fix links in doc

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)

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
 

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

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