refresh make stuff

jennybc · jennybc · commit c5d51d65f2be · 2015-11-19T01:26:36.000-08:00
diff --git a/automation00_index.html b/automation00_index.html
@@ -141,6 +141,7 @@ <h3>Hands-on activity</h3>
 <li>How to use <code>make</code> from the <a href="git09_shell.html">shell</a></li>
 <li>How Git facilitates the process of building a pipeline</li>
 </ul>
+<p><em>2015-11-19 Andrew MacDonald translated the above into a pipeline for the <a href="https://github.com/richfitz/remake"><code>remake</code> package</a> from Rich Fitzjohn: see <a href="https://gist.github.com/aammd/72a5b98356893c001001">this gist</a>.</em></p>
 </div>
 <div id="more-examples" class="section level3">
 <h3>More examples</h3>
diff --git a/automation00_index.md b/automation00_index.md
@@ -44,6 +44,8 @@ Walk before you run! Prove that `make` is actually installed and that it can be
   * The interface between RStudio and `make`
   * How to use `make` from the [shell](git09_shell.html)
   * How Git facilitates the process of building a pipeline
+  
+*2015-11-19 Andrew MacDonald translated the above into a pipeline for the [`remake` package](https://github.com/richfitz/remake) from Rich Fitzjohn: see [this gist](https://gist.github.com/aammd/72a5b98356893c001001).*
 
 ### More examples
 
diff --git a/automation02_windows.html b/automation02_windows.html
@@ -96,6 +96,7 @@ <h4 class="author"><em>Shaun Jackman, Dean Attali, Jenny Bryan</em></h4>
 
 
 <p><em>2015-11-17 NOTE: This year we made R packages before we used Make. The hope is, therefore, that the Make that ships with Rtools is all we need. So hopefully we can ignore this?</em></p>
+<p>back to <a href="automation00_index.html">All the automation things</a></p>
 <div id="install-make-on-microsoft-windows" class="section level3">
 <h3>Install <code>make</code> on Microsoft Windows</h3>
 <p>We are still working out the best way to install <code>make</code> on Windows. Our current best recommendation is to install <em>msysGit</em>, which includes <code>make</code> as well as <code>git</code> and <code>bash</code>.</p>
@@ -144,6 +145,7 @@ <h3>Issues we are still clarifying</h3>
 <li>See <a href="https://github.com/STAT545-UBC/Discussion/issues/54">issue 54</a> on the Discussion repo.</li>
 </ul></li>
 </ul>
+<p>back to <a href="automation00_index.html">All the automation things</a></p>
 </div>
 
 <div class="footer">
diff --git a/automation02_windows.md b/automation02_windows.md
@@ -10,6 +10,8 @@ output:
 
 *2015-11-17 NOTE: This year we made R packages before we used Make. The hope is, therefore, that the Make that ships with Rtools is all we need. So hopefully we can ignore this?*
 
+back to [All the automation things](automation00_index.html)
+
 ### Install `make` on Microsoft Windows
 
 We are still working out the best way to install `make` on Windows. Our current best recommendation is to install *msysGit*, which includes `make` as well as `git` and `bash`.
@@ -53,3 +55,5 @@ What are the tricky bits?
   * Ensuring `make`, `Rscript`, `pandoc`, `rm`, etc. can be found = updating `PATH`.
   * Getting `make` to use the correct [shell](git09_shell.html).
     - See [issue 54](https://github.com/STAT545-UBC/Discussion/issues/54) on the Discussion repo.
+
+back to [All the automation things](automation00_index.html)
diff --git a/automation03_make-test-drive.html b/automation03_make-test-drive.html
@@ -106,6 +106,7 @@ <h4 class="author"><em>Shaun Jackman, Jenny Bryan</em></h4>
 </div>
 
 <p>Before we use <code>make</code> for real work, we want to prove beyond a shadow of a doubt that it’s installed and findable from RStudio and/or the <a href="git09_shell.html">shell</a>.</p>
+<p>back to <a href="automation00_index.html">All the automation things</a></p>
 <div id="create-a-temporary-rstudio-project" class="section level3">
 <h3>Create a temporary RStudio Project</h3>
 <p>You can delete this project after this test drive, so don’t sweat too much about what you name it or where you put it.</p>
@@ -175,6 +176,7 @@ <h3>Run <code>make</code> from the <a href="git09_shell.html">shell</a></h3>
 </ul>
 <p>You should be seeing similar output as you saw in the Build tab of RStudio.</p>
 <p>If you are not, are you getting the error message that’s characteristic of a “spaces instead of tabs” problem? Or does it look more like <code>make</code> or other commands aren’t being found? If the latter, go back to the <a href="automation02_windows.html">Windows installation page</a> or reach out to the course staff.</p>
+<p>back to <a href="automation00_index.html">All the automation things</a></p>
 </div>
 
 <div class="footer">
diff --git a/automation03_make-test-drive.md b/automation03_make-test-drive.md
@@ -10,6 +10,8 @@ output:
 
 Before we use `make` for real work, we want to prove beyond a shadow of a doubt that it's installed and findable from RStudio and/or the [shell](git09_shell.html).
 
+back to [All the automation things](automation00_index.html)
+
 ### Create a temporary RStudio Project
 
 You can delete this project after this test drive, so don't sweat too much about what you name it or where you put it.
@@ -107,3 +109,5 @@ RStudio only provides access to a very limited bit of `make` -- it's even more l
 You should be seeing similar output as you saw in the Build tab of RStudio.
 
 If you are not, are you getting the error message that's characteristic of a "spaces instead of tabs" problem? Or does it look more like `make` or other commands aren't being found? If the latter, go back to the [Windows installation page](automation02_windows.html) or reach out to the course staff.
+
+back to [All the automation things](automation00_index.html)
diff --git a/automation04_make-activity.html b/automation04_make-activity.html
@@ -123,6 +123,7 @@ <h4 class="date"><em>2014-11-03</em></h4>
 <li>render a R Markdown report in HTML and PDF</li>
 </ul>
 <p>You will automate this pipeline using <code>make</code>!</p>
+<p>back to <a href="automation00_index.html">All the automation things</a></p>
 <div id="dependency-graph-of-the-pipeline" class="section level3">
 <h3>Dependency graph of the pipeline</h3>
 <!-- TO DO: remake the figure to say words.txt not words.tsv and the new words downloading strategy -->
@@ -133,11 +134,6 @@ <h3>Set up a new RStudio Project (and Git repo)</h3>
 <p>In RStudio: <em>File &gt; New Project &gt; New Directory &gt; Empty Project.</em> If you’re a Git user, we strongly encourage you to click on “Create a git repository.”</p>
 <p>This project will be useful as a reference in the future, so give it an informative name and location. If you’re a GitHub user, you may want to push it there as well.</p>
 <p>Git(Hub) users: from here on out, we assume you will be committing at regular intervals. At key points, we explicitly prompt you to commit.</p>
-<p>Configure this RStudio Project to work with <code>make</code>. Consult the <a href="automation03_make-test-drive.html"><code>make</code> test drive</a> for details:</p>
-<ul>
-<li>make sure tabs are NOT replaced with spaces</li>
-<li>set Project Build Tools to <code>Makefile</code></li>
-</ul>
 <p>Git folks: commit now.</p>
 </div>
 <div id="sample-project-and-git-repository" class="section level3">
@@ -148,6 +144,14 @@ <h3>Sample Project and Git repository</h3>
 <div id="create-the-makefile" class="section level3">
 <h3>Create the Makefile</h3>
 <p>In RStudio: <em>File &gt; New File &gt; Text File.</em> Save it with the name <code>Makefile</code>. Keep adding the rules we write below to this file, saving regularly.</p>
+<p>Once you’ve saved the file with the name <code>Makefile</code>, RStudio should indent with tabs instead of spaces. I recommend you display whitespace in order to visually confirm this: <em>RStudio &gt; Preferences &gt; Code &gt; Display &gt; Display whitespace characters</em>. A more extreme measure is to set Project or Global preferences to NOT replace tabs with spaces, but this will wreak havoc elsewhere.</p>
+<p>You also want RStudio to recognize the presence of the <code>Makefile</code>. Pick one:</p>
+<ul>
+<li>set Project Build Tools to <code>Makefile</code></li>
+<li>quit and relaunch</li>
+</ul>
+<p>You should see a “Build” tab now in the same pane as “Environment”, “History”, and, if applicable, “Git”.</p>
+<p>Git folks: commit now.</p>
 </div>
 <div id="get-the-dictionary-of-words" class="section level3">
 <h3>Get the dictionary of words</h3>
@@ -358,6 +362,7 @@ <h3>Appendix</h3>
 <p>The <code>.PHONY</code> line is where you declare which targets are <em>phony</em>, i.e. are not actual files to be made in the literal sense. It’s a good idea to explicitly tell <code>make</code> which targets are phony, instead of letting it try to deduce this. <code>make</code> can get confused if you create a file that has the same name as a phony target. If for example you create a directory named <code>clean</code> to hold your clean data and run <code>make clean</code>, then <code>make</code> will report <code>'clean' is up to date</code>, because a directory with that name already exists.</p>
 <p><code>.DELETE_ON_ERROR</code> causes <code>make</code> to “delete the target of a rule if it has changed and its recipe exits with a nonzero exit status”. In English, this means that – if a rule starts to run but then exits due to error – any outputs written in the course of that fiasco will be deleted. This can protect you from having half-baked, erroneous files lying around that will just confuse you later.</p>
 <p><code>.SECONDARY</code> tells <code>make</code> not to delete intermediate files of a chain of pattern rules. Consider creating a <code>Makefile</code> with two pattern rules, <code>%.md: %.rmd</code> and <code>%.html: %.md</code>, and then running <code>make report.html</code>. After <code>make</code> has created <code>report.md</code> and <code>report.html</code>, it will delete the intermediate file <code>report.md</code>. Adding <code>.SECONDARY</code> to your <code>Makefile</code> prevents the intermediate file from being deleted.</p>
+<p>back to <a href="automation00_index.html">All the automation things</a></p>
 </div>
 
 <div class="footer">
diff --git a/automation04_make-activity.md b/automation04_make-activity.md
@@ -19,6 +19,8 @@ The goal of this activity is to create a pipeline that will
 
 You will automate this pipeline using `make`!
 
+back to [All the automation things](automation00_index.html)
+
 ### Dependency graph of the pipeline
 
 <!-- TO DO: remake the figure to say words.txt not words.tsv and the new words downloading strategy -->
@@ -33,11 +35,6 @@ This project will be useful as a reference in the future, so give it an informat
 
 Git(Hub) users: from here on out, we assume you will be committing at regular intervals. At key points, we explicitly prompt you to commit.
 
-Configure this RStudio Project to work with `make`. Consult the [`make` test drive](automation03_make-test-drive.html) for details:
-
-  * make sure tabs are NOT replaced with spaces
-  * set Project Build Tools to `Makefile`
-
 Git folks: commit now.
 
 ### Sample Project and Git repository
@@ -50,6 +47,17 @@ The Project is set up for use with `make` at [this commit](https://github.com/ST
 
 In RStudio: *File > New File > Text File.* Save it with the name `Makefile`. Keep adding the rules we write below to this file, saving regularly.
 
+Once you've saved the file with the name `Makefile`, RStudio should indent with tabs instead of spaces. I recommend you display whitespace in order to visually confirm this: *RStudio > Preferences > Code > Display > Display whitespace characters*. A more extreme measure is to set Project or Global preferences to NOT replace tabs with spaces, but this will wreak havoc elsewhere.
+
+You also want RStudio to recognize the presence of the `Makefile`. Pick one:
+
+  * set Project Build Tools to `Makefile`
+  * quit and relaunch
+
+You should see a "Build" tab now in the same pane as "Environment", "History", and, if applicable, "Git".
+
+Git folks: commit now.
+
 ### Get the dictionary of words
 
 Depending on your OS and mood, you can get the file of English words by copying a local file or downloading from the internet.
@@ -312,3 +320,5 @@ The `.PHONY` line is where you declare which targets are *phony*, i.e. are not a
 `.DELETE_ON_ERROR` causes `make` to "delete the target of a rule if it has changed and its recipe exits with a nonzero exit status". In English, this means that -- if a rule starts to run but then exits due to error -- any outputs written in the course of that fiasco will be deleted. This can protect you from having half-baked, erroneous files lying around that will just confuse you later.
 
 `.SECONDARY` tells `make` not to delete intermediate files of a chain of pattern rules. Consider creating a `Makefile` with two pattern rules, `%.md: %.rmd` and `%.html: %.md`, and then running `make report.html`. After `make` has created `report.md` and `report.html`, it will delete the intermediate file `report.md`. Adding `.SECONDARY` to your `Makefile` prevents the intermediate file from being deleted.
+
+back to [All the automation things](automation00_index.html)
