pyhd8ed1ab_0
pandas=1.4.1=py38h43a58ef_0
pandoc=2.17.1.1=ha770c72_0
pandocfilters=1.5.0=pyhd8ed1ab_0
parso=0.7.1=pyh9f0ad1d_0
patsy=0.5.2=pyhd8ed1ab_0
pcre=8.45=h9c3ff4c_0
pexpect=4.8.0=pyh9f0ad1d_2
pickleshare=0.7.5=py_1003
pillow=9.0.1=py38h0ee0e06_2
pip=22.0.4=pyhd8ed1ab_0
platformdirs=2.5.1=pyhd8ed1ab_0
pluggy=1.0.0=py38h578d9bd_2
prometheus_client=0.13.1=pyhd8ed1ab_0
prompt-toolkit=3.0.27=pyha770c72_0
protobuf=3.18.1=py38h709712a_0
psutil=5.9.0=py38h497a2fe_0
pthread-stubs=0.4=h36c2ea0_1001
ptyprocess=0.7.0=pyhd3deb0d_0
pure_eval=0.2.2=pyhd8ed1ab_0
pyasn1=0.4.8=py_0
pyasn1-modules=0.2.7=py_0
pycodestyle=2.6.0=pyh9f0ad1d_0
pycparser=2.21=pyhd8ed1ab_0
pydocstyle=6.1.1=pyhd8ed1ab_0
pyflakes=2.2.0=pyh9f0ad1d_0
pygments=2.11.2=pyhd8ed1ab_0
pyjwt=2.3.0=pyhd8ed1ab_1
pylint=2.10.2=pyhd8ed1ab_0
pyopenssl=22.0.0=pyhd8ed1ab_0
pyparsing=3.0.7=pyhd8ed1ab_0
pyqt=5.12.3=py38h578d9bd_8
pyqt-impl=5.12.3=py38h0ffb2e6_8
pyqt5-sip=4.19.18=py38h709712a_8
pyqtchart=5.12=py38h7400c14_8
pyqtwebengine=5.12.1=py38h7400c14_8
pyrsistent=0.18.1=py38h497a2fe_0
pysocks=1.7.1=py38h578d9bd_4
python=3.8.13=h582c2e5_0_cpython
python-dateutil=2.8.2=pyhd8ed1ab_0
python-flatbuffers=1.12=pyhd8ed1ab_1
python-jsonrpc-server=0.4.0=pyh9f0ad1d_0
python-language-server=0.36.2=pyhd8ed1ab_0
python_abi=3.8=2_cp38
pytorch=1.11.0=py3.8_cuda10.2_cudnn7.6.5_0
pytorch-mutex=1.0=cuda
pytz=2022.1=pyhd8ed1ab_0
pyu2f=0.1.5=pyhd8ed1ab_0
pyyaml=6.0=py38h0a891b7_4
pyzmq=22.3.0=py38h2035c66_1
qt=5.12.9=h1304e3e_6
re2=2021.11.01=h9c3ff4c_0
readline=8.1=h46c0cb4_0
regex=2022.3.15=py38h0a891b7_0
requests=2.27.1=pyhd8ed1ab_0
requests-oauthlib=1.3.1=pyhd8ed1ab_0
rope=0.23.0=pyhd8ed1ab_0
rsa=4.8=pyhd8ed1ab_0
sacremoses=0.0.49=pyhd8ed1ab_0
scikit-learn=1.0.2=py38h1561384_0
scipy=1.8.0=py38h56a6a73_1
send2trash=1.8.0=pyhd8ed1ab_0
setuptools=61.2.0=py38h578d9bd_3
six=1.15.0=pyh9f0ad1d_0
smart_open=5.2.1=pyhd8ed1ab_0
snappy=1.1.8=he1b5a44_3
sniffio=1.2.0=py38h578d9bd_2
snowballstemmer=2.2.0=pyhd8ed1ab_0
soupsieve=2.3.1=pyhd8ed1ab_0
sqlite=3.37.1=h4ff8645_0
stack_data=0.2.0=pyhd8ed1ab_0
statsmodels=0.13.2=py38h6c62de6_0
tbb=2021.5.0=h4bd325d_0
tensorboard=2.6.0=pyhd8ed1ab_1
tensorboard-data-server=0.6.0=py38h3e25421_1
tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0
tensorflow=2.6.2=cuda102py38h4357c17_1
tensorflow-base=2.6.2=cuda102py38h62eeb6a_1
tensorflow-estimator=2.6.2=cuda102py38h4357c17_1
tensorflow-gpu=2.6.2=cuda102py38hf05f184_1
termcolor=1.1.0=py_2
terminado=0.13.3=py38h578d9bd_0
testpath=0.6.0=pyhd8ed1ab_0
threadpoolctl=3.1.0=pyh8a188c0_0
tk=8.6.12=h27826a3_0
tokenizers=0.10.3=py38hb63a372_1
toml=0.10.2=pyhd8ed1ab_0
tornado=6.1=py38h497a2fe_2
tqdm=4.63.1=pyhd8ed1ab_0
traitlets=5.1.1=pyhd8ed1ab_0
transformers=4.16.2=pyhd8ed1ab_0
typing-extensions=3.7.4.3=0
typing_extensions=3.7.4.3=py_0
ujson=5.1.0=py38hfa26641_1
unicodedata2=14.0.0=py38h497a2fe_0
urllib3=1.26.9=pyhd8ed1ab_0
wcwidth=0.2.5=pyh9f0ad1d_2
webencodings=0.5.1=py_1
websocket-client=1.3.2=pyhd8ed1ab_0
werkzeug=2.1.0=pyhd8ed1ab_0
wheel=0.37.1=pyhd8ed1ab_0
wrapt=1.12.1=py38h497a2fe_3
xorg-libxau=1.0.9=h7f98852_0
xorg-libxdmcp=1.1.3=h7f98852_0
xz=5.2.5=h516909a_1
yaml=0.2.5=h7f98852_2
yapf=0.32.0=pyhd8ed1ab_0
yarl=1.7.2=py38h497a2fe_1
zeromq=4.3.4=h9c3ff4c_1
zipp=3.7.0=pyhd8ed1ab_1
zlib=1.2.11=h166bdaf_1014
zstd=1.5.2=ha95c52a_0
pip:
- mat73==0.46 prefix: /home/mh6546/.conda/envs/247-main

miahong commented 2 years ago

hg-reqs.txt

zkokaja commented 2 years ago

@hvgazula some useful tools to list only what is relevant:

conda env export --from-history prints manually installed but not the version :/
full solution to output installed and versions in a script here

hvgazula commented 2 years ago

I like the first one. I guess that is what you did instead of manually :P.

zkokaja commented 2 years ago

@zkokaja @hvgazula @VeritasJoker @miahong run conda env export --from-history > ${USER}.txt from your 247-main conda environment and upload it here as a file.

miahong commented 2 years ago

mh6546.txt

zkokaja commented 2 years ago

zzada.txt

VeritasJoker commented 2 years ago

kw.txt sorry for the late file

hvgazula commented 2 years ago

Hello All, ultimately after some tests, I've come up with this requirements file for pickling and encoding. Please be aware that this environment does not include packages/modules supporting code that is not part of the final codebase.

https://github.com/hassonlab/247-encoding/blob/pkl_hierarchy/requirements.yml

zkokaja commented 2 years ago

Note for the above requirements file. I had to remove the torch lines with cuda versions and install manually using: pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu113

hassonlab / 247-main

Update requirements.yml #15