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Merge pull request #284 from Becksteinlab/update-rtd
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Update .readthedocs.yaml
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orbeckst authored Oct 10, 2024
2 parents ecd4da4 + 28ca1bd commit c4ffec7
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15 changes: 12 additions & 3 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,11 @@
# Required
version: 2

build:
os: "ubuntu-22.04"
tools:
python: "mambaforge-22.9"

# Build documentation in the docs/ directory with Sphinx
sphinx:
configuration: doc/sphinx/source/conf.py
Expand All @@ -13,8 +18,12 @@ sphinx:
formats:
- pdf

# Optionally set the version of Python and requirements required to build your docs
# install package
python:
version: 3.8
install:
- requirements: doc/requirements.txt
- method: pip
path: .

conda:
environment: devtools/conda-envs/readthedocs.yaml

26 changes: 26 additions & 0 deletions devtools/conda-envs/readthedocs.yaml
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@@ -0,0 +1,26 @@
name: readthedocs
channels:
- conda-forge
dependencies:
- python >=3.10
- six
- numpy
- scipy >=1.11.0
- matplotlib-base
- pandas
- scikit-learn
- pyyaml
- mdanalysis >=2
- numkit
- gromacswrapper
- alchemlyb >=2
- pymbar >=4
- rdkit
- seaborn
- svgutils
- cairosvg
- pypdf

# sphinx and RTD
- sphinx
- sphinx_rtd_theme
34 changes: 16 additions & 18 deletions doc/sphinx/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -55,9 +55,8 @@
# General information about the project.
project = "MDPOW"
now = datetime.datetime.now()
copyright = "2010–{}, Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein".format(
now.year
)
authors = "Shujie Fan, Ian Kenney, Alia Lescoulie, Bogdan Iorga, and Oliver Beckstein"
copyright = "2010–{}, ".format(now.year) + authors

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
Expand Down Expand Up @@ -220,16 +219,16 @@
latex_documents = [
(
"index",
"MDpow.tex",
"MDpow Documentation",
"Ian Kenney, Bogdan Iorga, and Oliver Beckstein",
"MDPOW.tex",
"MDPOW Documentation",
authors,
"manual",
),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
# latex_logo = None
latex_logo = html_logo

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
Expand All @@ -250,17 +249,16 @@
# intersphinx: reference standard lib and RecSQL
# http://sphinx.pocoo.org/latest/ext/intersphinx.html
intersphinx_mapping = {
"https://docs.python.org/": None,
"https://numpy.org/doc/stable/": None,
"https://docs.scipy.org/doc/scipy/reference/": None,
"https://gromacswrapper.readthedocs.io/en/latest": None,
"https://docs.mdanalysis.org/stable/": None,
"https://www.rdkit.org/docs/": None,
"https://pandas.pydata.org/docs/": None,
"https://seaborn.pydata.org": None,
"https://cairosvg.org/documentation/": None,
"https://svgutils.readthedocs.io/en/latest/": None,
"https://pypdf.readthedocs.io/en/stable/": None,
"python": ("https://docs.python.org/3", None),
"numpy": ("https://numpy.org/doc/stable/", None),
"scipy": ("https://docs.scipy.org/doc/scipy", None),
"GromacsWrapper": ("https://gromacswrapper.readthedocs.io/en/latest", None),
"MDAnalysis": ("https://docs.mdanalysis.org/stable/", None),
"RDKit": ("https://www.rdkit.org/docs/", None),
"pandas": ("https://pandas.pydata.org/docs/", None),
"seaborn": ("https://seaborn.pydata.org", None),
"svgutils": ("https://svgutils.readthedocs.io/en/latest/", None),
"pypdf": ("https://pypdf.readthedocs.io/en/stable/", None),
}


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38 changes: 19 additions & 19 deletions mdpow/workflows/dihedrals.py
Original file line number Diff line number Diff line change
Expand Up @@ -511,10 +511,12 @@ def periodic_angle_padding(df, padding=45):
def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None):
"""Plots kernel density estimates (KDE) of dihedral angle frequencies for
one dihedral atom group as violin plots, using as input the augmented
:class:`pandas.DataFrame` from :func:`~mdpow.workflows.dihedrals.periodic_angle_padding`.
:class:`pandas.DataFrame` from
:func:`~mdpow.workflows.dihedrals.periodic_angle_padding`.
Output is converted to SVG by :func:`~mdpow.workflows.dihedrals.build_svg`
and final output is saved as PDF by :func:`~mdpow.workflows.dihedrals.plot_dihedral_violins`
and final output is saved as PDF by
:func:`~mdpow.workflows.dihedrals.plot_dihedral_violins`
:keywords:
Expand All @@ -523,13 +525,13 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None):
:func:`~mdpow.workflows.dihedrals.periodic_angle_padding`
*width*
width of the violin element (>1 overlaps)
default: 0.9
width of the violin element (>1 overlaps); default: 0.9
*solvents*
The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
Normally takes a two-tuple, but analysis is compatible with single solvent selections.
Single solvent analyses will result in a figure with fully filled violins for the single solvent.
Normally takes a two-tuple, but analysis is compatible with single
solvent selections. Single solvent analyses will result in a figure
with fully filled violins for the single solvent.
*plot_title*
generated by :func:`~mdpow.workflows.dihedrals.build_svg` using
Expand Down Expand Up @@ -619,24 +621,22 @@ def build_svg(
solvents=SOLVENTS_DEFAULT,
width=0.9,
):
"""Converts and combines figure components into an
SVG object to be converted and saved as a publication
quality PDF.
"""Converts and combines figure components into an SVG object to be
converted and saved as a publication quality PDF.
:keywords:
*mol*
:class:`rdkit.Chem.rdchem.Mol` object converted from `solute`
*molname*
molecule name to be used for labelling
plots, if different from `resname`
(in this case, carried over from an upstream
decision between the two)
molecule name to be used for labelling plots, if different from
`resname` (in this case, carried over from an upstream decision between
the two)
*name_index_pairs*
dictionary with key-value pair for dihedral atom group,
atom indices, and bond indices
dictionary with key-value pair for dihedral atom group, atom indices,
and bond indices
.. seealso:: :func:`~mdpow.workflows.dihedrals.get_paired_indices`
Expand All @@ -647,12 +647,12 @@ def build_svg(
*solvents*
The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
Normally takes a two-tuple, but analysis is compatible with single solvent selections.
Single solvent analyses will result in a figure with fully filled violins for the single solvent.
Normally takes a two-tuple, but analysis is compatible with single
solvent selections. Single solvent analyses will result in a figure
with fully filled violins for the single solvent.
*width*
width of the violin element (>1 overlaps)
default: 0.9
width of the violin element (>1 overlaps); default: 0.9
:returns:
Expand Down

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