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facebookresearch / esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins
MIT License
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Adding console scripts #331

Closed andersoncarlosfs closed 1 year ago

andersoncarlosfs commented 1 year ago

199483762-870fb770-144d-42a3-af60-1342269fcea7

andersoncarlosfs commented 1 year ago

Hi @andersoncarlosfs thanks for submitting this PR! The goal of this PR is adding a CLI to the esm repo. This makes sense, I like it. A couple of things to point out:

* `scripts/extract.py → scripts/esmfold_extract.py` this is incorrect as the script allows extracting embeddings from ESM, not ESMFold.

* Instead let's rename `scripts/esmfold_inference.py` to `fold.py`, and make the CLI names `esm-extract` and `esm-fold` consistent with script names.

* Document CLI in README

Let us know if you can address those! And tagging @nikitos9000 to help support where needed and for a second look

Hello @tomsercu and @nikitos9000,

I updated the code and some notes in README following your recommendation. I would also inform you that I changed the environment.yml to use a requirements.txt, which can be part of the setup.py as requirement (listing the dependencies).

esm-extract esm-fold 
$ conda env create --name test --file=environment.yml
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Installing pip dependencies: ...working... Ran pip subprocess with arguments:
['/miniconda/envs/test/bin/python', '-m', 'pip', 'install', '-U', '-r', '/esm/condaenv.8db1ukvk.requirements.txt']
Pip subprocess output:
Collecting DLLogger@ git+https://github.com/NVIDIA/dllogger#egg=dllogger
  Cloning https://github.com/NVIDIA/dllogger to /private/var/folders/07/jg8wgn3j17b7nwbp0z668t_c0000gn/T/pip-install-o_eo3b9l/dllogger_a50df175eb114c91a68b82761b0bfafd
  Resolved https://github.com/NVIDIA/dllogger to commit 0540a43971f4a8a16693a9de9de73c1072020769
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pytest
  Using cached pytest-7.2.0-py3-none-any.whl (316 kB)
Collecting pandas
  Downloading pandas-1.3.5-cp37-cp37m-macosx_10_9_x86_64.whl (11.0 MB)
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Collecting biopython==1.79
  Using cached biopython-1.79-cp37-cp37m-macosx_10_9_x86_64.whl (2.3 MB)
Collecting deepspeed==0.5.9
  Using cached deepspeed-0.5.9-py3-none-any.whl
Collecting dm-tree==0.1.6
  Using cached dm_tree-0.1.6-cp37-cp37m-macosx_10_14_x86_64.whl (94 kB)
Collecting ml-collections==0.1.0
  Using cached ml_collections-0.1.0-py3-none-any.whl (88 kB)
Collecting numpy==1.21.2
  Using cached numpy-1.21.2-cp37-cp37m-macosx_10_9_x86_64.whl (16.9 MB)
Collecting PyYAML==5.4.1
  Using cached PyYAML-5.4.1-cp37-cp37m-macosx_10_9_x86_64.whl (249 kB)
Collecting requests==2.26.0
  Using cached requests-2.26.0-py2.py3-none-any.whl (62 kB)
Collecting scipy==1.7.1
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Collecting tqdm==4.62.2
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Collecting typing-extensions==3.10.0.2
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Collecting pytorch_lightning==1.5.10
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Collecting wandb==0.12.21
  Using cached wandb-0.12.21-py2.py3-none-any.whl (1.8 MB)
Requirement already satisfied: torch in /miniconda/envs/test/lib/python3.7/site-packages (from deepspeed==0.5.9->-r /esm/requirements.txt (line 4)) (1.12.1)
Requirement already satisfied: packaging in /miniconda/envs/test/lib/python3.7/site-packages (from deepspeed==0.5.9->-r /esm/requirements.txt (line 4)) (21.3)
Collecting hjson
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Collecting psutil
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Collecting ninja
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Collecting py-cpuinfo
  Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
Requirement already satisfied: six>=1.12.0 in /miniconda/envs/test/lib/python3.7/site-packages (from dm-tree==0.1.6->-r /esm/requirements.txt (line 5)) (1.16.0)
Collecting contextlib2
  Using cached contextlib2-21.6.0-py2.py3-none-any.whl (13 kB)
Collecting absl-py
  Using cached absl_py-1.3.0-py3-none-any.whl (124 kB)
Collecting certifi>=2017.4.17
  Using cached certifi-2022.9.24-py3-none-any.whl (161 kB)
Collecting idna<4,>=2.5
  Using cached idna-3.4-py3-none-any.whl (61 kB)
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting urllib3<1.27,>=1.21.1
  Using cached urllib3-1.26.12-py2.py3-none-any.whl (140 kB)
Collecting tensorboard>=2.2.0
  Using cached tensorboard-2.11.0-py3-none-any.whl (6.0 MB)
Collecting fsspec[http]!=2021.06.0,>=2021.05.0
  Using cached fsspec-2022.11.0-py3-none-any.whl (139 kB)
Collecting future>=0.17.1
  Using cached future-0.18.2-py3-none-any.whl
Collecting torchmetrics>=0.4.1
  Using cached torchmetrics-0.10.2-py3-none-any.whl (529 kB)
Requirement already satisfied: setuptools==59.5.0 in /miniconda/envs/test/lib/python3.7/site-packages (from pytorch_lightning==1.5.10->-r /esm/requirements.txt (line 13)) (59.5.0)
Collecting pyDeprecate==0.3.1
  Using cached pyDeprecate-0.3.1-py3-none-any.whl (10 kB)
Collecting setproctitle
  Using cached setproctitle-1.3.2-cp37-cp37m-macosx_10_9_x86_64.whl (11 kB)
Collecting promise<3,>=2.0
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Collecting docker-pycreds>=0.4.0
  Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting GitPython>=1.0.0
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Collecting pathtools
  Using cached pathtools-0.1.2-py3-none-any.whl
Requirement already satisfied: Click!=8.0.0,>=7.0 in /.local/lib/python3.7/site-packages (from wandb==0.12.21->-r /esm/requirements.txt (line 14)) (7.0)
Collecting protobuf<4.0dev,>=3.12.0
  Using cached protobuf-3.20.3-cp37-cp37m-macosx_10_9_x86_64.whl (981 kB)
Collecting sentry-sdk>=1.0.0
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Collecting shortuuid>=0.5.0
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Collecting attrs>=19.2.0
  Downloading attrs-22.1.0-py2.py3-none-any.whl (58 kB)
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Collecting importlib-metadata>=0.12
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Collecting tomli>=1.0.0
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Collecting pluggy<2.0,>=0.12
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Collecting iniconfig
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Collecting exceptiongroup>=1.0.0rc8
  Using cached exceptiongroup-1.0.4-py3-none-any.whl (14 kB)
Collecting pytz>=2017.3
  Downloading pytz-2022.6-py2.py3-none-any.whl (498 kB)
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Collecting python-dateutil>=2.7.3
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting aiohttp!=4.0.0a0,!=4.0.0a1
  Using cached aiohttp-3.8.3-cp37-cp37m-macosx_10_9_x86_64.whl (355 kB)
Collecting gitdb<5,>=4.0.1
  Using cached gitdb-4.0.9-py3-none-any.whl (63 kB)
Requirement already satisfied: zipp>=0.5 in /miniconda/envs/test/lib/python3.7/site-packages (from importlib-metadata>=0.12->pytest->-r /esm/requirements.txt (line 1)) (3.10.0)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /miniconda/envs/test/lib/python3.7/site-packages (from packaging->deepspeed==0.5.9->-r /esm/requirements.txt (line 4)) (3.0.9)
Collecting werkzeug>=1.0.1
  Using cached Werkzeug-2.2.2-py3-none-any.whl (232 kB)
Collecting google-auth-oauthlib<0.5,>=0.4.1
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Collecting google-auth<3,>=1.6.3
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Collecting tensorboard-data-server<0.7.0,>=0.6.0
  Using cached tensorboard_data_server-0.6.1-py3-none-macosx_10_9_x86_64.whl (3.5 MB)
Collecting tensorboard-plugin-wit>=1.6.0
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Collecting grpcio>=1.24.3
  Using cached grpcio-1.50.0-cp37-cp37m-macosx_10_10_x86_64.whl (4.5 MB)
Collecting markdown>=2.6.8
  Using cached Markdown-3.4.1-py3-none-any.whl (93 kB)
Requirement already satisfied: wheel>=0.26 in /miniconda/envs/test/lib/python3.7/site-packages (from tensorboard>=2.2.0->pytorch_lightning==1.5.10->-r /esm/requirements.txt (line 13)) (0.38.4)
Collecting aiosignal>=1.1.2
  Using cached aiosignal-1.3.1-py3-none-any.whl (7.6 kB)
Collecting frozenlist>=1.1.1
  Using cached frozenlist-1.3.3-cp37-cp37m-macosx_10_9_x86_64.whl (36 kB)
Collecting multidict<7.0,>=4.5
  Using cached multidict-6.0.2-cp37-cp37m-macosx_10_9_x86_64.whl (28 kB)
Collecting yarl<2.0,>=1.0
  Using cached yarl-1.8.1-cp37-cp37m-macosx_10_9_x86_64.whl (60 kB)
Collecting asynctest==0.13.0
  Using cached asynctest-0.13.0-py3-none-any.whl (26 kB)
Collecting async-timeout<5.0,>=4.0.0a3
  Using cached async_timeout-4.0.2-py3-none-any.whl (5.8 kB)
Collecting smmap<6,>=3.0.1
  Using cached smmap-5.0.0-py3-none-any.whl (24 kB)
Collecting cachetools<6.0,>=2.0.0
  Using cached cachetools-5.2.0-py3-none-any.whl (9.3 kB)
Collecting pyasn1-modules>=0.2.1
  Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
Collecting rsa<5,>=3.1.4
  Using cached rsa-4.9-py3-none-any.whl (34 kB)
Collecting requests-oauthlib>=0.7.0
  Using cached requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB)
Collecting MarkupSafe>=2.1.1
  Using cached MarkupSafe-2.1.1-cp37-cp37m-macosx_10_9_x86_64.whl (13 kB)
Collecting pyasn1<0.5.0,>=0.4.6
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting oauthlib>=3.0.0
  Using cached oauthlib-3.2.2-py3-none-any.whl (151 kB)
Building wheels for collected packages: DLLogger
  Building wheel for DLLogger (setup.py): started
  Building wheel for DLLogger (setup.py): finished with status 'done'
  Created wheel for DLLogger: filename=DLLogger-1.0.0-py3-none-any.whl size=5670 sha256=bd6190888b15c08ebb8257b3f0376b575ac4b79274390b9b01230b6c58e096fa
  Stored in directory: /private/var/folders/07/jg8wgn3j17b7nwbp0z668t_c0000gn/T/pip-ephem-wheel-cache-z2h_6dx7/wheels/f6/0b/e6/d9566189ca2a94642aa7060bbf15c51ec8c464053945b1358b
Successfully built DLLogger
Installing collected packages: typing-extensions, tensorboard-plugin-wit, pytz, pyasn1, py-cpuinfo, pathtools, ninja, iniconfig, hjson, urllib3, tqdm, tomli, tensorboard-data-server, smmap, shortuuid, setproctitle, rsa, PyYAML, python-dateutil, pyDeprecate, pyasn1-modules, psutil, protobuf, promise, oauthlib, numpy, multidict, MarkupSafe, importlib-metadata, idna, grpcio, future, fsspec, frozenlist, exceptiongroup, docker-pycreds, dm-tree, DLLogger, contextlib2, charset-normalizer, certifi, cachetools, attrs, asynctest, async-timeout, absl-py, yarl, werkzeug, torchmetrics, sentry-sdk, scipy, requests, pluggy, pandas, ml-collections, markdown, google-auth, gitdb, deepspeed, biopython, aiosignal, requests-oauthlib, pytest, GitPython, aiohttp, wandb, google-auth-oauthlib, tensorboard, pytorch_lightning
  Attempting uninstall: typing-extensions
    Found existing installation: typing_extensions 4.4.0
    Uninstalling typing_extensions-4.4.0:
      Successfully uninstalled typing_extensions-4.4.0
  Attempting uninstall: PyYAML
    Found existing installation: PyYAML 6.0
    Uninstalling PyYAML-6.0:
      Successfully uninstalled PyYAML-6.0
  Attempting uninstall: numpy
    Found existing installation: numpy 1.21.5
    Uninstalling numpy-1.21.5:
      Successfully uninstalled numpy-1.21.5
Successfully installed DLLogger-1.0.0 GitPython-3.1.29 MarkupSafe-2.1.1 PyYAML-5.4.1 absl-py-1.3.0 aiohttp-3.8.3 aiosignal-1.3.1 async-timeout-4.0.2 asynctest-0.13.0 attrs-22.1.0 biopython-1.79 cachetools-5.2.0 certifi-2022.9.24 charset-normalizer-2.0.12 contextlib2-21.6.0 deepspeed-0.5.9 dm-tree-0.1.6 docker-pycreds-0.4.0 exceptiongroup-1.0.4 frozenlist-1.3.3 fsspec-2022.11.0 future-0.18.2 gitdb-4.0.9 google-auth-2.14.1 google-auth-oauthlib-0.4.6 grpcio-1.50.0 hjson-3.1.0 idna-3.4 importlib-metadata-5.0.0 iniconfig-1.1.1 markdown-3.4.1 ml-collections-0.1.0 multidict-6.0.2 ninja-1.11.1 numpy-1.21.2 oauthlib-3.2.2 pandas-1.3.5 pathtools-0.1.2 pluggy-1.0.0 promise-2.3 protobuf-3.20.3 psutil-5.9.4 py-cpuinfo-9.0.0 pyDeprecate-0.3.1 pyasn1-0.4.8 pyasn1-modules-0.2.8 pytest-7.2.0 python-dateutil-2.8.2 pytorch_lightning-1.5.10 pytz-2022.6 requests-2.26.0 requests-oauthlib-1.3.1 rsa-4.9 scipy-1.7.1 sentry-sdk-1.11.0 setproctitle-1.3.2 shortuuid-1.0.11 smmap-5.0.0 tensorboard-2.11.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tomli-2.0.1 torchmetrics-0.10.2 tqdm-4.62.2 typing-extensions-3.10.0.2 urllib3-1.26.12 wandb-0.12.21 werkzeug-2.2.2 yarl-1.8.1

done
#
# To activate this environment, use
#
#     $ conda activate test
#
# To deactivate an active environment, use
#
#     $ conda deactivate
$ pip install ./
Processing /esm
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting DLLogger@ git+https://github.com/NVIDIA/dllogger#egg=dllogger
  Cloning https://github.com/NVIDIA/dllogger to /private/var/folders/07/jg8wgn3j17b7nwbp0z668t_c0000gn/T/pip-install-d57kfs4j/dllogger_2df039ccbdae49f3b01a7368a5aba1e6
  Resolved https://github.com/NVIDIA/dllogger to commit 0540a43971f4a8a16693a9de9de73c1072020769
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting numpy==1.21.2
  Using cached numpy-1.21.2-cp37-cp37m-macosx_10_9_x86_64.whl (16.9 MB)
Collecting dm-tree==0.1.6
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Collecting deepspeed==0.5.9
  Using cached deepspeed-0.5.9.tar.gz (510 kB)
  Preparing metadata (setup.py): started
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Collecting pytest
  Using cached pytest-7.2.0-py3-none-any.whl (316 kB)
Collecting pytorch-lightning==1.5.10
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Collecting wandb==0.12.21
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Collecting packaging
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Collecting six>=1.12.0
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Collecting future>=0.17.1
  Using cached future-0.18.2.tar.gz (829 kB)
  Preparing metadata (setup.py): started
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Collecting torchmetrics>=0.4.1
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Collecting setuptools==59.5.0
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Collecting tensorboard>=2.2.0
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tomsercu commented 1 year ago

@andersoncarlosfs I'd like to merge this PR! Can you undo the I changed the environment.yml to use a requirements.txt for now so we can rename and merge the CLI part?

andersoncarlosfs commented 1 year ago

@andersoncarlosfs I'd like to merge this PR! Can you undo the I changed the environment.yml to use a requirements.txt for now so we can rename and merge the CLI part?

I removed the pip options

tomsercu commented 1 year ago

After those last two small comments @andersoncarlosfs , and after @nikitos9000 you take a closer look and test it with pip install, we can merge this. After merging this we can roll this into a new minor pypi release.

andersoncarlosfs commented 1 year ago

After those last two small comments @andersoncarlosfs , and after @nikitos9000 you take a closer look and test it with pip install, we can merge this. After merging this we can roll this into a new minor pypi release.

Okidoki!

nikitos9000 commented 1 year ago

Thanks for the updates @andersoncarlosfs this looks really convenient! I had to create esm/scripts/__init__.py in order to make import esm.scripts work (as it's not a 'namespace' package) but otherwise I tested it and everything works good so merging it in.

andersoncarlosfs commented 1 year ago

Thanks for the updates @andersoncarlosfs this looks really convenient! I had to create esm/scripts/__init__.py in order to make import esm.scripts work (as it's not a 'namespace' package) but otherwise I tested it and everything works good so merging it in.

🙃