Devcontainer (#17)

* chore: clean up Makefile

* chore: update poetry env

* chore: add devcontainer for CUDA version

* docs: add dev environment notes

* build: edit devcontainer environment

* docs: add notes tab to site

* ci: remove quarto ci/cd

* ci: add poetry --with cpu key

* chore: Update poetry install command to include dev dependencies

.devcontainer/devcontainer.json

@@ -0,0 +1,16 @@
+{
+    "name": "moll-cuda",
+    "dockerFile": "../Dockerfile.devcontainer",
+    "context": "../",
+    "remoteUser": "moll",
+    "runArgs": [
+        "--gpus=all"
+    ],
+    "customizations": {
+        "vscode": {},
+        "settings": {
+            "terminal.integrated.shell.linux": "/bin/bash",
+            "editor.tabSize": 4
+        }
+    }
+}

.dockerignore

@@ -0,0 +1,3 @@
+.pytest_cache/
+.ruff_cache/
+.venv/

.github/workflows/pr-tests.yml

@@ -25,5 +25,5 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: poetry
       - run: poetry env use ${{ matrix.python-version }}
-      - run: poetry install -E cpu
+      - run: poetry install --with cpu,dev
       - run: poetry run pytest

.github/workflows/push-tests.yml

@@ -22,5 +22,5 @@ jobs:
           python-version: '${{ vars.TARGET_PYTHON_VERSION }}'
           cache: poetry
       - run: poetry env use '${{ vars.TARGET_PYTHON_VERSION }}'
-      - run: poetry install -E cpu
+      - run: poetry install --with cpu,dev
       - run: poetry run pytest

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
         with:
           python-version: "${{ vars.TARGET_PYTHON_VERSION }}"
           cache: poetry
-      - run: poetry install -E cpu
+      - run: poetry install --with cpu,dev
       - run: poetry build
       - uses: actions/upload-artifact@v3
         with:

Dockerfile.devcontainer

@@ -0,0 +1,16 @@
+FROM mcr.microsoft.com/devcontainers/python:3.10 as base
+
+ARG PROJECT_NAME=moll
+ARG USER_NAME=$PROJECT_NAME
+ARG SHELL=/bin/bash
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+
+RUN userdel -r vscode \
+    && groupadd --gid $USER_GID $USER_NAME \
+    && useradd --uid $USER_UID --gid $USER_GID --shell $SHELL --create-home $USER_NAME \
+    && echo $USER_NAME ALL=\(ALL\) NOPASSWD: ALL >> /etc/sudoers \
+    && pipx install poetry \
+    && apt-get install -y sudo
+
+USER $USER_NAME

Makefile

@@ -1,6 +1,3 @@
-render:
-	quarto render
-
 prep_docs:
 	rsync -av notebooks/ docs/notebooks/
 	rsync -av README.md docs/index.md
@@ -17,17 +14,10 @@ notebooks:
 clean:
 	rm -rf .venv .mypy* .pytest* .coverage* coverage.xml htmlcov **/__pycache__
 
-cpu: clean
-	poetry install -E cpu
-
-cuda12_local: clean
-	poetry install
-	poetry run pip install --upgrade "jax[cuda12_local]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
-
 metal: clean
 	# This is experimental
 	poetry env use 3.11
 	poetry install
 	poetry run pip install -U jax-metal==0.0.4 jax[cpu]==0.4.11 ml_dtypes==0.2.0 --extra-index-url https://storage.googleapis.com/jax-releases/jax_releases.html
 
-.PHONY: render docs notebooks clean
+.PHONY: docs notebooks clean

docs/notes/02-dev.md

@@ -0,0 +1,88 @@
+# Development Environment
+
+## Requirements
+
+- **JAX** is required to run the code.
+- **Poetry** is used for dependency management.
+- **NVIDIA Driver** and **NVIDIA Container Toolkit** are required for the CUDA version.
+
+
+
+## Installation
+
+### CPU Version
+
+To install the CPU-only development environment, run the following command:
+
+```bash
+poetry install --with cpu,dev
+```
+
+### CUDA Version
+
+1. Ensure the NVIDIA Driver is installed on your machine.
+2. Install Docker and NVIDIA Container Toolkit.
+3. Run the following command to install the GPU-supported development environment:
+
+```bash
+poetry install --with cuda,dev
+```
+
+### Manual JAX Installation
+
+To use the local JAX installation, install without specifying additional dependencies:
+
+```bash
+poetry install --with dev
+```
+
+
+
+## Docker Container for Development
+
+Optionally, you can run the development environment in a Docker container. Configuration files are `.devcontainer/*` and `Dockerfile.devcontainer`.
+
+### CPU Version
+
+To install the CPU version, run inside the devcontainer:
+
+```bash
+poetry install --with cpu,dev
+```
+
+### GPU Version
+
+Install NVIDIA Container Toolkit and run the devcontainer. Then, run the following command:
+
+```bash
+poetry install --with cuda,dev
+```
+
+
+
+## Running Tests
+
+To run the tests, use:
+
+```bash
+poetry run pytest
+```
+
+
+
+## Building Documentation
+
+1. Install documentation-specific dependencies:
+
+```bash
+poetry install --with docs
+```
+
+2. Build the documentation:
+
+```bash
+make docs
+```
+
+
+

mkdocs.yml

@@ -11,6 +11,7 @@ nav:
       - B: notebooks/chembl-1-percent.ipynb
       - C: notebooks/zinc20.ipynb
   - API: api/
+  - Notes: notes/
 
 theme:
   name: material