fixing docs

Author: giovanni-br

moha/api.py

@@ -24,14 +24,13 @@ class HamiltonianAPI(ABC):
     r"""Hamiltonian abstract base class."""
 
     def generate_connectivity_matrix(self):
-        r"""
-
-        Generate connectivity matrix.
+        r"""Generate connectivity matrix.
 
         Returns
         -------
         tuple
             (dictionary, np.ndarray)
+
         """
         # check if self.connectivity is a matrix
         # if so, put assign it to self.connectivity_matrix
@@ -76,8 +75,7 @@ def generate_zero_body_integral(self):
 
     @abstractmethod
     def generate_one_body_integral(self, dense: bool, basis: str):
-        r"""
-        Generate one body integral in spatial or spin orbital basis.
+        r"""Generate one body integral in spatial or spin orbital basis.
 
         Parameters
         ----------
@@ -89,13 +87,13 @@ def generate_one_body_integral(self, dense: bool, basis: str):
         Returns
         -------
         scipy.sparse.csr_matrix or np.ndarray
+
         """
         pass
 
     @abstractmethod
     def generate_two_body_integral(self, sym: int, basis: str, dense: bool):
-        r"""
-        Generate two body integral in spatial or spinorbital basis.
+        r"""Generate two body integral in spatial or spinorbital basis.
 
         Parameters
         ----------
@@ -109,12 +107,12 @@ def generate_two_body_integral(self, sym: int, basis: str, dense: bool):
         Returns
         -------
         scipy.sparse.csr_matrix or np.ndarray
+
         """
         pass
 
     def to_sparse(self, Md):
-        r"""
-        Convert dense array of integrals to sparse array in scipy csr format.
+        r"""Convert dense array of integrals to sparse array in scipy csr.
 
         Parameters
         ----------
@@ -124,6 +122,7 @@ def to_sparse(self, Md):
         Returns
         -------
         scipy.sparse.csr_matrix
+
         """
         # Finding indices for non-zero elements and shape of Md.
         indices = np.array(np.where(Md != 0)).astype(int).T
@@ -156,8 +155,7 @@ def to_sparse(self, Md):
             return
 
     def to_dense(self, Ms, dim=2):
-        r"""
-        Convert to dense matrix.
+        r"""Convert to dense matrix.
 
         Convert sparse array of integrals
         in scipy csr format to dense numpy array.
@@ -171,6 +169,7 @@ def to_dense(self, Ms, dim=2):
         Returns
         -------
         np.ndarray
+
         """
         # return dense 2D array (default).
         if dim == 2:
@@ -190,8 +189,7 @@ def to_dense(self, Ms, dim=2):
             raise ValueError("Target output dimension must be either 2 or 4.")
 
     def to_spatial(self, sym: int, dense: bool, nbody: int):
-        r"""
-        Convert one-/two- integral matrix from spin-orbital to spatial basis.
+        r"""Convert one/two integral matrix from spin-orbital to spatial basis.
 
         Parameters
         ----------
@@ -229,6 +227,7 @@ def to_spatial(self, sym: int, dense: bool, nbody: int):
         Assuming that :math:`v_{pqrs}^{abab} = v_{pqrs}^{baba}` and
         :math:`v_{pqrs}^{aaaa} = v_{pqrs}^{bbbb}`
         :math:`v_{pqrs} = 0.5*(v_{pqrs}^{aaaa} + v_{pqrs}^{abab})`
+
         """
         # Assumption: spatial components of alpha and beta
         # spin-orbitals are equivalent
@@ -275,8 +274,7 @@ def to_spatial(self, sym: int, dense: bool, nbody: int):
         return spatial_int
 
     def to_spinorbital(self, integral: np.ndarray, sym=1, dense=False):
-        r"""
-        Convert one-/two- integral matrix from spatial to spin-orbital basis.
+        r"""Convert one/two integral matrix from spatial to spin-orbital basis.
 
         Parameters
         ----------
@@ -290,12 +288,12 @@ def to_spinorbital(self, integral: np.ndarray, sym=1, dense=False):
         Returns
         -------
         None
+
         """
         pass
 
     def save_fcidump(self, f: Union[TextIO, str], nelec=0, spinpol=0):
-        r"""
-        Save all parts of hamiltonian in fcidump format.
+        r"""Save all parts of hamiltonian in fcidump format.
 
         Parameters
         ----------
@@ -313,6 +311,7 @@ def save_fcidump(self, f: Union[TextIO, str], nelec=0, spinpol=0):
         Returns
         -------
         None
+
         """
         # Open file if it is a string
         if isinstance(f, str):
@@ -358,8 +357,7 @@ def save_fcidump(self, f: Union[TextIO, str], nelec=0, spinpol=0):
             print(f"{core_energy:23.16e} {0:4d} {0:4d} {0:4d} {0:4d}", file=f)
 
     def save_triqs(self, fname: str, integral):
-        r"""
-        Save matrix in triqc format.
+        r"""Save matrix in triqc format.
 
         Parameters
         ----------
@@ -371,6 +369,7 @@ def save_triqs(self, fname: str, integral):
         Returns
         -------
         None
+
         """
         pass
 
@@ -392,6 +391,7 @@ def savez(self, f: Union[TextIO, str]):
         ```
         open("file.npz", "wb") as f:
         ```
+
         """
         if self.zero_energy is not None:
             e0 = self.zero_energy
@@ -412,8 +412,7 @@ def savez(self, f: Union[TextIO, str]):
 
 
 def expand_sym(sym, integral, nbody):
-    r"""
-    Restore permutational symmetry of one- and two-body terms.
+    r"""Restore permutational symmetry of one- and two-body terms.
 
     Parameters
     ----------
@@ -459,6 +458,7 @@ def expand_sym(sym, integral, nbody):
         permutations considered can be
         found in [this site]
         (http://vergil.chemistry.gatech.edu/notes/permsymm/permsymm.html).
+
     """
     if sym not in [1, 2, 4, 8]:
         raise ValueError("Wrong input symmetry")

moha/gpt/gpt.py

@@ -10,18 +10,18 @@
 
 
 def map_to_toml(funcs):
-    """
-    Functin that maps the dictionary to the toml-like dictionary.
+    """Functin that maps the dictionary to the toml-like dictionary.
 
     Parmaeters:
     -----------
     funcs: dict
         The dictionary that contains the function arguments
 
-    Returns:
-    --------
+    Returns
+    -------
     toml_dict: dict
         The dictionary that contains the toml-like arguments
+
     """
     toml_dict = {}
     toml_dict["control"] = {}
@@ -64,15 +64,15 @@ def map_to_toml(funcs):
 
 
 def load_config():
-    """
-    Load OpenAI API key and model type from config.txt file.
+    """Load OpenAI API key and model type from config.txt file.
 
-    Returns:
-    --------
+    Returns
+    -------
     OPENAI_API_KEY : str
         OpenAI API key
     GPT_MODEL : str
         GPT model type
+
     """
     config_path = Path(__file__).parent / "config.toml"
     config = toml.load(config_path)
@@ -87,11 +87,10 @@ def load_config():
 def chat_completion_request(messages, model, client,
                             tools=None,
                             tool_choice=None):
-    """
-    Request ChatCompletion from OpenAI API.
+    """Request ChatCompletion from OpenAI API.
 
-    Parameters:
-    -----------
+    Parameters
+    ----------
     messages : list
         List of messages
     model : str
@@ -103,10 +102,11 @@ def chat_completion_request(messages, model, client,
     tool_choice : dict
         Tool choice dictionary
 
-    Returns:
-    --------
+    Returns
+    -------
     response : dict
         ChatCompletion response
+
     """
     try:
         response = client.chat.completions.create(
@@ -123,31 +123,31 @@ def chat_completion_request(messages, model, client,
 
 
 def read_promt():
-    """
-    Read prompt from user.
+    """Read prompt from user.
 
-    Returns:
-    --------
+    Returns
+    -------
     prompt : str
         User input prompt
+
     """
     prompt = input("Describe Hamiltonian that needs to be generated: ")
     return prompt
 
 
 def generate_ham(prompt):
-    """
-    Generate Hamiltonian from prompt.
+    """Generate Hamiltonian from prompt.
 
-    Parameters:
-    -----------
+    Parameters
+    ----------
     prompt : str
         User input prompt
 
-    Returns:
-    --------
+    Returns
+    -------
     ham : dict
         Model Hamiltonian
+
     """
     # get api key and model type
     OPENAI_API_KEY, GPT_MODEL = load_config()

moha/gui/gui_utils.py

@@ -12,13 +12,13 @@
 
 
 def destroy_widgets(widgets):
-    r"""
-    Destroy list of widgets.
+    r"""Destroy list of widgets.
 
     Parameters
     ----------
     widgets: list
         list of widgets to be destroyed
+
     """
     # Destroy old form widgets if they exist
     for widget in widgets:
@@ -27,31 +27,31 @@ def destroy_widgets(widgets):
 
 
 def enable_dropdown_on_click(dropdown, prompt_text):
-    r"""
-    Enable dropdown and remove promt text on click.
+    r"""Enable dropdown and remove promt text on click.
 
     Parameters
     ----------
     dropdown: tk.Dropdown
         dropdown object to be enabled
     prompt_text: str
         initial prompt in the dropdown
+
     """
     if dropdown.get() == prompt_text:
         dropdown.state(["!disabled"])
         dropdown.set("")
 
 
 def set_prompt(dropdown, prompt_text):
-    r"""
-    Initialize dropdown text to default prompt.
+    r"""Initialize dropdown text to default prompt.
 
     Parameters
     ----------
     dropdown: tk.Dropdown
         dropdown object to be enabled
     prompt_text: str
         initial prompt in the dropdown
+
     """
     # Initialize dropdown text to default prompt
     dropdown.state(["disabled"])
@@ -65,8 +65,7 @@ def set_prompt(dropdown, prompt_text):
 
 
 def make_title(frame, title, pady=(0, 0), side=tk.TOP):
-    r"""
-    Make and display title in frame.
+    r"""Make and display title in frame.
 
     Parameters
     ----------
@@ -78,6 +77,7 @@ def make_title(frame, title, pady=(0, 0), side=tk.TOP):
         vertical padding of the title
     side: one of tk.TOP, tk.BOTTOM, tk.LEFT, tk.RIGHT
         the side which the title will be packed
+
     """
     title_font = ("Arial", 12, "bold")
     title_frame = tk.Frame(frame)