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eseiler/0001-DOC-Build-updated-3.0.1-docs-with-doxygen-1.8.16.patch

Last active February 18, 2020 08:34
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Build 3.0.1 docs with some cherry picked infrastructure commits
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0001-DOC-Build-updated-3.0.1-docs-with-doxygen-1.8.16.patch
From 5ba9423bc52b859ff91f779e4c86ac64f3450acd Mon Sep 17 00:00:00 2001
From: Enrico Seiler <[email protected]>
Date: Tue, 4 Feb 2020 07:57:26 +0100
Subject: [PATCH 1/1] [DOC] Build updated 3.0.1 docs with doxygen-1.8.16
---
include/seqan3/alphabet/all.hpp | 22 ++++-----
test/documentation/seqan3.css | 24 +++++++---
test/documentation/seqan3_doxygen_cfg.in | 3 ++
test/documentation/seqan3_footer.html | 23 +++++++++
test/documentation/version.js | 59 ++++++++++++++++++++++++
test/documentation/version.php | 32 +++++++++++++
6 files changed, 146 insertions(+), 17 deletions(-)
create mode 100644 test/documentation/seqan3_footer.html
create mode 100644 test/documentation/version.js
create mode 100644 test/documentation/version.php
diff --git a/include/seqan3/alphabet/all.hpp b/include/seqan3/alphabet/all.hpp
index e66ad3e4..0670b098 100644
--- a/include/seqan3/alphabet/all.hpp
+++ b/include/seqan3/alphabet/all.hpp
@@ -123,17 +123,17 @@
* seqan3::writable_alphabet whenever the values might be changed.
* Semi-alphabets are less useful in application code.
*
- * | | seqan3::semialphabet | seqan3::writable_semialphabet | seqan3::alphabet | seqan3::writable_alphabet | Aux |
- * |----------------------------------|:--------------------:|:----------------------------:|:----------------:|:------------------------:|:---:|
- * | seqan3::alphabet_size | ✅ | ✅ | ✅ | ✅ | |
- * | seqan3::to_rank | ✅ | ✅ | ✅ | ✅ | |
- * | seqan3::alphabet_rank_t | ✅ | ✅ | ✅ | ✅ | 🔗 |
- * | seqan3::assign_rank_to | | ✅ | | ✅ | |
- * | seqan3::to_char | | | ✅ | ✅ | |
- * | seqan3::alphabet_char_t | | | ✅ | ✅ | 🔗 |
- * | seqan3::assign_char_to | | | | ✅ | |
- * | seqan3::char_is_valid_for | | | | ✅ | |
- * | seqan3::assign_char_strictly_to | | | | ✅ | 🔗 |
+ * | | [semialphabet](@ref seqan3::semialphabet) | [writable_semialphabet](@ref seqan3::writable_semialphabet) | [alphabet](@ref seqan3::alphabet) | [writable_alphabet](@ref seqan3::writable_alphabet) | Aux |
+ * |-----------------------------------------------------------:|:------------------------------------:|:------------------------------------------------------:|:----------------------------:|:----------------------------------------------:|:---:|
+ * | [alphabet_size](@ref seqan3::alphabet_size) | ✅ | ✅ | ✅ | ✅ | |
+ * | [to_rank](@ref seqan3::to_rank) | ✅ | ✅ | ✅ | ✅ | |
+ * | [alphabet_rank_t](@ref seqan3::alphabet_rank_t) | ✅ | ✅ | ✅ | ✅ | 🔗 |
+ * | [assign_rank_to](@ref seqan3::assign_rank_to) | | ✅ | | ✅ | |
+ * | [to_char](@ref seqan3::to_char) | | | ✅ | ✅ | |
+ * | [alphabet_char_t](@ref seqan3::alphabet_char_t) | | | ✅ | ✅ | 🔗 |
+ * | [assign_char_to](@ref seqan3::assign_char_to) | | | | ✅ | |
+ * | [char_is_valid_for](@ref seqan3::char_is_valid_for) | | | | ✅ | |
+ * | [assign_char_strictly_to](@ref seqan3::assign_char_strictly_to) | | | | ✅ | 🔗 |
*
* The above table shows all alphabet concepts and related functions and type traits.
* The entities marked as "auxiliary" provide shortcuts to the other "essential" entitities.
diff --git a/test/documentation/seqan3.css b/test/documentation/seqan3.css
index 64aaef7e..b517af60 100644
--- a/test/documentation/seqan3.css
+++ b/test/documentation/seqan3.css
@@ -26,6 +26,17 @@ h1 {
table {
font-size: 12pt;
font-family: -apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";
+ table-layout: auto;
+ width: 100%;
+}
+
+.memItemLeft, .memTemplItemLeft {
+ white-space: normal;
+ width: 30%;
+}
+
+.memItemRight {
+ width: 70%;
}
div.contents {
@@ -45,6 +56,7 @@ div.contents {
#projectlogo {
padding: 10px;
+ width: 150px;
}
hr.footer {
@@ -109,30 +121,30 @@ hr {
}
/* markdown tables */
-table.doxtable {
+table.markdownTable {
empty-cells: show;
border: 1px solid #CBCBCB;
}
-table.doxtable caption {
+table.markdownTable caption {
color: #000;
font: italic 85%/1 arial,sans-serif;
padding: 1em 0;
text-align: center;
}
-table.doxtable td:first-child, table.doxtable th:first-child {
+table.markdownTable td:first-child, table.markdownTable th:first-child {
border-left-width: 0;
}
-table.doxtable thead {
+table.markdownTable thead {
background-color: #E0E0E0;
color: #000;
text-align: left;
vertical-align: bottom;
}
-table.doxtable td {
+table.markdownTable td {
background-color: transparent;
border: 0;
border-bottom: 2px solid #CBCBCB;
@@ -143,7 +155,7 @@ table.doxtable td {
padding: .5em 1em;
}
-table.doxtable th {
+table.markdownTable th {
border: 0;
border-width: 0 1 0 0px;
font-size: inherit;
diff --git a/test/documentation/seqan3_doxygen_cfg.in b/test/documentation/seqan3_doxygen_cfg.in
index 69b51c6f..f094d791 100644
--- a/test/documentation/seqan3_doxygen_cfg.in
+++ b/test/documentation/seqan3_doxygen_cfg.in
@@ -41,6 +41,7 @@ SKIP_FUNCTION_MACROS = NO
SORT_BRIEF_DOCS = YES
TOC_INCLUDE_HEADINGS = 2
HTML_EXTRA_STYLESHEET = ${SEQAN3_DOXYGEN_SOURCE_DIR}/test/documentation/seqan3.css
+HTML_FOOTER = ${SEQAN3_DOXYGEN_SOURCE_DIR}/test/documentation/seqan3_footer.html
INPUT_ENCODING = UTF-8
PREDEFINED = "CEREAL_SERIALIZE_FUNCTION_NAME=serialize" \
@@ -93,3 +94,5 @@ ALIASES += header_file{1}="\htmlonly<b>Header File</b><br><div style='text-inden
### Extra files that we can link to
HTML_EXTRA_FILES = ${SEQAN3_DOXYGEN_SOURCE_DIR}/doc/tutorial/alignment_file/example.sam
+HTML_EXTRA_FILES += ${SEQAN3_DOXYGEN_SOURCE_DIR}/test/documentation/version.js
+HTML_EXTRA_FILES += ${SEQAN3_DOXYGEN_SOURCE_DIR}/test/documentation/version.php
diff --git a/test/documentation/seqan3_footer.html b/test/documentation/seqan3_footer.html
new file mode 100644
index 00000000..55cce088
--- /dev/null
+++ b/test/documentation/seqan3_footer.html
@@ -0,0 +1,23 @@
+<!-- HTML footer for doxygen 1.8.16-->
+<!-- start footer part -->
+<!--BEGIN GENERATE_TREEVIEW-->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <div id="list_bottom_right" style="text-align:right; float:left; color:black; padding: 0px 0px 0px 10px"></div>
+ <script type="text/javascript" charset="utf-8" src="version.js"></script>
+ $navpath
+ <li class="footer">$generatedby
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion </li>
+ </ul>
+</div>
+<!--END GENERATE_TREEVIEW-->
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small>
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+</body>
+</html>
diff --git a/test/documentation/version.js b/test/documentation/version.js
new file mode 100644
index 00000000..b216b0ea
--- /dev/null
+++ b/test/documentation/version.js
@@ -0,0 +1,59 @@
+/* Jongkyu Kim ([email protected]), 2016.01.12
+ Adaptations by Enrico Seiler ([email protected]), 2020 */
+
+// Get the current script path https://stackoverflow.com/a/710996
+var scripts = document.getElementsByTagName('script');
+var lastScript = scripts[scripts.length-1];
+var scriptName = lastScript.src;
+// Remove the script name (version.js) from the path
+var split = scriptName.split("/");
+DOCUMENT_URL = split.slice(0, split.length - 2).join("/") + "/";
+
+VERSION_JSON_URL = "version.php";
+
+function changeVersion(formid)
+{
+ var frm = document.getElementById(formid);
+ window.top.location.href = DOCUMENT_URL + frm.options[frm.selectedIndex].value;
+}
+
+function addVersionSelection(arr)
+{
+ // add HTMLs
+ var version_select = document.createElement("select");
+ var version_div = document.createElement("div");
+
+ version_select.setAttribute("id","version_select");
+ version_div.setAttribute("style","vertical-align:middle; text-align:right;");
+ version_div.appendChild(document.createTextNode("Version: "));
+ version_div.appendChild(version_select);
+ document.getElementById("list_bottom_right").appendChild(version_div);
+
+ version_select.addEventListener("change", function(){changeVersion(this.id);}, false);
+
+ // current selection is..
+ cur_sel = window.location.pathname.split("/")[2];
+
+ for(i=0; i < arr.length; ++i)
+ {
+ var op = document.createElement("option");
+ op.value = arr[i];
+ op.text = arr[i];
+ op.selected = ( arr[i] == cur_sel ) ? true : false;
+ version_select.add(op);
+ }
+}
+
+// get JSON data & add selection form
+var req = new XMLHttpRequest();
+req.open("GET", VERSION_JSON_URL, true);
+req.setRequestHeader("Content-type", "application/json");
+req.onreadystatechange = function()
+{
+ if( req.readyState == 4 && req.status == 200 )
+ {
+ var response = JSON.parse(req.responseText);
+ addVersionSelection(response); // add selection form
+ }
+}
+req.send();
diff --git a/test/documentation/version.php b/test/documentation/version.php
new file mode 100644
index 00000000..966f3e37
--- /dev/null
+++ b/test/documentation/version.php
@@ -0,0 +1,32 @@
+<?php
+/* Jongkyu Kim([email protected]), 2016.01.12
+ Adaptations by Enrico Seiler ([email protected]), 2020 */
+$LOCALDIR = "../";
+
+$files = scandir($LOCALDIR, SCANDIR_SORT_DESCENDING);
+$list = array();
+foreach( $files as $file )
+{
+ if( strpos($file, "master_") !== FALSE ) // Skip directories starting with "master_"
+ continue;
+ if( $file == "master") // Skip SeqAn2 "master" documentation
+ continue;
+ if( $file == "index.html") // Skip seqan/index.html
+ continue;
+ if( strpos($file, "develop") !== FALSE ) // Skip SeqAn2 "develop" and "develop_" documentation
+ continue;
+ if( $file[0] == "1") // Skip SeqAn1 versioned documentation
+ continue;
+ if( $file[0] == "2") // Skip SeqAn2 versioned documentation
+ continue;
+ if( strpos($file, "learning-resources") !== FALSE ) // Skip learning resources
+ continue;
+ if( $file[0] == "." ) // Skip current directory
+ continue;
+
+ array_push($list, $file);
+}
+
+header("Content-Type: application/json");
+echo json_encode($list, JSON_PRETTY_PRINT);
+?>
--
2.21.1 (Apple Git-122.3)
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