New upstream version 2.4.13+git20190529+dfsg

# ignore other autotools generated content

Makefile

Makefile.in

configure

aclocal.m4

autom4te.cache

autoscan.log

depcomp

missing

compile

install-sh

config

config.*

.deps

stamp-h1

.dirstamp

ylwrap

tests/test-env.sh

src/ViennaRNA/vrna_config.h

libtool

# ignore libtoolize generated files

m4/libtool.m4

m4/lt*.m4

# ignore all tar.gz archives

*.tar.gz

# except the libsvm sources

!libsvm*.tar.gz

# logfiles of test suites

*.log

# libtool generated files

.libs

*.la

*.lo

*.o

# ignore pkg-config file

RNAlib2.pc

# ignore all postscript files that might be generated

*.ps

dist: xenial

compiler:

- gcc

- clang

addons:

  apt:

    sources:

    - ubuntu-toolchain-r-test

    packages:

    - gcc

    - g++

    - clang

    - gengetopt

    - flex

    - help2man

    - libgsl-dev

    - doxygen

    - doxygen-latex

    - libperl-dev

    - python-dev

    - python3-dev

    - graphviz

    - texlive-latex-base

    - texlive-latex-recommended

    - texlive-latex-extra

    - latex-beamer

    - check

    - texinfo

    - diffutils

before_script:

- autoreconf -i

install:

  - wget https://github.com/swig/swig/archive/rel-3.0.12.tar.gz

  - tar -xzvf rel-3.0.12.tar.gz

  - pushd swig-rel-3.0.12 && ./autogen.sh && ./configure --prefix=/usr && make && sudo make install && popd

script:

- cd src && tar xzf libsvm-3.23.tar.gz && cd ..

- ./configure --with-cluster --with-kinwalker --disable-lto

- make -j${CPU_COUNT}

- make check

before_deploy:

- make dist-gzip

- make dist-zip

- export DIST_GZIP=$(ls ViennaRNA-*.tar.gz)

- export DIST_ZIP=$(ls ViennaRNA-*.zip)

- echo "Deploying Changelog and autoconf's dists (${DIST_GZIP} and ${DIST_ZIP}) to GitHub releases"

deploy:

  provider: releases

  api-key:

    secure: 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

  skip_cleanup: true

  file_glob: true

  overwrite: true

  file:

  - "${DIST_GZIP}"

  - "${DIST_ZIP}"

  - CHANGELOG.md

  on:

    repo: ViennaRNA/ViennaRNA

    tags: true

# Contributing

If you wish to contribute to this project, please first discuss any proposed changes

with the owners and main developers. You may do that either through making an issue

at our official GitHub presence https://github.com/ViennaRNA/ViennaRNA, by email

(rna@tbi.univie.ac.at), or any other personal communication with the core developer

team.

Please note that we have a code of conduct. Please follow it in all your interactions

with this project.

## Reporting Bugs

1. Please make an issue at GitHub or notify us by emailing to rna@tbi.univie.ac.at

2. In your report, include as much information as possible, such that we are able

   to reproduce it. If possible, find a minimal example that triggers the bug.

3. Include the version number for the ViennaRNA Package you experience the bug with.

4. Include at least some minimal information regarding your operating system (Linux,

   Mac OS X, Windows, etc.)

## Pull Request Process

1. Ensure that you have not checked-in any files that are automatically build!

2. When contributing C source code, follow our code formatting guide lines. You

   may use the tool `uncrustify` together with our config located in `misc/uncrustify.cfg`

   to accomplish that.

3. Only expose symbols (functions, variables, etc.) to the libraries interface that are

   absolutely necessary! Hide all other symbols in the corresponding object file(s) by

   declaring them as `static`.

4. Use the prefixes `vrna_` for any symbol you add to the API of our library! Preprocessor

   macros in header files require the prefix in capital letters, i.e. `VRNA_`.

5. Use C-style comments at any place necessary to make sure your implementation can still

   be understood and followed in the future.

6. Add test cases for any new implementation! The test suite is located in the `tests`

   directory and is split into tests for the C-library, executable programs, and the

   individual scripting language interfaces.

7. Run `make check` to ensure that all other test suites still run properly with your

   applied changes!

8. When contributing via GitHub, make a personal fork of our project and create a separate

   branch for your changes. Then make a pull request to our `user-contrib` branch.

   Pull requests to the `master` branch will be rejected to keep its history clean.

9. Pull requests that have been successfully merged into the `user-contrib` branch

   usually find their way into the next release of the ViennaRNA Package. However, please

   note that the core developers may decide to include your changes in a later version.