Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix failing doc build #1177

Merged
merged 3 commits into from
Mar 26, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 0 additions & 5 deletions docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,6 @@
# documentation root, use os.path.abspath to make it absolute, like shown here.

MOCK_MODULES = [
"ele",
"ele.element",
"ele.exceptions",
"hoomd",
"hoomd.data",
"hoomd.md",
Expand All @@ -35,8 +32,6 @@
"hoomd.md.charge",
"hoomd.md.pair",
"hoomd.md.special_pair",
"numpy",
"numpy.linalg",
"mdtraj",
"mdtraj.core.element",
"networkx",
Expand Down
2 changes: 2 additions & 0 deletions docs/docs-env.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@ channels:
- jaimergp/label/unsupported-cudatoolkit-shim
- conda-forge
dependencies:
- ele
- numpy
- importlib_resources
- python=3.11
- ipython
Expand Down
8 changes: 5 additions & 3 deletions docs/getting_started/installation/installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -61,9 +61,9 @@ And (optional) all files can be checked by running::
Supported Python Versions
-------------------------

Python 3.6, 3.7 and 3.8 are officially supported, including testing during
Python 3.9, 3.10 and 3.11 are officially supported, including testing during
development and packaging. Support for Python 2.7 has been dropped as of
August 6, 2019. Other Python versions, such as 3.9 and 3.5 and older, may
August 6, 2019. Other Python versions, such as 3.12 and 3.8 and older, may
successfully build and function but no guarantee is made.

Testing your installation
Expand All @@ -79,5 +79,7 @@ Building the documentation

mBuild uses `sphinx <https://www.sphinx-doc.org/en/master/index.html>`_ to build its documentation. To build the docs locally, run the following while in the ``docs`` directory::

$ pip install -r requirements.txt
$ cd docs
$ conda env create -f docs-env.yml
$ conda activate mbuild-docs
$ make html
5 changes: 2 additions & 3 deletions docs/getting_started/writers/writers.rst
Original file line number Diff line number Diff line change
Expand Up @@ -17,22 +17,21 @@ field XML files (used by the `Foyer package <https://github.com/mosdef-hub/foyer
to the ``Compound.save`` function if Foyer is installed. If a force field is applied to a
Compound, the mBuild internal writers will also write angle and dihedral information
to the file in addition to labelling atoms by the atom types specified by the force
field. The CHARMM-style GOMC writers are the exception to this default rule since
field. The CHARMM-style GOMC writers (supported through the `MoSDeF-GOMC extension <https://github.com/GOMC-WSU/MoSDeF-GOMC>`_) are the exception to this default rule since
they need a force field to build the files, as these files depend on the force field parameters (Example: charge and MW in the PSF files).

The simulation engine writers that use mBuild or are currently contained in the mBuild library:


* `Cassandra <https://cassandra.nd.edu/>`_
* `GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu/>`_
* `GROMACS <https://www.gromacs.org/>`_
* `HOOMD-blue <http://glotzerlab.engin.umich.edu/hoomd-blue//>`_
* `Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) <https://lammps.sandia.gov/>`_

Support for `GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu/>`_ is also available through the `MoSDeF-GOMC library <https://github.com/GOMC-WSU/MoSDeF-GOMC>`_

.. toctree::

cassandra_file_writers
GOMC_file_writers
HOOMD_blue_file_writers
LAMMPS_file_writers
Loading