Merge branch 'main' into param_dict

.github/workflows/pytest.yml

@@ -40,7 +40,7 @@ jobs:
 
       - name: Pytest coverage comment
         id: coverageComment
-        uses: MishaKav/[email protected].52
+        uses: MishaKav/[email protected].53
         with:
           pytest-coverage-path: ./pytest-coverage.txt
           junitxml-path: ./pytest.xml

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: check-merge-conflict
@@ -14,19 +14,19 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.7
+    rev: v0.8.1
     hooks:
       - id: ruff # linter
         args: [--fix]
       - id: ruff-format # formatter
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.21.0
+    rev: typos-dict-v0.11.37
     hooks:
       - id: typos
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.13.0
     hooks:
       - id: mypy
         pass_filenames: false
@@ -38,3 +38,13 @@ repos:
           - pypulseq>=1.4.2
           - types-pyyaml
           - types-tqdm
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: ""
+  autoupdate_commit_msg: "[pre-commit] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [mypy]
+  submodules: false

src/bmctool/parameters/CESTPool.py

@@ -6,7 +6,7 @@
 class CESTPool(Pool):
     """Class to store CESTPool parameters."""
 
-    __slots__ = ['_r1', '_r2', '_k', '_f', '_dw']
+    __slots__ = ['_dw', '_f', '_k', '_r1', '_r2']
 
     def __init__(
         self,
@@ -44,16 +44,6 @@ def __init__(
         super().__init__(f=f, dw=dw, r1=r1, r2=r2, t1=t1, t2=t2)
         self.k = k
 
-    def __dict__(self):
-        """Return dictionary representation of CESTPool."""
-        return {
-            'f': self.f,
-            'r1': self.r1,
-            'r2': self.r2,
-            'k': self.k,
-            'dw': self.dw,
-        }
-
     @property
     def k(self) -> float:
         """Exchange rate [Hz]."""

src/bmctool/parameters/MTPool.py

@@ -9,7 +9,7 @@ class MTPool(Pool):
     """Class to store MTPool parameters."""
 
     valid_lineshapes: typing.ClassVar[list[str]] = ['lorentzian', 'superlorentzian']
-    __slots__ = ['_r1', '_r2', '_k', '_f', '_dw', '_lineshape']
+    __slots__ = ['_dw', '_f', '_k', '_lineshape', '_r1', '_r2']
 
     def __init__(
         self,
@@ -52,17 +52,6 @@ def __init__(
         self.k = k
         self.lineshape = lineshape
 
-    def __dict__(self):
-        """Return dictionary representation of MTPool."""
-        return {
-            'f': self.f,
-            'r1': self.r1,
-            'r2': self.r2,
-            'k': self.k,
-            'dw': self.dw,
-            'lineshape': self.lineshape,
-        }
-
     @property
     def k(self) -> float:
         """Exchange rate [Hz]."""

src/bmctool/parameters/Options.py

@@ -8,7 +8,7 @@
 class Options:
     """Class to store simulation options."""
 
-    __slots__ = ['_verbose', '_reset_init_mag', '_scale', '_max_pulse_samples']
+    __slots__ = ['_max_pulse_samples', '_reset_init_mag', '_scale', '_verbose']
 
     def __init__(
         self,
@@ -45,14 +45,9 @@ def __eq__(self, other: object) -> bool:
             return all(getter(self) == getter(other) for getter in attr_getters)
         return False
 
-    def __dict__(self):
-        """Return dictionary representation of Options."""
-        return {
-            'verbose': self.verbose,
-            'reset_init_mag': self.reset_init_mag,
-            'scale': self.scale,
-            'max_pulse_samples': self.max_pulse_samples,
-        }
+    def to_dict(self) -> dict:
+        """Return dictionary representation with leading underscores removed."""
+        return {slot.lstrip('_'): getattr(self, slot) for slot in self.__slots__}
 
     @property
     def verbose(self) -> bool:

src/bmctool/parameters/Parameters.py

@@ -120,6 +120,7 @@ def from_dict(cls, config: dict) -> Self:
         system = System(
             **{rename.get(key, key): value for key, value in config.items() if rename.get(key, key) in sys_keys}
         )
+
         options = Options(
             **{rename.get(key, key): value for key, value in config.items() if rename.get(key, key) in opt_keys}
         )
@@ -149,16 +150,16 @@ def to_yaml(self, yaml_file: str | Path) -> None:
             Path to yaml file.
         """
         if self.cest_pools:
-            cest_dict = {f'cest_{ii + 1}': pool.__dict__() for ii, pool in enumerate(self.cest_pools)}
+            cest_dict = {f'cest_{ii + 1}': pool.to_dict() for ii, pool in enumerate(self.cest_pools)}
 
         with Path(yaml_file).open('w') as file:
-            yaml.dump({'water_pool': self.water_pool.__dict__()}, file)
+            yaml.dump({'water_pool': self.water_pool.to_dict()}, file)
             if self.mt_pool:
-                yaml.dump({'mt_pool': self.mt_pool.__dict__()}, file)
+                yaml.dump({'mt_pool': self.mt_pool.to_dict()}, file)
             if self.cest_pools:
                 yaml.dump({'cest_pool': cest_dict}, file)
-            yaml.dump(self.system.__dict__(), file)
-            yaml.dump(self.options.__dict__(), file)
+            yaml.dump(self.system.to_dict(), file)
+            yaml.dump(self.options.to_dict(), file)
 
         file.close()
 

src/bmctool/parameters/Pool.py

@@ -8,7 +8,7 @@
 class Pool(ABC):
     """Base Class for Pools."""
 
-    __slots__ = ['_r1', '_r2', '_f', '_dw']
+    __slots__ = ['_dw', '_f', '_r1', '_r2']
 
     def __init__(
         self,
@@ -68,6 +68,10 @@ def __eq__(self, other: object) -> bool:
             return all(getter(self) == getter(other) for getter in attr_getters)
         return False
 
+    def to_dict(self) -> dict:
+        """Return dictionary representation with leading underscores removed."""
+        return {slot.lstrip('_'): getattr(self, slot) for slot in self.__slots__}
+
     @property
     def r1(self) -> float:
         """R1 relaxation rate [Hz] (1/T1)."""

src/bmctool/parameters/System.py

@@ -6,7 +6,7 @@
 class System:
     """Class to store system parameters."""
 
-    __slots__ = ['_b0', '_gamma', '_b0_inhom', '_rel_b1']
+    __slots__ = ['_b0', '_b0_inhom', '_gamma', '_rel_b1']
 
     def __init__(
         self,
@@ -43,14 +43,9 @@ def __eq__(self, other: object) -> bool:
             return all(getter(self) == getter(other) for getter in attr_getters)
         return False
 
-    def __dict__(self):
-        """Return dictionary representation of System."""
-        return {
-            'b0': self.b0,
-            'gamma': self.gamma,
-            'b0_inhom': self.b0_inhom,
-            'rel_b1': self.rel_b1,
-        }
+    def to_dict(self) -> dict:
+        """Return dictionary representation with leading underscores removed."""
+        return {slot.lstrip('_'): getattr(self, slot) for slot in self.__slots__}
 
     @property
     def b0(self) -> float:

src/bmctool/parameters/WaterPool.py

@@ -6,7 +6,7 @@
 class WaterPool(Pool):
     """Class to store WaterPool parameters."""
 
-    __slots__ = ['_f', '_dw', '_r1', '_r2']
+    __slots__ = ['_dw', '_f', '_r1', '_r2']
 
     def __init__(
         self,
@@ -37,13 +37,9 @@ def __init__(
         """
         super().__init__(f=f, dw=0, r1=r1, r2=r2, t1=t1, t2=t2)
 
-    def __dict__(self):
-        """Return dictionary representation of WaterPool."""
-        return {
-            'f': self.f,
-            'r1': self.r1,
-            'r2': self.r2,
-        }
+    def to_dict(self) -> dict:
+        """Return dictionary representation with leading underscores removed."""
+        return {slot.lstrip('_'): getattr(self, slot) for slot in self.__slots__ if slot != '_dw'}
 
     @property
     def dw(self) -> float:

src/bmctool/utils/eval.py

@@ -183,7 +183,7 @@ def plot_z(
         ax2 = ax1.twinx()
         ax2.set_ylim((round(min(mtr_asym) - 0.01, 2), round(max(mtr_asym) + 0.01, 2)))
         ax2.set_ylabel('$MTR_{asym}$', color='y')
-        ax2.plot(offsets, mtr_asym, label='$MTR_{asym}$', color='y')  # type: ignore
+        ax2.plot(offsets, mtr_asym, label='$MTR_{asym}$', color='y')
         ax2.tick_params(axis='y', labelcolor='y')
         fig.tight_layout()
 

src/bmctool/utils/misc.py

@@ -5,8 +5,8 @@ def truthy_check(value: bool | int | float | str) -> bool:
     """Check if input value is truthy."""
     if isinstance(value, str):
         value = value.lower()
-    if value in {True, 1, 1.0, 'true'}:
+    if value in {True, 'true'}:
         return True
-    elif value in {False, 0, 'false'}:
+    elif value in {False, 'false'}:
         return False
     raise ValueError('Input {value} cannot be converted to bool.')

src/bmctool/utils/pulses/calc_power_equivalents.py

@@ -33,8 +33,9 @@ def calc_power_equivalent(
     """
     amp = rf_pulse.signal / gamma_hz
     duty_cycle = tp / (tp + td)
+    cwpe = np.sqrt(np.trapz(amp**2, rf_pulse.t) / tp * duty_cycle)  # noqa: NPY201
 
-    return np.sqrt(np.trapz(amp**2, rf_pulse.t) / tp * duty_cycle)  # type: ignore
+    return cwpe  # type: ignore
 
 
 def calc_amplitude_equivalent(
@@ -62,6 +63,6 @@ def calc_amplitude_equivalent(
         Continuous wave amplitude equivalent value.
     """
     duty_cycle = tp / (tp + td)
-    alpha_rad = np.trapz(rf_pulse.signal * gamma_hz * 360, rf_pulse.t) * np.pi / 180
+    alpha_rad = np.trapz(rf_pulse.signal * gamma_hz * 360, rf_pulse.t) * np.pi / 180  # noqa: NPY201
 
     return alpha_rad / (gamma_hz * 2 * np.pi * tp) * duty_cycle  # type: ignore

src/bmctool/utils/pulses/make_hanning.py

@@ -51,5 +51,5 @@ def make_gauss_hanning(
     rf_pulse = pp.make_gauss_pulse(flip_angle=flip_angle, duration=pulse_duration, system=system, phase_offset=0)
     n_signal = rf_pulse.signal.size
     hanning_shape = hanning(n_signal)
-    rf_pulse.signal = hanning_shape / np.trapz(hanning_shape, x=rf_pulse.t) * (flip_angle / (2 * np.pi))
+    rf_pulse.signal = hanning_shape / np.trapz(hanning_shape, x=rf_pulse.t) * (flip_angle / (2 * np.pi))  # noqa: NPY201
     return rf_pulse  # type: ignore