diff --git a/CMakeLists.txt b/CMakeLists.txt index d708fa182e8ad9c1a99b868c0a5a96e78d6e5232..fa6ac65d3475358e0e6a3a6e70ed355bdcaa55da 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -84,7 +84,7 @@ if(NOT DISABLE_DOCUMENTATION) find_package(Sphinx ${PYTHON_VERSION} REQUIRED) set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}") # set this to the URL corresponding to the version of OST you are using - set(OST_DOC_URL "http://www.openstructure.org/docs/dev") + set(OST_DOC_URL "https://www.openstructure.org/docs/dev") endif() find_package(OPENSTRUCTURE 1.7 REQUIRED COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm) diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst index 4bb192686d60b60c60d52e9c0e8fb56b3334a91e..a601d619b695a46a2f15352e312e4bdaf91ab90f 100644 --- a/doc/buildsystem.rst +++ b/doc/buildsystem.rst @@ -143,11 +143,11 @@ safely delete the whole source folder. .. |qmean| replace:: QMEAN .. |eigen3| replace:: Eigen 3 .. |openmm| replace:: OpenMM -.. _qmean: http://swissmodel.expasy.org/qmean/cgi/index.cgi? -.. _ost_l: http://www.OpenStructure.org +.. _qmean: https://swissmodel.expasy.org/qmean/ +.. _ost_l: https://www.OpenStructure.org .. _cmake: https://cmake.org/ .. _python: https://www.python.org/ -.. _boost: http://www.boost.org/ +.. _boost: https://www.boost.org/ .. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page .. _openmm: http://openmm.org diff --git a/doc/conf.py.in b/doc/conf.py.in index 3453b6e9740f3b71777b6143d5e918808fd030a3..fddcc7ef702e11e7aa7d2f83910172e02a61f536 100644 --- a/doc/conf.py.in +++ b/doc/conf.py.in @@ -288,7 +288,7 @@ rst_epilog = """ .. |boost| replace:: Boost .. |git| replace:: Git .. |C++| replace:: C++ -.. _ost_s: http://www.OpenStructure.org +.. _ost_s: https://www.OpenStructure.org .. _nameattr: @PYTHON_DOC_URL@/library/__main__.html .. _mainattr: @PYTHON_DOC_URL@/library/__main__.html .. _descattr: @PYTHON_DOC_URL@/library/argparse.html#description diff --git a/doc/contributing.rst b/doc/contributing.rst index 832af70cc2e46a71d3850967a075a8f423ece6d8..ae3c842c641522624e55d208c51e6a146773a033 100644 --- a/doc/contributing.rst +++ b/doc/contributing.rst @@ -201,7 +201,7 @@ sporting a single monolithic :file:`test_sidechain_reconstruction.py`. |python| code is evaluated using its own :py_docs:`unit testing framework <library/unittest.html>` with a little help from |ost_s|_ (|C++| uses the |boost| `Test Library -<http://www.boost.org/doc/libs/1_47_0/libs/test/doc/html/index.html>`_). The +<https://www.boost.org/doc/libs/1_53_0/libs/test/doc/html/index.html>`_). The basic scheme is to import your module, subclass :class:`unittest.TestCase` and make the whole file runnable as script using the most common |nameattr|_ attribute. As an example we test the @@ -477,7 +477,7 @@ repository comes with a top-level :file:`doc` directory. While you should not spend to much time thinking about how to format documentation, here is a helpful list of standard formatters: -http://sphinx-doc.org/markup/inline.html +http://sphinx-doc.org/en/stable/markup/inline.html If you write new functionality for |project|, or fix bugs, feel free to extend the :file:`CHANGELOG` file. It will be automatically pulled into the