Add requirements.txt to install instructions

[jason-fries]

The current instructions don't cover all the dependencies needed to run CLMBR, we're missing packages like torch, tqdm, etc. Let's add a requirements.txt (currently not include in the instructions at https://github.com/som-shahlab/ehr_ml/blob/master/doc_src/source/setup.rst) to handle full install process.

[woffett]

I added some extra instructions to doc_src/source/setup.rst, but the current instructions are not great. Ideally we could just run poetry install once and wouldn't have to separately install PyTorch and embedding_dot (poetry allows for adding GitHub repositories as dependencies), but there are issues with getting Poetry to play nicely with each:

• Poetry doesn't allow for different downloads depending on CUDA version. This makes it difficult to include PyTorch in pyproject.toml as a dependency in a platform-agnostic way (for example, we would have to hard-code a specific PyTorch version with a CUDA version as a dependency, which would make ehr_ml unusable if the machine doesn't have the exact CUDA version specified)
• Poetry installs GitHub dependencies by allocating a temporary sub-shell to run the repository's setup.py, but this sub-shell doesn't inherit packages from the environment from which the command was run (poetry add git+<github_link>). The setup.py in embedding_dot imports PyTorch at the top, which causes the sub-shell install to fail since it doesn't have PyTorch. I tried this both with a fresh environment and my existing conda environment (which already had embedding_dot installed!) to no avail. There might be some extra things I can do with the poetry virtualenv to fix this, but I'm still looking into this.

There are a few existing GitHub issues / StackOverflow pages that confirm these are open issues that others are also experiencing:

• Some people use another tool called Poe the Poet to install PyTorch and the CUDA toolkit when running poetry install, but this still hard-codes specific versions of CUDA (Support for build variants/profiles python-poetry/poetry#2613)
• Allowing for a pip install -e . equivalent for GitHub repos appears to be a relatively new feature, but it doesn't address the issue of the sub-shell not inheriting dependencies for setup.py itself from the parent environment (pip install -e . equivalent? python-poetry/poetry#34).

[EthanSteinberg]

This is now fixed.