Make pylint more permissive about most names (#257)

.github/workflows/ci.yml

@@ -90,11 +90,11 @@ jobs:
       - name: Running pylint
         shell: bash -l {0}
         run: |
-          pylint --rcfile pylintrc_for_tests --recursive=y tests
-          pylint --recursive=y firecrown/connector
-          pylint --recursive=y firecrown/*.py
-          pylint --recursive=y firecrown/likelihood/*.py
-          pylint --recursive=y firecrown/likelihood/gauss_family/*.py
+          pylint --rcfile pylintrc_for_tests tests
+          pylint --rcfile pylintrc firecrown/connector
+          pylint --rcfile pylintrc firecrown/*.py
+          pylint --rcfile pylintrc firecrown/likelihood/*.py
+          pylint --rcfile pylintrc firecrown/likelihood/gauss_family/*.py
 
       - name: Running pytest
         shell: bash -l {0}

examples/des_y1_3x2pt/des_y1_cosmic_shear_TATT.py

@@ -100,7 +100,7 @@ def run_likelihood() -> None:
     sacc_data = sacc.Sacc.load_fits(saccfile)
 
     src0_tracer = sacc_data.get_tracer("src0")
-    z, nz = src0_tracer.z, src0_tracer.nz  # pylint: disable-msg=invalid-name
+    z, nz = src0_tracer.z, src0_tracer.nz
 
     # Define a ccl.Cosmology object using default parameters
     ccl_cosmo = ccl.CosmologyVanillaLCDM()
@@ -183,7 +183,6 @@ def run_likelihood() -> None:
         ia_bias=(z, np.ones_like(z)),
         use_A_ia=False,
     )
-    # pylint: disable=invalid-name
     cl_GI = ccl.angular_cl(ccl_cosmo, t_lens, t_ia, ells, p_of_k_a=pk_im)
     cl_II = ccl.angular_cl(ccl_cosmo, t_ia, t_ia, ells, p_of_k_a=pk_ii)
     # The weak gravitational lensing power spectrum
@@ -192,7 +191,6 @@ def run_likelihood() -> None:
     cl_theory = (
         cl_GG + 2 * cl_GI + cl_II
     )  # normally we would also have a third term, +cl_II).
-    # pylint: enable=invalid-name
 
     # plt.plot(x, y_theory, label="Total")
     plt.plot(ells, cells_gg, label="GG firecrown")

firecrown/connector/cobaya/ccl.py

@@ -33,10 +33,10 @@ def initialize(self):
         assert self.input_style
         self.map = mapping_builder(input_style=self.input_style)
 
-        self.a_bg = np.linspace(0.1, 1.0, 50)  # pylint: disable-msg=C0103
-        self.z_bg = 1.0 / self.a_bg - 1.0  # pylint: disable-msg=C0103
-        self.z_Pk = np.arange(0.2, 6.0, 1)  # pylint: disable-msg=C0103
-        self.Pk_kmax = 1.0  # pylint: disable-msg=C0103
+        self.a_bg = np.linspace(0.1, 1.0, 50)
+        self.z_bg = 1.0 / self.a_bg - 1.0
+        self.z_Pk = np.arange(0.2, 6.0, 1)
+        self.Pk_kmax = 1.0
 
     def get_param(self, p: str) -> None:
         """Return the current value of the parameter named 'p'.
@@ -119,9 +119,12 @@ def calculate(
 
         chi_arr = self.provider.get_comoving_radial_distance(self.z_bg)
         hoh0_arr = self.provider.get_Hubble(self.z_bg) / self.map.get_H0()
-        k, z, pk = self.provider.get_Pk_grid()  # pylint: disable-msg=C0103
+        k, z, pk = self.provider.get_Pk_grid()
 
-        # pylint: disable-next=W0201,C0103
+        # Note: we havae to define self.a_Pk here because Cobaya does not allow
+        # us to override the __init__ method.
+        #
+        # pylint: disable-next=attribute-defined-outside-init
         self.a_Pk = self.map.redshift_to_scale_factor(z)
         pk_a = self.map.redshift_to_scale_factor_p_k(pk)
 

firecrown/connector/mapping.py

@@ -101,7 +101,7 @@ def transform_p_k_h3_to_p_k(self, p_k_h3):
             category=DeprecationWarning,
         )
 
-    def transform_h_to_h_over_h0(self, h):  # pylint: disable-msg=C0103
+    def transform_h_to_h_over_h0(self, h):
         """Transform distances h to :math:`h/h_0`."""
         assert h is not None  # use assertion to silence pylint warning
         warnings.simplefilter("always", DeprecationWarning)
@@ -139,31 +139,31 @@ def set_params(
         # Typecheck is done automatically using the descriptors and is done to
         # avoid void very confusing error messages at a later time in case of
         # error.
-        self.Omega_c = Omega_c  # pylint: disable-msg=C0103
-        self.Omega_b = Omega_b  # pylint: disable-msg=C0103
-        self.h = h  # pylint: disable-msg=C0103
+        self.Omega_c = Omega_c
+        self.Omega_b = Omega_b
+        self.h = h
 
         if A_s is not None and sigma8 is not None:
             raise ValueError("Exactly one of A_s and sigma8 must be supplied")
         if sigma8 is None:
-            self.A_s = A_s  # pylint: disable-msg=C0103
-            self.sigma8 = None  # pylint: disable-msg=C0103
+            self.A_s = A_s
+            self.sigma8 = None
         else:
-            self.A_s = None  # pylint: disable-msg=C0103
-            self.sigma8 = sigma8  # pylint: disable-msg=C0103
+            self.A_s = None
+            self.sigma8 = sigma8
 
         self.n_s = n_s
-        self.Omega_k = Omega_k  # pylint: disable-msg=C0103
-        self.Omega_g = None  # pylint: disable-msg=C0103
-        self.Neff = Neff  # pylint: disable-msg=C0103
+        self.Omega_k = Omega_k
+        self.Omega_g = None
+        self.Neff = Neff
         self.m_nu = m_nu
         self.m_nu_type = m_nu_type
-        self.w0 = w0  # pylint: disable-msg=C0103
-        self.wa = wa  # pylint: disable-msg=C0103
-        self.T_CMB = T_CMB  # pylint: disable-msg=C0103
+        self.w0 = w0
+        self.wa = wa
+        self.T_CMB = T_CMB
 
     @staticmethod
-    def redshift_to_scale_factor(z):  # pylint: disable-msg=C0103
+    def redshift_to_scale_factor(z):
         """Given arrays of redshift returns an array of scale factor with the
         inverse order."""
 
@@ -198,7 +198,7 @@ def asdict(self) -> Dict[str, Union[Optional[float], List[float]]]:
             "T_CMB": self.T_CMB,
         }
 
-    def get_H0(self) -> float:  # pylint: disable-msg=C0103
+    def get_H0(self) -> float:  # pylint: disable-msg=invalid-name
         """Return the value of H0."""
         return self.h * 100.0
 
@@ -247,7 +247,6 @@ def set_params_from_cosmosis(self, cosmosis_params: NamedParameters):
         # TODO: Verify that CosmoSIS/CAMB does not use Omega_g
         # TODO: Verify that CosmoSIS/CAMB uses delta_neff, not N_eff
 
-        # pylint: disable=invalid-name
         h = cosmosis_params.get_float("h0")
         Omega_b = cosmosis_params.get_float("omega_b")
         Omega_c = cosmosis_params.get_float("omega_c")
@@ -263,7 +262,6 @@ def set_params_from_cosmosis(self, cosmosis_params: NamedParameters):
         m_nu_type = "normal"
         w0 = cosmosis_params.get_float("w")
         wa = cosmosis_params.get_float("wa")
-        # pylint: enable=invalid-name
 
         # pylint: disable=duplicate-code
         self.set_params(
@@ -388,23 +386,23 @@ def set_params_from_camb(self, **params_values):
         # CAMB can use different parameters in place of H0, we must deal with this
         # possibility here.
 
-        H0 = params_values["H0"]  # pylint: disable-msg=C0103
-        As = params_values["As"]  # pylint: disable-msg=C0103
-        ns = params_values["ns"]  # pylint: disable-msg=C0103
+        H0 = params_values["H0"]
+        As = params_values["As"]
+        ns = params_values["ns"]
         ombh2 = params_values["ombh2"]
         omch2 = params_values["omch2"]
-        Neff = params_values["nnu"]  # pylint: disable-msg=C0103
+        Neff = params_values["nnu"]
         m_nu = params_values["mnu"]
-        Omega_k0 = params_values["omk"]  # pylint: disable-msg=C0103
+        Omega_k0 = params_values["omk"]
 
         m_nu_type = "normal"
-        h0 = H0 / 100.0  # pylint: disable-msg=C0103
+        h0 = H0 / 100.0
         h02 = h0 * h0
-        Omega_b0 = ombh2 / h02  # pylint: disable-msg=C0103
-        Omega_c0 = omch2 / h02  # pylint: disable-msg=C0103
+        Omega_b0 = ombh2 / h02
+        Omega_c0 = omch2 / h02
 
-        w = params_values.get("w", -1.0)  # pylint: disable-msg=C0103
-        wa = params_values.get("wa", 0.0)  # pylint: disable-msg=C0103
+        w = params_values.get("w", -1.0)
+        wa = params_values.get("wa", 0.0)
 
         # Here we have the following problem, some parameters used by CAMB
         # are implicit, i.e., since they are not explicitly set the default

firecrown/connector/numcosmo/numcosmo.py

@@ -59,12 +59,12 @@ def set_params_from_numcosmo(
             self.p_mnl.prepare_if_needed(hi_cosmo)
         self.dist.prepare_if_needed(hi_cosmo)
 
-        h = hi_cosmo.h()  # pylint: disable-msg=C0103
-        Omega_b = hi_cosmo.Omega_b0()  # pylint: disable-msg=invalid-name
-        Omega_c = hi_cosmo.Omega_c0()  # pylint: disable-msg=invalid-name
-        Omega_k = hi_cosmo.Omega_k0()  # pylint: disable-msg=invalid-name
-        Neff = hi_cosmo.Neff()  # pylint: disable-msg=invalid-name
-        T_gamma0 = hi_cosmo.T_gamma0()  # pylint: disable-msg=invalid-name
+        h = hi_cosmo.h()
+        Omega_b = hi_cosmo.Omega_b0()
+        Omega_c = hi_cosmo.Omega_c0()
+        Omega_k = hi_cosmo.Omega_k0()
+        Neff = hi_cosmo.Neff()
+        T_gamma0 = hi_cosmo.T_gamma0()
 
         m_nu: Union[float, List[float]] = 0.0
         if hi_cosmo.NMassNu() == 0:
@@ -78,11 +78,11 @@ def set_params_from_numcosmo(
                 m_nu[i] = nu_info[0]
 
         if isinstance(hi_cosmo, Nc.HICosmoDEXcdm):
-            w0 = hi_cosmo.props.w  # pylint: disable-msg=C0103
-            wa = 0.0  # pylint: disable-msg=C0103
+            w0 = hi_cosmo.props.w
+            wa = 0.0
         elif isinstance(hi_cosmo, Nc.HICosmoDECpl):
-            w0 = hi_cosmo.props.w0  # pylint: disable-msg=C0103
-            wa = hi_cosmo.props.w1  # pylint: disable-msg=C0103
+            w0 = hi_cosmo.props.w0
+            wa = hi_cosmo.props.w1
         else:
             raise ValueError(f"NumCosmo object {type(hi_cosmo)} not supported.")
 
@@ -94,8 +94,8 @@ def set_params_from_numcosmo(
                 f"NumCosmo HIPrim object type {type(hiprim)} not supported."
             )
 
-        A_s = hiprim.SA_Ampl()  # pylint: disable-msg=invalid-name
-        n_s = hiprim.props.n_SA  # pylint: disable-msg=invalid-name
+        A_s = hiprim.SA_Ampl()
+        n_s = hiprim.props.n_SA
 
         # pylint: disable=duplicate-code
         self.set_params(
@@ -121,7 +121,7 @@ def calculate_ccl_args(self, mset: Ncm.MSet):  # pylint: disable-msg=too-many-lo
 
         if self.p_ml:
             p_m_spline = self.p_ml.get_spline_2d(hi_cosmo)
-            z = np.array(p_m_spline.xv.dup_array())  # pylint: disable-msg=invalid-name
+            z = np.array(p_m_spline.xv.dup_array())
             k = np.array(p_m_spline.yv.dup_array())
 
             scale = self.redshift_to_scale_factor(z)
@@ -138,7 +138,6 @@ def calculate_ccl_args(self, mset: Ncm.MSet):  # pylint: disable-msg=too-many-lo
 
         if self.p_mnl:
             p_mnl_spline = self.p_mnl.get_spline_2d(hi_cosmo)
-            # pylint: disable-next=invalid-name
             z = np.array(p_mnl_spline.xv.dup_array())
             k = np.array(p_mnl_spline.yv.dup_array())
 
@@ -353,7 +352,7 @@ def do_prepare(self, mset: Ncm.MSet):  # pylint: disable-msg=arguments-differ
         self.likelihood.update(firecrown_params)
         self.tools.prepare(self.ccl_cosmo)
 
-    # pylint: disable-next=invalid-name,arguments-differ
+    # pylint: disable-next=arguments-differ
     def do_mean_func(self, _, mean_vector):
         """
         Implements the virtual `Ncm.DataGaussCov` method `mean_func`.

firecrown/likelihood/gauss_family/gauss_family.py

@@ -122,7 +122,6 @@ def compute_chisq(self, tools: ModelingTools) -> float:
         self.predicted_data_vector: npt.NDArray[np.float64] = theory_vector
         self.measured_data_vector: npt.NDArray[np.float64] = data_vector
 
-        # pylint: disable-next=C0103
         x = scipy.linalg.solve_triangular(self.cholesky, residuals, lower=True)
         chisq = np.dot(x, x)
 

firecrown/likelihood/gauss_family/statistic/source/number_counts.py

@@ -32,7 +32,7 @@ class NumberCountsArgs:
     """Class for number counts tracer builder argument."""
 
     scale: float
-    z: npt.NDArray[np.float64]  # pylint: disable-msg=invalid-name
+    z: npt.NDArray[np.float64]
     dndz: npt.NDArray[np.float64]
     bias: Optional[npt.NDArray[np.float64]] = None
     mag_bias: Optional[Tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]] = None
@@ -169,7 +169,7 @@ def _get_derived_parameters(self) -> DerivedParameterCollection:
     def apply(
         self, tools: ModelingTools, tracer_arg: NumberCountsArgs
     ) -> NumberCountsArgs:
-        z = tracer_arg.z  # pylint: disable-msg=invalid-name
+        z = tracer_arg.z
         b_2_z = self.b_2 * np.ones_like(z)
         b_s_z = self.b_s * np.ones_like(z)
         # b_1 uses the "bias" field
@@ -245,7 +245,6 @@ def apply(
         z_bar = self.z_c + self.z_m * (self.r_lim - 24.0)
         # The slope of log(n_tot(z,r_lim)) with respect to r_lim
         # where n_tot(z,r_lim) is the luminosity function after using fit (C.1)
-        # pylint: disable-next=invalid-name
         s = (
             self.eta / self.r_lim
             - 3.0 * self.z_m / z_bar
@@ -421,11 +420,11 @@ def _read(self, sacc_data):
             The data in the sacc format.
         """
         tracer = sacc_data.get_tracer(self.sacc_tracer)
-        z = getattr(tracer, "z").copy().flatten()  # pylint: disable-msg=invalid-name
-        nz = getattr(tracer, "nz").copy().flatten()  # pylint: disable-msg=invalid-name
+        z = getattr(tracer, "z").copy().flatten()
+        nz = getattr(tracer, "nz").copy().flatten()
         indices = np.argsort(z)
-        z = z[indices]  # pylint: disable-msg=invalid-name
-        nz = nz[indices]  # pylint: disable-msg=invalid-name
+        z = z[indices]
+        nz = nz[indices]
 
         self.tracer_args = NumberCountsArgs(
             scale=self.scale, z=z, dndz=nz, bias=None, mag_bias=None

firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py

@@ -32,7 +32,7 @@ class WeakLensingArgs:
     """Class for weak lensing tracer builder argument."""
 
     scale: float
-    z: npt.NDArray[np.float64]  # pylint: disable-msg=invalid-name
+    z: npt.NDArray[np.float64]
     dndz: npt.NDArray[np.float64]
     ia_bias: Optional[Tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]]
 
@@ -236,7 +236,7 @@ def apply(
         tracer_arg, in the context of the given cosmology."""
 
         ccl_cosmo = tools.get_ccl_cosmology()
-        z = tracer_arg.z  # pylint: disable-msg=invalid-name
+        z = tracer_arg.z
         c_1, c_d, c_2 = pyccl.nl_pt.translate_IA_norm(
             ccl_cosmo,
             z,
@@ -353,11 +353,11 @@ def _read(self, sacc_data: sacc.Sacc) -> None:
         """
         tracer = sacc_data.get_tracer(self.sacc_tracer)
 
-        z = getattr(tracer, "z").copy().flatten()  # pylint: disable-msg=invalid-name
-        nz = getattr(tracer, "nz").copy().flatten()  # pylint: disable-msg=invalid-name
+        z = getattr(tracer, "z").copy().flatten()
+        nz = getattr(tracer, "nz").copy().flatten()
         indices = np.argsort(z)
-        z = z[indices]  # pylint: disable-msg=invalid-name
-        nz = nz[indices]  # pylint: disable-msg=invalid-name
+        z = z[indices]
+        nz = nz[indices]
 
         self.tracer_args = WeakLensingArgs(scale=self.scale, z=z, dndz=nz, ia_bias=None)
 

firecrown/likelihood/gauss_family/statistic/supernova.py

@@ -26,17 +26,15 @@ def __init__(self, sacc_tracer) -> None:
 
         self.sacc_tracer = sacc_tracer
         self.data_vector: Optional[DataVector] = None
-        # pylint: disable-next=invalid-name
         self.a: Optional[npt.NDArray[np.float64]] = None
-        self.M = parameters.create()  # pylint: disable-msg=invalid-name
+        self.M = parameters.create()
 
     def read(self, sacc_data: sacc.Sacc):
         """Read the data for this statistic from the SACC file."""
 
         data_points = sacc_data.get_data_points(
             data_type="supernova_distance_mu", tracers=(self.sacc_tracer,)
         )
-        # pylint: disable-next=invalid-name
         z = np.array([dp.get_tag("z") for dp in data_points])
         self.a = 1.0 / (1.0 + z)
         self.data_vector = DataVector.from_list([dp.value for dp in data_points])

firecrown/likelihood/gauss_family/statistic/two_point.py

@@ -336,7 +336,7 @@ def compute_theory_vector(self, tools: ModelingTools) -> TheoryVector:
                     continue
                 if tools.has_pk(pk_name):
                     # Use existing power spectrum
-                    pk = tools.get_pk(pk_name)  # pylint: disable-msg=invalid-name
+                    pk = tools.get_pk(pk_name)
                 elif tracer0.has_pt or tracer1.has_pt:
                     if not tracer0.has_pt and tracer1.has_pt:
                         # Mixture of PT and non-PT tracers
@@ -349,7 +349,7 @@ def compute_theory_vector(self, tools: ModelingTools) -> TheoryVector:
                     # Compute perturbation power spectrum
 
                     pt_calculator = tools.get_pt_calculator()
-                    pk = pyccl.nl_pt.get_pt_pk2d(  # pylint: disable-msg=invalid-name
+                    pk = pyccl.nl_pt.get_pt_pk2d(
                         ccl_cosmo,
                         tracer0.pt_tracer,
                         tracer2=tracer1.pt_tracer,
@@ -391,7 +391,7 @@ def compute_theory_vector(self, tools: ModelingTools) -> TheoryVector:
 
         if self.theory_window_function is not None:
 
-            def log_interpolator(x, y):  # pylint: disable-msg=invalid-name
+            def log_interpolator(x, y):
                 if np.all(y > 0):
                     # use log-log interpolation
                     intp = scipy.interpolate.InterpolatedUnivariateSpline(

firecrown/likelihood/gauss_family/student_t.py

@@ -32,7 +32,7 @@ def __init__(
         nu: Optional[float],
     ):
         super().__init__(statistics)
-        self.nu = parameters.create(nu)  # pylint: disable-msg=C0103
+        self.nu = parameters.create(nu)
 
     def compute_loglike(self, tools: ModelingTools):
         """Compute the log-likelihood.