Travis CI build and unit testing

.travis.yml

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+dist: focal
+
+addons:
+  apt:
+    sources:
+      - ubuntu-toolchain-r-test
+    packages:
+      - wget
+      - pkg-config
+
+cache:
+  directories:
+    - $HOME/.cache/apt
+
+before_install:
+  - echo "Installing C++ and Python"
+  - sudo apt-get update && sudo apt-get install -y --no-install-recommends --no-install-suggests build-essential g++ python-dev python3-dev python3-pip libc-dev python3-venv openmpi-bin libopenmpi-dev libomp-dev lammps
+  - sudo apt-get install gsl-bin libgsl0-dev libboost-all-dev imagemagick-6.q16 inkscape
+  - cp /var/cache/apt/archives/*.deb $HOME/.cache/apt/
+  - export BOOST_LIBDIR=/usr/lib/x86_64-linux-gnu/
+  - rm Gemfile.lock
+
+jobs:
+  include:
+    - stage: test
+      script:
+        - sed -i 's/%use/#%use/' bin/nanobind-frontend.ipynb
+        - sed -i 's/import hublib.use/#import hublib.use/' bin/nanobind-frontend.ipynb
+          #- sed -i 's/0000/000/' bin/infiles/in.lammps.template
+        - sed -i 's/lmp_g++/lmp/' bin/Makefile
+        - make all
+        - cd bin && ./test.sh
+      name: test

bin/test.sh

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+#!/bin/bash
+
+python3 -m venv ENV
+
+source ENV/bin/activate
+
+pip install hublib
+pip install jupyterlab
+pip install testbook
+pip install widgetsnbextension
+pip install svgwrite
+pip install pypng
+pip install pytest
+pip install matplotlib
+pip install ipywidgets
+jupyter nbextension enable --py widgetsnbextension
+
+export ENVIRON_CONFIG_DIRS=","
+pytest test || exit 1
+

bin/test/nanobind_test.py

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+import testbook
+import os
+from datetime import datetime
+import subprocess
+
+DEFAULT_EPSILON = 1
+DEFAULT_CONCENTRATION= 9
+DEFAULT_NCOMPLEXES = 108
+DEFAULT_WALLSPACING = 100
+DEFAULT_TIMEINMILS = 275
+
+@testbook.testbook('nanobind-frontend.ipynb', execute=True)
+def test_runPreprocessor(tb):
+    t0 = datetime.now()
+    func = tb.ref("runPreprocessor")
+    func(DEFAULT_EPSILON, DEFAULT_CONCENTRATION, DEFAULT_NCOMPLEXES, DEFAULT_WALLSPACING, DEFAULT_TIMEINMILS)
+    logf = "./preprocessor.log"
+    assert os.path.exists(logf) == 1
+    t1 = datetime.fromtimestamp(os.path.getmtime(logf))
+    assert (t1>t0)
+    os.remove(logf)
+
+'''
+def test_backend():
+    retcode1, retstr = subprocess.getstatusoutput("make run-preprocessor")
+    assert (retcode1 == 0)
+    retcode2, retstr = subprocess.getstatusoutput("time lmp < ./in.lammps")
+    #assert (retcode2 == 0)
+    print (retstr)
+    mk1 = "Total # of neighbors"
+    mk2 = "Ave neighs/atom"
+    assert ((mk1 in retstr) and (mk2 in retstr))
+'''