Refurbished documentation for meld, fixed doctest issues

CMakeLists.txt

@@ -16,7 +16,8 @@ include(PROMOD3)
 set(PROMOD3_VERSION_MAJOR 0)
 set(PROMOD3_VERSION_MINOR 1)
 set(PROMOD3_VERSION_PATCH 0)
-set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
+set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
+set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
 
 option(DISABLE_DOCUMENTATION "Do not build documentation" OFF)
 option(DISABLE_DISABLE_DOCTEST "Do not check examples in documentation" OFF)
@@ -85,6 +86,11 @@ if(NOT EIGEN3_FOUND)
   message(FATAL_ERROR "Eigen3 is essential for building ${PROJECT_NAME}.")
 endif()
 
+# This is somewhat experimental: Checking if Boost is compiled with the same
+# Python version used for Promod3. The very same macro is disabled in OST so
+# it may fail at some point.
+promod3_match_boost_python_version(${PYTHON_LIBRARIES})
+
 # basic environment
 include_directories(${Boost_INCLUDE_DIRS}
                     ${OST_INCLUDE_DIR}

doc/CMakeLists.txt

@@ -31,7 +31,10 @@ set(_SPHINX_CONF_SUBST_DICT PROMOD3_VERSION_MAJOR="${PROMOD3_VERSION_MAJOR}"
                             OST_ROOT="${OST_ROOT}"
                             OST_DOC_URL="${OST_DOC_URL}"
                             LIB_DIR="${LIB_DIR}")
-set(_CONF_SUBST_DICT -DINPUT_FILE=${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in -DOUT_FILE=${_SPHINX_CONF_PY})
+
+set(_CONF_SUBST_DICT -DINPUT_FILE=${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in)
+list(APPEND _CONF_SUBST_DICT -DOUT_FILE=${_SPHINX_CONF_PY})
+
 foreach(_subst ${_SPHINX_CONF_SUBST_DICT})
   list(APPEND _CONF_SUBST_DICT -D${_subst})
 endforeach()
@@ -45,7 +48,8 @@ add_custom_command(OUTPUT ${_SPHINX_CONF_PY}
 foreach(_rst_file ${_DOC_RST_FILES})
   add_custom_command(OUTPUT "${_RST_SOURCE_DIR}/${_rst_file}"
                      MAIN_DEPENDENCY "${CMAKE_CURRENT_SOURCE_DIR}/${_rst_file}"
-                     COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_CURRENT_SOURCE_DIR}/${_rst_file}" "${_RST_SOURCE_DIR}/${_rst_file}")
+                     COMMAND ${CMAKE_COMMAND} -E copy
+   "${CMAKE_CURRENT_SOURCE_DIR}/${_rst_file}" "${_RST_SOURCE_DIR}/${_rst_file}")
   set(_RST_DEPS ${_RST_DEPS} "${_RST_SOURCE_DIR}/${_rst_file}")
 endforeach()
 # care for a changelog file, if given
@@ -53,12 +57,13 @@ if(DEFINED PM3_DOC_CHANGELOG)
   # copy to different file name
   add_custom_command(OUTPUT "${_RST_SOURCE_DIR}/changelog.rst"
                      MAIN_DEPENDENCY "${PM3_DOC_CHANGELOG}"
-                     COMMAND ${CMAKE_COMMAND} -E copy "${PM3_DOC_CHANGELOG}" "${_RST_SOURCE_DIR}/changelog.rst")
+                     COMMAND ${CMAKE_COMMAND} -E copy
+                      "${PM3_DOC_CHANGELOG}" "${_RST_SOURCE_DIR}/changelog.rst")
   set(_RST_DEPS ${_RST_DEPS} "${_RST_SOURCE_DIR}/changelog.rst")
 endif()
 
 # iterate list of ALL modules registered by pymod()/ add_doc_source()
-foreach(mod ${PM3_MODULES})
+foreach(mod ${PM3_PY_MS})
   # only modules with dedicated rst files are considered for documentation, so
   # we check if a list PM3_RST_{module name} exists (filled by add_doc_source()
   # the following sets up copying for *.rst files only
@@ -98,7 +103,8 @@ set(_SPHINX_INDEX_HTML "${_SPHINX_HTML_DIR}/index.html")
 add_custom_command(OUTPUT ${_SPHINX_INDEX_HTML}
                    MAIN_DEPENDENCY "${_SPHINX_CONF_PY}"
                    DEPENDS ${_RST_DEPS} ${_DOC_MODULE_DEPS}
-                   COMMAND ${SPHINX_BINARY} -b html -c "${_RST_SOURCE_DIR}" "${_RST_SOURCE_DIR}" "${_SPHINX_HTML_DIR}")
+                   COMMAND ${SPHINX_BINARY} -b html -c "${_RST_SOURCE_DIR}"
+                                     "${_RST_SOURCE_DIR}" "${_SPHINX_HTML_DIR}")
 add_custom_target(html DEPENDS ${_SPHINX_INDEX_HTML})
 
 # man target
@@ -108,7 +114,8 @@ set(_SPHINX_MAN "${_SPHINX_MAN_DIR}/promod3.1")
 add_custom_command(OUTPUT ${_SPHINX_MAN}
                    MAIN_DEPENDENCY "${_SPHINX_CONF_PY}"
                    DEPENDS ${_RST_DEPS} ${_DOC_MODULE_DEPS}
-                   COMMAND ${SPHINX_BINARY} -b man -c "${_RST_SOURCE_DIR}" "${_RST_SOURCE_DIR}" "${_SPHINX_MAN_DIR}")
+                   COMMAND ${SPHINX_BINARY} -b man -c "${_RST_SOURCE_DIR}"
+                                      "${_RST_SOURCE_DIR}" "${_SPHINX_MAN_DIR}")
 add_custom_target(man DEPENDS ${_SPHINX_MAN})
 
 # doc target, registered with all
@@ -120,14 +127,17 @@ add_dependencies(doc man)
 set(_SPHINX_DOCTEST_DIR "${CMAKE_CURRENT_BINARY_DIR}/doctest")
 file(MAKE_DIRECTORY ${_SPHINX_DOCTEST_DIR})
 add_custom_target(doctest
-                  COMMAND ${SPHINX_BINARY} -b doctest -c "${_RST_SOURCE_DIR}" "${_RST_SOURCE_DIR}" "${_SPHINX_DOCTEST_DIR}"
-                  DEPENDS "${_SPHINX_CONF_PY}" ${_RST_DEPS} ${_DOC_MODULE_DEPS})
+                  COMMAND ${SPHINX_BINARY} -b doctest -c "${_RST_SOURCE_DIR}"
+                                   "${_RST_SOURCE_DIR}" "${_SPHINX_DOCTEST_DIR}"
+                  DEPENDS "${_SPHINX_CONF_PY}" ${_RST_DEPS} ${_DOC_MODULE_DEPS}
+                                         ${PM3_PYMODULES} ${PM3_UNIT_TEST_DATA})
 
 # linkcheck target
 set(_SPHINX_LINKCHECK_DIR "${CMAKE_CURRENT_BINARY_DIR}/linkcheck")
 file(MAKE_DIRECTORY ${_SPHINX_LINKCHECK_DIR})
 add_custom_target(linkcheck
-                  COMMAND ${SPHINX_BINARY} -b linkcheck -c "${_RST_SOURCE_DIR}" "${_RST_SOURCE_DIR}" "${_SPHINX_LINKCHECK_DIR}"
+                  COMMAND ${SPHINX_BINARY} -b linkcheck -c "${_RST_SOURCE_DIR}"
+                                 "${_RST_SOURCE_DIR}" "${_SPHINX_LINKCHECK_DIR}"
                   DEPENDS "${_SPHINX_CONF_PY}" ${_RST_DEPS} ${_DOC_MODULE_DEPS})
 
 # register doctest & linkcheck with check
@@ -147,6 +157,3 @@ endif()
 install(DIRECTORY ${_SPHINX_HTML_DIR} DESTINATION "share/promod3")
 # install man pages
 install(DIRECTORY ${_SPHINX_MAN_DIR} DESTINATION "share/promod3")
-
-# doctest & linkcheck goes into check, once its created, depend on rst
-# what about extratcting stuff from code? -> autofunction

extras/pre-commit

@@ -211,7 +211,7 @@ def CheckPythonCode(filepath):
   import_re = re.compile('import\s+\*')
   lno = 1
   for line in fh:
-    line = line.strip()
+    line = line.rstrip(os.linesep)
     TestLineWidthExit(line, lno, filepath)
     m_line = re.match('([^#]*)', line)
     ex_line = m_line.group(1)
@@ -228,7 +228,7 @@ def CheckRest(filepath):
   fh = open(filepath, "U")
   lno = 1
   for line in fh:
-    line = line.strip()
+    line = line.rstrip(os.linesep)
     TestLineWidthExit(line, lno, filepath)
     lno += 1
 
@@ -236,7 +236,7 @@ def CheckCmake(filepath):
   fh = open(filepath, "U")
   lno = 1
   for line in fh:
-    line = line.strip()
+    line = line.rstrip(os.linesep)
     TestLineWidthExit(line, lno, filepath)
     lno += 1
 
@@ -244,7 +244,7 @@ def CheckShellScript(filepath):
   fh = open(filepath, "U")
   lno = 1
   for line in fh:
-    line = line.strip()
+    line = line.rstrip(os.linesep)
     TestLineWidthExit(line, lno, filepath)
     lno += 1
 
@@ -252,7 +252,7 @@ def CheckCCode(filepath):
   fh = open(filepath, "U")
   lno = 1
   for line in fh:
-    line = line.strip()
+    line = line.rstrip(os.linesep)
     TestLineWidthExit(line, lno, filepath)
     lno += 1
 ### FUNCTIONS - END

meld/doc/CMakeLists.txt

 set(MELD_RST
 index.rst
-rawmodel.rst
 )
 
 add_doc_source(NAME meld RST ${MELD_RST})

meld/doc/index.rst

@@ -2,12 +2,98 @@
 ================================================================================
 
 .. module:: promod3.meld
-  :synopsis: Coordinate modeling and sampling
+  :synopsis: Raw Coordinate Model
+
+.. currentmodule:: promod3.meld
+
+Functionality to build raw (pseudo) models based on a sequence alignment.
+Here is an example of how to build a model from an alignment and a structure.
+
+.. testcode:: meld
+  :hide:
+
+  import os
+  import tempfile
+  from ost import io
+  from promod3 import meld
+
+  aln = io.LoadAlignment('../tests/meld/data/raw-modeling/seq.fasta')
+  template_structure = io.LoadPDB('../tests/meld/data/raw-modeling/gly.pdb',
+                                  restrict_chains='A')
+  aln.AttachView(1, template_structure.Select('peptide=true'))
+  result = meld.BuildRawModel(aln)
+  (fh, fn) = tempfile.mkstemp(suffix='.pdb')
+  io.SavePDB(result.model, fn)
+  os.remove(fn)
+
+.. doctest:: meld
+
+  from ost import io
+  from promod3 import meld
+
+  aln = io.LoadAlignment('seq.fasta')
+  template_structure = io.LoadPDB('gly.pdb', restrict_chains='A')
+  aln.AttachView(1, template_structure.Select('peptide=true'))
+  result = meld.BuildRawModel(aln)
+  io.SavePDB(result.model, 'model.pdb')
+
+
+Raw Coordinate Modeling API
+--------------------------------------------------------------------------------
+
+.. function:: BuildRawModel(alignment, calpha_only=False)
+              BuildRawModel(alignments, calpha_only=False)
+
+  Builds a raw (pseudo) model from the alignment. Can either take a single
+  alignment handle or an alignment handle list. Every list item is treated as a
+  single chain in the final raw model.
+
+  This is a basic protein core modeling algorithm that copies backbone
+  coordinates based on the sequence alignment. For matching residues, the
+  side chain coordinates are also copied. Gaps are ignored. Hydrogen an
+  deuterium atoms are not copied into the model.
+
+  The function tries to reuse as much as possible from the template. Modified
+  residues are treated as follows:
+
+    - Selenium methionine residues are converted to methionine
+
+    - Side chains which contain all atoms of the parent amino acid, e.g.
+      phosphoserine are copied as a whole with the modifications stripped off.
+
+  Residue numbers are set such that missing residue in gaps are honoured and
+  subsequent loop modeling can insert new residues without having to
+  renumber.
   
-This module contains functions and classes to build raw-models for protein
-structures from templates.
+  The returned :class:`RawModelingResult` stores the obtained raw model as well
+  as information about insertions and deletions in the gaps list.
+
+  :param calpha_only: If true, only Calpha atoms will be copied. Side chains
+                      and other backbone atoms are completely ignored.
+  :raises: A :exc:`RuntimeError` when the second sequence does not have an
+     attached structure
+
+.. class:: RawModelingResult
+
+  Holds the result of raw model building. Incredibly minimalistic for now. Will
+  most likely grow a few more members over time to, e.g. to store a detailed
+  report.
+
+  .. attribute:: model
+
+    The resulting model.
+
+    :type: :class:`~ost.mol.EntityHandle`
+
+  .. attribute:: gaps
+
+    List of gaps in the model that could not be copied from the template. These
+    gaps may be the result of insertions/deletions in the alignment or due to
+    missing or incomplete backbone coordinates in the template structure.
+
+
+    :type: :class:`StructuralGapList`
 
-.. toctree:: 
-  :maxdepth: 2
 
-  rawmodel
+..  LocalWords:  currentmodule promod aln AttachView BuildRawModel pdb calpha
+..  LocalWords:  RawModelingResult StructuralGapList

meld/doc/rawmodel.rst

-Raw Coordinate Modeling
-================================================================================
-
-.. currentmodule:: sm.meld
-
-Introduction
---------------------------------------------------------------------------------
-
-Contains function to build raw (pseudo) models based on a sequence alignment. Here is an example of how to build a model from an alignment and a structure.
-
-.. code-block:: python
-  
-  from promod3 import meld
-  
-  aln=io.LoadAlignment('parwise.fasta')
-  template_structure=io.LoadPDB('1ake.pdb', restrict_chains='A')
-  aln.AttachView(1, template_structure.Select('peptide=true'))
-  result=meld.BuildRawModel(aln)
-  io.SavePDB(result.model, 'model.pdb')
-  print 'remaining gaps:'
-  for gap in result.gaps:
-    print ' * %s' % str(gap)
-
-
-Raw Coordinate Modeling API
---------------------------------------------------------------------------------
-
-.. function:: BuildRawModel(alignment, calpha_only=False)
-              BuildRawModel(alignments, calpha_only=False)
-
-  Builds a raw (pseudo) model from the alignment.
-  Can either take a single alignment handle or an alignment handle list.
-  Every list item is treated as a single chain in the final raw model.
-  
-  This is a basic protein core modeling algorithm that copies backbone 
-  coordinates based on the sequence alignment. For matching residues, the 
-  sidechain coordinates are also copied. Gaps are ignored. Hydrogen an deuterium 
-  atoms are not copied into the model.
-  
-  The function tries to reuse as much as possible from the template. Modified 
-  residues are treated as follows:
-  
-    - Selenium methionine residues are converted to methionines
-    
-    - Sidechains which contain all atoms of the parent amino acid, e.g. 
-      phosphoserine are copied as a whole with the modifications stripped off.
-    
-  Residue numbers are set such that missing residue in gaps are honored and 
-  subsequent loop modeling can insert new residues without having to 
-  renumber.
-  
-  The returned :class:`RawModelingResult` stores the obtained raw model as well 
-  as information about insertions and deletions in the gaps list.
-  
-  :param calpha_only: If true, only Calpha atoms will be copied. Sidechains and 
-     other backbone atoms are completely ignored.
-  :raises: A :exc:`RuntimeError` when the second sequence does not have an 
-     attached structure
-
-.. class:: RawModelingResult
-
-  Holds the result of raw model building. Incredibly minimalistic for now. Will 
-  most likely grow a few more members over time to, e.g. to store a detailed 
-  report.
-  
-  .. attribute:: model
-  
-    The resulting model.
-    
-    :type: :class:`~ost.mol.EntityHandle`
-  
-  .. attribute:: gaps
-    
-    List of gaps in the model that could not be copied from the template. These 
-    gaps may be the result of insertions/deletions in the alignment or due to 
-    missing or incomplete backbone coordinates in the template structure.
-    
-    
-    :type: :class:`StructuralGapList`
-