improved workflows

.github/workflows/code_quality.yml

@@ -0,0 +1,67 @@
+name: Code Quality with pylint, pytest, black
+
+on: [push, pull_request]
+
+jobs:
+  pylint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+
+    - name: Run pylint
+      continue-on-error: true
+      run: |
+        find qDNA tools -type f -name "*.py" ! -name "__init__.py" | xargs pylint
+
+  pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+
+    - name: Run tests with pytest
+      run: python -m pytest
+
+  black:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install black
+
+    - name: Run black
+      continue-on-error: true
+      run: black --check .

.github/workflows/publish.yml

@@ -1,12 +1,8 @@
 name: Publish Python Package
 
 on:
-  push:
-    branches:
-      - main  
-  pull_request:
-    branches:
-      - main  
+  release:
+    types: [created]
 
 jobs:
   build-and-publish:

docs/sphinx_doc/conf.py

@@ -12,17 +12,18 @@
 
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'QuantumDNA'
-copyright = '2024, Dennis Herb'
-author = 'Dennis Herb'
+project = "QuantumDNA"
+copyright = "2024, Dennis Herb"
+author = "Dennis Herb"
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.0'
+release = "0.1.0"
 
 
 # -- General configuration ---------------------------------------------------
@@ -32,31 +33,31 @@
 # ones.
 
 extensions = [
-    'sphinx.ext.mathjax',
-    'matplotlib.sphinxext.plot_directive',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.doctest',
-    'sphinx.ext.autosummary',
-    'numpydoc',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.napoleon',
+    "sphinx.ext.mathjax",
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.todo",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autosummary",
+    "numpydoc",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.napoleon",
     #'sphinx_gallery.gen_gallery',
-    'sphinxcontrib.bibtex',
+    "sphinxcontrib.bibtex",
 ]
 
-bibtex_bibfiles = ['biblio.bib']
+bibtex_bibfiles = ["biblio.bib"]
 autosummary_generate = True
-                   
+
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -69,4 +70,4 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]

gui/__init__.py

@@ -13,4 +13,4 @@
 from .plotting_window import *
 from .scrollable_console_frame import ScrollableConsoleFrame
 
-from .qdna_app import *
+from .qdna_app import *

gui/config_frame.py

@@ -1,29 +1,38 @@
 import customtkinter as ctk
 
+
 class ConfigFrame(ctk.CTkFrame):
     def __init__(self, master, **kwargs):
         """
-        Notes: 
-            This frame is located in the main/ menu window. This means that the main window is its master. 
-            The frame uses the commands open_custom_window() and open_github() from the master 
-            
+        Notes:
+            This frame is located in the main/ menu window. This means that the main window is its master.
+            The frame uses the commands open_custom_window() and open_github() from the master
+
         Widgets with get() method:
             appearance_mode_combo
         """
-        
+
         # initialization of the ctk.CTkFrame class
         super().__init__(master)
-        
+
         # widgets
-        self.open_github_button = ctk.CTkButton(self, text="GitHub", command=master.open_github)
+        self.open_github_button = ctk.CTkButton(
+            self, text="GitHub", command=master.open_github
+        )
         self.open_github_button.grid(row=8, column=0, pady=10, padx=10)
-
-        self.open_custom_window_button = ctk.CTkButton(self, text="Customize", command=master.open_custom_window)
+
+        self.open_custom_window_button = ctk.CTkButton(
+            self, text="Customize", command=master.open_custom_window
+        )
         self.open_custom_window_button.grid(row=9, column=0, pady=10, padx=10)
-
-        self.appearance_mode_label = ctk.CTkLabel(self, text="Appearance Mode:", anchor="w")
+
+        self.appearance_mode_label = ctk.CTkLabel(
+            self, text="Appearance Mode:", anchor="w"
+        )
         self.appearance_mode_label.grid(row=10, column=0, pady=10, padx=10)
-
-        self.appearance_mode_combo = ctk.CTkComboBox(self, values=["Light", "Dark", "System"], command=ctk.set_appearance_mode)
+
+        self.appearance_mode_combo = ctk.CTkComboBox(
+            self, values=["Light", "Dark", "System"], command=ctk.set_appearance_mode
+        )
         self.appearance_mode_combo.grid(row=11, column=0, pady=10, padx=10)
-        self.appearance_mode_combo.set('System')
+        self.appearance_mode_combo.set("System")

gui/custom_window.py

@@ -3,78 +3,84 @@
 
 from qDNA import wrap_save_tb_params
 
+
 class CustomFrame(ctk.CTkFrame):
     def __init__(self, master, configs):
         """
-        Notes: 
-            This frame is located in the custom window. This means that the custom window is its master. 
-            The frame uses the commands save() and cancel() from the master 
-        
+        Notes:
+            This frame is located in the custom window. This means that the custom window is its master.
+            The frame uses the commands save() and cancel() from the master
+
         Widgets with get() method:
             tb_params_entry, source_entry, particle_combobox, tb_model_combobox, unit_combobox, methylation_checkbox
         """
-        
+
         # initialization of the ctk.CTkFrame class
         super().__init__(master)
         self.configs = configs
-        
+
         # widgets
         self.tb_params_label = ctk.CTkLabel(self, text="TB parameters:")
         self.tb_params_label.grid(row=0, column=0, columnspan=2, pady=10, padx=10)
-    
+
         self.tb_params_entry = ctk.CTkEntry(self)
         self.tb_params_entry.grid(row=1, column=0, columnspan=2, padx=10, pady=10)
 
         self.source_label = ctk.CTkLabel(self, text="Source:")
         self.source_label.grid(row=2, column=0, columnspan=2, padx=10, pady=10)
-    
+
         self.source_entry = ctk.CTkEntry(self)
         self.source_entry.grid(row=3, column=0, columnspan=2, padx=10, pady=10)
-        
+
         self.particle_label = ctk.CTkLabel(self, text="Particle:")
         self.particle_label.grid(row=4, column=0, columnspan=2, padx=10, pady=10)
 
-        self.particle_combobox = ctk.CTkComboBox(self, values=self.configs['PARTICLES'] )
+        self.particle_combobox = ctk.CTkComboBox(self, values=self.configs["PARTICLES"])
         self.particle_combobox.grid(row=5, column=0, columnspan=2, padx=10, pady=10)
 
         self.tb_model_label = ctk.CTkLabel(self, text="TB Model:")
         self.tb_model_label.grid(row=6, column=0, columnspan=2, padx=10, pady=10)
 
-        self.tb_model_combobox = ctk.CTkComboBox(self, values=self.configs['TB_MODELS'] )
+        self.tb_model_combobox = ctk.CTkComboBox(self, values=self.configs["TB_MODELS"])
         self.tb_model_combobox.grid(row=7, column=0, columnspan=2, padx=10, pady=10)
 
         self.unit_label = ctk.CTkLabel(self, text="Unit:")
         self.unit_label.grid(row=8, column=0, columnspan=2, padx=10, pady=10)
 
-        self.unit_combobox = ctk.CTkComboBox(self, values=self.configs['UNITS'] )
+        self.unit_combobox = ctk.CTkComboBox(self, values=self.configs["UNITS"])
         self.unit_combobox.grid(row=9, column=0, columnspan=2, padx=10, pady=10)
 
         check_var = ctk.BooleanVar(value=True)
-        self.methylation_checkbox = ctk.CTkCheckBox(self, text="Methylation", variable=check_var, onvalue=True, offvalue=False)
+        self.methylation_checkbox = ctk.CTkCheckBox(
+            self, text="Methylation", variable=check_var, onvalue=True, offvalue=False
+        )
         self.methylation_checkbox.grid(row=10, column=0, columnspan=2, padx=10, pady=10)
-       
+
         self.save_button = ctk.CTkButton(self, text="Save", command=master.save)
         self.save_button.grid(row=11, column=0, padx=10, pady=10)
-        
+
         self.cancel_button = ctk.CTkButton(self, text="Cancel", command=master.cancel)
         self.cancel_button.grid(row=11, column=1, padx=10, pady=10)
 
+
 class CustomWindow(ctk.CTkToplevel):
-    def __init__(self, master, configs): 
+    def __init__(self, master, configs):
         """
-        Notes: 
-            This window is a toplevel window of the main window. This means that the main window is its master. 
-            The frame uses the commands save() and cancel() from the master 
+        Notes:
+            This window is a toplevel window of the main window. This means that the main window is its master.
+            The frame uses the commands save() and cancel() from the master
         """
-        
+
         # initialization of the ctk.CTkToplevel class
         super().__init__(master)
         self.title("Customize")
-        
+
         # add a instance of CustomFrame to the window
         self.custom_frame = CustomFrame(self, configs)
-        self.custom_frame.grid(row=0, column=0, columnspan=2, padx=10, pady=10, sticky="nsew")
-
+        self.custom_frame.grid(
+            row=0, column=0, columnspan=2, padx=10, pady=10, sticky="nsew"
+        )
+
     def get_custom_frame_params(self):
         """
         Makes all parameters of custom_frame available in this window.
@@ -85,18 +91,25 @@ def get_custom_frame_params(self):
         self.tb_model_name = self.custom_frame.tb_model_combobox.get()
         self.unit = self.custom_frame.unit_combobox.get()
         self.methylated = self.custom_frame.methylation_checkbox.get()
-        
+
     def save(self):
         """
         Saves the tight-binding parameters and closes the window.
         """
         self.get_custom_frame_params()
         notes = f"methlation {self.methylated}"
-        wrap_save_tb_params(self.tb_param_dict, self.source, self.particle, self.tb_model_name, self.unit, notes=notes)
+        wrap_save_tb_params(
+            self.tb_param_dict,
+            self.source,
+            self.particle,
+            self.tb_model_name,
+            self.unit,
+            notes=notes,
+        )
         self.destroy()
-    
+
     def cancel(self):
         """
         Closes the window.
         """
-        self.destroy()
+        self.destroy()