Conda package for cpptraj

.github/workflows/merge-gate.yml

@@ -149,7 +149,7 @@ jobs:
     - name: Install conda packages
       run: |
         which conda
-        conda install conda=23.11.0 python=3.10
+        conda install conda=24.11.0 python=3.10
         conda --version
         conda env update --file devtools/ci/environment.yml --name base
     - name: Install cpptraj

Makefile

@@ -33,8 +33,8 @@ unittest: config.h
 # Clean up
 clean: config.h
 	cd src && $(MAKE) clean
-	cd test && $(MAKE) clean
-	cd unitTests && $(MAKE) clean
+#	cd test && $(MAKE) clean
+#	cd unitTests && $(MAKE) clean
 
 docs: src/cpptraj.Doxyfile
 	cd doc && make docs

configure

@@ -318,9 +318,9 @@ LIB_D_ON[$LFFTW3]='-DFFTW_FFT'
 LIB_DOFF[$LFFTW3]=''
 LIB_TYPE[$LFFTW3]='cpp'
 
-LIB_STAT[$LREADLINE]='bundled'
+LIB_STAT[$LREADLINE]='enabled'
 LIB_CKEY[$LREADLINE]='readline'
-LIB_HOME[$LREADLINE]='readline'
+LIB_HOME[$LREADLINE]=''
 LIB_FLAG[$LREADLINE]='-lreadline'
 LIB_STTC[$LREADLINE]='libreadline.a'
 LIB_D_ON[$LREADLINE]=''
@@ -1073,13 +1073,42 @@ EOF
 TestReadline() {
   cat > testp.cpp <<EOF
 #include <cstdio>
-#include <readline.h>
+#include <readline/readline.h>
 static char *line_read = (char *)NULL;
 // Do not want to actually run this so leave outside main
 void Unused() { line_read = readline(""); }
 int main() { return 0; }
 EOF
-  TestProgram "  Checking Readline" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]}"
+
+  if [ "${LIB_STAT[$LREADLINE]}" = 'specified' ] ; then
+    TestProgram "  Checking Readline" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]}"
+  else
+    # Test with just -lreadline
+    TestProgram silent "  Checking Readline" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]}"
+    lreadline_err=$?
+    if [ $lreadline_err -ne 0 ] ; then
+      # Try -ltermcap
+      TestProgram silent "  Checking Readline with termcap" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]} -ltermcap"
+      lreadline_err=$?
+      if [ $lreadline_err -eq 0 ] ; then
+        LIB_FLAG[$LREADLINE]="${LIB_FLAG[$LREADLINE]} -ltermcap"
+      fi
+    fi
+    if [ $lreadline_err -ne 0 ] ; then
+      # Try -lncurses
+      TestProgram silent "  Checking Readline with ncurses" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]} -lncurses"
+      lreadline_err=$?
+      if [ $lreadline_err -eq 0 ] ; then
+        LIB_FLAG[$LREADLINE]="${LIB_FLAG[$LREADLINE]} -lncurses"
+      fi
+    fi
+    if [ $lreadline_err -ne 0 ] ; then
+      echo "No readline available; using bundled readline."
+      LIB_STAT[$LREADLINE]='bundled'
+      LIB_FLAG[$LREADLINE]='readline/libreadline.a'
+      LIB_INCL[$LREADLINE]='-I.'
+    fi
+  fi
 }
 
 TestXdrfile() {
@@ -1503,22 +1532,22 @@ SetupLibraries() {
             lflag="-L$lhdir ${LIB_FLAG[$i]}"
           fi
           # Library-specific CPPTRAJ_INC fixes when home specified.
-          if [ $i -eq $LREADLINE ] ; then
-            linc="$linc/readline"
-          fi
+          #if [ $i -eq $LREADLINE ] ; then
+          #  linc="$linc/readline"
+          #fi
           if [ $i -eq $LXDRFILE ] ; then
             linc="$linc/xdrfile"
           fi
         fi
         # Library-specific flag fixes
-        if [ $i -eq $LREADLINE ] ; then
+#        if [ $i -eq $LREADLINE ] ; then
           # For external readline, we need to link libtermcap for windows
           # and libncurses for Linux
-          #if [ $USE_WINDOWS -eq 1 ]; then
+          if [ $USE_WINDOWS -eq 1 ]; then
             lflag="$lflag -ltermcap"
-          #else
-          #  lflag="$lflag -lncurses"
-          #fi
+          else
+            lflag="$lflag -lncurses"
+          fi
         elif [ $i -eq $LSANDER ] ; then
           # Always specify libsander location to prevent pulling in
           # other amber libraries.
@@ -1662,7 +1691,7 @@ SetupCompilers() {
       if [ -z "$FC" ]; then FC=gfortran; fi
       hostflags=''
       optflags='-O3'
-      ompflag='-fopenmp'
+      ompflag='-Xclang -fopenmp'
       freefmtflag='-ffree-form'
       foptflags='-O3'
       FLINK='-lgfortran'
@@ -1671,8 +1700,8 @@ SetupCompilers() {
       # Check the GNU compiler version
       CheckCompilerVersion gcc
       # Set version-specific flags
-      if [ $cc_version_major -ge 14 ] ; then
-        # Needed for readline with gcc >= 14
+      if [ $cc_version_major -ge 13 ] ; then
+        # Needed for readline with gcc >= 13
         CFLAGS="$CFLAGS -D_DEFAULT_SOURCE -D_XOPEN_SOURCE"
       fi
       ;;
@@ -2565,6 +2594,12 @@ if [ -z "`which grep`" ] ; then
   Err "CPPTRAJ configure requires 'grep'."
 fi
 
+# Check for the 'install/ binary
+INSTALL=`which install`
+if [ -z "$INSTALL" ] ; then
+  Err "CPPTRAJ configure requires 'install'."
+fi
+
 #echo "Path to configure: $WORKDIR"
 #echo "Current dir      : $CURRENTDIR"
 
@@ -2953,6 +2988,10 @@ CPPTRAJDAT="$CPPTRAJDAT"
 
 INSTALL_TARGETS=$INSTALL_TARGETS
 
+INSTALL=$INSTALL
+INSTALL_PROGRAM=$INSTALL
+INSTALL_DATA=$INSTALL -m 644
+
 EOF
 if [ ! -z "$DBGFLAGS" ] ; then
   echo "DBGFLAGS=$DBGFLAGS" >> config.h

devtools/GetHeaders.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Get all header files
+
+WORKDIR=`pwd`
+BASEDIR=`basename $WORKDIR`
+if [ "$BASEDIR" != 'src' ] ; then
+  echo "Should be executed from the CPPTRAJ src directory."
+  exit 1
+fi
+
+OUTFILE='cpptrajheaders'
+echo "# All cpptraj headers that should be installed for the cpptraj library." > $OUTFILE
+echo "CPPTRAJ_HEADERS = \\" >> $OUTFILE
+
+for DIR in . Cluster Structure Energy ; do
+  for FILE in `ls $DIR/*.h` ; do
+    echo "        $FILE \\" >> $OUTFILE
+  done
+done
+echo "" >> $OUTFILE
+
+exit 0

doc/CpptrajManual.lyx

@@ -1,26 +1,24 @@
 #LyX 2.4 created this file. For more info see https://www.lyx.org/
-\lyxformat 620
+\lyxformat 544
 \begin_document
 \begin_header
 \save_transient_properties true
 \origin unavailable
 \textclass article
 \use_default_options true
-\maintain_unincluded_children no
+\maintain_unincluded_children false
 \language english
 \language_package default
-\inputencoding auto-legacy
-\fontencoding auto
+\inputencoding auto
+\fontencoding global
 \font_roman "default" "default"
 \font_sans "default" "default"
 \font_typewriter "default" "default"
 \font_math "auto" "auto"
 \font_default_family default
 \use_non_tex_fonts false
 \font_sc false
-\font_roman_osf false
-\font_sans_osf false
-\font_typewriter_osf false
+\font_osf false
 \font_sf_scale 100 100
 \font_tt_scale 100 100
 \use_microtype false
@@ -64,9 +62,7 @@
 \suppress_date false
 \justification true
 \use_refstyle 1
-\use_formatted_ref 0
 \use_minted 0
-\use_lineno 0
 \index Index
 \shortcut idx
 \color #008000
@@ -82,16 +78,11 @@
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
-\tablestyle default
 \tracking_changes false
 \output_changes false
-\change_bars false
-\postpone_fragile_content false
 \html_math_output 0
 \html_css_as_file 0
 \html_be_strict false
-\docbook_table_output 0
-\docbook_mathml_prefix 1
 \end_header
 
 \begin_body
@@ -133,7 +124,6 @@ LatexCommand tableofcontents
 \begin_inset CommandInset include
 LatexCommand input
 filename "cpptraj.lyx"
-literal "true"
 
 \end_inset
 

doc/DocumentChecksums.txt

@@ -1,3 +1,3 @@
 b37726e7a841f6fc695ecd7fb040ffbf  CpptrajDevelopmentGuide.lyx
-786c4aec62d60a3f9265dec52b767e02  cpptraj.lyx
-07c4039e732fc2eb1df0c1e0863cb949  CpptrajManual.lyx
+1f4d9c647b6717314560290a4d3f9f06  cpptraj.lyx
+5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx