use script instead of globbing to avoid entering commands in multiple toctrees

doc/.gitignore

@@ -17,3 +17,10 @@
 *.el
 /utils/sphinx-config/_static/mathjax
 /utils/sphinx-config/_static/polyfill.js
+/src/pairs.rst
+/src/bonds.rst
+/src/angles.rst
+/src/dihedrals.rst
+/src/impropers.rst
+/src/computes.rst
+/src/fixes.rst

doc/Makefile

@@ -83,7 +83,11 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+globbed-tocs:
+	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
+	$(SHELL) $(BUILDDIR)/utils/make-globbed-tocs.sh $(RSTDIR)
+
+html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
@@ -113,7 +117,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p fasthtml
@@ -132,7 +136,7 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf fasthtml/PDF/.[sg]*
 	@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
 
-spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
+spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; \
@@ -143,7 +147,7 @@ spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives
 	)
 	@echo "Spell check finished."
 
-epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p epub/JPG
@@ -166,7 +170,7 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi

doc/src/angles.rst.in

@@ -3,6 +3,4 @@ Angle Styles
 
 .. toctree::
    :maxdepth: 1
-   :glob:
 
-   angle_*

doc/src/bonds.rst.in

@@ -3,6 +3,4 @@ Bond Styles
 
 .. toctree::
    :maxdepth: 1
-   :glob:
 
-   bond_*

doc/src/computes.rst.in

@@ -3,6 +3,4 @@ Computes
 
 .. toctree::
    :maxdepth: 1
-   :glob:
 
-   compute_*

doc/src/dihedrals.rst.in

@@ -3,6 +3,4 @@ Dihedral Styles
 
 .. toctree::
    :maxdepth: 1
-   :glob:
 
-   dihedral_*

doc/src/fixes.rst.in

@@ -3,6 +3,4 @@ Fixes
 
 .. toctree::
    :maxdepth: 1
-   :glob:
 
-   fix_*

doc/src/impropers.rst.in

@@ -3,6 +3,4 @@ Improper Styles
 
 .. toctree::
    :maxdepth: 1
-   :glob:
 
-   improper_*

doc/src/pairs.rst.in

@@ -3,6 +3,4 @@ Pair Styles
 
 .. toctree::
    :maxdepth: 1
-   :glob:
 
-   pair_*

doc/utils/make-globbed-tocs.sh

@@ -0,0 +1,75 @@
+#!/bin/bash
+# script to emulate globbed toctrees that allows to skip files that were entered already elsewhere
+
+if [ $# != 1 ]
+then
+    echo "Usage: $0 <rstdir>"
+    exit 1
+fi
+
+RSTDIR="$1"
+TMPNAM=${RANDOM}
+TMPDIR=${TMPDIR-/tmp}
+
+# pairs.rst
+cp ${RSTDIR}/pairs.rst.in ${TMPDIR}/${TMPNAM}.pairs.rst
+for f in $(echo ${RSTDIR}/pair_*.rst | sed -e "s@${RSTDIR}/@@g" -e 's@\.rst@@g' -e 's@pair_\(coeff\|modify\|style\|write\)@@g' | sort )
+do \
+    echo "   $f" >>  ${TMPDIR}/${TMPNAM}.pairs.rst
+done
+cmp -s ${TMPDIR}/${TMPNAM}.pairs.rst ${RSTDIR}/pairs.rst || mv -vf ${TMPDIR}/${TMPNAM}.pairs.rst ${RSTDIR}/pairs.rst
+rm -f  ${TMPDIR}/${TMPNAM}.pairs.rst
+
+# bonds.rst
+cp ${RSTDIR}/bonds.rst.in ${TMPDIR}/${TMPNAM}.bonds.rst
+for f in $(echo ${RSTDIR}/bond_*.rst | sed -e "s@${RSTDIR}/@@g" -e "s@\\.rst@@g" -e 's@bond_\(coeff\|modify\|style\|write\)@@g' | sort )
+do \
+    echo "   $f" >>  ${TMPDIR}/${TMPNAM}.bonds.rst
+done
+cmp -s ${TMPDIR}/${TMPNAM}.bonds.rst ${RSTDIR}/bonds.rst || mv -vf ${TMPDIR}/${TMPNAM}.bonds.rst ${RSTDIR}/bonds.rst
+rm -f  ${TMPDIR}/${TMPNAM}.bonds.rst
+
+# angles.rst
+cp ${RSTDIR}/angles.rst.in ${TMPDIR}/${TMPNAM}.angles.rst
+for f in $(echo ${RSTDIR}/angle_*.rst | sed -e "s@${RSTDIR}/@@g" -e "s@\\.rst@@g" -e 's@angle_\(coeff\|modify\|style\|write\)@@g' | sort )
+do \
+    echo "   $f" >>  ${TMPDIR}/${TMPNAM}.angles.rst
+done
+cmp -s ${TMPDIR}/${TMPNAM}.angles.rst ${RSTDIR}/angles.rst || mv -vf ${TMPDIR}/${TMPNAM}.angles.rst ${RSTDIR}/angles.rst
+rm -f  ${TMPDIR}/${TMPNAM}.angles.rst
+
+# dihedrals.rst
+cp ${RSTDIR}/dihedrals.rst.in ${TMPDIR}/${TMPNAM}.dihedrals.rst
+for f in $(echo ${RSTDIR}/dihedral_*.rst | sed -e "s@${RSTDIR}/@@g" -e "s@\\.rst@@g" -e 's@dihedral_\(coeff\|modify\|style\|write\)@@g' | sort )
+do \
+    echo "   $f" >>  ${TMPDIR}/${TMPNAM}.dihedrals.rst
+done
+cmp -s ${TMPDIR}/${TMPNAM}.dihedrals.rst ${RSTDIR}/dihedrals.rst || mv -vf ${TMPDIR}/${TMPNAM}.dihedrals.rst ${RSTDIR}/dihedrals.rst
+rm -f  ${TMPDIR}/${TMPNAM}.dihedrals.rst
+
+# impropers.rst
+cp ${RSTDIR}/impropers.rst.in ${TMPDIR}/${TMPNAM}.impropers.rst
+for f in $(echo ${RSTDIR}/improper_*.rst | sed -e "s@${RSTDIR}/@@g" -e "s@\\.rst@@g" -e 's@improper_\(coeff\|modify\|style\|write\)@@g' | sort )
+do \
+    echo "   $f" >>  ${TMPDIR}/${TMPNAM}.impropers.rst
+done
+cmp -s ${TMPDIR}/${TMPNAM}.impropers.rst ${RSTDIR}/impropers.rst || mv -vf ${TMPDIR}/${TMPNAM}.impropers.rst ${RSTDIR}/impropers.rst
+rm -f  ${TMPDIR}/${TMPNAM}.impropers.rst
+
+# computes.rst
+cp ${RSTDIR}/computes.rst.in ${TMPDIR}/${TMPNAM}.computes.rst
+for f in $(echo ${RSTDIR}/compute_*.rst | sed -e "s@${RSTDIR}/@@g" -e "s@\\.rst@@g" -e 's@compute_modify@@g' | sort )
+do \
+    echo "   $f" >>  ${TMPDIR}/${TMPNAM}.computes.rst
+done
+cmp -s ${TMPDIR}/${TMPNAM}.computes.rst ${RSTDIR}/computes.rst || mv -vf ${TMPDIR}/${TMPNAM}.computes.rst ${RSTDIR}/computes.rst
+rm -f  ${TMPDIR}/${TMPNAM}.computes.rst
+
+# fixs.rst
+cp ${RSTDIR}/fixes.rst.in ${TMPDIR}/${TMPNAM}.fixes.rst
+for f in $(echo ${RSTDIR}/fix_*.rst | sed -e "s@${RSTDIR}/@@g" -e "s@\\.rst@@g" -e 's@fix_\(modify\|modify_atc_commands\)@@g' | sort )
+do \
+    echo "   $f" >>  ${TMPDIR}/${TMPNAM}.fixes.rst
+done
+cmp -s ${TMPDIR}/${TMPNAM}.fixes.rst ${RSTDIR}/fixes.rst || mv -vf ${TMPDIR}/${TMPNAM}.fixes.rst ${RSTDIR}/fixes.rst
+rm -f  ${TMPDIR}/${TMPNAM}.fixes.rst