Refactor changes to documentation build

- Added CMake variables for readability
- Moved Mathjax files to _static to avoid special copy logic
- Moved JPG/lammps-logo.png to _static to avoid special copy logic
- Removed dead CMake code

cmake/Modules/Documentation.cmake

@@ -19,62 +19,70 @@ if(BUILD_DOC)
 
   file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
+
   add_custom_command(
     OUTPUT docenv
     COMMAND ${VIRTUALENV} docenv
   )
 
   set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+  set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
+
+  set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
+  set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
+  set(SPHINX_STATIC_DIR  ${SPHINX_CONFIG_DIR}/_static)
+
+  # configuration and static files are copied to binary dir to avoid collisions with parallel builds
+  set(DOC_BUILD_DIR ${CMAKE_CURRENT_BINARY_DIR}/doc)
+  set(DOC_BUILD_CONFIG_FILE ${DOC_BUILD_DIR}/conf.py)
+  set(DOC_BUILD_STATIC_DIR ${DOC_BUILD_DIR}/_static)
+  set(DOXYGEN_BUILD_DIR ${DOC_BUILD_DIR}/doxygen)
+  set(DOXYGEN_XML_DIR ${DOXYGEN_BUILD_DIR}/xml)
+
+  # copy entire configuration folder to doc build directory
+  # files in _static are automatically copied during sphinx-build, so no need to copy them individually
+  file(COPY ${SPHINX_CONFIG_DIR}/ DESTINATION ${DOC_BUILD_DIR})
+
+  # configure paths in conf.py, since relative paths change when file is copied
+  configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
 
   add_custom_command(
-    OUTPUT requirements.txt
+    OUTPUT ${DOC_BUILD_DIR}/requirements.txt
-    DEPENDS docenv
+    DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
-    COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
+    COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
   # download mathjax distribution and unpack to folder "mathjax"
-  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
+  if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
     file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
       "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
       EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
-    execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
+    execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
   endif()
-  file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
-  file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
 
   # for increased browser compatibility
-  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
+  if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)
     file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
-      "${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
+      "${DOC_BUILD_STATIC_DIR}/polyfill.js")
   endif()
 
   # set up doxygen and add targets to run it
-  file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doxygen)
+  file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})
-  set(DOXYGEN_XML_DIR ${CMAKE_CURRENT_BINARY_DIR}/doxygen/xml)
+  file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)
-  add_custom_command(
+  configure_file(${LAMMPS_DOC_DIR}/doxygen/Doxyfile.in ${DOXYGEN_BUILD_DIR}/Doxyfile)
-    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/doxygen/lammps-logo.png
-    DEPENDS ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png
-    COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png ${CMAKE_BINARY_DIR}/doxygen/lammps-logo.png
-  )
-  configure_file(${LAMMPS_DOC_DIR}/doxygen/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/doxygen/Doxyfile)
   get_target_property(LAMMPS_SOURCES lammps SOURCES)
-  # need to update timestamps on pg_*.rst files after running doxygen to have sphinx re-read them
-  file(GLOB PG_SOURCES ${LAMMPS_DOC_DIR}/src/pg_*.rst)
   add_custom_command(
     OUTPUT ${DOXYGEN_XML_DIR}/index.xml
     DEPENDS ${DOC_SOURCES} ${LAMMPS_SOURCES}
-    COMMAND Doxygen::doxygen ${CMAKE_CURRENT_BINARY_DIR}/doxygen/Doxyfile WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doxygen
+    COMMAND Doxygen::doxygen ${DOXYGEN_BUILD_DIR}/Doxyfile WORKING_DIRECTORY ${DOXYGEN_BUILD_DIR}
     COMMAND ${CMAKE_COMMAND} -E touch ${DOXYGEN_XML_DIR}/run.stamp
   )
 
-  # note, this may run in parallel with other tasks, so we must not use multiple processes here
-  file(COPY ${LAMMPS_DOC_DIR}/utils/sphinx-config DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/utils)
-  file(COPY ${LAMMPS_DOC_DIR}/src DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  configure_file(${CMAKE_CURRENT_BINARY_DIR}/utils/sphinx-config/conf.py.in ${CMAKE_CURRENT_BINARY_DIR}/utils/sphinx-config/conf.py)
   if(EXISTS ${DOXYGEN_XML_DIR}/run.stamp)
     set(SPHINX_EXTRA_OPTS "-E")
   else()
@@ -82,34 +90,17 @@ if(BUILD_DOC)
   endif()
   add_custom_command(
     OUTPUT html
-    DEPENDS ${DOC_SOURCES} docenv requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${CMAKE_CURRENT_BINARY_DIR}/utils/sphinx-config/conf.py
+    DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${CMAKE_BINARY_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
-    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
+    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
     COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp
   )
 
-  # copy selected image files to html output tree
-  file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/html/_images/wsl_tutorial)
-  file(GLOB HTML_EXTRA_IMAGES RELATIVE ${LAMMPS_DOC_DIR}/src/img/
-          ${LAMMPS_DOC_DIR}/src/img/[^.]*.jpg
-          ${LAMMPS_DOC_DIR}/src/img/[^.]*.gif
-          ${LAMMPS_DOC_DIR}/src/img/[^.]*.png
-          ${LAMMPS_DOC_DIR}/src/img/wsl_tutorial/[^.]*.png)
-  set(HTML_IMAGE_TARGETS "")
-  foreach(_IMG ${HTML_EXTRA_IMAGES})
-    list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/_images/${_IMG}")
-    add_custom_command(
-      OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/_images/${_IMG}
-      DEPENDS ${LAMMPS_DOC_DIR}/src/img/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/_images
-      COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/img/${_IMG} ${CMAKE_BINARY_DIR}/html/_images/${_IMG}
-    )
-  endforeach()
-
   add_custom_target(
     doc ALL
-    DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
+    DEPENDS html ${DOC_BUILD_STATIC_DIR}/mathjax/es5
     SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
   )
 
-  install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
+  install(DIRECTORY ${DOC_BUILD_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
 endif()

doc/.gitignore

@@ -15,3 +15,5 @@
 /utils/sphinx-config/conf.py
 /doxygen/Doxyfile
 *.el
+/utils/sphinx-config/_static/mathjax
+/utils/sphinx-config/_static/polyfill.js

doc/Makefile

@@ -4,11 +4,11 @@ SHELL          = /bin/bash
 BUILDDIR       = ${CURDIR}
 RSTDIR         = $(BUILDDIR)/src
 VENV           = $(BUILDDIR)/docenv
-MATHJAX        = $(BUILDDIR)/mathjax
-POLYFILL       = $(BUILDDIR)/mathjax/polyfill.js
 TXT2RST        = $(VENV)/bin/txt2rst
 ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
 SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
+MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
+POLYFILL       = $(SPHINXCONFIG)/_static/polyfill.js
 
 PYTHON         = $(shell which python3)
 DOXYGEN        = $(shell which doxygen)
@@ -106,9 +106,6 @@ html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
 	@mkdir -p html/JPG
 	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target: JPG' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
 	@rm -rf html/PDF/.[sg]*
-	@mkdir -p html/_static/mathjax
-	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
-	@cp $(POLYFILL) html/_static/
 	@echo "Build finished. The HTML pages are in doc/html."
 
 spelling: xmlgen $(VENV) $(SPHINXCONFIG)/false_positives.txt
@@ -125,7 +122,6 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
-	@cp src/JPG/lammps-logo.png epub/
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\

doc/utils/sphinx-config/conf.py.in

@@ -23,11 +23,16 @@ try:
 except:
     pass
 
+LAMMPS_DOC_DIR = '@LAMMPS_DOC_DIR@'
+LAMMPS_SOURCE_DIR = '@LAMMPS_SOURCE_DIR@'
+LAMMPS_PYTHON_DIR = '@LAMMPS_PYTHON_DIR@'
+LAMMPS_DOXYGEN_XML_DIR = '@DOXYGEN_XML_DIR@'
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
-sys.path.append(os.path.join('@LAMMPS_DOC_DIR@', 'src', '_ext'))
+sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'src', '_ext'))
 
 # -- General configuration ------------------------------------------------
 
@@ -74,7 +79,7 @@ copyright = '2003-2020 Sandia Corporation'
 def get_lammps_version():
     import os
     script_dir = os.path.dirname(os.path.realpath(__file__))
-    with open(os.path.join('@LAMMPS_SOURCE_DIR@', 'version.h'), 'r') as f:
+    with open(os.path.join(LAMMPS_SOURCE_DIR, 'version.h'), 'r') as f:
         line = f.readline()
         start_pos = line.find('"')+1
         end_pos = line.find('"', start_pos)
@@ -167,7 +172,7 @@ html_title = "LAMMPS documentation"
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = 'lammps-logo.png'
+html_logo = '_static/lammps-logo.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -328,7 +333,7 @@ texinfo_documents = [
 
 epub_title = 'LAMMPS Documentation - ' + get_lammps_version()
 
-epub_cover = ('lammps-logo.png', '')
+epub_cover = ('_static/lammps-logo.png', '')
 
 epub_description = """
 This is the Manual for the LAMMPS software package.
@@ -363,7 +368,7 @@ from sphinx.highlighting import lexers
 
 lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
 
-sys.path.append('@LAMMPS_PYTHON_DIR@')
+sys.path.append(LAMMPS_PYTHON_DIR)
 
 # avoid syntax highlighting in blocks that don't specify language
 highlight_language = 'none'
@@ -375,7 +380,7 @@ autodoc_member_order = 'bysource'
 
 # breathe configuration
 
-breathe_projects = { 'progguide' : '@DOXYGEN_XML_DIR@' }
+breathe_projects = { 'progguide' : LAMMPS_DOXYGEN_XML_DIR }
 breathe_default_project = 'progguide'
 breathe_show_define_initializer = True
 breathe_domain_by_extension = { 'h'   : 'cpp',

doc/utils/sphinx-config/lammps-logo.png

@@ -1 +0,0 @@
-../../src/JPG/lammps-logo.png