Some suggestions

.gitignore

@@ -1,6 +1,8 @@
 .venv
 .vscode
 
+.devcontainer/
+
 __pycache__
 
 build
@@ -16,4 +18,6 @@ work
 
 key.asc
 .~*
-VERSION*
+VERSION*
+
+test/test_data/*.xlsx

examples/build_a_well_from_sections.py

@@ -85,7 +85,7 @@
 
 # make a mesh
 mesh = WellMesh(survey, method='circle')
-
+    
 # finally, plot it
 plot([mesh.mesh], interactive=False)
 

setup.py

@@ -52,12 +52,15 @@
 
 # if someone wants to output a requirements file
 # `python setup.py --list-all > requirements.txt`
-if '--list-all' in sys.argv:
-    # will not include default requirements (numpy)
-    print('\n'.join(requirements_all))
+if '--list-default' in sys.argv:
+    print('\n'.join(requirements_default))
+    exit()
+elif '--list-all' in sys.argv:
+    requirements = requirements_all.union(requirements_default)
+    print('\n'.join(requirements))
     exit()
 elif '--list-easy' in sys.argv:
-    # again will not include numpy+setuptools
+    requirements = requirements_easy.union(requirements_default)
     print('\n'.join(requirements_easy))
     exit()
 

welleng/errors/tool_errors.py

@@ -1,12 +1,11 @@
+import os
+
 import numpy as np
-from numpy import sin, cos, tan, pi, sqrt
-from numpy.core.defchararray import index
 import yaml
-import os
+
 from collections import OrderedDict
-# import imp
+from numpy import sin, cos, tan, pi, sqrt
 
-# import welleng.error
 from ..utils import NEV_to_HLA
 
 # since this is running on different OS flavors

welleng/survey.py

@@ -49,11 +49,7 @@ def __init__(
         deg=True,
         depth_unit='meters',
         surface_unit='meters',
-        mag_defaults={
-            'b_total': 50_000.,
-            'dip': 70.,
-            'declination': 0.,
-        },
+        mag_defaults=None,
         **kwargs
     ):
         """
@@ -142,7 +138,11 @@ def __init__(
         self.G = G
         self.azi_reference = azi_reference
 
-        self.mag_defaults = mag_defaults
+        self.mag_defaults = mag_defaults or {
+            'b_total': 50_000.,
+            'dip': 70.,
+            'declination': 0.,
+        }
         self._get_mag_data(deg)
 
     def _get_mag_data(self, deg):
@@ -234,8 +234,8 @@ def __init__(
         cov_nev=None,
         cov_hla=None,
         error_model=None,
-        start_xyz=[0., 0., 0.],
-        start_nev=[0., 0., 0.],
+        start_xyz=None,
+        start_nev=None,
         start_cov_nev=None,
         deg=True,
         unit="meters",
@@ -325,8 +325,10 @@ def __init__(
         )
         self.unit = unit
         self.deg = deg
-        self.start_xyz = start_xyz
-        self.start_nev = start_nev
+
+        self.start_xyz = start_xyz or [0., 0., 0.]
+        self.start_nev = start_nev or [0., 0., 0.]
+
         self.md = np.array(md).astype('float64')
         self.start_cov_nev = start_cov_nev
 
@@ -384,6 +386,7 @@ def _process_azi_ref(self, inc, azi, deg):
                 self.azi_true_deg - math.degrees(self.header.declination)
             )
             self._get_azi_mag_and_true_rad()
+
         elif self.header.azi_reference == 'true':
             if deg:
                 self.azi_true_deg = np.array(azi).astype('float64')
@@ -400,6 +403,7 @@ def _process_azi_ref(self, inc, azi, deg):
                 self._get_azi_mag_and_true_deg()
                 azi_temp = self._get_azi_temp(deg)
             self._make_angles(inc, azi_temp, deg)
+
         else:  # azi_reference is "magnetic"
             if deg:
                 self.azi_mag_deg = np.array(azi).astype('float64')
@@ -444,8 +448,10 @@ def _get_azi_mag_and_true_deg(self):
     def _get_radius(self, radius=None):
         if radius is None:
             self.radius = np.full_like(self.md.astype(float), 0.3048)
+
         elif np.array([radius]).shape[-1] == 1:
             self.radius = np.full_like(self.md.astype(float), radius)
+
         else:
             assert len(radius) == len(self.md), "Check radius"
             self.radius = np.array(radius)
@@ -469,8 +475,10 @@ def _min_curve(self, vec):
         if self.x is None:
             # self.x, self.y, self.z = (mc.poss + self.start_xyz).T
             self.x, self.y, self.z = (mc.poss).T
+
         if self.n is None:
             self._get_nev()
+
         if vec is None:
             self.vec_xyz = get_vec(self.inc_rad, self.azi_grid_rad, deg=False)
             self.vec_nev = get_vec(
@@ -512,27 +520,29 @@ def get_error(self, error_model, return_error=False):
 
         if return_error:
             return self.err
-        else:
-            return self
+
+        return self
 
     def _get_errors(self):
         """
         Initiate a welleng.error.ErrorModel object and calculate the
         covariance matrices with the specified error model.
         """
         if self.error_model:
-            # if self.error_model == "iscwsa_mwd_rev4":
             self.err = ErrorModel(
                 self,
                 error_model=self.error_model
             )
             self.cov_hla = self.err.errors.cov_HLAs.T
             self.cov_nev = self.err.errors.cov_NEVs.T
+
         else:
             if self.cov_nev is not None and self.cov_hla is None:
                 self.cov_hla = NEV_to_HLA(self.survey_rad, self.cov_nev.T).T
+
             elif self.cov_nev is None and self.cov_hla is not None:
                 self.cov_nev = HLA_to_NEV(self.survey_rad, self.cov_hla.T).T
+
             else:
                 pass
 
@@ -547,10 +557,7 @@ def _curvature_to_rate(self, curvature):
         with np.errstate(divide='ignore', invalid='ignore'):
             radius = 1 / curvature
         circumference = 2 * np.pi * radius
-        if self.unit == 'meters':
-            x = 30
-        else:
-            x = 100
+        x = 30 if self.unit == 'meters' else 100
         rate = np.absolute(np.degrees(2 * np.pi / circumference) * x)
 
         return rate
@@ -563,10 +570,7 @@ def _get_toolface_and_rates(self):
         # split the survey
         s = SplitSurvey(self)
 
-        if self.unit == 'meters':
-            x = 30
-        else:
-            x = 100
+        x = 30 if self.unit == 'meters' else 100
 
         # this is lazy I know, but I'm using this mostly for flags
         with np.errstate(divide='ignore', invalid='ignore'):
@@ -732,6 +736,7 @@ def project_to_bit(self, delta_md, dls=None, toolface=None):
         """
         if dls is None:
             dls = self.dls[-1]
+
         if toolface is None:
             toolface = self.toolface[-1]
 
@@ -817,10 +822,10 @@ def interpolate_md(survey, md):
     x = md - survey.md[idx]
     assert x >= 0
 
-    return _interpolate_survey(survey, x=x, index=idx)
+    return _interpolate_survey(survey, md=x, index=idx)
 
 
-def _interpolate_survey(survey, x=0, index=0):
+def _interpolate_survey(survey, md=0, index=0):
     """
     Interpolates a point distance x between two survey stations
     using minimum curvature.
@@ -829,7 +834,7 @@ def _interpolate_survey(survey, x=0, index=0):
     ----------
         survey: welleng.Survey
             A survey object with at least two survey stations.
-        x: float
+        md: float
             Length along well path from indexed survey station to
             perform the interpolate at. Must be less than length
             to the next survey station.
@@ -861,7 +866,7 @@ def _interpolate_survey(survey, x=0, index=0):
 
         total_dogleg = survey.dogleg[index + 1]
 
-        dogleg = x * (total_dogleg / survey.delta_md[index + 1])
+        dogleg = md * (total_dogleg / survey.delta_md[index + 1])
 
         t = (
             (math.sin(total_dogleg - dogleg) / math.sin(total_dogleg)) * t1
@@ -876,7 +881,7 @@ def _interpolate_survey(survey, x=0, index=0):
     sh.azi_reference = 'grid'
 
     s = Survey(
-        md=np.array([survey.md[index], survey.md[index] + x]),
+        md=np.array([survey.md[index], survey.md[index] + md]),
         inc=np.array([survey.inc_rad[index], inc]),
         azi=np.array([survey.azi_grid_rad[index], azi]),
         start_xyz=np.array([survey.x, survey.y, survey.z]).T[index],
@@ -885,8 +890,8 @@ def _interpolate_survey(survey, x=0, index=0):
         deg=False,
     )
     interpolated = False if any((
-        x == 0,
-        x == survey.md[index + 1] - survey.md[index]
+        md == 0,
+        md == survey.md[index + 1] - survey.md[index]
      )) else True
     s.interpolated = [False, interpolated]
 
@@ -932,7 +937,7 @@ def tidy_up_angle(d):
         dogleg = s_temp.dogleg[-1]
 
     if np.isnan(dogleg):
-        return _interpolate_survey(survey, x=0, index=idx)
+        return _interpolate_survey(survey, md=0, index=idx)
 
     if dogleg == 0:
         x = (
@@ -989,7 +994,7 @@ def tidy_up_angle(d):
 
         assert x <= delta_md
 
-    interpolated_survey = _interpolate_survey(survey, x=x, index=idx)
+    interpolated_survey = _interpolate_survey(survey, md=x, index=idx)
 
     interpolated = True if x > 0 else False
     node = get_node(interpolated_survey, 1, interpolated=interpolated)

welleng/utils.py

@@ -161,6 +161,7 @@ def get_vec(inc, azi, nev=False, r=1, deg=True):
     else:
         inc_rad = inc
         azi_rad = azi
+
     y = r * np.sin(inc_rad) * np.cos(azi_rad)
     x = r * np.sin(inc_rad) * np.sin(azi_rad)
     z = r * np.cos(inc_rad)
@@ -173,34 +174,35 @@ def get_vec(inc, azi, nev=False, r=1, deg=True):
     return vec / np.linalg.norm(vec, axis=-1).reshape(-1, 1)
 
 
-def get_nev(
-    pos, start_xyz=np.array([0., 0., 0.]), start_nev=np.array([0., 0., 0.])
-):
+def get_nev(pos, start_xyz=None, start_nev=None):
     """
     Convert [x, y, z] coordinates to [n, e, tvd] coordinates.
 
     Params:
         pos: (n,3) array of floats
             Array of [x, y, z] coordinates
         start_xyz: (,3) array of floats
-            The datum of the [x, y, z] cooardinates
+            The datum of the [x, y, z] coordinates
         start_nev: (,3) array of floats
             The datum of the [n, e, tvd] coordinates
 
     Returns:
         An (n,3) array of [n, e, tvd] coordinates.
     """
-    # e, n, v = (
-    #     np.array([pos]).reshape(-1,3) - np.array([start_xyz])
-    # ).T
+    start_xyz = start_xyz or np.array([0., 0., 0.])
+    start_nev = start_nev or np.array([0., 0., 0.])
+
     e, n, v = (
-        np.array([pos]).reshape(-1,3) - np.array([start_xyz])
+        np.array([pos]).reshape(-1, 3) - np.array([start_xyz])
     ).T
 
     return (np.array([n, e, v]).T + np.array([start_nev]))
 
 
-def get_xyz(pos, start_xyz=[0., 0., 0.], start_nev=[0., 0., 0.]):
+def get_xyz(pos, start_xyz=None, start_nev=None):
+    start_xyz = start_xyz or [0., 0., 0.]
+    start_nev = start_nev or [0., 0., 0.]
+
     y, x, z = (
         np.array([pos]).reshape(-1, 3) - np.array([start_nev])
     ).T
@@ -215,7 +217,6 @@ def _get_angles(vec):
 
     return np.stack((inc, azi), axis=1)
 
-
 if NUMBA:
     _get_angles = njit(_get_angles)
 
@@ -284,6 +285,7 @@ def get_transform(
 
     # return trans
 
+
 def NEV_to_HLA(survey, NEV, cov=True):
     """
     Transform from NEV to HLA coordinate system.
@@ -295,11 +297,11 @@ def NEV_to_HLA(survey, NEV, cov=True):
             The NEV coordinates or covariance matrices.
         cov: boolean
             If cov is True then a (3,3,d) array of covariance matrices
-            is expecte, else a (d,3) array of coordinates.
+            is expected, else a (d,3) array of coordinates.
 
     Returns:
         Either a transformed (n,3) array of HLA coordinates or an
-        (3,3,n) array of HLA covariance matrices. 
+        (3,3,n) array of HLA covariance matrices.
     """
 
     trans = get_transform(survey)
@@ -309,10 +311,10 @@ def NEV_to_HLA(survey, NEV, cov=True):
             np.dot(np.dot(t, NEV.T[i]), t.T) for i, t in enumerate(trans)
         ]
 
-        HLAs = np.vstack(HLAs).reshape(-1,3,3).T
+        HLAs = np.vstack(HLAs).reshape(-1, 3, 3).T
 
     else:
-        NEV = NEV.reshape(-1,3)
+        NEV = NEV.reshape(-1, 3)
         HLAs = [
             np.dot(NEV[i], t.T) for i, t in enumerate(trans)
         ]
@@ -328,7 +330,7 @@ def HLA_to_NEV(survey, HLA, cov=True, trans=None):
             np.dot(np.dot(t.T, HLA.T[i]), t) for i, t in enumerate(trans)
         ]
 
-        NEVs = np.vstack(NEVs).reshape(-1,3,3).T
+        NEVs = np.vstack(NEVs).reshape(-1, 3, 3).T
 
     else:
         NEVs = [