Exclude PMI1 from doxygen docs

Don't document IMP.pmi1 as we should not be
using this module in any new applications,
and most of its classes shadow PMI classes.

tools/build/doxygen_add_ref_nav.py

@@ -28,7 +28,8 @@ def get_module_readme(module):
 
 def main():
     source = sys.argv[1]
-    modules = [m[0] for m in tools.get_modules(source)]
+    # Exclude obsolete modules
+    modules = [m[0] for m in tools.get_modules(source) if m[0] != 'pmi1']
     docs = Docs(xml_dir='doxygen/ref/xml',
                 html_dir='doc/ref',
                 top_source_dir=source,

tools/build/doxygen_templates/Doxyfile.in

@@ -728,7 +728,7 @@ EXCLUDE_SYMLINKS       = NO
 
 # We really want _[a-zA-Z]* here (because we don't want to hide things
 # # like __init__) but doxygen patterns aren't that flexible
-EXCLUDE_PATTERNS       = */internal/* */_*/* */_a* */_b* */_c* */_d* */_e* */_f* */_g* */_h* */_i* */_j* */_k* */_l* */_m* */_n* */_o* */_p* */_q* */_r* */_s* */_t* */_u* */_v* */_w* */_x* */_y* */_z* */_A* */_B* */_C* */_D* */_E* */_F* */_G* */_H* */_I* */_J* */_K* */_L* */_M* */_N* */_O* */_P* */_Q* */_R* */_S* */_T* */_U* */_V* */_W* */_X* */_Y* */_Z* @EXCLUDE_PATTERNS@
+EXCLUDE_PATTERNS       = */internal/* */pmi1/* */pmi1.h */IMP_pmi1.dox */_*/* */_a* */_b* */_c* */_d* */_e* */_f* */_g* */_h* */_i* */_j* */_k* */_l* */_m* */_n* */_o* */_p* */_q* */_r* */_s* */_t* */_u* */_v* */_w* */_x* */_y* */_z* */_A* */_B* */_C* */_D* */_E* */_F* */_G* */_H* */_I* */_J* */_K* */_L* */_M* */_N* */_O* */_P* */_Q* */_R* */_S* */_T* */_U* */_V* */_W* */_X* */_Y* */_Z* @EXCLUDE_PATTERNS@
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -738,7 +738,7 @@ EXCLUDE_PATTERNS       = */internal/* */_*/* */_a* */_b* */_c* */_d* */_e* */_f*
 
 # We really want _[a-zA-Z]* here (because we don't want to hide things
 # like __init__) but doxygen patterns aren't that flexible
-EXCLUDE_SYMBOLS        = _a* _b* _c* _d* _e* _f* _g* _h* _i* _j* _k* _l* _m* _n* _o* _p* _q* _r* _s* _t* _u* _v* _w* _x* _y* _z* _A* _B* _C* _D* _E* _F* _G* _H* _I* _J* _K* _L* _M* _N* _O* _P* _Q* _R* _S* _T* _U* _V* _W* _X* _Y* _Z*
+EXCLUDE_SYMBOLS        = _a* _b* _c* _d* _e* _f* _g* _h* _i* _j* _k* _l* _m* _n* _o* _p* _q* _r* _s* _t* _u* _v* _w* _x* _y* _z* _A* _B* _C* _D* _E* _F* _G* _H* _I* _J* _K* _L* _M* _N* _O* _P* _Q* _R* _S* _T* _U* _V* _W* _X* _Y* _Z* IMP::pmi1
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or
 # directories that contain example code fragments that are included (see

tools/build/setup_doxygen_config.py

@@ -71,7 +71,7 @@ def get_output_file_contents(self, output):
                                       "doxygen/manual-tags.xml=../manual")
             doxygen = doxygen.replace("@XML_OUTPUT@", "doxygen/ref/xml/")
             doxygen = doxygen.replace("@EXCLUDE@",
-                                      "lib/IMP/kernel lib/IMP/base")
+                                      "lib/IMP/pmi1")
         doxygen = doxygen.replace("@NAME@", "IMP")
         doxygen = doxygen.replace("@IMP_SOURCE_PATH@", source) \
                          .replace("@VERSION@", version)
@@ -97,6 +97,9 @@ def get_output_file_contents(self, output):
             inputsh = ["doxygen/generated", source + "/doc/ref",
                        "include", "doc/examples", "lib/IMP"]
             for m, p in tools.get_modules(source):
+                # Don't document obsolete modules
+                if m == 'pmi1':
+                    continue
                 doc = os.path.join(p, "doc")
                 if os.path.exists(doc):
                     inputsh.append(doc + "/")
@@ -123,6 +126,9 @@ def generate_overview_pages(source):
 IMP modules provide a number of command line tools.
 These are listed below under their parent module:""")
     for bs, g in tools.get_modules(source):
+        # Don't document obsolete modules
+        if bs == 'pmi1':
+            continue
         if tools.get_module_info(bs, '')['ok']:
             with open(os.path.join("build_info", "IMP_%s.pck" % bs),
                       'rb') as fh: