V3.4

.github/workflows/ccpp.yml

@@ -4,10 +4,34 @@ on: [push]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-    
+
     steps:
-    - uses: actions/checkout@v2
-    - name: compile POPSC
-      run: cd POPSC; ./bootstrap; ./configure; make
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Ensure submodules are present
+        run: |
+          git submodule sync --recursive
+          git submodule update --init --recursive
+          echo "Submodule status:"
+          git submodule status --recursive
+          echo "Checking Gemmi headers:"
+          ls -l POPSC/gemmi/include/gemmi/cif.hpp
+
+      - name: Install build deps
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y autoconf automake libtool pkg-config \
+            g++ make \
+            libxml2-dev zlib1g-dev
+
+      - name: Compile POPSC
+        run: |
+          cd POPSC
+          ./bootstrap
+          ./configure
+          make -j$(nproc) V=1

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "POPSC/gemmi"]
+	path = POPSC/gemmi
+	url = https://github.com/project-gemmi/gemmi.git

ChangeLog

@@ -5,6 +5,10 @@
 ## Docker image released at version 3.1
 #===============================================================================
 
+- 3.4
+Fri 20 Feb 11:18:33 GMT 2026
+	Added mmcif capability.
+
 - 3.3
 Thu 29 Feb 08:39:24 GMT 2024
 	Added README file of C code as new tab to the interface.

POPSC/Makefile

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.18.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.5 from Makefile.am.
 # Makefile.  Generated from Makefile.in by configure.
 
-# Copyright (C) 1994-2025 Free Software Foundation, Inc.
+# Copyright (C) 1994-2021 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -73,8 +73,6 @@ am__make_running_with_option = \
   test $$has_opt = yes
 am__make_dryrun = (target_option=n; $(am__make_running_with_option))
 am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
-am__rm_f = rm -f $(am__rm_f_notfound)
-am__rm_rf = rm -rf $(am__rm_f_notfound)
 pkgdatadir = $(datadir)/pops
 pkgincludedir = $(includedir)/pops
 pkglibdir = $(libdir)/pops
@@ -91,8 +89,8 @@ POST_INSTALL = :
 NORMAL_UNINSTALL = :
 PRE_UNINSTALL = :
 POST_UNINSTALL = :
-build_triplet = aarch64-apple-darwin24.6.0
-host_triplet = aarch64-apple-darwin24.6.0
+build_triplet = x86_64-pc-linux-gnu
+host_triplet = x86_64-pc-linux-gnu
 subdir = .
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/ax_openmp.m4 \
@@ -168,8 +166,8 @@ distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
 am__remove_distdir = \
   if test -d "$(distdir)"; then \
-    find "$(distdir)" -type d ! -perm -700 -exec chmod u+rwx {} ';' \
-      ; rm -rf "$(distdir)" \
+    find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
+      && rm -rf "$(distdir)" \
       || { sleep 5 && rm -rf "$(distdir)"; }; \
   else :; fi
 am__post_remove_distdir = $(am__remove_distdir)
@@ -199,23 +197,21 @@ am__relativize = \
   done; \
   reldir="$$dir2"
 DIST_ARCHIVES = $(distdir).tar.gz
-GZIP_ENV = -9
+GZIP_ENV = --best
 DIST_TARGETS = dist-gzip
 # Exists only to be overridden by the user if desired.
 AM_DISTCHECK_DVI_TARGET = dvi
 distuninstallcheck_listfiles = find . -type f -print
 am__distuninstallcheck_listfiles = $(distuninstallcheck_listfiles) \
   | sed 's|^\./|$(prefix)/|' | grep -v '$(infodir)/dir$$'
-distcleancheck_listfiles = \
-  find . \( -type f -a \! \
-            \( -name .nfs* -o -name .smb* -o -name .__afs* \) \) -print
-ACLOCAL = ${SHELL} '/Users/jkleinj/software/develop/POPScomp/POPSC/missing' aclocal-1.18
+distcleancheck_listfiles = find . -type f -print
+ACLOCAL = ${SHELL} '/home/jkleinj/develop/POPScomp/POPSC/missing' aclocal-1.16
 AMTAR = $${TAR-tar}
 AM_DEFAULT_VERBOSITY = 1
-AUTOCONF = ${SHELL} '/Users/jkleinj/software/develop/POPScomp/POPSC/missing' autoconf
-AUTOHEADER = ${SHELL} '/Users/jkleinj/software/develop/POPScomp/POPSC/missing' autoheader
-AUTOMAKE = ${SHELL} '/Users/jkleinj/software/develop/POPScomp/POPSC/missing' automake-1.18
-AWK = awk
+AUTOCONF = ${SHELL} '/home/jkleinj/develop/POPScomp/POPSC/missing' autoconf
+AUTOHEADER = ${SHELL} '/home/jkleinj/develop/POPScomp/POPSC/missing' autoheader
+AUTOMAKE = ${SHELL} '/home/jkleinj/develop/POPScomp/POPSC/missing' automake-1.16
+AWK = mawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2
@@ -228,8 +224,8 @@ CXXFLAGS = -g -O2
 CYGPATH_W = echo
 DEFS = -DHAVE_CONFIG_H
 DEPDIR = .deps
-ECHO_C = \c
-ECHO_N = 
+ECHO_C = 
+ECHO_N = -n
 ECHO_T = 
 ETAGS = etags
 EXEEXT = 
@@ -242,63 +238,61 @@ LDFLAGS =
 LIBOBJS = 
 LIBS = -lm 
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} '/Users/jkleinj/software/develop/POPScomp/POPSC/missing' makeinfo
-MKDIR_P = mkdir -p
+MAKEINFO = ${SHELL} '/home/jkleinj/develop/POPScomp/POPSC/missing' makeinfo
+MKDIR_P = /usr/bin/mkdir -p
 OBJEXT = o
-OPENMP_CFLAGS = 
+OPENMP_CFLAGS = -fopenmp
 PACKAGE = pops
 PACKAGE_BUGREPORT = jens@jkleinj.eu
 PACKAGE_NAME = pops
-PACKAGE_STRING = pops 3.2.2
+PACKAGE_STRING = pops 3.4
 PACKAGE_TARNAME = pops
 PACKAGE_URL = 
-PACKAGE_VERSION = 3.2.2
+PACKAGE_VERSION = 3.4
 PATH_SEPARATOR = :
-PKG_CONFIG = /opt/homebrew/bin/pkg-config
+PKG_CONFIG = /usr/bin/pkg-config
 PKG_CONFIG_LIBDIR = 
 PKG_CONFIG_PATH = 
 SET_MAKE = 
-SHELL = /bin/sh
+SHELL = /bin/bash
 STRIP = 
-VERSION = 3.2.2
-XML_CFLAGS = 
-XML_LIBS = -lxml2
+VERSION = 3.4
+XML_CFLAGS = -I/usr/include/libxml2 
+XML_LIBS = -lxml2 
 ZLIB_CFLAGS = 
-ZLIB_LIBS = -lz
-abs_builddir = /Users/jkleinj/software/develop/POPScomp/POPSC
-abs_srcdir = /Users/jkleinj/software/develop/POPScomp/POPSC
-abs_top_builddir = /Users/jkleinj/software/develop/POPScomp/POPSC
-abs_top_srcdir = /Users/jkleinj/software/develop/POPScomp/POPSC
+ZLIB_LIBS = -lz 
+abs_builddir = /home/jkleinj/develop/POPScomp/POPSC
+abs_srcdir = /home/jkleinj/develop/POPScomp/POPSC
+abs_top_builddir = /home/jkleinj/develop/POPScomp/POPSC
+abs_top_srcdir = /home/jkleinj/develop/POPScomp/POPSC
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
 am__leading_dot = .
 am__quote = 
-am__rm_f_notfound = 
-am__tar = tar --format=ustar -chf - "$$tardir"
-am__untar = tar -xf -
-am__xargs_n = xargs -n
+am__tar = $${TAR-tar} chof - "$$tardir"
+am__untar = $${TAR-tar} xf -
 bindir = ${exec_prefix}/bin
-build = aarch64-apple-darwin24.6.0
+build = x86_64-pc-linux-gnu
 build_alias = 
-build_cpu = aarch64
-build_os = darwin24.6.0
-build_vendor = apple
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = pc
 builddir = .
 datadir = ${datarootdir}
 datarootdir = ${prefix}/share
 docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
 dvidir = ${docdir}
 exec_prefix = ${prefix}
-host = aarch64-apple-darwin24.6.0
+host = x86_64-pc-linux-gnu
 host_alias = 
-host_cpu = aarch64
-host_os = darwin24.6.0
-host_vendor = apple
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = pc
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = ${SHELL} /Users/jkleinj/software/develop/POPScomp/POPSC/install-sh
+install_sh = ${SHELL} /home/jkleinj/develop/POPScomp/POPSC/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
@@ -462,13 +456,12 @@ cscopelist-am: $(am__tagged_files)
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
 	-rm -f cscope.out cscope.in.out cscope.po.out cscope.files
-
 distdir: $(BUILT_SOURCES)
 	$(MAKE) $(AM_MAKEFLAGS) distdir-am
 
 distdir-am: $(DISTFILES)
 	$(am__remove_distdir)
-	$(AM_V_at)$(MKDIR_P) "$(distdir)"
+	test -d "$(distdir)" || mkdir "$(distdir)"
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	list='$(DISTFILES)'; \
@@ -538,10 +531,6 @@ dist-bzip2: distdir
 	tardir=$(distdir) && $(am__tar) | BZIP2=$${BZIP2--9} bzip2 -c >$(distdir).tar.bz2
 	$(am__post_remove_distdir)
 
-dist-bzip3: distdir
-	tardir=$(distdir) && $(am__tar) | bzip3 -c >$(distdir).tar.bz3
-	$(am__post_remove_distdir)
-
 dist-lzip: distdir
 	tardir=$(distdir) && $(am__tar) | lzip -c $${LZIP_OPT--9} >$(distdir).tar.lz
 	$(am__post_remove_distdir)
@@ -583,19 +572,17 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  eval GZIP= gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
-	*.tar.bz3*) \
-	  bzip3 -dc $(distdir).tar.bz3 | $(am__untar) ;;\
 	*.tar.lz*) \
 	  lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
 	*.tar.xz*) \
 	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  eval GZIP= gzip -dc $(distdir).shar.gz | unshar ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	*.tar.zst*) \
@@ -695,8 +682,8 @@ mostlyclean-generic:
 clean-generic:
 
 distclean-generic:
-	-$(am__rm_f) $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || $(am__rm_f) $(CONFIG_CLEAN_VPATH_FILES)
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
 
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
@@ -775,29 +762,21 @@ uninstall-am:
 .PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
 	am--refresh check check-am clean clean-cscope clean-generic \
 	cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
-	dist-bzip3 dist-gzip dist-lzip dist-shar dist-tarZ dist-xz \
-	dist-zip dist-zstd distcheck distclean distclean-generic \
-	distclean-tags distcleancheck distdir distuninstallcheck dvi \
-	dvi-am html html-am info info-am install install-am \
-	install-data install-data-am install-dvi install-dvi-am \
-	install-exec install-exec-am install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs installdirs-am \
-	maintainer-clean maintainer-clean-generic mostlyclean \
-	mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
-	uninstall-am
+	dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
+	dist-zstd distcheck distclean distclean-generic distclean-tags \
+	distcleancheck distdir distuninstallcheck dvi dvi-am html \
+	html-am info info-am install install-am install-data \
+	install-data-am install-dvi install-dvi-am install-exec \
+	install-exec-am install-html install-html-am install-info \
+	install-info-am install-man install-pdf install-pdf-am \
+	install-ps install-ps-am install-strip installcheck \
+	installcheck-am installdirs installdirs-am maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am tags tags-am uninstall uninstall-am
 
 .PRECIOUS: Makefile
 
 
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:
-
-# Tell GNU make to disable its built-in pattern rules.
-%:: %,v
-%:: RCS/%,v
-%:: RCS/%
-%:: s.%
-%:: SCCS/s.%