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Managing Python environments with mamba and pip-tools

Some time ago I published a post about managing Conda environments. My workflow has changed quite a bit since then, and I’ve moved to venv + pip-tools, but I’ll leave that for another post. Today I want to talk about new experiments I’m making with mamba + pip-tools. If you don’t know about mamba, it’s kind of a miniconda replacement. It just works a lot better, and it’s VERY fast.

Triggered by this tweet, I feel like writing about this new experimental workflow. We will see how it works, some problems that may come up and workarounds to fix them.

Creating a “dev” conda environment

Thanks to the new features in JupyterLab 3.0, installing Jupyter extensions is a lot easier. I create my “dev” environment with this script:

#!/usr/bin/env bash

set -e
set -x

if [ $# -eq 0 ]; then
    echo "Usage: conda_base.sh [VERSION]
Example: conda_base.sh 3.7"
    exit 1
fi

NAME="dev"
VERSION=$1

echo "Creating environment with name: $NAME"
echo "Using Python version: $VERSION"


conda create --name "$NAME" python="$VERSION"
mamba install -y --name "$NAME" -c conda-forge ipython jupyterlab=3 nb_conda_kernels black isort
mamba install -y --name "$NAME" -c conda-forge jupyterlab_code_formatter ipywidgets

One of the key libraries is nb_conda_kernels, it makes this conda environment the ability to “discover” ipython kernels in other conda environments.

TL;DR / managing environments

We create the environment (called “tester”) for our new project and install what we need:

mamba create --name "tester" python=3.7

mamba install -y --name "tester" -c conda-forge numpy pandas ipykernel pip-tools fastapi

NOTE: pip-tools has to be installed in the same environment from which you are going to use it

Now we write our file for pip-tools requirements.in.

# requirements.in
numpy
pandas
fastapi

And compile it with:

# activate the conda environment (conda activate tester)
pip-compile -v --output-file requirements.txt requirements.in

Finally, write a Dockerfile, build and run it:

FROM python:3.7-slim-buster

COPY requirements.txt .

RUN pip install -r requirements.txt
# `csq` is just a random name I gave the image

docker image build -t csq . && docker run --rm csq

Problems with pip extras

Some Python packages can include “extras”. For example, you can run pip install fastapi[all] to install FastAPI + many other dependencies. However, maybe you don’t want to install everything.

The extras syntax pip install somepackage[extras] is not available in conda.

Without this kind of control, some dependencies may sneak in your projects. One option is installing them with pip, but then you lose some advantages of using conda.

Problems with PyTorch

We now need to add PyTorch to our project, and we run:

mamba install -y --name "tester" pytorch torchvision -c pytorch

Update your requirements.in file:

# requirements.in
# file in macOS
numpy
pandas
fastapi
torch
torchvision

Finally, we run the pip-compile command again to generate the requirements.txt file with pinned versions,

Let’s build the Dockerfile you will some something like:

Downloading torch-1.7.1-cp39-cp39-manylinux1_x86_64.whl (776.8 MB)

Wait! 776.8 MB?! Exactly, now we are trying to install PyTorch with CUDA. If you check the PyTorch site, you’ll see that the installation on Linux vs. Mac needs different versions.

Ok, the PyTorch site tells us to specify the version with +cpu to install it on Linux. We can try that:

# requirements.in
# file in macOS
torch==1.7.1+cpu
torchvision==0.8.2+cpu

We run again our pip-compile command and… surprise!

pip._internal.exceptions.DistributionNotFound: No matching distribution found for torchvision==0.8.2+cpu (from -r requirements.in (line 2))

The problem is that this version is for Linux, not macOS. There are some GitHub issues open about this bug, and so far, I have not found how to solve it.

Maybe we can run the installation of PyTorch as a separate step in our Dockerfile. Let’s add this line:

RUN pip install torch==1.7.1+cpu

Build it, and… another error!

# error building Dockerfile
ERROR: Could not find a version that satisfies the requirement torch==1.7.1+cpu
ERROR: No matching distribution found for torch==1.7.1+cpu

It can’t find the appropriate version. The solution for this is using the --find-links flag.

Thanks to this Stack Overflow answer I learned how to specify that inside a requirements.txt/.in file:

# requirements.in
# file in macOS
--find-links https://download.pytorch.org/whl/torch_stable.html
torch
torchvision

However, that won’t give us the versions with +cpu. We can try:

# requirements.in
# file in mac=S
--find-links https://download.pytorch.org/whl/torch_stable.html
torch==1.7.1+cpu
torchvision==0.8.2+cpu

But it will try to find that packages for macOS, which don’t exist.

We have “quick and dirty” a workaround for the problem, adding this to our Dockerfile:

RUN pip install --find-links https://download.pytorch.org/whl/torch_stable.html torch==1.7.1+cpu torchvision==0.8.2+cpu

But now our dependencies management is becoming problematic. We need to find a different solution.

We could consider exporting the whole conda environment with conda env export --no-build --name tester > env.yml and using conda inside our docker. For that, we must install the cpuonly package. With that package installed, torch will work in macOS and in Linux, it will install the CPU versions. Regardless, porting conda environments across operating systems has a ton of problems. We could use --from-history but if we did not install dependencies with a specific version, it will create an environment file without versions.

There are libraries to help, but I don’t want to install something else. We can use some conda functionalities to write a short python script that will clean our environment file. We will need to install pyyaml to read the exported conda environment. We can export it as json but then we would need to write it as yaml (conda can’t create and environment from a json file).

# conda_cleaner.py
from pathlib import Path
import re
import yaml
import subprocess

# load our original requirements.in files
# split and clean it
r = [s.strip() for s in Path("requirements.in").read_text().split("\n") if s != ""]
# ['numpy', 'pandas', 'fastapi', 'torch', 'torchvision']

pat = re.compile("|".join(r))
# re.compile(r'numpy|pandas|fastapi|torch|torchvision', re.UNICODE)

env_dict = yaml.full_load(
    subprocess.run(
        ["conda", "env", "export", "--no-build", "--name", "tester"],
        capture_output=True,
    ).stdout
)

clean_deps = [dep for dep in env_dict["dependencies"] if pat.search(dep)]

print(f"Keeping dependencies:\n{clean_deps}")
env_dict["dependencies"] = clean_deps
print("Removing prefix")
del env_dict["prefix"]

Path("docker_env.yaml").write_text(yaml.dump(env_dict))

Run python3 conda_cleaner.py. Our environment definition now looks like:

channels:
- pytorch
- conda-forge
- defaults
dependencies:
- cpuonly=1.0
- fastapi=0.63.0
- numpy=1.19.5
- pandas=1.2.0
- pytorch=1.7.1
- torchvision=0.8.2
name: tester

Finally, we can use micromamba to create a docker image:

FROM bitnami/minideb:buster

# Use bash in RUN commands and make sure bashrc is sourced when executing commands with /bin/bash -c
# Needed to have the micromamba activate command configured etc.
# from: https://gist.github.com/wolfv/fe1ea521979973ab1d016d95a589dcde#gistcomment-3525280
# Install basic commands and mamba

RUN install_packages wget tar bzip2 ca-certificates bash
SHELL ["/bin/bash", "-c"]
ENV BASH_ENV ~/.bashrc

RUN wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba --strip-components=1 && \
        ./micromamba shell init -s bash -p ~/micromamba

COPY ./docker_env.yaml .
RUN micromamba create -f ./docker_env.yaml -y

ENTRYPOINT micromamba activate tester && python -c "import torch; print('success!')"

But… oh no!

# Installing:
# ...
 cudatoolkit         11.0.221  h6bb024c_0                       pkgs/main/linux-64       623 MB
 # ...

  It’s installing CUDA again.   Ok. Little detour. I cancelled the building of that Dockerfile. Here I started going crazy, I tried tons of different ways of building my Dockerfile and my docker_env.yaml. I think I spent more than 4 hours on it, only to later find this:

When I teach Python courses I repeat the same thing over and over, “Programming is more about searching for the correct information than knowing the syntax by heart”. Well, now I’m telling that to myself too.

Anyway, getting back to what we were doing, we need to find a way to automate this. We know that pip-compile kind of works, we are just missing +cpu at the end of each dependency, why don’t we use python again?

# cpu_fixer.py
import re
from pathlib import Path

data = Path("requirements.txt").read_text()
pat = re.compile(r"torch\w*\=\=\d.*\d")

new_data = []

for l in data.split("\n"):
    if pat.match(l):
        new_data.append(l + "+cpu")
    else:
        new_data.append(l)


Path("requirements.txt").write_text("\n".join(new_data))

That script will replace torch==1.7.1 with torch==1.7.1+cpu and torchvision==0.8.2 torchvision==0.8.2+cpu. We could achieve the same using re.sub but I’ll leave it like that.

Just kidding, we can do it better like this:

import re
from pathlib import Path
from sys import argv

requirements = argv[1]
data = Path(requirements).read_text()

fixed = re.sub(
    r"^(torch\w*==[\d|\.]+)\b", lambda x: x.group(0) + "+cpu", data, flags=re.MULTILINE,
)


Path(requirements).write_text(fixed)

Let’s try now, I’ve modified the entrypoint of the Dockerfile to import torch instead of numpy:

FROM python:3.7-slim-buster
COPY requirements.txt .
RUN pip install -r requirements.txt
ENTRYPOINT python -c "import torch; print('working!!')"

IT’S WORKING!! Sorry for the euphoria, when I started writing about this I didn’t think it would take me so much time.

What we learned:

  • Use whatever you want to create your environment
  • Mamba is amazing!
  • Pip-tools is amazing! The good thing about pip-tools is that it does not “lock” you into any dependency manager, we can use conda/mamba and then compile the requirements with pip-tools so that we can just pip install in our Dockerfile.
  • Searching for open GitHub issues before spending hours trying 100 things is highly recommended.

About the workflow

This article was initially about workflows. As I said, now I use venv + pip-tools, but I’m enjoying using mamba to manage local environments. Now I’m also using pyenv to manage Python versions. With mamba you don’t need pyenv.

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