Fix check source not parsing errors and warnings correctly

Fixes #3487

Change-Id: I6161e02f66a9c34a56a7475f986ab94a5cc83d91

diff --git a/admin/gitlab-ci/lint.gitlab-ci.yml b/admin/gitlab-ci/lint.gitlab-ci.yml
index 03343bbcee6fe94bba2c8f947a4f3f8714ffeac3..21a7003e0a6e3d5ec30dd827c12d0980914d3058 100644 (file)
--- a/admin/gitlab-ci/lint.gitlab-ci.yml
+++ b/admin/gitlab-ci/lint.gitlab-ci.yml
@@ -140,8 +140,9 @@ check-source:
   script:
     - cd $BUILD_DIR
     - cmake --build . --target check-source
-    - grep -qi "error" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee doxygenError.txt || true
-    - grep -qi "warning" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee -a doxygenError.txt || true
+    - awk '/warning.*include style.*order/,/You can use.*rst|^$/' docs/doxygen/check-source.log | tee doxygenError.txt || true
+    - awk '/Traceback/,/.*rror|^$/' docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee -a doxygenError.txt || true
+    - awk '/warning:/,/in doxygen.*|^$/' docs/doxygen/doxygen*log | tee -a doxygenError.txt || true
     - if [ -s doxygenError.txt ] ; then echo "Found errors while running doxygen"; exit 1; fi
   artifacts:
     name: docs-artifacts-$CI_COMMIT_REF_SLUG

diff --git a/src/gromacs/domdec/utility.h b/src/gromacs/domdec/utility.h
index 4e36029e2e40b913591ed2b1a244bcc9e8835af7..89e804aaf62d69c18bfde9de9b23f51427b0d4bc 100644 (file)
--- a/src/gromacs/domdec/utility.h
+++ b/src/gromacs/domdec/utility.h
@@ -42,9 +42,9 @@
 #ifndef GMX_DOMDEC_DOMDEC_UTILITY_H
 #define GMX_DOMDEC_DOMDEC_UTILITY_H
 
+#include "gromacs/math/vectypes.h"
 #include "gromacs/mdtypes/forcerec.h"
 #include "gromacs/utility/arrayref.h"
-#include "gromacs/math/vectypes.h"
 
 #include "domdec_internal.h"
 

diff --git a/src/gromacs/imd/imd.cpp b/src/gromacs/imd/imd.cpp
index 9c84d7718b6445cbe7ab4206f29597d2829ce2f7..6b5d3d28f4443d9cb9669b039dc264b81daf27df 100644 (file)
--- a/src/gromacs/imd/imd.cpp
+++ b/src/gromacs/imd/imd.cpp
@@ -71,12 +71,12 @@
 #include "gromacs/mdlib/stat.h"
 #include "gromacs/mdrunutility/handlerestart.h"
 #include "gromacs/mdrunutility/multisim.h"
+#include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/mdtypes/imdmodule.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/mdrunoptions.h"
-#include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"

diff --git a/src/gromacs/selection/compiler.cpp b/src/gromacs/selection/compiler.cpp
index bf9fd86f9afd770058a81ddedf096dc45f07ad9d..52a26628d936f2b75bb2a1fd77c2674c7708e4a7 100644 (file)
--- a/src/gromacs/selection/compiler.cpp
+++ b/src/gromacs/selection/compiler.cpp
@@ -2586,18 +2586,6 @@ static void free_item_compilerdata(const SelectionTreeElementPointer& sel)
 namespace gmx
 {
 
-/*!
- * \param[in,out] coll Selection collection to be compiled.
- *
- * Before compilation, the selection collection should have been initialized
- * with gmx_ana_selcollection_parse_*().
- * The compiled selection collection can be passed to
- * gmx_ana_selcollection_evaluate() to evaluate the selection for a frame.
- * If an error occurs, \p sc is cleared.
- *
- * The covered fraction information in \p sc is initialized to
- * \ref CFRAC_NONE.
- */
 void compileSelection(SelectionCollection* coll)
 {
     gmx_ana_selcollection_t*    sc = &coll->impl_->sc_;

diff --git a/src/gromacs/selection/compiler.h b/src/gromacs/selection/compiler.h
index 6602835a7516411c8bf07bc195f1e1c332835825..97c9fb99f8a7f20c245446f0f96487f516f78d98 100644 (file)
--- a/src/gromacs/selection/compiler.h
+++ b/src/gromacs/selection/compiler.h
@@ -55,8 +55,19 @@ class SelectionCollection;
  * It prepares the selections in a selection collection for evaluation and
  * performs some optimizations.
  *
+ * Before compilation, the selection collection should have been initialized
+ * with gmx_ana_selcollection_parse_*().
+ * The compiled selection collection can be passed to
+ * gmx_ana_selcollection_evaluate() to evaluate the selection for a frame.
+ * If an error occurs, \p coll is cleared.
+ *
+ * The covered fraction information in \p coll is initialized to
+ * \ref CFRAC_NONE.
+ *
  * See \ref page_module_selection_compiler.
  *
+ * \param[in, out] coll Selection collection to work on.
+ *
  * \ingroup module_selection
  */
 void compileSelection(SelectionCollection* coll);

diff --git a/src/gromacs/selection/selectioncollection.h b/src/gromacs/selection/selectioncollection.h
index 886bb898a0491580c5093f57bb118db91de3cf0c..a168aaa1b22551c138fb6c977d38579550944284 100644 (file)
--- a/src/gromacs/selection/selectioncollection.h
+++ b/src/gromacs/selection/selectioncollection.h
@@ -416,13 +416,9 @@ private:
 
     PrivateImplPointer<Impl> impl_;
 
-    /*! \brief
-     * Needed for the compiler to freely modify the collection.
-     */
-    friend void compileSelection(SelectionCollection* /*coll*/);
-    /*! \brief
-     * Needed for the evaluator to freely modify the collection.
-     */
+    // Needed for the compiler to freely modify the collection.
+    friend void compileSelection(SelectionCollection* coll);
+    // Needed for the evaluator to freely modify the collection.
     friend class SelectionEvaluator;
 };