Merge pull request #43 from Zabamund/drop-pandas

Drop pandas

README.md

@@ -1,7 +1,7 @@
 # README
 
-[wellpathpy/master](https://github.com/Zabamund/wellpathpy/tree/master):[![Build Status](https://travis-ci.com/Zabamund/wellpathpy.svg?branch=master)](https://travis-ci.com/Zabamund/wellpathpy)
-[wellpathpy/api_models](https://github.com/Zabamund/wellpathpy/tree/api_models):[![Build Status](https://travis-ci.com/Zabamund/wellpathpy.svg?branch=api_models)](https://travis-ci.com/Zabamund/wellpathpy)
+[wellpathpy/master](https://github.com/Zabamund/wellpathpy/tree/master):
+[![Build Status](https://travis-ci.com/Zabamund/wellpathpy.svg?branch=master)](https://travis-ci.com/Zabamund/wellpathpy)
 
 ## Contributors:
 
@@ -18,16 +18,16 @@
 - load well deviation in (md, inc, azi) format:
     * meta data (header, rkb, dfe, rt)
     * md, incl, azi
-- interpolate survey using one of these methods:
+- calculate position log survey using one of these methods:
     * minimum curvature method
     * radius of curvature method
-    * tangential method
-- calculate dog-leg severity
+    * tangential methods
+- calculate dog-leg severity from minimum curvature
 - calculate depth references using header data if available: MD, TVD, TVDSS
 - return interpolated deviation in (tvd, northing, easting) format
 - move surface location to (0, 0, 0) or to (kb, mE, mN)
 - convert to tvdss based on kb elevation
-- resample deviation on regular steps
+- resample deviation on regular steps with minimum curvature only
 
 ## Installation
 
@@ -39,14 +39,12 @@ From [pypi](https://pypi.org/project/wellpathpy/) with:
 
 ## Requirements
 
-- [pandas](https://pandas.pydata.org/) version 0.24.2 or greater
 - [numpy](https://numpy.org/) version 1.16.2 or greater
-- [pytest](https://pytest.org/) version 4.3.1 or greater
 - [pint](https://github.com/hgrecco/pint) version 0.9 or greater
 
 ## Tutorials
 
-Currently work-in-progress in [branch:api_models](https://github.com/Zabamund/wellpathpy/tree/api_models).
+A tutorial is available on [wellpathpy.readthedocs.io](https://wellpathpy.readthedocs.io/en/latest/tutorial.html)
 
 ## Contributing
 

docs/source/tutorial.rst

@@ -59,21 +59,35 @@ A valid input file must be a CSV file containing the columns: md, inc, azi in th
     150,78.5,254
     252.5,90,359.9
 
-- column headers are **required**
+- column headers are generally expected but will be skipped when the file is read
+- if no headers are provided, the ``skiprows`` argument can be set to ``0``
 - md must increase monotonically
 - as inc and azi cannot be distinguished numerically it is the user's responsibility to ensure the data are passed in this order
-- inc must be in range 0-180 (to allow for horizontal wells to climb)
-- azi must be in range 0-360
+- inc must be in range 0 <= inc < 180 (to allow for horizontal wells to climb)
+- azi must be in range 0 <= azi < 360
 
 You can then load them into wellpathpy using:
 
 .. code-block:: python
 
    md, inc, azi = wp.read_csv(fname)
 
+``wp.read_csv`` simply calls ``np.loadtxt`` with ``delimiter=','`` and ``skiprows=1``.
+These can be changed if required; for example the ``delimiter`` and ``skiprows`` can be changed with:
+
+.. code-block:: python
+
+   md, inc, azi = wp.read_csv(fname, delimiter='\t', skiprows=0)
+
+Additional ``kwargs`` accepted by ``np.loadtxt`` can also be passed in, for example:
+
+.. code-block:: python
+
+   md, inc, azi = wp.read_csv(fname, comments='$')
+
 **Notes**:
 
-Some simple sanity checks are performed to reject bad CSVs. ``wp.read_csv`` supports all options ``pd.read_csv``
+Some simple sanity checks are performed to reject bad CSVs. ``wp.read_csv`` supports all options ``np.loadtxt``
 supports. Only those columns named md, inc, azi will be read.
 
 If the deviation survey is not in CSV, is generated in a different place in your
@@ -105,7 +119,7 @@ With this, it is then possible to resample the depths using the ``minimum_curvat
 
    step = 30
    depths = list(range(0, int(dev.md[-1]) + 1, step))
-   pos = dev.mininum_curvature().resample(depths = depths)
+   pos = dev.minimum_curvature().resample(depths = depths)
    dev2 = pos.deviation()
 
 **Notes**:
@@ -370,8 +384,9 @@ Exporting results
 #################
 
 The two main ``wellpathpy`` objects; ``deviation`` and ``position`` logs can be written to CSV via
-object methods as shown below. These simply use ``pd.DataFrame.to_csv`` under the hood with the
-``pandas`` ``kwarg`` ``index`` set to ``False`` so that the index is not written out.
+object methods as shown below. These both call ``np.savetxt`` with ``fmt='%.3f'`` and ``delimiter=','``.
+The ``deviation`` also has ``header='md,inc,azi'`` and the ``postition`` has ``header='easting,northing,depth'``.
+Other ``kwargs`` accepted by ``np.savetxt`` are also accepted.
 
 - for a deviation survey:
 
@@ -385,5 +400,12 @@ object methods as shown below. These simply use ``pd.DataFrame.to_csv`` under th
 
     pos.to_csv('./position.csv')
 
+Additional ``kwargs`` can be passed like:
+
+.. code-block:: python
+
+    dev.to_csv('./deviation.csv', fmt='%.2e')
+    pos.to_csv('./position.csv', header='X,Y,Z', comments='$')
+
 This is a pretty straight-forward function convenient CSV writing. If you need
 more control, or more sophisticated output, you must implement your own writer.

requirements-dev.txt

@@ -1,5 +1,4 @@
 pytest
-pandas
 numpy
 pint
 setuptools-scm

requirements.txt

@@ -1,3 +1,2 @@
-pandas
 numpy
 pint

setup.py

@@ -14,7 +14,7 @@
       packages=['wellpathpy'],
       license='LGPL-3.0',
       platforms='any',
-      install_requires=['numpy >=1.10', 'pandas', 'pint'],
+      install_requires=['numpy >=1.10', 'pint'],
       setup_requires=['setuptools >=28', 'setuptools_scm', 'pytest-runner'],
       tests_require=['pytest', 'hypothesis'],
       use_scm_version=True,

wellpathpy/position_log.py

@@ -77,15 +77,15 @@ def tan_method(self, choice = 'avg'):
         )
         return tan_method(self, tvd, n, e)
 
-    def to_csv(self, fname):
+    def to_csv(self, fname, **kwargs):
         """This function calls write.deviation_to_csv with self
 
         Notes
         -----
             You can access help with `wp.write.deviation_to_csv?`
             in `ipython`
         """
-        return deviation_to_csv(fname, self.md, self.inc, self.azi)
+        return deviation_to_csv(fname, self.md, self.inc, self.azi, **kwargs)
 
 class position_log:
     """Position log
@@ -207,15 +207,15 @@ def resample(self, *args, **kwargs):
     def deviation(self, *args, **kwargs):
         raise NotImplementedError
 
-    def to_csv(self, fname):
+    def to_csv(self, fname, **kwargs):
         """This function calls write.position_to_csv with self
 
         Notes
         -----
             You can access help with `wp.write.position_to_csv?`
             in `ipython`
         """
-        return position_to_csv(fname, self.depth, self.northing, self.easting)
+        return position_to_csv(fname, self.depth, self.northing, self.easting, **kwargs)
 
 def spherical_interpolate(p0, p1, t, omega):
     """

wellpathpy/read.py

@@ -1,23 +1,36 @@
-import pandas as pd
+import numpy as np
 
 from .checkarrays import checkarrays
 
-def read_csv(fname, md = 'md', inc = 'inc', azi = 'azi', **kwargs):
+def read_csv(fname, delimiter=',', skiprows=1, **kwargs):
     """Read a deviation file in CSV format
 
-    Read a deviation survey from a CSV file. Columns can be specified with the
-    md, inc, and azi parameters.
+    A header row containing the column names `md`, `inc`, `azi` in
+    that order is generally expected to be included as the first row
+    in the file. By default, this header is skipped with the `skiprows`
+    argument set to `1` but this can be changed to `0` if no header is
+    inclduded.
+    The data must be ordered as `md`, `inc`, `azi` as the data cannot
+    be distinguished numerically.
 
     Parameters
     ----------
     fname : str
         path to a CSV file with this format:
-    md : str
-        measured depth column name
-    inc : str
-        inclination column name
-    azi : str
-        azimuth column name
+        ```md,inc,azi
+        0,0,244
+        10,11,220
+        50,43,254
+        150,78.5,254
+        252.5,90,359.9```
+    delimiter: str
+        the character used as a delimiter in the CSV
+    skiprows : int
+        number of rows to skip, normally the header row
+
+    Other Parameters
+    ----------------
+    **kwargs : All other keyword arguments are passed to `np.loadtxt`
 
     Returns
     -------
@@ -31,11 +44,10 @@ def read_csv(fname, md = 'md', inc = 'inc', azi = 'azi', **kwargs):
     inc : float
         well inclination in degrees from vertical
     azi : float
-        well azimuth in degrees from North
+        well azimuth in degrees from Grid North
     """
-    df = pd.read_csv(fname, header=0, **kwargs)
-
-    md, inc, azi = df[md].values, df[inc].values, df[azi].values
+    dev = np.loadtxt(fname, delimiter=delimiter, skiprows=skiprows, **kwargs)
+    md, inc, azi = np.split(dev[:,0:3], 3, 1)
     md, inc, azi = checkarrays(md, inc, azi)
 
     return md, inc, azi

wellpathpy/test/test_calculations.py

@@ -1,5 +1,4 @@
 import pytest
-import pandas as pd
 import numpy as np
 
 import hypothesis
@@ -11,28 +10,27 @@
 from ..position_log import deviation, position_log as mc
 
 # import test well data
-well9 = pd.read_csv('./wellpathpy/test/fixtures/well9.csv', sep=",")
-well10 = pd.read_csv('./wellpathpy/test/fixtures/well10.csv', sep=",")
-
+well9 = np.loadtxt('./wellpathpy/test/fixtures/well9.csv', delimiter=",", skiprows=1)
+well10 = np.loadtxt('./wellpathpy/test/fixtures/well10.csv', delimiter=",", skiprows=1)
 # get data series
-well9_true_md_m = well9['Measured Depth ( ft )'].values * 0.3048 # converting feet to meters
-well9_true_inc = well9['Inclination ( deg )'].values
-well9_true_azi = well9['Azimuth Grid ( deg )'].values
-well9_true_tvd_m = well9['TVD ( ft )'].values * 0.3048 # converting feet to meters
-well9_true_northing = well9['Northing ( m )'].values
-well9_true_easting = well9['Easting ( m )'].values
-well9_true_dls = well9['DLS ( deg/100 ft )'].values
+well9_true_md_m = well9[:,0] * 0.3048 # converting feet to meters
+well9_true_inc = well9[:,1]
+well9_true_azi = well9[:,2]
+well9_true_tvd_m = well9[:,3] * 0.3048 # converting feet to meters
+well9_true_northing = well9[:,5]
+well9_true_easting = well9[:,6]
+well9_true_dls = well9[:,4]
 well9_true_surface_northing = 39998.454
 well9_true_surface_easting = 655701.278
 well9_true_datum_elevation = 100 * 0.3048 # converting feet to meters
 
-well10_true_md_m = well10['Measured Depth ( ft )'].values * 0.3048 # converting feet to meters
-well10_true_inc = well10['Inclination ( deg )'].values
-well10_true_azi = well10['Azimuth Grid ( deg )'].values
-well10_true_tvd_m = well10['TVD ( ft )'].values * 0.3048 # converting feet to meters
-well10_true_northing = well10['Northing ( m )'].values
-well10_true_easting = well10['Easting ( m )'].values
-well10_true_dls = well10['DLS ( deg/100 ft )'].values
+well10_true_md_m = well10[:,0] * 0.3048 # converting feet to meters
+well10_true_inc = well10[:,1]
+well10_true_azi = well10[:,2]
+well10_true_tvd_m = well10[:,3] * 0.3048 # converting feet to meters
+well10_true_northing = well10[:,5]
+well10_true_easting = well10[:,6]
+well10_true_dls = well10[:,4]
 well10_true_surface_northing = 40004.564
 well10_true_surface_easting = 655701.377
 well10_true_datum_elevation = 100 * 0.3048 # converting feet to meters

wellpathpy/test/test_location.py

@@ -1,31 +1,32 @@
 import pytest
 import numpy as np
-import pandas as pd
 
 from ..mincurve import minimum_curvature
 from ..location import loc_to_wellhead, loc_to_zero, loc_to_tvdss
 
 # import test well data
-well9 = pd.read_csv('./wellpathpy/test/fixtures/well9.csv', sep=",")
-well10 = pd.read_csv('./wellpathpy/test/fixtures/well10.csv', sep=",")
+well9 = np.loadtxt('./wellpathpy/test/fixtures/well9.csv', delimiter=",", skiprows=1)
+well10 = np.loadtxt('./wellpathpy/test/fixtures/well10.csv', delimiter=",", skiprows=1)
 
 # get data series
-well9_true_md_m = well9['Measured Depth ( ft )'].values * 0.3048 # converting feet to meters
-well9_true_inc = well9['Inclination ( deg )'].values
-well9_true_azi = well9['Azimuth Grid ( deg )'].values
-well9_true_tvd_m = well9['TVD ( ft )'].values * 0.3048 # converting feet to meters
-well9_true_northing = well9['Northing ( m )'].values
-well9_true_easting = well9['Easting ( m )'].values
+well9_true_md_m = well9[:,0] * 0.3048 # converting feet to meters
+well9_true_inc = well9[:,1]
+well9_true_azi = well9[:,2]
+well9_true_tvd_m = well9[:,3] * 0.3048 # converting feet to meters
+well9_true_northing = well9[:,5]
+well9_true_easting = well9[:,6]
+well9_true_dls = well9[:,4]
 well9_true_surface_northing = 39998.454
 well9_true_surface_easting = 655701.278
 well9_true_datum_elevation = 100 * 0.3048 # converting feet to meters
 
-well10_true_md_m = well10['Measured Depth ( ft )'].values * 0.3048 # converting feet to meters
-well10_true_inc = well10['Inclination ( deg )'].values
-well10_true_azi = well10['Azimuth Grid ( deg )'].values
-well10_true_tvd_m = well10['TVD ( ft )'].values * 0.3048 # converting feet to meters
-well10_true_northing = well10['Northing ( m )'].values
-well10_true_easting = well10['Easting ( m )'].values
+well10_true_md_m = well10[:,0] * 0.3048 # converting feet to meters
+well10_true_inc = well10[:,1]
+well10_true_azi = well10[:,2]
+well10_true_tvd_m = well10[:,3] * 0.3048 # converting feet to meters
+well10_true_northing = well10[:,5]
+well10_true_easting = well10[:,6]
+well10_true_dls = well10[:,4]
 well10_true_surface_northing = 40004.564
 well10_true_surface_easting = 655701.377
 well10_true_datum_elevation = 100 * 0.3048 # converting feet to meters