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	<title>Avoiding common annoyances in bioinformatics</title>
	<meta name="author" content="Pieter Moris">

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			<section style="font-size: 0.7em;">
				<h1>1111 rules for avoiding misery in bioinformatics</h1>
				<h3>or a bunch of stupid things I've done</h3>
				<h3>or an excuse to spout my opinion and act smug</h3>
				<p>
					<medium>Created by Pieter Moris</medium>
				</p>
			</section>

			<!-- GIT -->
			<section>
				<section data-background-transition="zoom" data-background="#a6e22e">
					<h1>Use version control</h1>
					<h4 class="fragment visible">Preferably <code>git</code></h4>
				</section>
				<!-- <section>
						<h4>Use version control - preferably <code>git</code>.</h4>
						<p>Nuff' said.</p>
					</section> -->

				<!-- <section>
						<p>Why?</p>
						</br>
						<span class="fragment">
							<img  class="fragment visible" data-src="assets/why-you-need-vcs.jpg" alt="version-control-r-files">
						</br>
							<ul style="font-size: 0.7em">
								<li class="fragment visible">Safety</li>
								<li class="fragment visible">History</li>
								<li class="fragment visible">Organization</li>
							</ul>
						</span>
					</section> -->

				<section>
					<p>Why?</p>

					<div class="column_container">
						<div class="col">
							<img class="fragment visible" data-src="assets/why-you-need-vcs.jpg"
								alt="version-control-r-files">
						</div>

						<div class="col">
							<ul style="vertical-align: middle;">
								<li class="fragment visible">Safety</li>
								<li class="fragment visible">History</li>
								<li class="fragment visible">Organization</li>
							</ul>
						</div>
					</div>

					<!-- Notes: use it so you don't end up with this nonsense. It's safe because you'll be able to re-trace your steps and get a free backup. You get an overview of your history and attempts, because you sure as hell won't remember what you were doing two weeks from now. It also allows you to be better organized, by avoiding these redundant naming schemes and making you think about which files should be available and where they should be located. -->
				</section>

				<section>
					<p>How?</p>
					<ul class="fragment">
						<li style="padding: 10px;">My git internals tutorial: <a
								href=https://pmoris.github.io/git-gud>https://pmoris.github.io/git-gud </a> </li> <li
								style="padding: 10px;">Various other resources and tutorials are collected in my
								computational skill set primer.</li>
					</ul>
				</section>
				<section style="font-size: 0.65em">
					<h4>Beware git GUIs</h4>
					<p><span class="emphasized">Use the command line</span> as much as possible for interacting with
						<code>git</code> and only rely on a GUI for visualisation of history and file diffs.</p>
					</br>
					<p class="fragment">Reason: GUIs sometimes hide steps, use slightly different naming conventions or
						try to be smart and automate certain steps, which can cause a lot of confusion, anxiety and/or
						horror.</p>
					<p class="fragment">Or they just choke completely after a <code>git rebase -i</code>.</p>
					<div style="font-size: 0.9em" class="fragment">
						</br>
						<p>Read more in the primer, important aspects include: </p>
						<ul>
							<li>How to generate SSH keys and how to use them in other git-aware tools.</li>
							<li>Use a private commit e-mail address and don't accidentally overwrite it.</li>
							<li><code>git clone</code> is just a way to download a repository to your computer.</li>
						</ul>
					</div>
				</section>

				<!-- <section data-menu-title="git SSH vs HTTPS"> -->
				<section>
					<h4>These are not the same!</h4>
					<img style="border: 0;" height="100%" data-src="assets/ssh-https.png" alt="ssh-https-github">
					<p>GitHub recommends HTTPS, but SSH allows you to use your SSH key instead of requiring login
						credentials for each remote action.</p>
					<ul style="font-size: 0.6em">
						<li><a
								href="https://help.github.com/en/articles/which-remote-url-should-i-use">https://help.github.com/en/articles/which-remote-url-should-i-use</a>
						</li>
						<li><a
								href="https://stackoverflow.com/questions/11041729/why-does-github-recommend-https-over-ssh">https://stackoverflow.com/questions/11041729/why-does-github-recommend-https-over-ssh</a>
						</li>
					</ul>
				</section>
				<section style="font-size: 0.8em">
					<!-- <section style="font-size: 0.8em" data-menu-title="GitKraken"> -->
					<h3>Side note for those that use <span style="color: #a6e22e">GitKraken</span>: </h3>
					<ul>
						<li>GitKraken account != GitHub account != git username</li>
						<li>Profile overwrites your git e-mail <code>git config --list</code></li>
					</ul>
				</section>
			</section>

			<!-- EXCEL -->
			<section>
				<section data-menu-title="Spreadsheet software woes">
					<h2>Be careful when using <span style="color: #a6e22e">Excel</span> or equivalents</h2>
					<img class="stretch" data-src="assets/excel.png" alt="excel">
				</section>

				<section style="font-size: 0.4em">
					<img class="stretch" data-src="assets/gene-names-dates.png" alt="gene-names-dates">

					<blockquote>
						Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in
						bioinformatics (Zeeberg et al., 2004. <a
							href="https://doi.org/10.1186/1471-2105-5-80">https://doi.org/10.1186/1471-2105-5-80</a>)
					</blockquote>

					<blockquote>
						Gene name errors are widespread in the scientific literature (Ziemann et al., 2016. <a
							href="https://doi.org/10.1186/s13059-016-1044-7">https://doi.org/10.1186/s13059-016-1044-7</a>)
					</blockquote>
				</section>

				<section style="font-size: 0.6em">
					<img class="stretch" data-src="assets/encoding.png" alt="encoding">
					<p class="fragment">Other lessons to learn: encapsulate fields (<code>"entry-filled with, separators
							you use to separate; columns"</code>) and mind character encoding (almost always opt for
						<code>UTF-8</code>).</p>

					<p class="fragment">Similar issues can crop up when importing data into <code>R</code> or
						<code>pandas</code> dataframes, so be explicit and specify the encoding!</p>
				</section>
			</section>

			<!-- HOTKEYS -->
			<section>
				<section data-background-transition="zoom" data-background="#a6e22e">
					<h1>Familiarise yourself with hotkeys and shortcuts ⌨</h1>
				</section>
				<!-- <section data-background-transition="zoom" data-background="#191919">
						<h1 style="color: #a6e22e">Familarise yourself with hotkeys and shortcuts</h1>
					</section> -->
				<!-- <section data-background-transition="zoom" data-background="#466111">
						<h1>Familarise yourself with hotkeys and shortcuts</h1>
					</section> -->

				<section>
					<p>Seeing other people navigate their computer sometimes triggers a deep silent rage within me.</p>
					<img class="stretch" data-src="assets/screaming.gif" alt="screaming">
				</section>

				<section style="font-size: 0.9em">
					<h3>Notorious examples include:</h3>
					</br>
					<ul>
						<li>Not using <span class="emphasized">tab-completion</span> whenever possible (and mistyping
							file paths as a consequence).</li>
						<li>Re-typing commands in a terminal instead of using the <span
								class="emphasized">history</span> <span style="font-size: 70%">(<code>↑</code> key or
								history search function <code>ctrl + r</code>)</span>.</li>
						<li>Using the mouse and GUI buttons to run code in notebooks or IDEs.</li>
					</ul>
				</section>

				<section>
					<blockquote>Spend 10 minutes now to save many more in the future.</blockquote>

					</br>

					<p class="fragment">Especially important in your <span class="emphasized">terminal</span>, <span
							class="emphasized">file manager</span> and <span class="emphasized">IDE</span> or <span
							class="emphasized">text editor</span>.</p>
				</section>

				<section style="font-size: 0.75em">
					<h4>Additional examples and resources</h4>

					<ul>
						<li>Your <span class="emphasized">terminal</span> has dozens of neat shortcuts, like moving the
							cursor to the start/end of a line, deleting whole words, etc.</li>
						<li class="fragment">R and Jupyter <span class="emphasized">notebooks</span> have hotkeys to
							create cells, switch between cell types, run the current/above/below/all cells</li>
						<li class="fragment">In RStudio select lines and use <code>ctrl + return</code> to run just them
							(or all lines).</li>
						<li class="fragment">Use automatic docstring <span class="emphasized">generators</span>. <span
								style="font-style: italic">You are writing docstrings, aren't you?</span></li>
						<li class="fragment">Decide on a code <span class="emphasized">formatter + linter</span> and use
							it consistently, most editors can do this for you (e.g. VS code + <code>black</code> and
							<code>flake8</code>).</li>
					</ul>

					<p>Check out the primer for more resources on this topic.</p>
				</section>
			</section>

			<!-- COPYING CODE -->
			<section>
				<section data-background-transition="zoom" data-background="#a6e22e">
					<h1>Be careful when copying code from the web ✂📋</h1>
				</section>

				<section>
					<pre><code class="sh" data-trim data-noescape>
								pieter  🐍 base  ~  sudo apt install –y cowsay
								[sudo] password for pieter:
								Reading package lists... Done
								Building dependency tree
								Reading state information... Done
								E: Unable to locate package –y
						</code></pre>

					<p class="fragment" style="font-size: 0.7em"><code>—</code> (em dash) VS <code>–</code> (en dash) VS
						<code>-</code> (hyphen ~= hyphen-minus)</p>

					</br>

					<pre class="fragment"><code class="sh" data-trim data-noescape>
							  pieter  🐍 base  ~  echo “something profound”
							“something profound”
							 pieter  🐍 base  ~  echo "something else"
							something else
						</code></pre>

					<span class="fragment" style="font-size: 0.7em">
						<p>curly or smart and straight or vertical quotation marks</p>
						<p><code>“ ”</code> VS <code>" "</code></p>
						<p><code>‘ ’</code> VS <code>' '</code></p>
					</span>
				</section>
			</section>

			<!-- TERMINAL TIPS -->
			<section>
				<section data-background-transition="zoom" data-background="#a6e22e">
					<h1>Terminal tips <i class="fas fa-terminal"></i></h1>
				</section>
				<section>
					<ul>
						<li>Increase the length of your bash history: <br> <code>echo "HISTFILESIZE=100000" >>
								~/.bashrc</code> and use <code>ctrl + r</code> to search through it.</li>
						<br>
						<li class="fragment">Create aliases and save short scripts: <br> <code>echo alias vpn="sudo
								openconnect vpn.uantwerpen.be" >> ~/.bash_aliases</code> </li>
					</ul>
				</section>
				<section>
					<h4>Be careful when using <code>rm</code>.</h4>
					<ul style="font-size: 0.8em">
						<li><code>cd /so/very/deep/in/a/path && rm -rf dir</code></li>
						<li>Place dangerous flags after the path: <code>rm /path/to/dir -r</code>. <small>Accidentally
								pressing enter too soon is less likely to cause harm.</small></li>
						<li>Tab completion helps!</li>
						<li><code>touch -- -i</code> in important directories.</li>
						<li>Use <a href="https://launchpad.net/safe-rm">https://launchpad.net/safe-rm</a></li>
						<li>Don't use trailing slashes or dot-slash starts in your filepaths: <br> <code>rm -rf ./* # *;
								rm -rf $FOO/ # $FOO</code></li>
					</ul>
				</section>
				<section id="path">
					<h4>What is the <span class="emphasized">PATH</span>?!‽‽‽</h4>
					<span class="fragment" style="font-size: 0.8em">
						<p>List of directories where the shell searches for executable files.</p>
						<div class="column_container">
							<div style="font-size: 0.55em;" class="fragment" class="col">
								<h6>Windows</h6>

								<img width="65%" data-src="assets/windows-path.jpg" alt="path-windows">
							</div>

							<div style="font-size: 0.55em; margin-left: 50px !important; text-align:left !important"
								class="col">
								<span class="fragment">
									<h6>Unix</h6>
									<code class="shell" data-trim>
										$ echo $PATH <br>
										/home/pieter/.nvm/versions/node/v10.5.0/bin:/home/pieter/.rbenv/shims:/home/pieter/.rbenv/bin:/opt/pycharm/bin:/home/pieter/miniconda3/bin:/home/pieter/miniconda3/condabin:/home/pieter/bin:/home/pieter/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/java-10-oracle/bin:/usr/lib/jvm/java-10-oracle/db/bin:/usr/lib/jvm/java-11-openjdk-amd64/bin:/home/pieter/miniconda3/envs/tools/bin
									</code>
								</span>
								<br><br>
								<code class="fragment">
									echo 'export PATH="$PATH:/home/pieter/miniconda3/envs/tools/bin"' >> .bash_rc
								</code>
							</div>
						</div>

						<ul style="font-size: 0.5em">
							<li><a
									href="https://astrobiomike.github.io/unix/modifying_your_path">https://astrobiomike.github.io/unix/modifying_your_path</a>
							</li>
							<li><a
									href="https://superuser.com/questions/284342/what-are-path-and-other-environment-variables-and-how-can-i-set-or-use-them">https://superuser.com/questions/284342/what-are-path-and-other-environment-variables-and-how-can-i-set-or-use-them</a>
							</li>
						</ul>
					</span>
				</section>
				<section>
					<p>You can use the following commands to find out where a command is located:</p>

					<pre class="stretch"><code class="sh" data-trim data-noescape>
							 $ which python # only works if binary is included in $PATH
							/home/pieter/miniconda3/bin/python
							 $ conda activate tools
							 $ which python
							/home/pieter/miniconda3/envs/tools/bin/python

							 $ whereis python # searches hard-coded paths regardless of $PATH
							python: /usr/bin/python3.6 /usr/bin/python3.5 /usr/bin/python3.6m-config /usr/bin/python3.6m /usr/bin/python3.5m /usr/bin/python3.6-config /usr/bin/python2.7 /usr/bin/python /usr/lib/python3.6 /usr/lib/python3.5 /usr/lib/python2.7 /usr/lib/python3.7 /etc/python3.6 /etc/python3.5 /etc/python2.7 /etc/python /usr/local/lib/python3.6 /usr/local/lib/python3.5 /usr/local/lib/python2.7 /usr/include/python3.6 /usr/include/python3.6m /usr/include/python2.7 /usr/share/python /home/pieter/miniconda3/envs/tools/bin/python3.7 /home/pieter/miniconda3/envs/tools/bin/python3.7m /home/pieter/miniconda3/envs/tools/bin/python3.7m-config /home/pieter/miniconda3/envs/tools/bin/python3.7-config /home/pieter/miniconda3/envs/tools/bin/python /usr/share/man/man1/python.1.gz

							 $ echo alias vpn=openconnect vpn.uantwerpen.be >> .bash_aliases
							 $ type vpn # searches environment including $PATH and aliases (or "command -v")
							vpn is aliased to `sudo openconnect vpn.uantwerpen.be'
						</code></pre>

					<p>cf. version managers</p>
				</section>

				<!--
					<section>
						<h4>How not do to it</h4>
						<pre><code class="sh" data-trim data-noescape>
							$ pip install redis
							$ sudo apt install python2
							$ bash ./install_conda.sh
							$ conda install
							$ R
							$ install.packages
						</code></pre>
						<p>Learn how different methods of install work behind the scenes.</p>
						SEE INSTALLATION MANAGEMENT PYTHON/R
					</section> -->


				<section>
					<img width="60%" data-src="assets/bash-windows.jpg" alt="bash-windows">
				</section>
				<section style="font-size: 0.5em">
					<p>Windows Command Prompt and Powershell are not the same as a Unix-shell, although they have their
						uses.</p>
					<p>Install the Windows Subsystem for Linux on W10 <a
							href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">https://docs.microsoft.com/en-us/windows/wsl/install-win10</a>,
						rather than running a virtual machine (for most scenarios).</p>
					<p>Caveat: things like Python are <span class="emphasized">not automatically shared</span> between
						Windows and the Subsystem.</p>
					<p>Even GUI apps work if you install an X server!</p>
					<p>Can even be linked to your IDE e.g. VS Code: <a
							href="https://medium.com/@janelgbrandon/a-guide-for-using-wsl-for-development-d135670313a6">https://medium.com/@janelgbrandon/a-guide-for-using-wsl-for-development-d135670313a6</a>
						& <a
							href="https://code.visualstudio.com/docs/remote/wsl">https://code.visualstudio.com/docs/remote/wsl</a>
						as if it's a remote server</p>
					<p>For the full write-up, see the primer.</p>
					<a
						href="https://askubuntu.com/questions/1051525/windows-subsystem-for-linux-wsl-what-cant-i-do-with-the-ubuntu-application-f">https://askubuntu.com/questions/1051525/windows-subsystem-for-linux-wsl-what-cant-i-do-with-the-ubuntu-application-f</a>
				</section>

				<section>
					<img width="60%" data-src="assets/exit-vim.jpeg" alt="bash-windows">
				</section>

				<section>
					<h2>Learn how to exit vim</h2>

					<code style="text-decoration: line-through;">Press the X button</code><br>
					<span style="text-decoration: line-through;"><code>$ killall -9 vim</code></span><br>
					<code data-noescape> &lt;esc&gt;:wq&lt;enter&gt;</code><br>
					<code>Shift-Z-Z</code>

					<p style="font-size:0.6em"><a
							href="https://stackoverflow.blog/2017/05/23/stack-overflow-helping-one-million-developers-exit-vim/">https://stackoverflow.blog/2017/05/23/stack-overflow-helping-one-million-developers-exit-vim/</a>
					</p>

				</section>

				<section>
					<h4>Learn (at least) a few Bash/PowerShell tools</h4>

					<p><code>grep</code> (and by extension regular expressions) can help when your IDE decides to be an
						idiot.</p>

					<img class="stretch" data-src="assets/grep-ide.png" alt="ide-vs-grep">
				</section>
				<!-- counting lines
					head or tail
					checking columns
					editing line-by-line sed
					low memory editing vim -->
				<section>
					<h4>Spend some time on a bash primer</h4>
					<pre>
							<code class="sh" data-trim data-noescape>
								 $ rsync --help | grep "-z"
								Usage: grep [OPTION]... PATTERN [FILE]...
								Try 'grep --help' for more information.

								 $ rsync -h | grep "\-z"
								-z, --compress              compress file data during the transfer

								 $ rsync -h | grep '\-z'
								-z, --compress              compress file data during the transfer

								 $ rsync --help | grep -- -z
								-z, --compress              compress file data during the transfer

							</code>
						</pre>
				</section>

				<section>
					<h4>Things worth your time</h4>

					<ul style="font-size: 0.7em">
						<li>File permissions: <a
								href="https://linuxjourney.com/lesson/file-permissions">https://linuxjourney.com/lesson/file-permissions</a>
						</li>
						<li>File redirection: <a
								href="https://catonmat.net/bash-one-liners-explained-part-three">https://catonmat.net/bash-one-liners-explained-part-three</a>
							e.g. <code>foo >outfile1 2>&1 >outfile2</code> (<a
								href="https://stackoverflow.com/questions/818255/in-the-shell-what-does-21-mean">see
								SO</a>)</li>
						<li>Regular expressions and <code>grep / sed / awk</code>: <a
								href="https://regexone.com/">https://regexone.com/</a></li>
						<li><a href="https://mywiki.wooledge.org/BashGuide">https://mywiki.wooledge.org/BashGuide</a>
						</li>
						<li><a
								href="https://mywiki.wooledge.org/BashPitfalls">https://mywiki.wooledge.org/BashPitfalls</a>
							(even just number 1 is useful)</li>
						<li><a
								href="https://zwischenzugs.com/2018/01/06/ten-things-i-wish-id-known-about-bash/">https://zwischenzugs.com/2018/01/06/ten-things-i-wish-id-known-about-bash/</a>
						</li>
					</ul>
				</section>

				<!-- MENTION TEE? -->
				<!-- counting lines

					head or tail

					checking columns

					editing line-by-line sed

					low memory editing vim -->
			</section>

			<!-- SSH TIPS -->
			<section>
				<section data-background-transition="zoom" data-background="#a6e22e">
					<h1>SSH tips 🔑 </h1>
				</section>
				<section>
					<h4>Use <code>~/.ssh/config</code></h4>
					<pre>
							<code class="sh" data-trim data-noescape>
								Host calcua
								HostName login-leibniz.uantwerpen.be
								#Port 22000
								User vsc20380
								IdentityFile ~/.ssh/id_rsa
							</code>
						</pre>

					<pre>
							<code class="sh" data-trim data-noescape>
								$ ssh calcua
								$ rsync -avhzP *.tar.gz calcua:/scratch/antwerpen/203/vsc20380/pmc/
							</code>
						</pre>
				</section>

				<section>
					<h4>When working on a remote server over <span class="emphasized">SSH</span> (or <span
							class="emphasized">PuTTY</span>), you can keep jobs alive after disconnecting:</h4>

					<ul style="font-size: 0.8em">
						<li class="fragment">After already starting a process: <code>^Z</code> followed by <code>bg
								%1</code> and <code>disown (-h) %1</code></li>
						<li class="fragment"><code>nohup bash my_amazing_script.sh > output.log 2>&1 &</code> (cf.
							redirection)</li>
						<li class="fragment"><code style="text-decoration: line-through">screen</code> /
							<code>tmux</code></li>
					</ul>

					<span class="fragment">
						<p>Process needs to be immune to SIGHUP.</p>

						<ul style="font-size: 0.5em">
							<li><a
									href="https://serverfault.com/questions/311593/keeping-a-linux-process-running-after-i-logout">https://serverfault.com/questions/311593/keeping-a-linux-process-running-after-i-logout</a>
							</li>
							<li><a
									href="https://unix.stackexchange.com/questions/3886/difference-between-nohup-disown-and">https://unix.stackexchange.com/questions/3886/difference-between-nohup-disown-and</a>
							</li>
							<li><a
									href="https://unix.stackexchange.com/questions/484276/do-disown-h-and-nohup-work-effectively-the-same">https://unix.stackexchange.com/questions/484276/do-disown-h-and-nohup-work-effectively-the-same</a>
							</li>
							<li><a
									href="https://unix.stackexchange.com/questions/57166/disown-wont-take-h-option">https://unix.stackexchange.com/questions/57166/disown-wont-take-h-option</a>
							</li>
						</ul>
					</span>
				</section>

				<section style="font-size: 0.85em">
					<p>If you cannot connect to a server using SSH keys (and <code>ssh -vvv</code> is cryptic), check
						your <span class="emphasized">file permissions</span>.</p>
					</br>
					<ul>
						<li>.ssh directory: 700 (<code>drwx------</code>)</li>
						<li>public key (.pub file): 644 (<code>-rw-r--r--</code>)</li>
						<li>private key (id_rsa): 600 (<code>-rw-------</code>)</li>
						<li>home directory should not be writeable by the group or others, at most 755
							(<code>drwxr-xr-x</code>)</li>
					</ul>
				</section>

				<section>
					<p>
						Windows users: be aware than when you create <span class="emphasized">keys in WSL</span> the
						keys won't automatically be picked up by other Windows programs (PuTTY, git GUIs, etc.)
					</p>
				</section>
			</section>

			<!-- PYTHON DEBUGGING -->
			<section>
				<section data-menu-title="Debugging">
					<img class="stretch" data-src="assets/python-debug.jpg" alt="python-debug">
				</section>
				<!-- <section data-background-transition="zoom" data-background="#a6e22e"> -->
				<section>
					<h4>When you have more than a few <code>print()</code> statements in your Python code, it's time to
						use a proper <span class="emphasized">debugger</span>.</h4>

					<pre class="fragment"><code class="python" data-trim>
							import pdb # or import ipdb as pdb

							# insert this line where you want a breakpoint
							pdb.set_trace()
						</code></pre>

					<p class="fragment">Or use a solution built into your IDE e.g. PyCharm.</p>
					<br>
					<ul class="fragment" style="font-size: 0.5em">
						<li><a
								href="https://realpython.com/python-debugging-pdb/">https://realpython.com/python-debugging-pdb/</a>
						</li>
						<li><a
								href="https://github.com/spiside/pdb-tutorial">https://github.com/spiside/pdb-tutorial</a>
						</li>
						<li>Changing breakpoint statement: <a
								href="https://www.andreagrandi.it/2018/10/16/using-ipdb-with-python-37-breakpoint/">https://www.andreagrandi.it/2018/10/16/using-ipdb-with-python-37-breakpoint/</a>
						</li>
					</ul>
				</section>
				<!-- R equivalents? -->
			</section>

			<!-- Managing python -->
			<section>
				<section data-menu-title="Managing Python">
					<h2>Managing Python <i class="fab fa-python"></i></h2>
					<img class="stretch" style="border: 0px" data-src="assets/python_environment.png" alt="python-hell">
				</section>
				<section>
					<h3>Use <code>conda</code></h3>
					<ul style="font-size: 0.8em">
						<li class="fragment">Actually, use <code>miniconda</code> to avoid bloat.</li>
						<li class="fragment">Lives side-by-side your system-wide Python install, but uses an alias to
							become the default <code>which python</code></li>
						<li class="fragment">Use <code>conda</code> <span class="emphasized">environments</span> to keep
							projects and specific package versions separated and documented cf. version control.</li>
						<li class="fragment">Use <code>virtualenv</code> when deploying code on a remote server or
							docker container.</li>
					</ul>
					<p class="fragment" style="font-size: 0.6em">Check the documentation for a list of command commands:
						creating/listing/exporting environments, installing/removing packages, etc. <a
							href="https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html">https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html</a>
					</p>
				</section>
				<section>
					<h3><code>conda</code> and <code>pip</code> are separate things</h3>

					<p class="fragment" style="font-size: 0.8em">Use <code>conda install</code> by default.</p>
					<p class="fragment" style="font-size: 0.8em">If a package is missing, check out different channels
						e.g. <code>conda install --channel forge</code> (bioconda is also nice).</p<>
						<p class="fragment" style="font-size: 0.8em">If that fails, <span class="emphasized">first
								install pip inside the conda environment</span>.</p>
						<p class="fragment">cf. <a href="#/path">What is <code>PATH</code>?</a></p>
				</section>
				<section>
					<h4>Never use <code>sudo conda/pip install</code>!</h4>
					<p>You should always be able to install packages for just your user. This is more secure and ensures
						all packages can see one another.</p>
				</section>
				<section>
					<h4><code>pip</code> is not installed by default!</h4>
					<pre><code class="sh" data-trim data-noescape>
							 $ conda create -n newenv python=3.7
							......
							 $ which python
							/home/pieter/miniconda3/envs/newenv/bin/python
							 $ which pip
							/home/pieter/miniconda3/envs/newenv/bin/pip

							 $ conda create -n newerenv
							......
							 $ conda activate newerenv
							 $ which python
							/usr/bin/python
							 $ which pip
							/home/pieter/miniconda3/envs/tools/bin/pip 
							# due to custom PATH append statement inside my .bashrc
						</code></pre>
				</section>

				<section>
					<h4>Install <code>nb_conda</code> for managing environments inside notebooks</h4>
					<div style="font-size: 0.75em" class="fragment">
						<img width="100%" data-src="assets/nb_conda.png" alt="nb_conda">
						<p>Add <code>nb_conda</code> to whatever environment you want to launch Jupyter notebooks from
							(I use the base environment).</p>
						<p>Install <code>ipykernel / r-irkernel</code> into any environment you want to use inside
							notebooks.</p>
					</div>
				</section>
				<section>
					<p>For <code>ruby</code> use <code><a href="https://github.com/rbenv/rbenv">rbenv</a></code>.</p>
					<p>For <code>node.js</code> use <code><a href="https://github.com/creationix/nvm">nvm</a></code>.
					</p>
				</section>
				<section>
					<h4>Use <code>pathlib</code> to mange i/o.</h4>
					<ul>
						<li><a
								href="https://treyhunner.com/2018/12/why-you-should-be-using-pathlib/">https://treyhunner.com/2018/12/why-you-should-be-using-pathlib/</a>
						</li>
						<li><a
								href="https://pbpython.com/pathlib-intro.html">https://pbpython.com/pathlib-intro.html</a>
						</li>
						<li>
							<a href="https://realpython.com/python-pathlib/">https://realpython.com/python-pathlib/</a>
						</li>
					</ul>
				</section>
			</section>

			<!-- Managing R -->
			<section data-menu-title="Managing R">
				<section data-background-transition="zoom" data-background="#a6e22e" data-menu-title="Managing R">
					<h1>Managing <i class="fab fa-r-project"></i></h1>
				</section>
				<section>
						<ul>
							<li>Use (RStudio) projects.</li>
							<li class="fragment">Never use <code>setwd()!</code></li>
							<li class="fragment"><span class="emphasized">Do</span> use the <code>here</code> package and create paths relative to the top
								level of your project.</li>
							<small>
								<li class="fragment">See: <a
										href="https://www.tidyverse.org/articles/2017/12/workflow-vs-script" />https://www.tidyverse.org/articles/2017/12/workflow-vs-script/</a>
									<!-- https://stackoverflow.com/questions/53433955/relative-paths-in-r-how-to-avoid-my-computer-being-set-on-fire
									https://whattheyforgot.org/project-oriented-workflow.html
									http://plantarum.ca/code/setwd/
									https://malco.io/2018/11/05/why-should-i-use-the-here-package/ -->
								</li>
							</small>
						</ul>
						<pre class="fragment">
							<code class="r" data-trim data-noescape>
								> here("data","raw","input.dat")
								[1] "/home/pieter/projects/dot-project-directory/data/raw/input.dat"
							</code>
						</pre>
					</section>
					<section>
						<p>Don't preserve your workspace, since previously stored variables can
							silently mess up your results.</p>
						<img width="45%"
							data-src="assets/rstudio-workspace.png" alt="rstudio-workspace">
					</section>
				<section>
					<h4>For package management, check out <code>renv</code>. <small>(or <code>packrat</code>)</small>
					</h4>
					<br>
					<p class="fragment">Don't install packages via your system package manager, only use
						<code>install.packages()</code>.</p>
					<p class="fragment"><code>conda</code> can also manage R environments, but might not act nicely with
						R_LIBS <small>(<a
								href="https://waoverholt.com/conda-and-R/">https://waoverholt.com/conda-and-R/</a>)</small>
					</p>
				</section>
				<section>
					<code>renv</code>: if things go awry, install package into the base environment, purge the renv
					files (`renv` dir, `renv.lock` and a line in `.RProfile`) and start over.
				</section>
				<section>
					<p>
						The default R installation directory might not be writeable for a user, so a user library should
						be created (rather than installing packages as an admin).
					</p>

					<pre>
						<code>
							install.packages('random')

							Installing package into ‘/usr/local/lib/R/site-library’
							(as ‘lib’ is unspecified)
							Warning in install.packages("random") :
							'lib = "/usr/local/lib/R/site-library"' is not writable

							Would you like to use a personal library instead?  (y/n) y

							Would you like to create a personal library
							~/R/pc-linux-gnu-library/3.2
							to install packages into?  (y/n) y
						</code>
					</pre>

					<p>You can also set this in a file:</p>

					<pre>
						<code>
							echo R_LIBS_USER="~/lib/R/library" > .Renviron
						</code>
					</pre>
				</section>
			</section>

			<!-- Notebooks -->
			<section>
				<section data-background-transition="zoom" data-background="#a6e22e">
					<h1>Use interactive coding notebooks responsibly 📓</h1>
				</section>

				<section>
					<h4>Notebooks (Jupyter and R) are great for: </h4>
					<ul>
						<li class="fragment">Exploration</li>
						<li class="fragment">Prototyping</li>
						<li class="fragment">Sharing results, visualisation and adding remarks</li>
					</ul>
				</section>
				<section>
					<h4>But notebooks suffer from: </h4>
					<ul>
						<li class="fragment">Hidden states (<a
								href="https://docs.google.com/presentation/d/1n2RlMdmv1p25Xy5thJUhkKGvjtV-dkAIsUXP-AL4ffI/edit#slide=id.g3a428e2eb8_0_223">see
								example</a>)</li>
						<li class="fragment">Out-of-order execution</li>
						<li class="fragment">Horrible for sharing code</li>
					</ul>
					<br>
					<p class="fragment">Use them appropriately, for <span class="emphasized">exploration, not
							reproducing</span>.</p>
					<p class="fragment">Write functions in separate files or create a local package (see primer).</p>
					<br>
					<ul class="fragment" style="font-size: 0.6em">
						<li>Excellent talk by Joel Grus: <a
								href="https://www.youtube.com/watch?v=7jiPeIFXb6U">https://www.youtube.com/watch?v=7jiPeIFXb6U</a>
						</li>
						<li>Thoughts of the amazing author of <code>knitr</code>: <a
								href="https://yihui.name/en/2018/09/notebook-war/#summary">https://yihui.name/en/2018/09/notebook-war/#summary</a>
						</li>
					</ul>
				</section>
				<section data-transition="slide none">
					<img width="100%" data-src="assets/notebook1.png">
				</section>
				<section data-transition="none side">
					<img width="100%" data-src="assets/notebook2.png">
				</section>
				<section data-transition="none side">
					<img width="100%" data-src="assets/notebook3.png">
				</section>
				<section>
					<p>As a side note, everyone who uses Jupyter Notebooks should check out its successor JupyterLab and
						Binder-like cloud solutions. <small>(<a
								href="https://www.dataschool.io/cloud-services-for-jupyter-notebook/">https://www.dataschool.io/cloud-services-for-jupyter-notebook/</a>)</small>
					</p>
				</section>
			</section>

			<!-- unit testing -->
			<section>
				<section data-menu-title="Unit tests" style="font-size: 0.52em">
					<pre><code style="max-height: 100%; max-width: 100%;" data-trim data-noescape>
							    ,@@@@@@@@@@,,@@@@@@@%  .#&@@@&&.,@@@@@@@@@@,      %@@@@@@%*   ,@@@%     .#&@@@&&.  *&@@@@&(  ,@@@@@@@%  %@@@@@,     ,@@,
								,@@,    ,@@,      ,@@/   ./.    ,@@,          %@%   ,&@# .&@&@@(   .@@/   ./. #@&.  .,/  ,@@,       %@%  *&@&.  ,@@,
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								,@@,    ,@@/,,,,    ./#&@@@(    ,@@,          %@@@@@@%* /@@,  #@&.   ./#&@@@(   *(%&@@&. ,@@/,,,,   %@%    &@#  .&&.
								,@@,    ,@@,      ./,   .&@#    ,@@,          %@%      ,@@@@@@@@@% ./.   .&@# /*.   /@@. ,@@,       %@%  *&@&.   ,,
								,@@,    ,@@@@@@@% .#&@@@@&/     ,@@,          %@%     .&@#     ,@@/.#&@@@@&/   /%&@@@@.  ,@@@@@@@%  %@@@@@.     ,@@,
					,*************,,*/(((((//,,*(#%%%%%%%%%%%%%%%#(*,,,****************************************************,*/(((((((((/((((////****/((##%%%%%%
					,*************,,//((((((//,,*(%%%%%%%%%%%%%%%%%##/*****************************************************,,*/(///(//////****//((##%%%%%%%%%%%
					,************,,*/(((((((//***/#%%%%%%%%%%%%%%%%%%%#(/***************************************************,*//////////*//((#%%%%%%%%%%%%%%%%%
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					,*******,.,,***********************,,,,*(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%##(//**//
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					,***,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,,*(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%#(/*******************
					,**,,.,,,,,,,,,,,,,,,,,,,,,,,,,,.......,,,,,,/#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%#####%%%%%%%%%%%%%%%%#(/******************
					,**,..,,,,,,,,,,,,,,,,,,,,,,,,,......,,,*,,,*(#%%%%%%%%##(((/(##%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%##(((/*/((#%%%%%%%%%%%%%%#(/*****************
					,*,..,,,,,,,,,,,,,,,,,,,,,,,,,,,.....,,**,,*/#%%%%%%%##((((*,**/#%%%%%%%%%%%%%%%%%%%%%%%%%%%%##((##/,,,*(#%%%%%%%%%%%%%%#(*****************
					.*,.,,,**,,,,,,,,,,,,,,,,,,,,,,,,,,*****,,,/(%%%%%%%%#(//(#/,..*/#%%%%%%%%%%%%%%%%%%%%%%%%%%%#(//(#/,..,/(#%%%%%%%%%%%%%%#/*****///////////
					.,..,,,,,,,,,,,,,,,,,,,,,,,,,,*,,*******,,,(#%%%%%%%%#(*,,,....,/#%%%%%%%%%%%%%%%%%%%%%%%%%%%#(*,,,....,/(#%%%%%%%%%%%%%%#(*,**////////////
					.,..,,,,,,,,,...........,,,,,,*,********,,*(#%%%%%%%%%#(/*,,...,/#%%%%%%%%%%%%%%%%%%%%%%%%%%%%#(/*,,..,*/##%%%%%%%%%%%%%%%#(***////////////
					...,,,,,,,................,,*,**********,,/#%%%%%%%%%%%%#((////((#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%##((///(#%%%%%%%%%%%%%%%%%%(/**////////////
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					.,,,,,,,,.................,,***********,,/(####%%%%%%%%%%%%%%%%%%%%%%%%#(/*,,,*(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%#(/*////////////
					.,***,,,,,,..............,,,**********,..,***//((##%%%%%%%%%%%%%%%%%%%%%%%##((##%%%%%%%%%%%%%%%%%%%%%%%%%##(((((((((###%%%%%#/**///////////
					.*****,,,,,,,,,,,,,,,,,,,*************,..,*******/(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%##///*//////((#%%%%%#(**///////////
					.****************/******/***////*****,.,*///////**/#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%#(////////////(#%%%%%#/**//////////
					.***********************/////*******,..,*//////////(#%%%%%%%%%%%%%%%%%%%%##########%%%%%%%%%%%%%%%%%%%%#(///////////*/(#%%%%%#(***/////////
					.************************///********,..,*//////////#%%%%%%%%%%%%%%%%%%#(//*****///(((##%%%%%%%%%%%%%%%%#(///////////**/##%%%%##/***////////
					.***********************************,.,,***///////(#%%%%%%%%%%%%%%%%#(/*,,,*//((((////(#%%%%%%%%%%%%%%%#((////////////(#%%%%%%#(*********//
					,***********,,,*,,*,,**************,,,*//******//(#%%%%%%%%%%%%%%%%%#(*,,*/(((#####(((((#%%%%%%%%%%%%%%%##///////////(#%%%%%%%%#(***///////
					,*************,,**,,,************,,,,,/(##((((####%%%%%%%%%%%%%%%%%%%(/**/(((#((((#((//(#%%%%%%%%%%%%%%%%%#(((((((((##%%%%%%%%%%#/**///////
					,******************************,,,,,,,*(#%#%%%%%%%%%%%%%%%%%%%%%%%%%%#(**/((#(#(((#((//(#%%%%%%%%%%%%%%%%%%%%%%%#%#%%%%%%%%%%%%%#(**///////
					,*************,**************,****,,,,,/(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%#(/*/((((#((((///(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%(/*///////
					,*************************************,*/#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%##(////////////(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%#/**/////*
					,******////****///////////////////////***/#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%####(((((((###%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%#(********
					.,*,****///////////////////////////////***/#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%#(/*******
					.,,,,*****//////////////////////////*******(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%##(*******
					.,,,,,,***********/////////////////********/(#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%(*******
						</code></pre>
				</section>

				<section style="font-size: 0.8em">
					<p>Try to incorporate unit testing into your workflow. </p>
					<p class="fragment">Even something as simple as an <code>assert</code> statement checking the number
						of columns after reading a .csv file goes a long way.</p>
					<p class="fragment">For more information, check out this talk aimed specifically at data scientists
						(as opposed to software engineers): <a
							href="https://www.youtube.com/watch?v=0ysyWk-ox-8">https://www.youtube.com/watch?v=0ysyWk-ox-8</a>
					</p>
				</section>
			</section>

			<!-- dos2unix -->
			<section data-menu-title="dos2unix">
				<p>When sharing files between Windows and Unix systems, use the <code>dos2unix / unix2dos</code> command
					to convert line breaks (<code>"\r\n" <=> "\n"</code>).</p>
			</section>

			<!-- Python / coding conventions
				wout's talk
				type hinting
				etc.

				+ project organization => cookie cutters => README for data or workflow managers-->

			<!-- python environments
					conda != pip
					nb_conda for kernel switching -->

			<section>
				<section data-background-transition="zoom" data-background="#a6e22e"
					data-menu-title="Project organization">
					<h2>Structure your projects and your code</h2>
				</section>
				<section>
					<p>Go through Wout's presentations and/or the primer.</p>
				</section>
				<section style="font-size: 0.8em">
					<p>Add <span class="emphasized">docstrings</span> to your functions.</p>
					<p class="fragment">Create <span class="emphasized">functions</span>.</p>
					<p class="fragment">Be consistent in <span class="emphasized">code style</span> (cf. use a
						formatter).</p>
					<p class="fragment">Decide on a sane <span class="emphasized">project directory structure</span>.
						<small>(e.g. <a
								href="https://drivendata.github.io/cookiecutter-data-science/">https://drivendata.github.io/cookiecutter-data-science/</a>,
							<a
								href="https://community.rstudio.com/t/data-science-project-template-for-r/3230">https://community.rstudio.com/t/data-science-project-template-for-r/3230</a>,
							<a
								href="https://www.r-bloggers.com/structuring-r-projects/">https://www.r-bloggers.com/structuring-r-projects/</a>,
							<a
								href="https://nicercode.github.io/blog/2013-04-05-projects/">https://nicercode.github.io/blog/2013-04-05-projects/</a>)</small>
					</p>
					<p class="fragment">For all one-off commands, download sources and general meta-data, create <span
							class="emphasized">READMEs</span> in the relevant directories.</p>
					<p class="fragment">For repeated pipelines, use a workflow manager (<code>Make</code> is fine, but
						more feature-rich variants exist). <small>(e.g. <code>snakemake</code> and
							<code>nextflow</code>, discussion here: <a
								href="https://www.biostars.org/p/258436/">https://www.biostars.org/p/258436/</a>)</small>
					</p>
				</section>
				<section style="font-size: 0.8em">
					<p>Python imports are weird.</p>

					<p>My prefered approach is to use a locally installed package.</p>
					<p>Store all your functions in a <code>src</code> directory and <code>pip install -e .</code> it
						using a <code>setup.py</code> in the project root directory.
					</p>

					<p>More reading material on this:</p>

					<ul style="font-size: 0.5em">
						<li>https://dev.to/codemouse92/dead-simple-python-project-structure-and-imports-38c6</li>
						<li>https://towardsdatascience.com/whats-init-for-me-d70a312da583</li>
						<li>https://towardsdatascience.com/building-package-for-machine-learning-project-in-python-3fc16f541693
						</li>
						<li>https://realpython.com/absolute-vs-relative-python-imports/</li>
						<li>https://chrisyeh96.github.io/2017/08/08/definitive-guide-python-imports.html</li>
						<li>https://alex.dzyoba.com/blog/python-import/</li>
						<li>https://hackernoon.com/pip-install-abra-cadabra-or-python-packages-for-beginners-33a989834975
						</li>
						<li>https://stackoverflow.com/questions/22840671/what-is-the-difference-between-importing-python-sub-modules-from-numpy-matplotl
						</li>
						<li>https://stackoverflow.com/questions/16475129/clean-name-space-and-init-py</li>
						<li>https://stackoverflow.com/questions/13093665/python-import-statement-semantics</li>
						<li>https://stackoverflow.com/questions/19989179/modules-expose-imported-packages</li>
					</ul>
				</section>
			</section>

			<section>
				<h1>Just use a password manager already</h1>
			</section>

			<section>
				<h1>And Zotero for managing your literature</h1>
			</section>

			<section>
				That's all folks.
			</section>

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