Update .readthedocs.yaml

.readthedocs.yaml

@@ -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
@@ -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
+

devtools/conda-envs/readthedocs.yaml

@@ -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

doc/sphinx/source/conf.py

@@ -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
@@ -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.
@@ -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),
 }
 
 

mdpow/workflows/dihedrals.py

@@ -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:
 
@@ -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
@@ -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`
 
@@ -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: