Fix failing doc build (#1177)

* move numpy and ele to docs-env, re-link mosdef-gomc

* update docs build instruction

* fix syntax in installation.rst

docs/conf.py

@@ -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",
@@ -35,8 +32,6 @@
     "hoomd.md.charge",
     "hoomd.md.pair",
     "hoomd.md.special_pair",
-    "numpy",
-    "numpy.linalg",
     "mdtraj",
     "mdtraj.core.element",
     "networkx",

docs/docs-env.yml

@@ -3,6 +3,8 @@ channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
+  - ele
+  - numpy
   - importlib_resources
   - python=3.11
   - ipython

docs/getting_started/installation/installation.rst

@@ -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
@@ -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

docs/getting_started/writers/writers.rst

@@ -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