[med-svn] [Git][med-team/mmseqs2][master] 3 commits: Fix LGPL license to match /usr/share/common-licenses
Shayan Doust
gitlab at salsa.debian.org
Thu Jul 18 14:48:34 BST 2019
Shayan Doust pushed to branch master at Debian Med / mmseqs2
Commits:
cb93ddb2 by Shayan Doust at 2019-07-17T06:59:29Z
Fix LGPL license to match /usr/share/common-licenses
- - - - -
7e87d256 by Shayan Doust at 2019-07-17T07:53:05Z
Missing sources are userguide PDF sources. Not in upstream tarball
- - - - -
0b3dea19 by Shayan Doust at 2019-07-17T07:55:40Z
Close ITP bug
- - - - -
6 changed files:
- debian/changelog
- debian/copyright
- + debian/missing-sources/userguide/Home.md
- + debian/missing-sources/userguide/MMseqs2-Developer-Guide.md
- + debian/missing-sources/userguide/eisvogel.tex
- + debian/missing-sources/userguide/make-pdf.sh
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
mmseqs2 (9-d36de-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #932369)
-- Shayan Doust <hello at shayandoust.me> Mon, 15 Jul 2019 13:45:03 +0100
=====================================
debian/copyright
=====================================
@@ -37,61 +37,47 @@ Copyright: 2019 Shayan Doust <hello at shayandoust.me>
License: GPLv3
License: GPLv3
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
- .
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-License: LGPL
- This version of the GNU Lesser General Public License incorporates
+ This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.
.
0. Additional Definitions.
.
- As used herein, "this License" refers to version 3 of the GNU Lesser
+ As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.
.
- "The Library" refers to a covered work governed by this License,
+ "The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.
.
- An "Application" is any work that makes use of an interface provided
+ An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.
.
- A "Combined Work" is a work produced by combining or linking an
+ A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
with which the Combined Work was made is also called the "Linked
Version".
.
- The "Minimal Corresponding Source" for a Combined Work means the
+ The "Minimal Corresponding Source" for a Combined Work means the
Corresponding Source for the Combined Work, excluding any source code
for portions of the Combined Work that, considered in isolation, are
based on the Application, and not on the Linked Version.
.
- The "Corresponding Application Code" for a Combined Work means the
+ The "Corresponding Application Code" for a Combined Work means the
object code and/or source code for the Application, including any data
and utility programs needed for reproducing the Combined Work from the
Application, but excluding the System Libraries of the Combined Work.
.
1. Exception to Section 3 of the GNU GPL.
.
- You may convey a covered work under sections 3 and 4 of this License
+ You may convey a covered work under sections 3 and 4 of this License
without being bound by section 3 of the GNU GPL.
.
2. Conveying Modified Versions.
.
- If you modify a copy of the Library, and, in your modifications, a
+ If you modify a copy of the Library, and, in your modifications, a
facility refers to a function or data to be supplied by an Application
that uses the facility (other than as an argument passed when the
facility is invoked), then you may convey a copy of the modified
@@ -107,7 +93,7 @@ License: LGPL
.
3. Object Code Incorporating Material from Library Header Files.
.
- The object code form of an Application may incorporate material from
+ The object code form of an Application may incorporate material from
a header file that is part of the Library. You may convey such object
code under terms of your choice, provided that, if the incorporated
material is not limited to numerical parameters, data structure
@@ -123,7 +109,7 @@ License: LGPL
.
4. Combined Works.
.
- You may convey a Combined Work under terms of your choice that,
+ You may convey a Combined Work under terms of your choice that,
taken together, effectively do not restrict modification of the
portions of the Library contained in the Combined Work and reverse
engineering for debugging such modifications, if you also do each of
@@ -141,7 +127,7 @@ License: LGPL
these notices, as well as a reference directing the user to the
copies of the GNU GPL and this license document.
.
- d) Do one of the following:
+ d) Do one of the following:
.
0) Convey the Minimal Corresponding Source under the terms of this
License, and the Corresponding Application Code in a form
@@ -172,7 +158,7 @@ License: LGPL
.
5. Combined Libraries.
.
- You may place library facilities that are a work based on the
+ You may place library facilities that are a work based on the
Library side by side in a single library together with other library
facilities that are not Applications and are not covered by this
License, and convey such a combined library under terms of your
@@ -188,12 +174,12 @@ License: LGPL
.
6. Revised Versions of the GNU Lesser General Public License.
.
- The Free Software Foundation may publish revised and/or new versions
+ The Free Software Foundation may publish revised and/or new versions
of the GNU Lesser General Public License from time to time. Such new
versions will be similar in spirit to the present version, but may
differ in detail to address new problems or concerns.
.
- Each version is given a distinguishing version number. If the
+ Each version is given a distinguishing version number. If the
Library as you received it specifies that a certain numbered version
of the GNU Lesser General Public License "or any later version"
applies to it, you have the option of following the terms and
@@ -203,7 +189,7 @@ License: LGPL
General Public License, you may choose any version of the GNU Lesser
General Public License ever published by the Free Software Foundation.
.
- If the Library as you received it specifies that a proxy can decide
+ If the Library as you received it specifies that a proxy can decide
whether future versions of the GNU Lesser General Public License shall
apply, that proxy's public statement of acceptance of any version is
permanent authorization for you to choose that version for the
=====================================
debian/missing-sources/userguide/Home.md
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/missing-sources/userguide/MMseqs2-Developer-Guide.md
=====================================
@@ -0,0 +1,280 @@
+# Code Style
+## Braces
+Braces are also used where they would be optional
+Braces are used with if, else, for, do and while statements, even when the body is empty or contains only a single statement.
+
+For example, a preprocessor macro that could go wrong when leaving out braces:
+
+```
+#define MACRO test1; \
+test2;
+
+if (true)
+ MACRO
+
+```
+
+This would get expanded to the following:
+
+```
+if (true) {
+ test1;
+}
+test2;
+```
+
+Keep the beginning brace in the same line as control structures, functions, etc.:
+
+```
+if (true) {
+```
+
+Please avoid:
+```
+if (true)
+{
+```
+
+## Naming guideline
+Write your names as descriptive and long as necessary, but also as short as possible.
+Example: Use `weights` instead of `wg`. Do not unnecessarily expand the name to `sequenceWeights`, if its clear from the context that you are dealing with a sequence. However, if you dealing with `profileWeights` and `sequenceWeights` in the same context, feel free to use longer names.
+
+Only iterator variables are supposed to be one letter long (`i`, `j`, `k`).
+
+### Class names
+Class names are written in UpperCamelCase.
+Example: `ClusterAlgorithm`
+
+### Method names
+Method names are written in lowerCamelCase.
+Method names are typically verbs or verb phrases.
+Example: `sendMessage`, `stop`, `clusterMethod`
+
+### Constant names
+Constant names use CONSTANT_CASE: all uppercase letters, with each word separated from the next by a single underscore.
+Example: `CLUSTER_ALGORITHM`
+
+### Non-constant field names
+Non-constant field names (static or otherwise) are written in lowerCamelCase.
+These names are typically nouns or noun phrases.
+Example: `computedValues` or `index`
+
+### Local variable names
+Local variable names are written in lowerCamelCase.
+Even when final and immutable, local variables are not considered to be constants, and should not be styled as constants.
+
+## Whitespace
+Be generous with white spacing horizontally, but try to keep code compact vertically.
+
+Here a `_` characters indicates where you should be placing a space character:
+```
+if_(int_name)_{
+____int_test_=_1_+_(1_+_x);
+}
+```
+
+Use empty lines to structure code in logical blocks or tasks.
+
+# Programming Practices
+## Logging errors or info messages
+Do not use `printf`, `std::cout`, `std::err` (etc.) for printing messages. All output have to go through the `Debug` logging class.
+
+## Error handling
+We do not use Exceptions in our code. We have two types of errors in MMseqs2.
+Exceptions are disabled per compile flag.
+
+#### 1) Errors which stop the run completly
+Write a descriptive error message with `Debug(Debug::ERROR)` and exit out immediatly with the `EXIT` macro.
+Dot not use `exit` directly. `EXIT` handles cleaning up remaining MPI instances (if compiled with MPI).
+
+```
+size_t written = write(dataFilefd, buffer, bufferSize);
+if (written != bufferSize) {
+ Debug(Debug::ERROR) << "Could not write to data file " << dataFileNames[0] << "\n";
+ EXIT(EXIT_FAILURE);
+}
+```
+
+### 2) Warning which can be handled
+Write to `Debug(Debug::WARNING)` and continue with the next loop iteration or whatever is appropriate.
+
+```
+if (std::remove(dataFileNames[i]) != 0) {
+ Debug(Debug::WARNING) << "Could not remove file " << dataFileNames[i] << "\n";
+}
+```
+
+## Parallel Computing
+We use OpenMP to run multiple threads for parallel computing.
+Do not use `pthreads` or `std::thread`.
+
+The standard pattern for doing anything with OpenMP looks something like this:
+
+```
+// Declare only thread-safe stuff here
+#pragma omp parallel
+{
+ // PER THREAD VARIABLE DECLARATION
+ unsigned int threadIdx = 0;
+#ifdef OPENMP
+ threadIdx = (unsigned int) omp_get_thread_num();
+#endif
+
+// somtimes you want schedule(static)
+#pragma omp for schedule(dynamic, 1)
+ for (...) {
+ // DO YOUR WORK
+ }
+ // CLEAN UP MEMORY IF NECCECARY
+}
+```
+
+Try to avoid `#pragma omp critical` and `#pragma omp atomic`. Consider using atomic instructions instead (e.g. `__sync_fetch_and_add`).
+
+## Advice on memory allocation
+
+Allocate memory as early as possible. Try not to allocate memory on the heap inside your hot loops:
+
+```
+#pragma omp parallel
+{
+ // try to allocate once here
+ char MEMORY[1024 * 1024 * 1024];
+ // also for containers
+ std::vector<int> results;
+ results.reserve(1024);
+#pragma omp for schedule(static)
+ for (...) {
+ // not here
+ }
+```
+
+# C++ Standard
+
+Try to avoid using too many C++ features. MMseqs2 is coded in a way where we do not use not too many concepts from modern C++.
+Generally you have to support GCC 4.8, this is enforced by the Continous Integration system.
+It is more like C style C++. We do use classes to organize code. Some STL functionality should be used `std::string`, `std::vector`, sometimes also `std::map` (careful!).
+However, weight any new C++ concept heavily and try to avoid them as much as possible.
+
+Especially, do not use:
+* `auto`
+* streams (they can be extremely slow, instead use `std::string s; s.reserve(10000);` outside a loop and inside `s.append(...); s.clear();`)
+* smart pointers (try to use RAII for allocation as much as possible)
+* functional programming
+* inheritance (think about it very carefully, its usually a lot less useful than it appears)
+
+You will still find some `std::stringstream` littered throughout our codebase, we are trying to progressivly get rid of those and not to add any new ones.
+
+Some modern C++ features are very useful.
+For example, `std::vector::emplace_back` can avoid memory allocations for example:
+```
+// two allocations
+vector.push_back(Struct(1, 2, 3));
+// one allocation
+vector.emplace_back(1, 2, 3);
+```
+
+# MMseqs2 specific advice
+
+## Code reuse
+Take a look at all the classes in the `src/common` subfolder.
+They contain a lot of useful stuff like `Util`, `FileUtil`, `MathUtil`, `Itoa`, etc.
+Try not to reimplement stuff that exists already.
+
+For bioinformatics, understand how to use the `Sequence`, `QueryMatcher`, `Matcher`, etc. classes.
+
+## Development of modules
+To add a workflow or an util tool to MMseqs2 you need register your workflow or module in the `src/mmseqs.cpp` file.
+A new command generally looks something like this:
+
+```
+{"search", search, &par.searchworkflow, COMMAND_MAIN,
+ "Search with query sequence or profile DB (iteratively) through target sequence DB",
+ "Searches with the sequences or profiles query DB through the target sequence DB by running the prefilter tool and the align tool for Smith-Waterman alignment. For each query a results file with sequence matches is written as entry into a database of search results (alignmentDB).\nIn iterative profile search mode, the detected sequences satisfying user-specified criteria are aligned to the query MSA, and the resulting query profile is used for the next search iteration. Iterative profile searches are usually much more sensitive than (and at least as sensitive as) searches with single query sequences.",
+ "Martin Steinegger <martin.steinegger at mpibpc.mpg.de>",
+ "<i:queryDB> <i:targetDB> <o:alignmentDB> <tmpDir>",
+ CITATION_MMSEQS2},
+```
+
+# Before commiting code
+## Compiler warnings
+Do not leave any compiler warnings in your code. Most of the time they might be false positives.
+However, sometimes they hide real issues. Continous integration runs with `-Werror` and will fail when it finds any warnings.
+Since, the CI system runs on many compilers and compiler versions the kinf of warnigs reported might differ between your local environment and the CI>
+
+### Shellcheck
+(Shellcheck)[https://www.shellcheck.net] runs on all workflow shell scripts and will fail in the continous integration if it finds any issues.
+Make sure to not use Bash specific features. `#!/bin/sh` means that are POSIX shell compliant.
+
+The MMseqs2 Windows builds run with the busybox ash shell, if you are a bit careful about your scripts, you will automatically gain Windows support.
+
+## Regression test
+The regression test runs most workflows such as search, profile search, profile-profile, target-profile, clustering, linclustm etc. after every commit.
+It compares their values against known good ones and fails if they don't match.
+
+To run a search regression test execute the following steps:
+
+ # download the runner script and set permissions
+ $ wget https://bitbucket.org/martin_steinegger/mmseqs-benchmark/raw/master/scripts/run_codeship_pipeline.sh
+ $ chmod +x run_codeship_pipeline.sh
+
+ # change three variables in this file edit the following variables:
+ # If you dont have AVX2 on the machine just comment all lines containing MMSEQSAVX
+
+`BASE_DIR="$HOME/clone/regression_test”`
+`MMSEQSSSE="$HOME/clone/build/src/mmseqs”`
+`MMSEQSAVX="$HOME/clone/build_avx2/src/mmseqs"`
+
+ # run script and set CI_COMMIT_ID to some non-empty string (in our CI system this is automatically set to the git commit).
+ $ CI_COMMIT_ID="TESTING" ./run_codeship_pipeline.sh
+
+ # The script will return an error code != 0 if there is a regression in sensitivity of MMseqs2. The error code can be checked with "echo $?".
+ $ [ $? -eq 1 ] && echo "Error"
+
+It will print a report with sensitivity AUCs it achieved and then error out if it did not achieve the minimum AUCs. Currently 0.235 for normal sequence searches and 0.331 for profile searches.
+
+You can also use our Docker images to run this benchmark:
+
+ cd mmseqs-folder
+ docker build -t mmseqs2 .
+ git clone https://bitbucket.org/martin_steinegger/mmseqs-benchmark.git
+ cd mmseqs-benchmark
+ docker build -t mmseqs-benchmark .
+
+The regression test passed, if the second image exits cleanly.
+Please note, some users don't have permissions to access the unix socket to communicate with the Docker engine.
+In such a case, run the commands above as "sudo docker build ..."
+
+The script that runs the regression test is found here:
+
+https://bitbucket.org/martin_steinegger/mmseqs-benchmark/raw/master/scripts/run_codeship_pipeline.sh
+
+There is also a docker image that runs the regression test:
+
+https://bitbucket.org/martin_steinegger/mmseqs-benchmark/raw/master/Dockerfile
+
+## Inspecting crashes on real data
+MMseqs2 is designed for large-scale data analysis so if a crash occurs on real data it is often not possible to reproduce the run and debug it in a source-code editor (e.g., visual studio code). It is therefore recommended to compile MMseqs2 with
+```
+-DCMAKE_BUILD_TYPE=RelWithDebInfo
+```
+Any post-crash core dump file can then be inspected by running:
+```
+gdb /path/to/mmseqs path/to/core/file
+```
+You can first inspect the stack trace with 'bt'. This should give you an idea of the mmseqs function and line of code that started the trouble. using 'frame number' can allow zooming in on a particular frame. Other useful options include re-running the code using gdb and setting breakpoints. For example, 'b abort' and 'b exit' will set breakpoints upon any exit of abort in the code.
+
+To run gdb on mmseqs2 with its arguments type:
+```
+gdb --args /path/to/mmseqs mmseqs2-arg1 mmseqs2-arg2 mmseqs2-arg3 ...
+```
+
+## Sanitizers
+
+MMseqs2 can be built with [ASan](https://github.com/google/sanitizers/wiki/AddressSanitizer)/[MSan](https://github.com/google/sanitizers/wiki/MemorySanitizer)/[UBSan](https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html)/[TSan](https://clang.llvm.org/docs/ThreadSanitizer.html) support by specifying calling:
+
+```
+cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=ASan ..
+```
+
+Replace ASan with MSan, UBsan or TSan for the other sanitizers. CMake will error and abort if your compiler does not support the respective sanitizer.
\ No newline at end of file
=====================================
debian/missing-sources/userguide/eisvogel.tex
=====================================
@@ -0,0 +1,860 @@
+%%
+% Copyright (c) 2017 - 2019, Pascal Wagler;
+% Copyright (c) 2014 - 2019, John MacFarlane
+%
+% All rights reserved.
+%
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+%
+% - Redistributions of source code must retain the above copyright
+% notice, this list of conditions and the following disclaimer.
+%
+% - Redistributions in binary form must reproduce the above copyright
+% notice, this list of conditions and the following disclaimer in the
+% documentation and/or other materials provided with the distribution.
+%
+% - Neither the name of John MacFarlane nor the names of other
+% contributors may be used to endorse or promote products derived
+% from this software without specific prior written permission.
+%
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+% "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+% LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+% FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+% COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+% INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+% BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+% LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+% LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+% ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+% POSSIBILITY OF SUCH DAMAGE.
+%%
+
+%%
+% This is the Eisvogel pandoc LaTeX template.
+%
+% For usage information and examples visit the official GitHub page:
+% https://github.com/Wandmalfarbe/pandoc-latex-template
+%%
+
+\PassOptionsToPackage{unicode=true$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref} % options for packages loaded elsewhere
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+$endif$
+$if(colortheme)$
+\usecolortheme{$colortheme$}
+$endif$
+$if(fonttheme)$
+\usefonttheme{$fonttheme$}
+$endif$
+%$if(mainfont)$
+%\usefonttheme{serif} % use mainfont rather than sansfont for slide text
+%$endif$
+$if(innertheme)$
+\useinnertheme{$innertheme$}
+$endif$
+$if(outertheme)$
+\useoutertheme{$outertheme$}
+$endif$
+$endif$
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\IfFileExists{microtype.sty}{% use microtype if available
+ \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
+ \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+$if(indent)$
+$else$
+\makeatletter
+\@ifundefined{KOMAClassName}{% if non-KOMA class
+ \IfFileExists{parskip.sty}{%
+ \usepackage{parskip}
+ }{% else
+ \setlength{\parindent}{0pt}
+ \setlength{\parskip}{6pt plus 2pt minus 1pt}}
+}{% if KOMA class
+ \KOMAoptions{parskip=half}}
+\makeatother
+$endif$
+$if(verbatim-in-note)$
+\usepackage{fancyvrb}
+$endif$
+\usepackage{xcolor}
+\definecolor{default-linkcolor}{HTML}{A50000}
+\definecolor{default-filecolor}{HTML}{A50000}
+\definecolor{default-citecolor}{HTML}{4077C0}
+\definecolor{default-urlcolor}{HTML}{4077C0}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
+\hypersetup{
+$if(title-meta)$
+ pdftitle={$title-meta$},
+$endif$
+$if(author-meta)$
+ pdfauthor={$author-meta$},
+$endif$
+$if(subject)$
+ pdfsubject={$subject$},
+$endif$
+$if(keywords)$
+ pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
+$endif$
+$if(colorlinks)$
+ colorlinks=true,
+ linkcolor=$if(linkcolor)$$linkcolor$$else$default-linkcolor$endif$,
+ filecolor=$if(filecolor)$$filecolor$$else$default-filecolor$endif$,
+ citecolor=$if(citecolor)$$citecolor$$else$default-citecolor$endif$,
+ urlcolor=$if(urlcolor)$$urlcolor$$else$default-urlcolor$endif$,
+$else$
+ pdfborder={0 0 0},
+$endif$
+ breaklinks=true}
+\urlstyle{same} % don't use monospace font for urls
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+$if(geometry)$
+\usepackage[margin=2.5cm,includehead=true,includefoot=true,centering,$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
+$else$
+\usepackage[margin=2.5cm,includehead=true,includefoot=true,centering]{geometry}
+$endif$
+$if(logo)$
+\usepackage[export]{adjustbox}
+\usepackage{graphicx}
+$endif$
+$if(beamer)$
+\newif\ifbibliography
+$endif$
+$if(listings)$
+\usepackage{listings}
+\newcommand{\passthrough}[1]{#1}
+\lstset{defaultdialect=[5.3]Lua}
+\lstset{defaultdialect=[x86masm]Assembler}
+$endif$
+$if(listings-no-page-break)$
+\usepackage{etoolbox}
+\BeforeBeginEnvironment{lstlisting}{\par\noindent\begin{minipage}{\linewidth}}
+\AfterEndEnvironment{lstlisting}{\end{minipage}\par\addvspace{\topskip}}
+$endif$
+$if(lhs)$
+\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
+$endif$
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+$if(tables)$
+\usepackage{longtable,booktabs}
+$if(beamer)$
+\usepackage{caption}
+% These lines are needed to make table captions work with longtable:
+\makeatletter
+\def\fnum at table{\tablename~\thetable}
+\makeatother
+$else$
+% Allow footnotes in longtable head/foot
+\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
+\makesavenoteenv{longtable}
+$endif$
+$endif$
+$if(graphics)$
+\usepackage{graphicx,grffile}
+\makeatletter
+\def\maxwidth{\ifdim\Gin at nat@width>\linewidth\linewidth\else\Gin at nat@width\fi}
+\def\maxheight{\ifdim\Gin at nat@height>\textheight\textheight\else\Gin at nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+$endif$
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(strikeout)$
+\usepackage[normalem]{ulem}
+% avoid problems with \sout in headers with hyperref:
+\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
+$endif$
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+\providecommand{\tightlist}{%
+ \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+$if(numbersections)$
+\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
+$else$
+\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
+$endif$
+$if(beamer)$
+$else$
+$if(subparagraph)$
+$else$
+% Redefines (sub)paragraphs to behave more like sections
+\ifx\paragraph\undefined\else
+ \let\oldparagraph\paragraph
+ \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+ \let\oldsubparagraph\subparagraph
+ \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+$endif$
+$endif$
+$if(pagestyle)$
+\pagestyle{$pagestyle$}
+$endif$
+
+% Make use of float-package and set default placement for figures to H
+\usepackage{float}
+\floatplacement{figure}{H}
+
+$for(header-includes)$
+$header-includes$
+$endfor$
+$if(lang)$
+\ifnum 0\ifxetex 1\fi=0 % if pdftex or luatex
+ \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
+$if(babel-newcommands)$
+ $babel-newcommands$
+$endif$
+\else % if xetex
+ $if(mainfont)$
+ $else$
+ % See issue https://github.com/reutenauer/polyglossia/issues/127
+ \renewcommand*\familydefault{\sfdefault}
+ $endif$
+ % load polyglossia as late as possible as it *could* call bidi if RTL lang (e.g. Hebrew or Arabic)
+ \usepackage{polyglossia}
+ \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
+$for(polyglossia-otherlangs)$
+ \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
+$endfor$
+\fi
+$endif$
+$if(dir)$
+\ifxetex
+ % load bidi as late as possible as it modifies e.g. graphicx
+ \usepackage{bidi}
+\fi
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+ \TeXXeTstate=1
+ \newcommand{\RL}[1]{\beginR #1\endR}
+ \newcommand{\LR}[1]{\beginL #1\endL}
+ \newenvironment{RTL}{\beginR}{\endR}
+ \newenvironment{LTR}{\beginL}{\endL}
+\fi
+$endif$
+$if(natbib)$
+\usepackage[$natbiboptions$]{natbib}
+\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+$endif$
+$if(biblatex)$
+\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
+$for(bibliography)$
+\addbibresource{$bibliography$}
+$endfor$
+$endif$
+
+$if(title)$
+\title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
+$endif$
+$if(subtitle)$
+$if(beamer)$
+$else$
+\usepackage{etoolbox}
+\makeatletter
+\providecommand{\subtitle}[1]{% add subtitle to \maketitle
+ \apptocmd{\@title}{\par {\large #1 \par}}{}{}
+}
+\makeatother
+$endif$
+\subtitle{$subtitle$}
+$endif$
+$if(author)$
+\author{$for(author)$$author$$sep$ \and $endfor$}
+$endif$
+\date{$date$}
+$if(beamer)$
+$if(institute)$
+\institute{$for(institute)$$institute$$sep$ \and $endfor$}
+$endif$
+$if(titlegraphic)$
+\titlegraphic{\includegraphics{$titlegraphic$}}
+$endif$
+$if(logo)$
+\logo{\includegraphics{$logo$}}
+$endif$
+$endif$
+
+
+
+
+
+%%
+%% added
+%%
+
+%
+% language specification
+%
+% If no language is specified, use English as the default main document language.
+%
+$if(lang)$$else$
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+ \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=english]{babel}
+$if(babel-newcommands)$
+ $babel-newcommands$
+$endif$
+\else
+ $if(mainfont)$
+ $else$
+ % Workaround for bug in Polyglossia that breaks `\familydefault` when `\setmainlanguage` is used.
+ % See https://github.com/Wandmalfarbe/pandoc-latex-template/issues/8
+ % See https://github.com/reutenauer/polyglossia/issues/186
+ % See https://github.com/reutenauer/polyglossia/issues/127
+ \renewcommand*\familydefault{\sfdefault}
+ $endif$
+ % load polyglossia as late as possible as it *could* call bidi if RTL lang (e.g. Hebrew or Arabic)
+ \usepackage{polyglossia}
+ \setmainlanguage[]{english}
+$for(polyglossia-otherlangs)$
+ \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
+$endfor$
+\fi
+$endif$
+
+%
+% for the background color of the title page
+%
+$if(titlepage)$
+\usepackage{pagecolor}
+\usepackage{afterpage}
+$endif$
+
+%
+% TOC depth and
+% section numbering depth
+%
+\setcounter{tocdepth}{3}
+$if(numbersections)$
+\setcounter{secnumdepth}{3}
+$endif$
+
+%
+% break urls
+%
+\PassOptionsToPackage{hyphens}{url}
+
+%
+% When using babel or polyglossia with biblatex, loading csquotes is recommended
+% to ensure that quoted texts are typeset according to the rules of your main language.
+%
+\usepackage{csquotes}
+
+%
+% captions
+%
+\definecolor{caption-color}{HTML}{777777}
+\usepackage[font={stretch=1.2}, textfont={color=caption-color}, position=top, skip=4mm, labelfont=bf, singlelinecheck=false, justification=$if(caption-justification)$$caption-justification$$else$raggedright$endif$]{caption}
+\setcapindent{0em}
+
+%
+% blockquote
+%
+\definecolor{blockquote-border}{RGB}{221,221,221}
+\definecolor{blockquote-text}{RGB}{119,119,119}
+\usepackage{mdframed}
+\newmdenv[rightline=false,bottomline=false,topline=false,linewidth=3pt,linecolor=blockquote-border,skipabove=\parskip]{customblockquote}
+\renewenvironment{quote}{\begin{customblockquote}\list{}{\rightmargin=0em\leftmargin=0em}%
+\item\relax\color{blockquote-text}\ignorespaces}{\unskip\unskip\endlist\end{customblockquote}}
+
+%
+% Source Sans Pro as the default font family
+% Source Code Pro for monospace text
+%
+% 'default' option sets the default
+% font family to Source Sans Pro, not \sfdefault.
+%
+$if(mainfont)$
+$else$
+$endif$
+
+%
+% heading color
+%
+\definecolor{heading-color}{RGB}{40,40,40}
+\addtokomafont{section}{\color{heading-color}}
+% When using the classes report, scrreprt, book,
+% scrbook or memoir, uncomment the following line.
+%\addtokomafont{chapter}{\color{heading-color}}
+
+%
+% variables for title and author
+%
+\usepackage{titling}
+\title{$title$}
+\author{$for(author)$$author$$sep$, $endfor$}
+
+%
+% tables
+%
+$if(tables)$
+
+\definecolor{table-row-color}{HTML}{F5F5F5}
+\definecolor{table-rule-color}{HTML}{999999}
+
+%\arrayrulecolor{black!40}
+\arrayrulecolor{table-rule-color} % color of \toprule, \midrule, \bottomrule
+\setlength\heavyrulewidth{0.3ex} % thickness of \toprule, \bottomrule
+\renewcommand{\arraystretch}{1.3} % spacing (padding)
+
+% Reset rownum counter so that each table
+% starts with the same row colors.
+% https://tex.stackexchange.com/questions/170637/restarting-rowcolors
+\let\oldlongtable\longtable
+\let\endoldlongtable\endlongtable
+\renewenvironment{longtable}{
+\rowcolors{3}{}{table-row-color!100} % row color
+\oldlongtable} {
+\endoldlongtable
+\global\rownum=0\relax}
+
+% Unfortunately the colored cells extend beyond the edge of the
+% table because pandoc uses @-expressions (@{}) like so:
+%
+% \begin{longtable}[]{@{}ll@{}}
+% \end{longtable}
+%
+% https://en.wikibooks.org/wiki/LaTeX/Tables#.40-expressions
+$endif$
+
+%
+% remove paragraph indention
+%
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{6pt plus 2pt minus 1pt}
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+
+%
+%
+% Listings
+%
+%
+
+$if(listings)$
+
+%
+% listing colors
+%
+\definecolor{listing-background}{HTML}{F7F7F7}
+\definecolor{listing-rule}{HTML}{B3B2B3}
+\definecolor{listing-numbers}{HTML}{B3B2B3}
+\definecolor{listing-text-color}{HTML}{000000}
+\definecolor{listing-keyword}{HTML}{435489}
+\definecolor{listing-identifier}{HTML}{435489}
+\definecolor{listing-string}{HTML}{00999A}
+\definecolor{listing-comment}{HTML}{8E8E8E}
+\definecolor{listing-javadoc-comment}{HTML}{006CA9}
+
+\lstdefinestyle{eisvogel_listing_style}{
+ language = java,
+$if(listings-disable-line-numbers)$
+ xleftmargin = 0.6em,
+ framexleftmargin = 0.4em,
+$else$
+ numbers = left,
+ xleftmargin = 2.7em,
+ framexleftmargin = 2.5em,
+$endif$
+ backgroundcolor = \color{listing-background},
+ basicstyle = \color{listing-text-color}\small\ttfamily{}\linespread{1.15}, % print whole listing small
+ breaklines = true,
+ frame = single,
+ framesep = 0.19em,
+ rulecolor = \color{listing-rule},
+ frameround = ffff,
+ tabsize = 4,
+ numberstyle = \color{listing-numbers},
+ aboveskip = -0.7em,
+ belowskip = 0.1em,
+ abovecaptionskip = 0em,
+ belowcaptionskip = 1em,
+ keywordstyle = \color{listing-keyword}\bfseries,
+ classoffset = 0,
+ sensitive = true,
+ identifierstyle = \color{listing-identifier},
+ commentstyle = \color{listing-comment},
+ morecomment = [s][\color{listing-javadoc-comment}]{/**}{*/},
+ stringstyle = \color{listing-string},
+ showstringspaces = false,
+ escapeinside = {/*@}{@*/}, % Allow LaTeX inside these special comments
+ literate =
+ {á}{{\'a}}1 {é}{{\'e}}1 {í}{{\'i}}1 {ó}{{\'o}}1 {ú}{{\'u}}1
+ {Á}{{\'A}}1 {É}{{\'E}}1 {Í}{{\'I}}1 {Ó}{{\'O}}1 {Ú}{{\'U}}1
+ {à}{{\`a}}1 {è}{{\'e}}1 {ì}{{\`i}}1 {ò}{{\`o}}1 {ù}{{\`u}}1
+ {À}{{\`A}}1 {È}{{\'E}}1 {Ì}{{\`I}}1 {Ò}{{\`O}}1 {Ù}{{\`U}}1
+ {ä}{{\"a}}1 {ë}{{\"e}}1 {ï}{{\"i}}1 {ö}{{\"o}}1 {ü}{{\"u}}1
+ {Ä}{{\"A}}1 {Ë}{{\"E}}1 {Ï}{{\"I}}1 {Ö}{{\"O}}1 {Ü}{{\"U}}1
+ {â}{{\^a}}1 {ê}{{\^e}}1 {î}{{\^i}}1 {ô}{{\^o}}1 {û}{{\^u}}1
+ {Â}{{\^A}}1 {Ê}{{\^E}}1 {Î}{{\^I}}1 {Ô}{{\^O}}1 {Û}{{\^U}}1
+ {œ}{{\oe}}1 {Œ}{{\OE}}1 {æ}{{\ae}}1 {Æ}{{\AE}}1 {ß}{{\ss}}1
+ {ç}{{\c c}}1 {Ç}{{\c C}}1 {ø}{{\o}}1 {å}{{\r a}}1 {Å}{{\r A}}1
+ {€}{{\EUR}}1 {£}{{\pounds}}1 {«}{{\guillemotleft}}1
+ {»}{{\guillemotright}}1 {ñ}{{\~n}}1 {Ñ}{{\~N}}1 {¿}{{?`}}1
+ {…}{{\ldots}}1 {≥}{{>=}}1 {≤}{{<=}}1 {„}{{\glqq}}1 {“}{{\grqq}}1
+ {”}{{''}}1
+}
+\lstset{style=eisvogel_listing_style}
+
+\lstdefinelanguage{XML}{
+ morestring = [b]",
+ moredelim = [s][\bfseries\color{listing-keyword}]{<}{\ },
+ moredelim = [s][\bfseries\color{listing-keyword}]{</}{>},
+ moredelim = [l][\bfseries\color{listing-keyword}]{/>},
+ moredelim = [l][\bfseries\color{listing-keyword}]{>},
+ morecomment = [s]{<?}{?>},
+ morecomment = [s]{<!--}{-->},
+ commentstyle = \color{listing-comment},
+ stringstyle = \color{listing-string},
+ identifierstyle = \color{listing-identifier}
+}
+$endif$
+
+%
+% header and footer
+%
+$if(disable-header-and-footer)$
+$else$
+\usepackage{fancyhdr}
+
+\fancypagestyle{eisvogel-header-footer}{
+ \fancyhead{}
+ \fancyfoot{}
+ \lhead[$if(header-right)$$header-right$$else$$date$$endif$]{$if(header-left)$$header-left$$else$$title$$endif$}
+ \chead[$if(header-center)$$header-center$$else$$endif$]{$if(header-center)$$header-center$$else$$endif$}
+ \rhead[$if(header-left)$$header-left$$else$$title$$endif$]{$if(header-right)$$header-right$$else$$date$$endif$}
+ \lfoot[$if(footer-right)$$footer-right$$else$\thepage$endif$]{$if(footer-left)$$footer-left$$else$$for(author)$$author$$sep$, $endfor$$endif$}
+ \cfoot[$if(footer-center)$$footer-center$$else$$endif$]{$if(footer-center)$$footer-center$$else$$endif$}
+ \rfoot[$if(footer-left)$$footer-left$$else$$for(author)$$author$$sep$, $endfor$$endif$]{$if(footer-right)$$footer-right$$else$\thepage$endif$}
+ \renewcommand{\headrulewidth}{0.4pt}
+ \renewcommand{\footrulewidth}{0.4pt}
+}
+\pagestyle{eisvogel-header-footer}
+$endif$
+
+%%
+%% end added
+%%
+
+\begin{document}
+
+%%
+%% begin titlepage
+%%
+
+$if(titlepage)$
+\begin{titlepage}
+\newgeometry{left=6cm}
+$if(titlepage-color)$
+\definecolor{titlepage-color}{HTML}{$titlepage-color$}
+\newpagecolor{titlepage-color}\afterpage{\restorepagecolor}
+$endif$
+\newcommand{\colorRule}[3][black]{\textcolor[HTML]{#1}{\rule{#2}{#3}}}
+\begin{flushleft}
+\noindent
+\\[-1em]
+\color[HTML]{$if(titlepage-text-color)$$titlepage-text-color$$else$5F5F5F$endif$}
+\makebox[0pt][l]{\colorRule[$if(titlepage-rule-color)$$titlepage-rule-color$$else$435488$endif$]{1.3\textwidth}{$if(titlepage-rule-height)$$titlepage-rule-height$$else$4$endif$pt}}
+\par
+\noindent
+
+{ \setstretch{1.4}
+\vfill
+\noindent {\huge \textbf{\textsf{$title$}}}
+$if(subtitle)$
+\vskip 1em
+{\Large \textsf{$subtitle$}}
+$endif$
+\vskip 2em
+\noindent
+{\Large \textsf{$for(author)$$author$$sep$, $endfor$}
+\vfill
+}
+
+$if(logo)$
+\noindent
+\includegraphics[width=$if(logo-width)$$logo-width$$else$100$endif$pt, left]{$logo$}
+$endif$
+
+\textsf{$date$}}
+\end{flushleft}
+\end{titlepage}
+\restoregeometry
+$endif$
+
+%%
+%% end titlepage
+%%
+
+$if(has-frontmatter)$
+\frontmatter
+$endif$
+$if(title)$
+$if(beamer)$
+\frame{\titlepage}
+$endif$
+$if(abstract)$
+\begin{abstract}
+$abstract$
+\end{abstract}
+$endif$
+$endif$
+
+$if(first-chapter)$
+\setcounter{chapter}{$first-chapter$}
+\addtocounter{chapter}{-1}
+$endif$
+
+$for(include-before)$
+$include-before$
+
+$endfor$
+$if(toc)$
+$if(toc-title)$
+\renewcommand*\contentsname{$toc-title$}
+$endif$
+$if(beamer)$
+\begin{frame}
+$if(toc-title)$
+ \frametitle{$toc-title$}
+$endif$
+ \tableofcontents[hideallsubsections]
+\end{frame}
+$if(toc-own-page)$
+\newpage
+$endif$
+$else$
+{
+$if(colorlinks)$
+\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
+$endif$
+\setcounter{tocdepth}{$toc-depth$}
+\tableofcontents
+$if(toc-own-page)$
+\newpage
+$endif$
+}
+$endif$
+$endif$
+$if(lot)$
+\listoftables
+$endif$
+$if(lof)$
+\listoffigures
+$endif$
+$if(has-frontmatter)$
+\mainmatter
+$endif$
+$body$
+
+$if(has-frontmatter)$
+\backmatter
+$endif$
+$if(natbib)$
+$if(bibliography)$
+$if(biblio-title)$
+$if(has-frontmatter)$
+\renewcommand\bibname{$biblio-title$}
+$else$
+\renewcommand\refname{$biblio-title$}
+$endif$
+$endif$
+$if(beamer)$
+\begin{frame}[allowframebreaks]{$biblio-title$}
+ \bibliographytrue
+$endif$
+ \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
+$if(beamer)$
+\end{frame}
+$endif$
+
+$endif$
+$endif$
+$if(biblatex)$
+$if(beamer)$
+\begin{frame}[allowframebreaks]{$biblio-title$}
+ \bibliographytrue
+ \printbibliography[heading=none]
+\end{frame}
+$else$
+\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
+$endif$
+
+$endif$
+$for(include-after)$
+$include-after$
+
+$endfor$
+\end{document}
+
=====================================
debian/missing-sources/userguide/make-pdf.sh
=====================================
@@ -0,0 +1,13 @@
+#!/bin/sh -e
+
+cat Home.md \
+ | sed '1,/<!--- TOC END -->/d' \
+ | cat .pandoc/meta.yaml - \
+ | pandoc \
+ --from=markdown \
+ -o userguide.pdf \
+ --template=.pandoc/eisvogel.tex \
+ --toc
+
+chmod a+r userguide.pdf
+
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/59d0956bf05f275a8e40eed6e65f67f7dfd4391f...0b3dea19ff958b170f043d269bd7125676047345
--
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/59d0956bf05f275a8e40eed6e65f67f7dfd4391f...0b3dea19ff958b170f043d269bd7125676047345
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