Update Tutorial with links to 1.77 api docs (#2903)

Changed links from API docs built with epydoc to those built with Sphinx
biopython · May 25, 2020 · a353d84 · a353d84
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diff --git a/Doc/Tutorial/chapter_align.tex b/Doc/Tutorial/chapter_align.tex
@@ -168,7 +168,7 @@ \subsection{Single Alignments}
 
 Note that rather than using the Sanger website, you could have used \verb|Bio.AlignIO| to convert the original Stockholm format file into a FASTA file yourself (see below).
 
-With any supported file format, you can load an alignment in exactly the same way just by changing the format string.  For example, use ``phylip'' for PHYLIP files, ``nexus'' for NEXUS files or ``emboss'' for the alignments output by the EMBOSS tools.  There is a full listing on the wiki page (\url{http://biopython.org/wiki/AlignIO}) and in the built in documentation (also \href{http://biopython.org/DIST/docs/api/Bio.AlignIO-module.html}{online}):
+With any supported file format, you can load an alignment in exactly the same way just by changing the format string.  For example, use ``phylip'' for PHYLIP files, ``nexus'' for NEXUS files or ``emboss'' for the alignments output by the EMBOSS tools.  There is a full listing on the wiki page (\url{http://biopython.org/wiki/AlignIO}) and in the built in documentation (also \href{http://biopython.org/docs/1.77/api/Bio.AlignIO.html}{online}):
 
 \begin{minted}{pycon}
 >>> from Bio import AlignIO
@@ -1469,7 +1469,7 @@ \subsection{pairwise2}
 The first letter decodes the match score, e.g. \texttt{x} means that a match counts
 1 while mismatches have no costs. With \texttt{m} general values for either matches
 or mismatches can be defined
-(for more options see \href{http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html}{Biopython's API}).
+(for more options see \href{http://biopython.org/docs/1.77/api/Bio.pairwise2.html}{Biopython's API}).
 The second letter decodes the cost for gaps; \texttt{x} means no gap costs at all,
 with \texttt{s} different penalties for opening and extending a gap can be assigned.
 So, \verb|globalxx| means that only matches between both sequences are counted.
@@ -1624,7 +1624,7 @@ \subsection{pairwise2}
 residues that are encoded by more than one character), etc. These features
 are hard (if at all) to realize with other alignment tools. For more details
 see the modules documentation in
-\href{http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html}{Biopython's API}.
+\href{http://biopython.org/docs/1.77/api/Bio.pairwise2.html}{Biopython's API}.
 
 \subsection{PairwiseAligner}
 \label{sec:pairwisealigner}

diff --git a/Doc/Tutorial/chapter_cookbook.tex b/Doc/Tutorial/chapter_cookbook.tex
@@ -724,7 +724,7 @@ \subsection{Converting FASTQ files}
 very different from the original FASTQ standard as used by Sanger,
 the NCBI, and elsewhere (format name \texttt{fastq} or \texttt{fastq-sanger}).
 
-For more details, see the built in help (also \href{http://www.biopython.org/DIST/docs/api/Bio.SeqIO.QualityIO-module.html}{online}):
+For more details, see the built in help (also \href{http://www.biopython.org/docs/1.77/api/Bio.SeqIO.QualityIO.html}{online}):
 
 \begin{minted}{pycon}
 >>> from Bio.SeqIO import QualityIO

diff --git a/Doc/Tutorial/chapter_quick_start.tex b/Doc/Tutorial/chapter_quick_start.tex
@@ -11,7 +11,7 @@ \section{General overview of what Biopython provides}
 
 As mentioned in the introduction, Biopython is a set of libraries to provide the ability to deal with ``things'' of interest to biologists working on the computer. In general this means that you will need to have at least some programming experience (in Python, of course!) or at least an interest in learning to program. Biopython's job is to make your job easier as a programmer by supplying reusable libraries so that you can focus on answering your specific question of interest, instead of focusing on the internals of parsing a particular file format (of course, if you want to help by writing a parser that doesn't exist and contributing it to Biopython, please go ahead!). So Biopython's job is to make you happy!
 
-One thing to note about Biopython is that it often provides multiple ways of ``doing the same thing.'' Things have improved in recent releases, but this can still be frustrating as in Python there should ideally be one right way to do something. However, this can also be a real benefit because it gives you lots of flexibility and control over the libraries. The tutorial helps to show you the common or easy ways to do things so that you can just make things work. To learn more about the alternative possibilities, look in the Cookbook (Chapter~\ref{chapter:cookbook}, this has some cools tricks and tips), the Advanced section (Chapter~\ref{chapter:advanced}), the built in ``docstrings'' (via the Python help command, or the \href{http://biopython.org/DIST/docs/api/}{API documentation}) or ultimately the code itself.
+One thing to note about Biopython is that it often provides multiple ways of ``doing the same thing.'' Things have improved in recent releases, but this can still be frustrating as in Python there should ideally be one right way to do something. However, this can also be a real benefit because it gives you lots of flexibility and control over the libraries. The tutorial helps to show you the common or easy ways to do things so that you can just make things work. To learn more about the alternative possibilities, look in the Cookbook (Chapter~\ref{chapter:cookbook}, this has some cools tricks and tips), the Advanced section (Chapter~\ref{chapter:advanced}), the built in ``docstrings'' (via the Python help command, or the \href{http://biopython.org/docs/1.77/api/}{API documentation}) or ultimately the code itself.
 
 \section{Working with sequences}
 \label{sec:sequences}

diff --git a/Doc/Tutorial/chapter_searchio.tex b/Doc/Tutorial/chapter_searchio.tex
@@ -235,9 +235,9 @@ \subsection{QueryResult}
 
 For a complete list of accessible attributes, you can check each format-specific
 documentation. Here are the ones
-\href{http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html}{for BLAST}
+\href{http://biopython.org/docs/1.77/api/Bio.SearchIO.BlastIO.html}{for BLAST}
 and for
-\href{http://biopython.org/DIST/docs/api/Bio.SearchIO.BlatIO-module.html}{BLAT}.
+\href{http://biopython.org/docs/1.77/api/Bio.SearchIO.BlatIO.html}{BLAT}.
 
 Having looked at using \verb|print| on \verb|QueryResult| objects, let's drill
 down deeper. What exactly is a \verb|QueryResult|? In terms of Python objects,
@@ -693,7 +693,7 @@ \subsection{HSP}
 \end{minted}
 
 Check out the \verb|HSP|
-\href{http://biopython.org/DIST/docs/api/Bio.SearchIO._model.hsp-module.html}{documentation}
+\href{http://biopython.org/docs/1.77/api/Bio.SearchIO.html#module-Bio.SearchIO#module-Bio.SearchIO}{documentation}
 for a full list of these predefined properties.
 
 Furthermore, each sequence search tool usually computes its own statistics /
@@ -880,7 +880,7 @@ \subsection{HSP}
 \verb|hit_all|, and \verb|aln_all|. These properties will return a list containing
 \verb|SeqRecord| or \verb|MultipleSeqAlignment| objects from each of the HSP
 fragment. There are other attributes that behave similarly, i.e. they only work
-for HSPs with one fragment. Check out the \verb|HSP| \href{http://biopython.org/DIST/docs/api/Bio.SearchIO._model.hsp-module.html}{documentation}
+for HSPs with one fragment. Check out the \verb|HSP| \href{http://biopython.org/docs/1.77/api/Bio.SearchIO.html#module-Bio.SearchIO}{documentation}
 for a full list.
 
 Finally, to check whether you have multiple fragments or not, you can use the

diff --git a/Doc/Tutorial/chapter_seq_annot.tex b/Doc/Tutorial/chapter_seq_annot.tex
@@ -7,7 +7,7 @@ \chapter{Sequence annotation objects}
 for now. If on the other hand you are going to be using richly annotated sequence data, say from GenBank
 or EMBL files, this information is quite important.
 
-While this chapter should cover most things to do with the \verb|SeqRecord| and \verb|SeqFeature| objects in this chapter, you may also want to read the \verb|SeqRecord| wiki page (\url{http://biopython.org/wiki/SeqRecord}), and the built in documentation (also online -- \href{http://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html}{SeqRecord} and \href{http://biopython.org/DIST/docs/api/Bio.SeqFeature.SeqFeature-class.html}{SeqFeature}):
+While this chapter should cover most things to do with the \verb|SeqRecord| and \verb|SeqFeature| objects in this chapter, you may also want to read the \verb|SeqRecord| wiki page (\url{http://biopython.org/wiki/SeqRecord}), and the built in documentation (also online -- \href{http://biopython.org/docs/1.77/api/Bio.SeqRecord.html}{SeqRecord} and \href{http://biopython.org/docs/1.77/api/Bio.SeqFeature.html}{SeqFeature}):
 
 \begin{minted}{pycon}
 >>> from Bio.SeqRecord import SeqRecord

diff --git a/Doc/Tutorial/chapter_seqio.tex b/Doc/Tutorial/chapter_seqio.tex
@@ -2,7 +2,7 @@ \chapter{Sequence Input/Output}
 \label{chapter:seqio}
 
 In this chapter we'll discuss in more detail the \verb|Bio.SeqIO| module, which was briefly introduced in Chapter~\ref{chapter:quick_start} and also used in Chapter~\ref{chapter:seq_annot}. This aims to provide a simple interface for working with assorted sequence file formats in a uniform way.
-See also the \verb|Bio.SeqIO| wiki page (\url{http://biopython.org/wiki/SeqIO}), and the built in documentation (also \href{http://biopython.org/DIST/docs/api/Bio.SeqIO-module.html}{online}):
+See also the \verb|Bio.SeqIO| wiki page (\url{http://biopython.org/wiki/SeqIO}), and the built in documentation (also \href{http://biopython.org/docs/1.77/api/Bio.SeqIO.html}{online}):
 
 \begin{minted}{pycon}
 >>> from Bio import SeqIO
@@ -54,7 +54,7 @@ \subsection{Reading Sequence Files}
     print(len(seq_record))
 \end{minted}
 
-Similarly, if you wanted to read in a file in another file format, then assuming \verb|Bio.SeqIO.parse()| supports it you would just need to change the format string as appropriate, for example ``swiss'' for SwissProt files or ``embl'' for EMBL text files. There is a full listing on the wiki page (\url{http://biopython.org/wiki/SeqIO}) and in the built in documentation (also \href{http://biopython.org/DIST/docs/api/Bio.SeqIO-module.html}{online}).
+Similarly, if you wanted to read in a file in another file format, then assuming \verb|Bio.SeqIO.parse()| supports it you would just need to change the format string as appropriate, for example ``swiss'' for SwissProt files or ``embl'' for EMBL text files. There is a full listing on the wiki page (\url{http://biopython.org/wiki/SeqIO}) and in the built in documentation (also \href{http://biopython.org/docs/1.77/api/Bio.SeqIO.html}{online}).
 
 Another very common way to use a Python iterator is within a list comprehension (or
 a generator expression).  For example, if all you wanted to extract from the file was