Installation¶
oxmol
is currently not listed in any package repos while deployment is
worked out, but installation from source is fairly easy. Installation has
only been tested on Linux (Ubuntu 18.04) and with Python 3.7, but should
be possible for any system compatible with PyO3. This includes Windows,
macOS, Linux and BSD systems and both the Python and PyPy interpreters.
Toolchain¶
The easiest way to build the Python wheels is to use Maturin, which can be installed via pip.
pip install maturin
You will also need the nightly Rust compiler. If you have not yet installed the Rust toolchain, see the instructions here. The nightly compiler can then be installed and and enabled by running the following two commands:
rustup install nightly
rustup default nightly
To set the default compiler back to stable, run the following command:
rustup default stable
If compiling on macOS, you will need to create a a file at ~/.cargo/config
with the following contents in order to set the linker options:
[target.x86_64-apple-darwin]
rustflags = [
"-C", "link-arg=-undefined",
"-C", "link-arg=dynamic_lookup",
]
Dependencies¶
The Rust component of oxmol
depends upon pyo3
, molecule
and
gamma
(a graph library) but these should be automatically fetched by Cargo
when compiling so there are no dependencies to install manually.
Installation Steps¶
Clone the repo using git and move into the root folder:
git clone https://github.com/thesketh/oxmol
cd oxmol
Execute the following command from the root of the repo.
maturin build --release
Maturin will compile the Rust component of the library and create a Python
wheel containing the Rust and Python components, which are placed in
./target/wheels
.
As Maturin will compile a wheel for each interpreter it finds (e.g. the
system Python and the interpreter from a Conda environment), there may be
multiple versions. You will have to install the version most relevant to
your version of Python (e.g. oxmol-0.1.0-cp36...
for Python 3.6 and
oxmol-0.1.0-cp37...
for Python 3.7). The full name of the file
will vary depending on your platform.
cd into ./target/wheels
and use pip to install the most relevant wheel
cd ./target/wheels
# Update the following command with the most relevant version.
pip install ./oxmol-0.1.0-cp37-cp37m-manylinux1_x86_64.whl
You should now be ready to start using oxmol
. If you are interested in
compiling against a specific version of Python, you can specify the path
to the interetreter using the -i
flag for Maturin:
maturin build -i $(which python3) --release
For information about other flags, use the Maturin docs.
Installing against PyPy¶
The latest version of PyPy changed the ABI string format and Maturin hasn’t yet been updated, so you may have to rename the wheel file.
To compile oxmol against PyPy3, use the -i
flag for Maturin:
maturin build -i $(which pypy3) --release
cd target/wheels
If you’re using PyPy3 version >= 7.3.1 (where SYSTEM
is e.g. linux_x86_64
):
mv oxmol-0.1.0-pp3pp73-pypy3_pp73-SYSTEM.whl oxmol-0.1.0-pp36-pypy36_pp73-SYSTEM.whl
Install using PyPy’s pip:
pypy3 -m pip install oxmol-0.1.0-pp36-pypy36_pp73-SYSTEM.whl