bow · May 15, 2019 · May 15, 2019 · May 15, 2019 · May 15, 2019 · May 15, 2019
diff --git a/2018_BOSC/presentation/README.md b/2018_BOSC/presentation/README.md
@@ -0,0 +1,5 @@
+The presentation source is on GitHub here, in Peter's personal talks repository:
+https://github.com/peterjc/peter-talks/tree/master/Biopython-Update-2018
+
+It was uploaded to F1000 after the meeting, citable here:
+https://doi.org/10.7490/f1000research.1115739.1
diff --git a/2019_BOSC/abstract/abstract.tex b/2019_BOSC/abstract/abstract.tex
@@ -0,0 +1,99 @@
+\documentclass[10pt,oneside]{article}
+
+%%%%%%%%%%%%%
+\setlength{\textheight}{8.75in} %Letter is 11in, less 2 for margins, less 0.25 for footer
+\setlength{\oddsidemargin}{0.0in} %gets +1inc
+\setlength{\evensidemargin}{0.0in} %gets +1inch
+\setlength{\textwidth}{6.50in} %Letter is 8.5, less 2 inches for margins
+\setlength{\topmargin}{0.5in}
+\setlength{\headheight}{0in}
+\setlength{\headsep}{0in}
+\setlength{\parindent}{0.25in}
+%%%%%%%%%%%%
+
+% use letters instead of symbols to accommodate >7 authors
+\makeatletter
+\let\@fnsymbol\@alph
+\makeatother
+
+\usepackage[utf8]{inputenc}
+\usepackage[numbers]{natbib}
+\usepackage{graphicx}
+\usepackage[colorlinks=true,citecolor=black,urlcolor=blue]{hyperref}
+
+\title{%Hack to get the logo on the PDF front page:
+\vspace{-1.5in}
+\includegraphics[width=0.3\textwidth]{biopython_logo_s.png} \\
+\vspace{3mm}Biopython Project Update 2019}
+\author{
+    Peter Cock\thanks{Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, UK},\\
+    and the Biopython Contributors\thanks{See \href{https://github.com/biopython/biopython/blob/master/CONTRIB.rst}{contributor listing on GitHub}.}}
+\date{20\textsuperscript{th} Bioinformatics Open Source Conference (BOSC) 2019, Basel, Switzerland}
+
+\begin{document}
+\maketitle
+\thispagestyle{empty}
+
+\vspace{-0.2in}
+\noindent
+Website: \url{http://biopython.org} \\
+Repository: \url{https://github.com/biopython/biopython} \\
+License: Biopython License Agreement (BSD like, see \url{http://www.biopython.org/DIST/LICENSE}) \\
+
+The Biopython Project is a long-running distributed collaborative effort,
+supported by the Open Bioinformatics Foundation, which develops a freely
+available Python library for biological computation \cite{AppNote}. This
+talk will look ahead to the year to come, and give a summary of the project
+news since the 1.72 release in June 2018, and the talk at GCCBOSC 2018.
+
+While there were no major new modules introduced in Biopython 1.73
+(December 2018) or Biopython 1.74 (expected May/June 2019), there have
+been lots of incremental improvements.
+In terms of lines of code changed, a substantial proportion has been
+in-line documentation (Python docstrings), used to generate human-readable
+API documentation. While we are still using \texttt{epydoc} for this, our continuous
+integration system has been generating more modern HTML output using \texttt{sphinx},
+which we hope to host on our domain, or at Read The Docs, making this work
+much more visible to the world. We have been using the tool \texttt{flake8}
+with various plugins for this (as well as checking coding style), showing
+a steady improvement in best practice compliance - every public API should
+be documented this year.
+
+In 2017 we started a re-licensing plan, to transition away
+from our liberal but unique \emph{Biopython License Agreement} to the similar
+but very widely used \emph{3-Clause BSD License}. We are reviewing the code
+base authorship file-by-file, to gradually dual license the entire project.
+All new contributions are dual licensed, and currently, half the Python files
+in the main library have been dual licensed.
+
+Another important going effort is improving the unit test coverage. Sadly
+this is currently fairly static at about $85\%$ (excluding online tests),
+but can be viewed online at
+\href{https://codecov.io/github/biopython/biopython/}{CodeCov.io}.
+
+We are using GitHub-integrated continuous integration testing on Linux (using
+\href{https://travis-ci.org/biopython/biopython/builds}{TravisCI}) and Windows
+(using \href{https://ci.appveyor.com/project/biopython/biopython/history}{AppVeyor}),
+including enforcing the Python PEP8 and PEP257 coding style guidelines.
+We hope to be able to recommend a simple \texttt{git pre-commit} hook
+for our contributors shortly, and have discussed the idea of adopting the
+new yet popular Python code formatting style tool \texttt{black} to reduce
+the human time costs in writing compliant code.
+
+Looking further ahead, in 2020, in line with most major scientific Python
+libraries, we will be dropping support for Python 2. See \url{https://python3statement.org/}
+
+Finally, since our last update talk in June 2018, Biopython has had 32 named
+contributors including 14 newcomers. This reflects our policy of trying to
+encourage even small contributions.
+% Removed repeated use of 'This'
+Our total named contributor count is now at 248 since the project began, and
+looks likely to break 250 by our 20th Birthday in August 2019.
+
+\begin{thebibliography}{}
+
+\bibitem[Cock {\it et al}., 2009]{AppNote}Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., de Hoon, M.J. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. {\it Bioinformatics} {\bf 25}(11) 1422-3. \href{http://dx.doi.org/10.1093/bioinformatics/btp163}{doi:10.1093/bioinformatics/btp163}
+
+\end{thebibliography}
+
+\end{document}
diff --git a/2019_BOSC/abstract/abstract.txt b/2019_BOSC/abstract/abstract.txt
@@ -0,0 +1,9 @@
+(200 word limit for all ISMB/ECCB abstracts; the PDF is limited to one page for BOSC)
+
+Biopython is a long-running collaboration that provides a freely available Python library for biological computation. We summarise recent project news, and look ahead.
+
+Releases 1.73 (December 2018) and 1.74 (expected May/June 2019) include improvements to various modules of the code base and continue the effort to document our public APIs, which we expect to complete this year. We have also focused on improving test coverage, currently at 85% (excluding online tests). Tests and Python PEP8/PEP257 style are checked with continuous integration on Linux (TravisCI) and Windows (AppVeyor). We are considering adopting the Python code formatting style tool 'black' to reduce human time writing compliant code.
+
+In 2017 we started transitioning from our liberal but unique Biopython License Agreement to the similar but very widely used 3-Clause BSD License. Already half the files in the main library have been dual licensed after reviewing authorship, and all new contributions are dual licensed.
+
+Finally, in the last year, Biopython had 32 named contributors, including 14 newcomers, reflecting our policy of encouraging even small contributions. We expect to reach 250 contributors by our 20th Birthday in August 2019.
diff --git a/2019_BOSC/abstract/biopython_logo_s.png b/2019_BOSC/abstract/biopython_logo_s.png
@@ -0,0 +1 @@
+../../2018_BOSC/abstract/biopython_logo_s.png
diff --git a/2020_BOSC/abstract/abstract.tex b/2020_BOSC/abstract/abstract.tex
@@ -0,0 +1,84 @@
+\documentclass[10pt,oneside]{article}
+
+%%%%%%%%%%%%%
+\setlength{\textheight}{8.75in} %Letter is 11in, less 2 for margins, less 0.25 for footer
+\setlength{\oddsidemargin}{0.0in} %gets +1inc
+\setlength{\evensidemargin}{0.0in} %gets +1inch
+\setlength{\textwidth}{6.50in} %Letter is 8.5, less 2 inches for margins
+\setlength{\topmargin}{0.5in}
+\setlength{\headheight}{0in}
+\setlength{\headsep}{0in}
+\setlength{\parindent}{0.25in}
+%%%%%%%%%%%%
+
+% use letters instead of symbols to accommodate >7 authors
+\makeatletter
+\let\@fnsymbol\@alph
+\makeatother
+
+\usepackage[utf8]{inputenc}
+\usepackage[numbers]{natbib}
+\usepackage{graphicx}
+\usepackage[colorlinks=true,citecolor=black,urlcolor=blue]{hyperref}
+
+\title{%Hack to get the logo on the PDF front page:
+\vspace{-1.5in}
+\includegraphics[width=0.3\textwidth]{biopython_logo_s.png} \\
+\vspace{3mm}Biopython Project Update 2020}
+\author{
+    Peter Cock\thanks{Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, UK},\\
+    and the Biopython Contributors\thanks{See \href{https://github.com/biopython/biopython/blob/master/CONTRIB.rst}{contributor listing on GitHub}.}}
+\date{Bioinformatics Open Source Conference (BOSC),\\Bioinformatics Community Conference 2020}
+
+\begin{document}
+\maketitle
+\thispagestyle{empty}
+
+\vspace{-0.2in}
+\noindent
+Website: \url{http://biopython.org} \\
+Repository: \url{https://github.com/biopython/biopython} \\
+License: Biopython License Agreement (BSD like, see \url{http://www.biopython.org/DIST/LICENSE}) \\
+
+The Biopython Project is a long-running distributed collaborative effort,
+supported by the Open Bioinformatics Foundation, which develops a freely
+available Python library for biological computation \cite{AppNote}. This
+talk will look ahead to the year to come, and give a summary of the project
+news since the 1.74 release in July 2019, and the talk at BOSC 2019.
+
+There have been three releases: Biopython 1.75 (November 2019), Biopython 1.76
+(December 2019), and Biopython 1.77 (expected May/June 2020). This year saw
+the adoption of the \texttt{black} Python coding style, our final release to
+support Python 2, and substantial code cleanup to focus on Python 3 only.
+
+In 2017 we started a re-licensing plan, to transition away
+from our liberal but unique \emph{Biopython License Agreement} to the similar
+but very widely used \emph{3-Clause BSD License}. We are reviewing the code
+base authorship file-by-file, to gradually dual license the entire project.
+All new contributions are dual licensed, and currently over $75\%$ of the
+Python and C files in the main library have been dual licensed.
+
+Another important effort had been improving the unit test coverage, which can
+be viewed at \href{https://codecov.io/github/biopython/biopython/}{CodeCov.io}.
+Sadly, this has stalled at about $85\%$ (excluding online tests) for some time.
+
+We are using GitHub-integrated continuous integration testing on Linux (using
+\href{https://travis-ci.org/biopython/biopython/builds}{TravisCI}) and Windows
+(using \href{https://ci.appveyor.com/project/biopython/biopython/history}{AppVeyor}),
+including enforcing the Python PEP8, PEP257 and black coding style guidelines.
+We recommend a simple \texttt{git pre-commit} hook using \textit{flake8} for
+our contributors, which aims to reduce the human time costs in writing
+compliant code.
+
+Finally, since our last update talk in July 2019, Biopython has had 37 named
+contributors including 15 newcomers. This reflects our policy of trying to
+encourage even small contributions. Our total named contributor count is now
+at 275 since the project began, over twenty year ago.
+
+\begin{thebibliography}{}
+
+\bibitem[Cock {\it et al}., 2009]{AppNote}Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., de Hoon, M.J. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. {\it Bioinformatics} {\bf 25}(11) 1422-3. \href{http://dx.doi.org/10.1093/bioinformatics/btp163}{doi:10.1093/bioinformatics/btp163}
+
+\end{thebibliography}
+
+\end{document}
diff --git a/2020_BOSC/abstract/abstract.txt b/2020_BOSC/abstract/abstract.txt
@@ -0,0 +1,35 @@
+(One page PDF limit)
+
+The Biopython Project is a long-running distributed collaborative effort,
+supported by the Open Bioinformatics Foundation, which develops a freely
+available Python library for biological computation \cite{AppNote}. This
+talk will look ahead to the year to come, and give a summary of the project
+news since the 1.74 release in July 2019, and the talk at BOSC 2019.
+
+There have been three releases: Biopython 1.75 (November 2019), Biopython 1.76
+(December 2019), and Biopython 1.77 (expected May/June 2020). This year saw
+the adoption of the black Python coding style, our final release to
+support Python 2, and substantial code cleanup to focus on Python 3 only.
+
+In 2017 we started a re-licensing plan, to transition away
+from our liberal but unique Biopython License Agreement to the similar
+but very widely used 3-Clause BSD License. We are reviewing the code
+base authorship file-by-file, to gradually dual license the entire project.
+All new contributions are dual licensed, and currently over 75% of the Python
+and C files in the main library have been dual licensed.
+
+Another important effort had been improving the unit test coverage, which can
+be viewed at CodeCov.io.
+Sadly, this has stalled at about 85% (excluding online tests) for some time.
+
+We are using GitHub-integrated continuous integration testing on Linux (using
+TravisCI) and Windows (using AppVeyor),
+including enforcing the Python PEP8, PEP257 and black coding style guidelines.
+We recommend a simple git pre-commit hook using flake8 for
+our contributors, which aims to reduce the human time costs in writing
+compliant code.
+
+Finally, since our last update talk in July 2019, Biopython has had 37 named
+contributors including 15 newcomers. This reflects our policy of trying to
+encourage even small contributions. Our total named contributor count is now
+at 275 since the project began, over twenty year ago.
diff --git a/2020_BOSC/abstract/biopython_logo_s.png b/2020_BOSC/abstract/biopython_logo_s.png
@@ -0,0 +1 @@
+../../2018_BOSC/abstract/biopython_logo_s.png