Fix install instructions

Author: Yoshanuikabundi

README.md

@@ -6,69 +6,59 @@ OpenFF Pablo
 | :----------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | **Status**         | [![GH Actions Status](https://github.com/openforcefield/openff-pablo/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/openforcefield/openff-pablo/actions?query=branch%3Amain+workflow%3Agh-ci) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/openforcefield/openff-pablo/main.svg)](https://results.pre-commit.ci/latest/github/openforcefield/openff-pablo/main) |
 
-New, independent implementation of `Topology.from_pdb`
+New, independent implementation of OpenFF's `Topology.from_pdb`
 
 OpenFF Pablo is bound by a [Code of Conduct](https://github.com/openforcefield/openff-pablo/blob/main/CODE_OF_CONDUCT.md).
 
 ### Installation
 
-To build OpenFF Pablo from source,
-we highly recommend using virtual environments.
-If possible, we strongly recommend that you use
-[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
-Below we provide instructions both for `conda` and
-for `pip`.
+This is a pre-release of Pablo and is not yet published in any package manager.
+You can install it by managing your own Conda environment and installing it manually.
 
-#### With conda
+Here we describe dependency and environment management with Micromamba, but other Conda-compatible package managers such as Conda and Mamba work the same way - just change the name of the executable.
 
-Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
-
-Create a virtual environment and activate it:
+Download the user environment YAML file and create a virtual environment from it:
 
 ```
-conda create --name pablo
-conda activate pablo
+curl https://raw.githubusercontent.com/openforcefield/openff-pablo/refs/heads/main/devtools/conda-envs/user_env.yaml | micromamba env create --name pablo -f /dev/stdin
 ```
 
-Install the development and documentation dependencies:
+#### Development build
+
+Clone the repository:
 
 ```
-conda env update --name pablo --file devtools/conda-envs/test_env.yaml
-conda env update --name pablo --file docs/requirements.yaml
+git clone https://github.com/openforcefield/openff-pablo
 ```
 
-Build this package from source:
+Create a virtual environment:
 
 ```
-pip install -e .
+micromamba create --name pablo-dev
 ```
 
-If you want to update your dependencies (which can be risky!), run:
+Install the development and documentation dependencies:
 
 ```
-conda update --all
+micromamba env update -n pablo-dev --file openff-pablo/devtools/conda-envs/test_env.yaml
+micromamba env update -n pablo-dev --file openff-pablo/docs/requirements.yaml
 ```
 
-And when you are finished, you can exit the virtual environment with:
+Install this package in editable mode:
 
 ```
-conda deactivate
+micromamba run -n pablo-dev pip install -e openff-pablo
 ```
 
-#### With pip
+If you want to update your dependencies, rebuild the environment from scratch.
 
-To build the package from source, run:
+Then activate the environment to run commands in it:
 
 ```
-pip install -e .
+micromamba activate pablo-dev
 ```
 
-If you want to create a development environment, install
-the dependencies required for tests and docs with:
-
-```
-pip install -e ".[test,doc]"
-```
+Or use `micromamba run -n pablo-dev`.
 
 ### Copyright
 

devtools/conda-envs/user_env.yaml

@@ -0,0 +1,16 @@
+name: pablo
+channels:
+  - conda-forge
+dependencies:
+  # Base depends (runtime and imports)
+  - pip
+  - python>=3.11
+  - openff-toolkit-base>=0.17.0
+  - rdkit
+  - openmm
+  - pyxdg
+  - rustworkx
+  - gemmi
+
+  - pip:
+      - git+https://github.com/openforcefield/openff-pablo.git@main

openff/pablo/_utils.py

@@ -18,7 +18,6 @@
 import rdkit.Chem.Draw
 import rdkit.Chem.rdDepictor
 import rdkit.Geometry
-from IPython.display import SVG
 from openff.toolkit import Molecule
 from openff.toolkit.topology._mm_molecule import _SimpleMolecule
 from openff.toolkit.topology.molecule import MoleculeLike
@@ -348,9 +347,11 @@ def draw_molecule(
     emphasize_atoms: list[int] | None = None,
     explicit_hydrogens: bool | None = None,
     color_by_element: bool | None = None,
-) -> SVG:
+) -> str:
     """Draw a molecule
 
+    Returns a string encoding an XML with the requested drawing.
+
     Parameters
     ==========
 
@@ -391,6 +392,14 @@ def draw_molecule(
     KeyError
         When an atom or bond in highlight_atoms or highlight_bonds is missing
         from the image, including when it is present in the molecule but hidden.
+
+    Examples
+    ========
+
+    >>> from IPython.display import SVG
+    >>>
+    >>> SVG(draw_molecule(...))
+
     """
 
     # We're working in RDKit
@@ -543,4 +552,4 @@ def draw_molecule(
 
     # Return an SVG object that we can view in notebook
     svg_contents = drawer.GetDrawingText()
-    return SVG(svg_contents)
+    return svg_contents