Merge pull request #43 from gruenewald-lab/fixdocs

Fixdocs

.github/workflows/python-app.yml

@@ -82,4 +82,4 @@ jobs:
       - name: Run docs
         run: |
           mkdir -p docs/source/_static
-          sphinx-build -E -b html docs/source/ docs/build/html
+          sphinx-build -WnE -b html docs/source/ docs/build/html

README.rst

@@ -65,10 +65,17 @@ Martini 3 Benzene
     # Draw molecule at different resolutions
     ax, pos = draw_molecule(mol_graph)
 
-Resources
-=========
+Installation
+============
 
-- here go some resources
+The easiest ways to install **cgsmiles** is using pip:
+
+.. code:: bash
+
+   pip install git+https://github.com/gruenewald-lab/CGsmiles.git
+
+In the future we will also distribute it through the Pypi
+package index but that is currently not supported.
 
 Related Tools
 =============

cgsmiles/cgsmiles_utils.py

@@ -47,8 +47,8 @@ def find_open_bonds(molecule, target_nodes=None):
 
     Parameters
     ----------
-    molecule: nx.Graph
-    target_nodes: list[abc.hashable]
+    molecule: networkx.Graph
+    target_nodes: list[collections.abc.Hashable]
         a list of node keys matching molecule
 
     Return
@@ -85,7 +85,7 @@ def read_fragment_cgsmiles(cgsmiles_str,
 
     Returns
     -------
-    nx.Graph
+    networkx.Graph
         the graph of the molecular fragment
     """
     mol_graph = read_cgsmiles(cgsmiles_str)

cgsmiles/dialects.py

@@ -36,9 +36,9 @@ def _parse_dialect_string(string_iterable,
 
     Parameters
     ----------
-    string_iterable: iter
+    string_iterable: :type data: iter
         the string or iter object that contains the string
-    dialect_signature: cls.inspec.Signature
+    dialect_signature: inspect.Signature
         a signature defineing args, kwargs, default values
         and types
     arg_to_fullname: dict

cgsmiles/drawing.py

@@ -86,9 +86,9 @@ def draw_molecule(graph,
 
     Parameters
     ----------
-    ax: :class:`matplotlib.pyplot.axis`
+    ax: matplotlib.axes.Axes
         mpl axis object
-    layout_method:
+    layout_method: str
         choice of vespr, vespr_refined, circular
         (default: 'vespr_refined')
     pos: dict
@@ -106,7 +106,7 @@ def draw_molecule(graph,
         draw an outline around each node
     use_weights: bool
         color nodes according to weight attribute (default: False)
-    align_with: str or np.ndarray
+    align_with: str or :class:`numpy.ndarray`
         align the longest distance in molecule with one of x, y, diag
         or a custom axis as numpy 2D array
     fontsize: float
@@ -124,7 +124,7 @@ def draw_molecule(graph,
 
     Returns
     -------
-    :class:`matplotlib.pyplot.axis`
+    matplotlib.axes.Axes
         the updated axis object
     dict
         a dict of positions

cgsmiles/drawing_utils.py

@@ -28,8 +28,8 @@ def make_edge(p0, p1, bond_order, spacing=0.1, sep=0.0):
 
     Parameters
     ----------
-    p0: np.ndarray(2)
-    p1: np.ndarray(2)
+    p0: :class:`numpy.ndarray` of shape 2
+    p1: :class:`numpy.ndarray` of shape 2
     bond_order: int
     spacing: float
     sep: float
@@ -74,9 +74,9 @@ def make_graph_edges(graph, pos, spacing=0.1, sep=0.2):
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
         Graph with bond oder attribute
-    pos: np.ndarray((2, len(graph)))
+    pos: :class:`numpy.ndarray` of shape ((2, len(graph)))
         2D positions for the nodes
     spacing: float
         distance between pos and start of edge
@@ -124,9 +124,9 @@ def make_mapped_edges(graph, plain_edges):
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
         graph of the molecule with 'fragid' attribute
-    plain_edges: dict[frozenset([abc.hashable])]
+    plain_edges: dict[frozenset([collections.abc.Hashable])]
         dict of edge coordinates indexed by node keys
 
     Returns
@@ -168,9 +168,9 @@ def make_node_pies(graph,
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
         graph of the molecule
-    pos: dict[np.array]
+    pos: dict[:class:`numpy.ndarray`]
         dict of 2D node positions
     cgmapping: bool
         if the drawing includes a cgmapping;
@@ -189,7 +189,7 @@ def make_node_pies(graph,
 
     Yields
     ------
-    np.array, dict
+    :class:`numpy.ndarray`, dict
         array slices and keyword arguments to be given
         to mpl.Pie class
     """

cgsmiles/graph_layout.py

@@ -14,11 +14,11 @@ def vespr_layout(graph, default_bond=1, align_with=None):
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
         the molecule to draw
     default_bond: float
         the default bond length
-    align_with: np.ndarray
+    align_with: :class:`numpy.ndarray`
         axis to align longest axis with
 
     Returns
@@ -73,11 +73,11 @@ def circular_layout(graph, radius, align_with=None):
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
         the molecule to draw
     radius: float
         the radius of the circle
-    align_with: np.ndarray
+    align_with: :class:`numpy.ndarray`
         axis to align longest axis with
 
     Returns
@@ -116,11 +116,11 @@ def vespr_refined_layout(graph,
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
         the molecule to draw
     default_bond: float
         the default bond length
-    align_with: np.ndarray
+    align_with: :class:`numpy.ndarray`
         axis to align longest axis with
     default_angle: float
         the default angle in degrees

cgsmiles/graph_layout_utils.py

@@ -24,11 +24,11 @@ def rotate_subgraph(graph, anchor, reference, target, points, angle=120):
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
         the graph
-    target: tuple(abc.hashable, abc.hashable)
+    target: tuple(collections.abc.Hashable, collections.abc.Hashable)
         the target edge
-    points: dict[abc.hashable: np.array]
+    points: dict[collections.abc.Hashable: :class:`numpy.ndarray`]
         the dict of 2D positions
     angle: float
         the angle to rotate by
@@ -86,11 +86,11 @@ def find_triplets(graph):
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
 
     Returns
     -------
-    tuple([abc.hashable,abc.hashable,abc.hashable])
+    tuple([collections.abc.Hashable,collections.abc.Hashable,collections.abc.Hashable])
         the node keys corresponding to the triplet
         the central node is the common one.
     """
@@ -115,11 +115,11 @@ def assign_angles(graph, default_angle=120):
 
     Parameters
     ----------
-    graph: nx.Graph
+    graph: networkx.Graph
 
     Returns
     -------
-    tuple([[abc.hashable,abc.hashable,abc.hashable,int])
+    tuple([[collections.abc.Hashable,collections.abc.Hashable,collections.abc.Hashable,int])
         tuple with node keys corresponding to the angle
         and the reference angle value
     """
@@ -161,14 +161,14 @@ def assign_bonds(graph, pos, default_bond=None):
 
     Parameters
     ----------
-    graph: nx.Graph
-    pos: np.ndarray((n,2))
+    graph: networkx.Graph
+    pos: :class:`numpy.ndarray` of shape ((n,2))
     default_bond: float
         default bond distance
 
     Returns
     -------
-    tuple([abc.hashable, abc.hashable, float])
+    tuple([collections.abc.Hashable, collections.abc.Hashable, float])
         tuple of node keys and distance
     """
     bonds = []
@@ -235,7 +235,7 @@ def _optimize_geometry_2D(positions,
 
     Parameters
     ----------
-    positions: np.ndarray((n, 2))
+    positions: :class:`numpy.ndarray` of shape ((n, 2))
         the inital positions
     atom_to_idx: dict
         dict mapping node keys to indices in the position
@@ -254,7 +254,7 @@ def _optimize_geometry_2D(positions,
 
     Returns
     -------
-    np.ndarray((n, 2)), float
+    :class:`numpy.ndarray` of shape ((n, 2)), float
         the optimized positions and final energy
     """
     def target_function(positions):
@@ -319,7 +319,7 @@ def _generate_circle_coordinates(radius, num_points, center=(0, 0)):
 
     Returns
     -------
-    np.ndarray((num_points, 2))
+    :class:`numpy.ndarray` of shape ((num_points, 2))
         array of the point coordinates
     """
     # Generate angles in clockwise order (start at 0 and go to -2π)

cgsmiles/graph_utils.py

@@ -17,7 +17,7 @@ def merge_graphs(source_graph, target_graph, max_node=None):
 
     Parameters
     ----------
-    molecule: Molecule
+    molecule: networkx.Graph
         The molecule to merge at the end.
 
     Returns
@@ -66,9 +66,9 @@ def sort_nodes_by_attr(graph,
 
     Parameters
     ----------
-    graph: :class:`nx.Graph`
+    graph: networkx.Graph
         the graph to sort nodes of
-    sort_attr: `abc.hashable`
+    sort_attr: collections.abc.Hashable
         the attribute to use for sorting
     relative_attr: tuple(str, bool)
         a list of attributes that are sensetive
@@ -80,7 +80,7 @@ def sort_nodes_by_attr(graph,
 
     Returns
     -------
-    nx.Graph
+    networkx.Graph
         graph with nodes sorted in correct order
     """
     fragids = nx.get_node_attributes(graph, sort_attr)
@@ -154,9 +154,9 @@ def set_atom_names_atomistic(molecule, meta_graph=None):
 
     Parameters
     ----------
-    molecule: nx.Graph
+    molecule: networkx.Graph
         the molecule for which to adjust the atomnames
-    meta_graph: nx.Graph
+    meta_graph: networkx.Graph
         optional; get the fragments from the meta_graph
         attributes which is faster in some cases
     """

cgsmiles/linalg_functions.py

@@ -8,11 +8,11 @@ def u_vect(vect):
 
     Parameters
     ----------
-    vect: np.array
+    vect: :class:`numpy.ndarray`
 
     Returns
     -----------
-    np.array
+    :class:`numpy.ndarray`
     """
     u_vect = vect/np.linalg.norm(vect)
     return u_vect
@@ -24,8 +24,8 @@ def vector_angle_degrees(v1, v2):
 
     Parameters
     ----------
-    v1: np.array
-    v2: np.array
+    v1: :class:`numpy.ndarray`
+    v2: :class:`numpy.ndarray`
 
     Returns
     ---------

cgsmiles/pysmiles_utils.py

@@ -13,7 +13,7 @@ def compute_mass(input_molecule):
 
     Parameters
     ----------
-    molecule: nx.Graph
+    molecule: networkx.Graph
         molecule which must have element specified per node
 
     Returns
@@ -61,9 +61,9 @@ def rebuild_h_atoms(mol_graph,
 
     Parameters
     ----------
-    mol_graph: :class:`nx.Graph`
+    mol_graph: networkx.Graph
         graph describing the full molecule without hydrogen atoms
-    copy_attrs: list[abc.hashable]
+    copy_attrs: list[collections.abc.Hashable]
         a list of attributes to copy from the parent node to the
         hydrogen atom
     keep_bonding: bool
@@ -110,7 +110,7 @@ def annotate_ez_isomers_cgsmiles(molecule):
 
     Parameters
     ----------
-    molecule: nx.Graph
+    molecule: networkx.Graph
         The molecule of interest, which must of ez_isomer_pairs
         and ez_isomer_class set as node attributes
     """
@@ -147,7 +147,7 @@ def read_fragment_smiles(smiles_str,
 
     Returns
     -------
-    nx.Graph
+    networkx.Graph
         the graph of the molecular fragment
     """
     if smiles_str == 'H':