From da474de074e8d68c751b157f0b6ed09037d8d0fc Mon Sep 17 00:00:00 2001 From: Co Quach Date: Fri, 22 Mar 2024 16:13:36 -0500 Subject: [PATCH 1/3] move numpy and ele to docs-env, re-link mosdef-gomc --- docs/conf.py | 5 ----- docs/docs-env.yml | 2 ++ docs/getting_started/installation/installation.rst | 4 ++-- docs/getting_started/writers/writers.rst | 5 ++--- 4 files changed, 6 insertions(+), 10 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index b5dc288a2..29d2ef3b8 100755 --- a/docs/conf.py +++ b/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", diff --git a/docs/docs-env.yml b/docs/docs-env.yml index 24ada5ee0..6810337bc 100644 --- a/docs/docs-env.yml +++ b/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 diff --git a/docs/getting_started/installation/installation.rst b/docs/getting_started/installation/installation.rst index 50fceae15..17e398a1b 100644 --- a/docs/getting_started/installation/installation.rst +++ b/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 diff --git a/docs/getting_started/writers/writers.rst b/docs/getting_started/writers/writers.rst index eecffc49b..65d819f02 100644 --- a/docs/getting_started/writers/writers.rst +++ b/docs/getting_started/writers/writers.rst @@ -17,22 +17,21 @@ field XML files (used by the `Foyer package `_) 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 `_ -* `GPU Optimized Monte Carlo (GOMC) `_ * `GROMACS `_ * `HOOMD-blue `_ * `Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) `_ +Support for `GPU Optimized Monte Carlo (GOMC) `_ is also available through the `MoSDeF-GOMC library `_ .. toctree:: cassandra_file_writers - GOMC_file_writers HOOMD_blue_file_writers LAMMPS_file_writers From 23d82524b09b26213fab66c55a51cc0fa88b3211 Mon Sep 17 00:00:00 2001 From: Co Quach Date: Fri, 22 Mar 2024 16:19:33 -0500 Subject: [PATCH 2/3] update docs build instruction --- docs/getting_started/installation/installation.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/getting_started/installation/installation.rst b/docs/getting_started/installation/installation.rst index 17e398a1b..3cad8a5c4 100644 --- a/docs/getting_started/installation/installation.rst +++ b/docs/getting_started/installation/installation.rst @@ -79,5 +79,7 @@ Building the documentation mBuild uses `sphinx `_ 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 create -f docs-env.yml + $ conda activate mbuild-docs $ make html From 7c5708de2313c6844bc628ea5c0a99872650ab93 Mon Sep 17 00:00:00 2001 From: Co Quach Date: Mon, 25 Mar 2024 10:28:55 -0500 Subject: [PATCH 3/3] fix syntax in installation.rst --- docs/getting_started/installation/installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/getting_started/installation/installation.rst b/docs/getting_started/installation/installation.rst index 3cad8a5c4..ba2241706 100644 --- a/docs/getting_started/installation/installation.rst +++ b/docs/getting_started/installation/installation.rst @@ -80,6 +80,6 @@ Building the documentation mBuild uses `sphinx `_ to build its documentation. To build the docs locally, run the following while in the ``docs`` directory:: $ cd docs - $ conda create -f docs-env.yml + $ conda env create -f docs-env.yml $ conda activate mbuild-docs $ make html