Changeset 13e5be

Timestamp:

Oct 22, 2025, 5:19:15 PM (29 hours ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

stable

Parents:

91c409

git-author:

Frederik Heber <frederik.heber@…> (10/22/25 17:10:11)

git-committer:

Frederik Heber <frederik.heber@…> (10/22/25 17:19:15)

Message:

Set version to 1.7.0.

• MoleCuilder library is now 19:0:0.
• Codename "Seven Years" (because seven years passed since the last release).
• Added to debian/changelog.
• Adapted k8s and docker files.

Files:

• README (modified) (2 diffs)
• configure.ac (modified) (3 diffs)
• debian/changelog (modified) (1 diff)
• docker/Dockerfile (modified) (5 diffs)
• k8s/server-deployment.yaml (modified) (2 diffs)
• k8s/worker-deployment.yaml (modified) (1 diff)

README

@@ -1 +1 @@
 # Project: MoleCuilder
 #
-# heber@ins.uni-bonn.de
+# frederik.heber@gmail.com
 
         MoleCuilder
@@ -21 +21 @@
 * GCC or alike
 * GSL (GNU Scientific Library, available at http://www.gnu.org/software/gsl)
-* Boost 1.4 or newer
+* Boost 1.69 or newer
 * PugiXML (is provided in src/Parser/pugixml)
-
-LINKS
-=====
-[1] http://www.ins.uni-bonn.de/

configure.ac

@@ -3 +3 @@
 
 AC_PREREQ(2.59)
-AC_INIT(MoleCuilder, 1.6.1, [bug@molecuilder.de], [molecuilder], [http://www.molecuilder.de/])
+AC_INIT(MoleCuilder, 1.7.0, [bug@molecuilder.de], [molecuilder], [http://www.molecuilder.de/])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_SRCDIR([src/builder.cpp])
@@ -43 +43 @@
 AS_IF([test x"$enable_python" != x"no"],[
   # Python (for boost::python)
-  AM_PATH_PYTHON([2.2])
+  AM_PATH_PYTHON([3.0])
   AC_DEFINE(HAVE_PYTHON,1, ["Build python module and scripts."])
 ])
@@ -181 +181 @@
 # refer to the libtool manual, section "Updating library version information":
 # http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
-AC_SUBST([MOLECUILDER_SO_VERSION], [18:0:1])
-AC_SUBST([MOLECUILDER_API_VERSION], [1.6.1])
+AC_SUBST([MOLECUILDER_SO_VERSION], [19:0:0])
+AC_SUBST([MOLECUILDER_API_VERSION], [1.7.0])
 
 dnl this macro is used to get the arguments supplied

debian/changelog

@@ +1 @@
+molecuilder (1.7.0-1) UNRELEASED; urgency=low
+
+  Major
+  * saturate (fixes to polyhedra and scaling) and bondify (new)
+  * potentials are first class citizens
+  * proper path from molecule, to automated fragmentation, computation, homologies and finally potential training (and visualizing in the UI).
+  * convenience changes in the UI: bigger icons, context menu in gl view, potential tab with plotting
+  * enhancements to python scripting: numpy compatibility, wait returns status, python3
+  * works inside jupyter notebooks.
+  * can be deployed to k8s for large-scale computations.
+  * graph6 strings, evaluating stability and chemical space evaluation
+  * more selection actions
+
+  Minor
+  * switch to simpler kubernetes-aimed worker-server setup (health probes, workers don't register but accessed through load balancer)
+  * potential list shown in UI, new actions to add and remove, also potential curves are plotted in UI
+  * general fixes to potential setup to make them work as compound potentials
+  * undomark action
+  * Undo is again without dialog, undo mark is an extra action now.
+  * context menu (right-click) in gl view to manipulate atoms directly
+  * docker file contained in repo
+  * bondify has undo/redo
+  * switched all python to python3
+  * graph6 fixes and writing strings
+  * generatePotentialAction generates all combinations
+  * full numpy getter and setter to atom position, velocities, and forces.
+  * saturate action allows for just using outer shell (unocc and occ orbitals, only unocc used for adding hydrogens) 
+  * stretch bond falls back to tabled distances for element pairs on zero length
+  * select atom's bond neighbors
+  * select atoms randomly
+  * calculate pair correlation between element and selected atoms.
+
+  Fixes
+  * corrected units and computation in SaveEnergies, renamed from SaveTemperatures
+  * InputAction will also save that file on exit
+
+ -- Frederik Heber <heber@molecuilder.com>  Wed, 22 Oct 2025 19:13:00 +0100
+
 molecuilder (1.6.1-1) UNRELEASED; urgency=low
 

docker/Dockerfile

@@ -46 +46 @@
 FROM ubuntu:18.04 as build-molecuilder-stage
 WORKDIR /home/molecuilder
-ENV MOLECUILDER_VERSION 1.6.1
+ENV MOLECUILDER_VERSION 1.7.0
 
 # copy build boost
@@ -70 +70 @@
 RUN ln -s /home/molecuilder/_pkgs/boost-1.69/lib/libboost_numpy36-mt-x64.so /home/molecuilder/_pkgs/boost-1.69/lib/libboost_numpy3-mt-x64.so
 
-ENV ARCHIVE molecuilder-1.6.1.tar.bz2
+ENV ARCHIVE molecuilder-1.7.0.tar.bz2
 COPY dependencies_ubuntu18_04.txt .
 RUN apt-get update && apt-get install -y \
@@ -86 +86 @@
 RUN (cp `basename $ARCHIVE` `basename $ARCHIVE | sed -e "s#-#_#" -e "s#\(\.tar\.${suffix}\)#.orig\1#"`)
 RUN ( tar -jxvf $ARCHIVE && \
-        cd molecuilder-1.6.1 && \
+        cd molecuilder-1.7.0 && \
         mkdir -p build64 && \
         cd build64 && \
@@ -112 +112 @@
                 'QT_LDFLAGS=-L/usr/lib/x86_64-linux-gnu -L/usr/lib' \
                 'QT_LIBS=-lQtCore -lQtGui -lQtOpenGL -lQt3D' \
-                '--prefix=/home/molecuilder/_pkgs/molecuilder-1.6.1')
-RUN (cd molecuilder-1.6.1/build64 && \
+                '--prefix=/home/molecuilder/_pkgs/molecuilder-1.7.0')
+RUN (cd molecuilder-1.7.0/build64 && \
         make -j8 && \
         make install)
-#RUN (cd molecuilder-1.6.1/ && \
+#RUN (cd molecuilder-1.7.0/ && \
 #       debuild -j6 -ub -uc)
-#RUN mv molecuilder-1.6.1/build64/*.deb . && \
+#RUN mv molecuilder-1.7.0/build64/*.deb . && \
 #       rm -rf molecuilder
 
@@ -154 +154 @@
         rm -f /tmp/libqt4-3d_1.0-tp2_amd64.deb
 ENV OMPI_MCA_plm_rsh_agent /bin/false
-ENV PATH "$PATH:/home/molecuilder/_pkgs/molecuilder-1.6.1"
+ENV PATH "$PATH:/home/molecuilder/_pkgs/molecuilder-1.7.0"
 
 # install for taking screenshots

k8s/server-deployment.yaml

@@ -26 +26 @@
           - name: WORKER_ADDRESS
             value: "molecuilder-worker:20026"
-        command: ["/home/molecuilder/_pkgs/molecuilder-1.6.1/bin/molecuilder_server"]
+        command: ["/home/molecuilder/_pkgs/molecuilder-1.7.0/bin/molecuilder_server"]
         args: ["--signal", "15", "--workeraddress", "$(WORKER_ADDRESS)", "--controllerport", "$(CONTROLLER_PORT)", "--workerport", "$(SERVER_PORT)", "--verbosity", "4", "--timeout", "60"]
         ports:
@@ -36 +36 @@
           exec:
             command:
-              - /home/molecuilder/_pkgs/molecuilder-1.6.1/bin/molecuilder_controller
+              - /home/molecuilder/_pkgs/molecuilder-1.7.0/bin/molecuilder_controller
               - --server
               - localhost:20024

k8s/worker-deployment.yaml

@@ -25 +25 @@
           - name: WORKER_PORT
             value: "20026"
-        command: ["/home/molecuilder/_pkgs/molecuilder-1.6.1/bin/molecuilder_poolworker"]
+        command: ["/home/molecuilder/_pkgs/molecuilder-1.7.0/bin/molecuilder_poolworker"]
         args: ["--signal", "15", "--listen", "$(WORKER_PORT)", "--server", "$(SERVER_HOST):$(SERVER_PORT)", "--verbosity", "2", "--healthport", "8092"]
         # command: ["mpirun"]
-        # args: ["--allow-run-as-root", "-np", "1", "/home/molecuilder/_pkgs/molecuilder-1.6.1/bin/molecuilder_poolworker", "--signal", "15", "--listen", "$(WORKER_PORT)", "--server", "$(SERVER_HOST):$(SERVER_PORT)", "--verbosity", "2", "--healthport", "8092"]
+        # args: ["--allow-run-as-root", "-np", "1", "/home/molecuilder/_pkgs/molecuilder-1.7.0/bin/molecuilder_poolworker", "--signal", "15", "--listen", "$(WORKER_PORT)", "--server", "$(SERVER_HOST):$(SERVER_PORT)", "--verbosity", "2", "--healthport", "8092"]
         ports:
         - containerPort: 20026