Remove star imports

Author: jdehning

mrestimator/__init__.py

@@ -1,17 +1,16 @@
 from importlib import metadata as importlib_metadata
 
 from . import utility as ut
-
-ut.initialize()
-log = ut.log
-
 from .coefficients import CoefficientResult, coefficients
 from .fit import *
 from .input_output import *
 from .simulate import *
 from .utility import disable_progressbar, enable_progressbar
 from .wrapper import *
 
+ut.initialize()
+log = ut.log
+
 
 def _get_version():
     try:

mrestimator/fit.py

@@ -6,11 +6,11 @@
 import scipy.optimize
 import scipy.stats
 
+from mrestimator import CoefficientResult
 from mrestimator import utility as ut
 
 log = ut.log
 tqdm = ut.tqdm
-from mrestimator import CoefficientResult
 
 
 def f_linear(k, A, O):

mrestimator/input_output.py

@@ -3,15 +3,16 @@
 import os
 import re
 
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+
 from mrestimator import utility as ut
 from mrestimator._version import __version__
 from mrestimator.coefficients import CoefficientResult
 from mrestimator.fit import FitResult
 
 log = ut.log
-import matplotlib
-import matplotlib.pyplot as plt
-import numpy as np
 
 
 def input_handler(items, **kwargs):

mrestimator/wrapper.py

@@ -1,15 +1,27 @@
 import logging
 import os
 
+import matplotlib.pyplot as plt
 import numpy as np
 from matplotlib import rc_context
+from matplotlib.axes import Axes
 
 from mrestimator import utility as ut
+from mrestimator.coefficients import coefficients
+from mrestimator.fit import (
+    f_complex,
+    f_exponential,
+    f_exponential_offset,
+    fit,
+    fitfunc_check,
+)
+from mrestimator.input_output import (
+    OutputHandler,
+    input_handler,
+    overview,
+)
 
 log = ut.log
-from mrestimator.coefficients import coefficients
-from mrestimator.fit import *
-from mrestimator.input_output import *
 
 
 def full_analysis(
@@ -342,7 +354,7 @@ def full_analysis(
         )
         raise TypeError
 
-    if targetplot is not None and not isinstance(targetplot, matplotlib.axes.Axes):
+    if targetplot is not None and not isinstance(targetplot, Axes):
         log.exception(
             "Optional argument 'targetplot' needs "
             + "to be an instance of 'matplotlib.axes.Axes'"

pyproject.toml

@@ -68,11 +68,7 @@ ignore = [
     "E741", # ignore ambiguous variable names, because of the example of the S,I,R model
     "UP007", # don't reformat Optional[...] to ... | None as it isn't supported by
              # autodoc
-    "F405",
-    "F403",
-    "F402",
     "E722", # bare excepts
-    "E402", # module level import not at top of file
 ]
 select = [
     "E", # pycodestyle
@@ -84,7 +80,8 @@ select = [
 
 [tool.ruff.lint.per-file-ignores]
 # Ignore `F401` (unused imports) in all `__init__.py` files.
-"__init__.py" = ["F401"]
+"__init__.py" = ["F401", "F403", "F405"]
+"tests/__init__.py" = ["F401", "F403", "F405", "E402"]
 
 
 [tool.ruff.lint.pydocstyle]

tests/__init__.py

@@ -1,7 +1,7 @@
 import os
+import sys
 
 os.chdir(os.path.dirname(__file__))
-import sys
 
 sys.path.append("../../")
 

tests/test_coefficients.py

@@ -5,6 +5,14 @@
 import numpy as np
 
 import mrestimator as mre
+from mrestimator.coefficients import (
+    coefficients,
+    sm_method,
+    sm_precompute,
+    ts_method,
+    ts_precompute,
+)
+from mrestimator.simulate import simulate_branching
 from mrestimator.utility import log
 
 
@@ -140,10 +148,6 @@ def test_separate(self):
             )
 
 
-from mrestimator.coefficients import *
-from mrestimator.simulate import simulate_branching
-
-
 class TestCCKnownMean(unittest.TestCase):
     def test_sm(self):
         print("Testing knownmean argument to sm_method")

tests/test_mr_estimator.py

@@ -4,17 +4,15 @@
 import numpy as np
 import scipy.optimize
 
-print(__name__)
-
-
 # import mrestimator as mre
 import mrestimator as mre
 from tests.test_coefficients import (
     calc_corr_arr_stationary,
     check_similarity,
 )
 
-# Currently not working...
+print(__name__)
+
 
 ######################