diff --git a/cmake_support/doc/index.rst b/cmake_support/doc/index.rst index 8fb98c962d01b733a99644e1d3d0d1bc7be3fb9e..ca224d7d0eb730c29dc1409317d30ebc68739963 100644 --- a/cmake_support/doc/index.rst +++ b/cmake_support/doc/index.rst @@ -1,3 +1,5 @@ +.. _pm3-cmake-doc: + |project|'s Share Of |cmake| =============================================================================== diff --git a/doc/contributing.rst b/doc/contributing.rst index be7f6cf077eddf29fe179c6deafbd8a39105dc6d..fb68988ffa2af49d1d37c477704ed9d93e92bf8c 100644 --- a/doc/contributing.rst +++ b/doc/contributing.rst @@ -169,10 +169,10 @@ tell it which files have to be considered packaging, compiling, etc.. Also documentation. |cmake| is a rather complex topic (unfortunately all usable build systems seem to be) so we skip a detailed view, here, and just advice you to go by example. There is a tiny bit of documentation on our additions to -|cmake| in the top-level :file:`cmake_support` directory. If you really need to -make changes to the build system, other than adding new files and modules, you -have to dive into |cmake| documentation all by yourself and on your own -responsibility. You have been warned. +|cmake| :ref:`here <pm3-cmake-doc>`. If you really need to make changes to the +build system, other than adding new files and modules, you have to dive into +|cmake| documentation all by yourself and on your own responsibility. You have +been warned. -------------------------------------------------------------------------------- The :file:`stage` Directory @@ -191,7 +191,7 @@ tutorial on unit testing here. Again, have a look at how other modules treat this topic and then there is quite a lot of educated material to be found on the Internet. Nevertheless, here is a short list of most important advices: -* Tests go into dedicated scripts in the :file:`tests` directory +* Tests go into dedicated scripts/ source files in the :file:`tests` directory * No external data dependencies, if tests need data, they find it in :file:`tests/data` * If 'exotic' |python| modules are used, consider making the test aware of the @@ -431,7 +431,7 @@ top level :file:`CMakeLists.txt`: COMPONENTS io mol seq seq_alg mol_alg conop) find_package(QMEAN 1.0 REQUIRED) - #The KIC loop closing algorithm requires a solver for a generalized eigen + #The KIC loop closing algorithm requires a solver for a generalised eigen #problem. Eigen3 would provide such a solver, but only allows to extract #the resulting eigenvalues and not the eigenvectors. #As soon as there is an Eigen3 release with the required functionality, @@ -643,4 +643,6 @@ contributions to web pages using |project|. .. LocalWords: changelog Optimized DOPTIMIZE gitignore cd conf subtree attr .. LocalWords: unittest TestCase nameattr testcode staticmethod builtin cp .. LocalWords: SomethingTests testFileExistsFalse testutils RunTests DQMEAN -.. LocalWords: pre +.. LocalWords: pre API inline CMake hh ProMod Bienchen OST OPENSTRUCTURE +.. LocalWords: mol alg conop QMEAN KIC eigen eigenvectors Lapack rawmodel +.. LocalWords: OpenStructure ost diff --git a/extras/pre_commit/pm3_csc/filecheck/rest.py b/extras/pre_commit/pm3_csc/filecheck/rest.py index d234a14b57c3c1d14d1987dec187fd92bd478a78..0ae713cc18da993e899f8c781778a09aaf34f922 100644 --- a/extras/pre_commit/pm3_csc/filecheck/rest.py +++ b/extras/pre_commit/pm3_csc/filecheck/rest.py @@ -24,9 +24,11 @@ class Rest(base.FileCheck): if re_head1.match(line) and len(last_line): ma_title = re_title1.match(last_line) if ma_title: - wl_title = ma_title.group(1).split() + wl_title = ma_title.group(1).split(' ()') for wrd in wl_title: if wrd not in ['-', 'a', 'an', 'the'] and wrd[0] != '|': + if re.match(r':.+:`.+`', wrd): + continue if not wrd[0].isupper(): pm3_csc.FailMsg("Line %d"%(self.current_line-1)+ " seems to be a headline "+