From 8902a4382e98eda406338bcb15bf576391c985a1 Mon Sep 17 00:00:00 2001
From: Oliver Stocks <ojs1g14@soton.ac.uk>
Date: Mon, 9 Jul 2018 09:43:55 +0100
Subject: [PATCH] retweaked align.py

---
 AmpScan/align.py          | 159 +++++++++++++++++++-------------------
 AmpScan/docstringstuff.py |  18 +++++
 Internship_Diary/main.tex |  12 +++
 3 files changed, 110 insertions(+), 79 deletions(-)
 create mode 100644 AmpScan/docstringstuff.py

diff --git a/AmpScan/align.py b/AmpScan/align.py
index 6fbbb0a..2bb153d 100644
--- a/AmpScan/align.py
+++ b/AmpScan/align.py
@@ -11,7 +11,86 @@ from scipy.optimize import minimize
 
 
 def align(moving, static, method = 'P2P'):
-    
+    """
+    Using this function for sample docstring (one line desc).
+
+    A more extended description that provides details of how the function works.
+
+    Parameters
+    ----------
+    moving : array_like
+        Rot has a structure that can be iterated through implying it should be an
+        array like structure
+    static : data_type
+        Description of tTree input and what it does.
+    method : data_type
+        Desc of method
+
+    Returns
+    -------
+    type
+        Explanation of anonymous return value of type ``type``.
+    describe : type
+        Explanation of return value named `describe`.
+    out : type
+        Explanation of `out`.
+    type_without_description
+
+    Other Parameters
+    ----------------
+    only_seldom_used_keywords : type
+        Explanation
+    common_parameters_listed_above : type
+        Explanation
+
+    Raises
+    ------
+    BadException
+        Because you shouldn't have done that.
+
+    See Also
+    --------
+    otherfunc : relationship (optional)
+    newfunc : Relationship (optional), which could be fairly long, in which
+              case the line wraps here.
+    thirdfunc, fourthfunc, fifthfunc
+
+    Notes
+    -----
+    Notes about the implementation algorithm (if needed).
+
+    This can have multiple paragraphs.
+
+    You may include some math:
+
+    .. math:: X(e^{j\omega } ) = x(n)e^{ - j\omega n}
+
+    And even use a Greek symbol like :math:`\omega` inline.
+
+    References
+    ----------
+    Cite the relevant literature, e.g. [1]_.  You may also cite these
+    references in the notes section above.
+
+    .. [1] O. McNoleg, "The integration of GIS, remote sensing,
+       expert systems and adaptive co-kriging for environmental habitat
+       modelling of the Highland Haggis using object-oriented, fuzzy-logic
+       and neural-network techniques," Computers & Geosciences, vol. 22,
+       pp. 585-588, 1996.
+
+    Examples
+    --------
+    These are written in doctest format, and should illustrate how to
+    use the function.
+
+    >>> a = [1, 2, 3]
+    >>> print [x + 3 for x in a]
+    [4, 5, 6]
+    >>> print "a\n\nb"
+    a
+    b
+
+    """    
 
     def icp():
         """
@@ -24,84 +103,6 @@ def align(moving, static, method = 'P2P'):
         
         
     def calcDistError(rot, tTree):
-        """
-        Using this function for sample docstring (one line desc).
-        
-        A more extended description that provides details of how the function works.
-        
-        Parameters
-        ----------
-        rot : array_like
-            Rot has a structure that can be iterated through implying it should be an
-            array like structure
-        tTree : data_type
-            Description of tTree input and what it does.
-        
-        Returns
-        -------
-        type
-            Explanation of anonymous return value of type ``type``.
-        describe : type
-            Explanation of return value named `describe`.
-        out : type
-            Explanation of `out`.
-        type_without_description
-
-        Other Parameters
-        ----------------
-        only_seldom_used_keywords : type
-            Explanation
-        common_parameters_listed_above : type
-            Explanation
-
-        Raises
-        ------
-        BadException
-            Because you shouldn't have done that.
-
-        See Also
-        --------
-        otherfunc : relationship (optional)
-        newfunc : Relationship (optional), which could be fairly long, in which
-                  case the line wraps here.
-        thirdfunc, fourthfunc, fifthfunc
-
-        Notes
-        -----
-        Notes about the implementation algorithm (if needed).
-
-        This can have multiple paragraphs.
-
-        You may include some math:
-
-        .. math:: X(e^{j\omega } ) = x(n)e^{ - j\omega n}
-
-        And even use a Greek symbol like :math:`\omega` inline.
-
-        References
-        ----------
-        Cite the relevant literature, e.g. [1]_.  You may also cite these
-        references in the notes section above.
-
-        .. [1] O. McNoleg, "The integration of GIS, remote sensing,
-           expert systems and adaptive co-kriging for environmental habitat
-           modelling of the Highland Haggis using object-oriented, fuzzy-logic
-           and neural-network techniques," Computers & Geosciences, vol. 22,
-           pp. 585-588, 1996.
-
-        Examples
-        --------
-        These are written in doctest format, and should illustrate how to
-        use the function.
-
-        >>> a = [1, 2, 3]
-        >>> print [x + 3 for x in a]
-        [4, 5, 6]
-        >>> print "a\n\nb"
-        a
-        b
-
-        """
         Id = np.identity(3)
         for i in range(3):
             if rot[i] != 0:
diff --git a/AmpScan/docstringstuff.py b/AmpScan/docstringstuff.py
new file mode 100644
index 0000000..1d7b1c5
--- /dev/null
+++ b/AmpScan/docstringstuff.py
@@ -0,0 +1,18 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu July 05 11:10:30 2018
+
+@author: ojs1g14
+"""
+
+
+def add_docs(input_file):
+    """
+    docstring yo
+    """
+    f = open(input_file, r+)
+    for line in f.readlines():
+        if "def " in line:
+            print(str(line))
+    
+    f.close()
\ No newline at end of file
diff --git a/Internship_Diary/main.tex b/Internship_Diary/main.tex
index 3f3ca0f..e43d579 100644
--- a/Internship_Diary/main.tex
+++ b/Internship_Diary/main.tex
@@ -135,5 +135,17 @@ pip install numpydoc
 
 An example docstring is provided in the inline documentation - I added this to the \_doctemplates folder in the top level directory with some tweaks to make it more relevant to the project. Copyright infringement may be worth considering before future deployment.
 
+\noindent\fbox{%
+    \parbox{\textwidth}{%
+        Quick Note on Git:
+
+I spent some time finding that I could not add changes made to my branch. Changes were listed but would not be staged when I used \lstinline{git add .}. This turned out to be because I was not in the root directory of the branch.
+    }%
+}
+
+...
+
+\subsection{Gitlab Wiki}
+Gitlab provides in built documentation associated with the project...
 
 \end{document}
-- 
GitLab