New feature/tensor network

.github/workflows/code-quality.yml

@@ -1,6 +1,10 @@
-name: Code quality
+name: Code Quality
 
-on: [push, pull_request]
+on:
+  push:
+    branches: [master, main, development]
+  pull_request:
+    branches: [master, main, development]
 
 jobs:
   build:
@@ -18,27 +22,13 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install black pylint pytest coverage coveralls
-        pip install -r requirements/requirements.txt
-
-    - name: Run black
-      continue-on-error: true
-      run: black --check .
+        pip install black pylint
 
     - name: Run lint with pylint
       continue-on-error: true
       run: |
-        find qDNA tools -type f -name "*.py" ! -name "__init__.py" | xargs pylint
-
-    - name: Run tests with pytest
-      run: python -m pytest
+        pylint --rcfile=.pylintrc $(git ls-files 'qDNA/*.py')
 
-    - name: Run tests with coverage
-      run: |
-        coverage run -m pytest
-
-    - name: Upload coverage to Coveralls
+    - name: Run black
       continue-on-error: true
-      env:
-        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-      run: coveralls
+      run: black --check .

.gitignore

@@ -20,9 +20,6 @@ docs/_templates/
 __pycache__
 .pytest_cache/
 
-# created for pylint
-.pylintrc
-
 # created by coverage
 .coverage
 htmlcov/

.pylintrc

@@ -0,0 +1,57 @@
+[MASTER]
+ignore=tests
+jobs=1
+load-plugins=
+extension-pkg-whitelist=
+
+[MESSAGES CONTROL]
+disable=
+    C0114,  # missing-module-docstring
+    C0116,  # missing-function-docstring
+    C0301,  # line-too-long
+    R0903,  # too-few-public-methods
+    R0801,  # duplicate-code
+    W0511,  # fixme
+    R0902,  # too-many-instance-attributes
+    R0912,  # too-many-branches
+    R0913,  # too-many-arguments
+    R0914,  # too-many-locals
+    R0915,  # too-many-statements
+    R0917,  # too-many-positional-arguments
+    R0401,  # cyclic-import
+    E0401,  # import-error
+
+[REPORTS]
+output-format=colorized
+reports=no
+score=yes
+
+[BASIC]
+good-names=
+bad-names=
+variable-rgx=.*
+attr-rgx=.*
+argument-rgx=.*
+method-rgx=.*
+module-rgx=.*
+class-rgx=.*
+function-rgx=.*
+
+
+[TYPECHECK]
+ignored-modules=
+ignored-classes=optparse.Values,thread._local,_thread._local
+generated-members=numpy.*,torch.*
+
+[FORMAT]
+max-line-length=120
+indent-string='    '
+
+[DESIGN]
+max-args=7
+max-attributes=10
+max-locals=20
+max-returns=6
+max-branches=12
+max-statements=50
+max-line-length=100

docs/conf.py

@@ -50,9 +50,7 @@
 # Do not add full module names
 add_module_names = False
 
-numpydoc_show_inherited_class_members = (
-    False  # Show inherited class members in the documentation
-)
+numpydoc_show_inherited_class_members = False  # Show inherited class members in the documentation
 numpydoc_show_property_with_doc = (
     False  # Show properties with documentation in the class documentation
 )

pyproject.toml

@@ -40,6 +40,6 @@ requires = ["setuptools>=61.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.black]
-line-length = 120
+line-length = 100
 target-version = ['py311']
 skip-string-normalization = true

qDNA/__init__.py

@@ -18,5 +18,3 @@
 from .evaluation import *
 from .visualization import *
 from .legacy import *
-
-# some nice comment...

qDNA/environment/observables.py

@@ -124,15 +124,11 @@ def get_eh_observable(tb_basis, particle, start_state, end_state):
 
     # Create the electron observable
     if particle == "electron":
-        eh_observable = np.kron(
-            get_observable(tb_basis, start_state, end_state), np.eye(num_sites)
-        )
+        eh_observable = np.kron(get_observable(tb_basis, start_state, end_state), np.eye(num_sites))
 
     # Create the hole observable
     elif particle == "hole":
-        eh_observable = np.kron(
-            np.eye(num_sites), get_observable(tb_basis, start_state, end_state)
-        )
+        eh_observable = np.kron(np.eye(num_sites), get_observable(tb_basis, start_state, end_state))
 
     # Create the exciton observable
     elif particle == "exciton":

qDNA/environment/therm_ops.py

@@ -106,11 +106,7 @@ def get_loc_therm_op(eigv, eigs, unique, site_m, relaxation, matrix_dim):
         omega_i, omega_j = eigv[i], eigv[j]
         state_i, state_j = eigs[:, i], eigs[:, j]
         if omega_i - omega_j == unique:
-            op += (
-                state_j[site_m].conjugate()
-                * state_i[site_m]
-                * np.outer(state_j, state_i)
-            )
+            op += state_j[site_m].conjugate() * state_i[site_m] * np.outer(state_j, state_i)
     if relaxation:
         op = add_groundstate(op)
 

qDNA/environment/therm_rates.py

@@ -53,9 +53,7 @@ def ohmic_spectral_density(omega, cutoff_freq, reorg_energy, exponent):
     """
     if omega <= 0:
         return 0
-    return (np.pi * reorg_energy * omega**exponent / cutoff_freq) * np.exp(
-        -omega / cutoff_freq
-    )
+    return (np.pi * reorg_energy * omega**exponent / cutoff_freq) * np.exp(-omega / cutoff_freq)
 
 
 # ----------------------------------------------------------------------
@@ -76,9 +74,7 @@ def bose_einstein_distrib(omega, temperature):
     float
         Bose-Einstein distribution.
     """
-    assert (
-        temperature != 0 and omega != 0
-    ), "Temperature and frequency must be non-zero."
+    assert temperature != 0 and omega != 0, "Temperature and frequency must be non-zero."
     return 1.0 / (np.exp(c.hbar * omega * 1e12 / (c.k * temperature)) - 1)
 
 
@@ -142,12 +138,8 @@ def rate_constant_redfield(
         spec_omega_ji = debye_spectral_density(-omega, cutoff_freq, reorg_energy)
 
     elif spectral_density == "ohmic":
-        spec_omega_ij = ohmic_spectral_density(
-            omega, cutoff_freq, reorg_energy, exponent
-        )
-        spec_omega_ji = ohmic_spectral_density(
-            -omega, cutoff_freq, reorg_energy, exponent
-        )
+        spec_omega_ij = ohmic_spectral_density(omega, cutoff_freq, reorg_energy, exponent)
+        spec_omega_ji = ohmic_spectral_density(-omega, cutoff_freq, reorg_energy, exponent)
 
     n_omega_ij = bose_einstein_distrib(omega, temperature)
     n_omega_ji = bose_einstein_distrib(-omega, temperature)

qDNA/evaluation/evaluation.py

@@ -78,9 +78,7 @@ def calc_lifetime(self):
         start_time = time.time()
         gs_pop = self.get_groundstate_pop()["groundstate"]
         try:
-            _, index = next(
-                (val, i) for i, val in enumerate(gs_pop) if val >= 1 - 1 / np.e
-            )
+            _, index = next((val, i) for i, val in enumerate(gs_pop) if val >= 1 - 1 / np.e)
             self.lifetime = self.times[index]
             if self.t_unit == "ps":
                 self.lifetime *= 1000
@@ -136,9 +134,7 @@ def calc_charge_separation(self, average=True):
 
         # Calculate the electron-hole distance
         distance_list = 3.4 * get_eh_distance(self.eh_basis)
-        self.charge_separation = [
-            distance_list @ dm.diag()[1:] for dm in self.get_result()
-        ]
+        self.charge_separation = [distance_list @ dm.diag()[1:] for dm in self.get_result()]
         if average:
             self.charge_separation = np.mean(self.charge_separation).real
         return self.charge_separation
@@ -203,9 +199,7 @@ def calc_backbone_transfer(self, average=True):
             If the backbone attribute is not set, indicating the model is not a Fishbone model.
         """
 
-        assert (
-            self.backbone
-        ), "Backbone population can only be calculated for Fishbone models"
+        assert self.backbone, "Backbone population can only be calculated for Fishbone models"
         self._back_to_unitary()
 
         upper_backbone_sites, lower_backbone_sites = [], []
@@ -250,9 +244,7 @@ def calc_exciton_transfer(self, average=True):
         assert (
             self.double_stranded
         ), "Exciton transfer can only be calculated for double-stranded models"
-        assert (
-            not self.backbone
-        ), "Exciton transfer can only be calculated for non-backbone models"
+        assert not self.backbone, "Exciton transfer can only be calculated for non-backbone models"
         self._back_to_unitary()
 
         upper_sites, lower_sites = [], []
@@ -334,10 +326,7 @@ def __init__(self, evaluation_list, **kwargs):
             "observables", ["lifetime", "charge_separation", "dipole_moment"]
         )
 
-        self.args = [
-            (i, self.observables, self.evaluation_list)
-            for i in range(self.num_sequences)
-        ]
+        self.args = [(i, self.observables, self.evaluation_list) for i in range(self.num_sequences)]
 
     def calc_results(self, filepath=None, save=True):
         """

qDNA/gui/advanced_frame.py

@@ -54,15 +54,11 @@ def __init__(self, master):
         super().__init__(master)
 
         # help label
-        self.help_label = ctk.CTkLabel(
-            self, text="Help", font=ctk.CTkFont(size=15, weight="bold")
-        )
+        self.help_label = ctk.CTkLabel(self, text="Help", font=ctk.CTkFont(size=15, weight="bold"))
         self.help_label.grid(row=0, column=0, pady=10, padx=10)
 
         # github link
-        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=1, column=0, pady=10, padx=10)
 
         # documentation link

qDNA/gui/fasta_window.py

@@ -98,9 +98,7 @@ def __init__(self, master):
             text="Calculate Exciton Population",
             variable=self.exciton_transfer_var,
         )
-        self.exciton_transfer_checkbox.grid(
-            row=3, column=1, padx=10, pady=10, sticky="w"
-        )
+        self.exciton_transfer_checkbox.grid(row=3, column=1, padx=10, pady=10, sticky="w")
 
         # --------------------------------------------------------------
 
@@ -113,12 +111,8 @@ def __init__(self, master):
         )
 
         # submit button
-        self.submit_button = ctk.CTkButton(
-            self, text="Submit", command=self.process_files
-        )
-        self.submit_button.grid(
-            row=5, column=0, columnspan=2, padx=10, pady=10, sticky="ew"
-        )
+        self.submit_button = ctk.CTkButton(self, text="Submit", command=self.process_files)
+        self.submit_button.grid(row=5, column=0, columnspan=2, padx=10, pady=10, sticky="ew")
 
         # console frame
         self.scrollable_console_frame = ScrollableConsoleFrame(self)
@@ -183,10 +177,7 @@ def estimate_comp_time(self):
         for upper_strand in self.upper_strands:
             comp_time += comp_time_dict[self.tb_model_name][len(upper_strand) - 2]
         comp_time /= min(self.num_cpu, len(self.upper_strands))
-        print(
-            f"Estimated Computation Time {comp_time}"
-            + f"\nUsing {self.num_cpu} kernels"
-        )
+        print(f"Estimated Computation Time {comp_time}" + f"\nUsing {self.num_cpu} kernels")
 
     # ------------------------------------------------------------------
 
@@ -213,9 +204,7 @@ def process_files(self):
             tb_sites = get_tb_sites(upper_strand, tb_model_name=self.tb_model_name)
             tb_sites_list.append(tb_sites)
 
-        evaluation_list = [
-            Evaluation(tb_sites, **self.kwargs) for tb_sites in tb_sites_list
-        ]
+        evaluation_list = [Evaluation(tb_sites, **self.kwargs) for tb_sites in tb_sites_list]
         parallel = EvaluationParallel(evaluation_list, observables=observables)
         results = parallel.calc_results(
             filepath=os.path.join(DATA_DIR, "gui", "result.json"), save=True

qDNA/gui/gui_utils.py

@@ -7,13 +7,9 @@
 
 def change_state_all_widgets(frame, state):
     for widget in frame.winfo_children():
-        if isinstance(
-            widget, ctk.CTkBaseClass
-        ):  # Check if the widget is a customtkinter widget
+        if isinstance(widget, ctk.CTkBaseClass):  # Check if the widget is a customtkinter widget
             widget.configure(state=state)
-        elif isinstance(
-            widget, ctk.CTkFrame
-        ):  # Recursively disable widgets in nested frames
+        elif isinstance(widget, ctk.CTkFrame):  # Recursively disable widgets in nested frames
             change_state_all_widgets(widget, state)
 
 

qDNA/gui/initial_frame.py

@@ -37,9 +37,7 @@ def __init__(self, master):
         # --------------------------------------------------------------
 
         # upper strand label
-        self.upper_strand_label = ctk.CTkLabel(
-            self, text="Upper DNA Strand \n(5'-3' direction):"
-        )
+        self.upper_strand_label = ctk.CTkLabel(self, text="Upper DNA Strand \n(5'-3' direction):")
         self.upper_strand_label.grid(row=2, column=0, pady=0, padx=10)
 
         # upper strand entry
@@ -50,9 +48,7 @@ def __init__(self, master):
         # --------------------------------------------------------------
 
         # lower strand label
-        self.lower_strand_label = ctk.CTkLabel(
-            self, text="Lower DNA Strand \n(3'-5' direction):"
-        )
+        self.lower_strand_label = ctk.CTkLabel(self, text="Lower DNA Strand \n(3'-5' direction):")
         self.lower_strand_label.grid(row=4, column=0, pady=0, padx=10)
 
         # lower strand entry

qDNA/gui/lind_diss_frame.py

@@ -74,16 +74,12 @@ def __init__(self, master):
 
         # local thermalization checkbox
         self.loc_therm_var = ctk.BooleanVar(value=self.defaults["loc_therm"])
-        self.loc_therm_check = ctk.CTkCheckBox(
-            self, text="Local", variable=self.loc_therm_var
-        )
+        self.loc_therm_check = ctk.CTkCheckBox(self, text="Local", variable=self.loc_therm_var)
         self.loc_therm_check.grid(row=6, column=0, padx=10, pady=10)
 
         # global thermalization checkbox
         self.glob_therm_var = ctk.BooleanVar(value=self.defaults["glob_therm"])
-        self.glob_therm_check = ctk.CTkCheckBox(
-            self, text="Global", variable=self.glob_therm_var
-        )
+        self.glob_therm_check = ctk.CTkCheckBox(self, text="Global", variable=self.glob_therm_var)
         self.glob_therm_check.grid(row=6, column=1, padx=10, pady=10)
 
         # --------------------------------------------------------------