updated scripts to build, run, test all sample projects

beta/test_build_samples.sh

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+#  Copy this file to the root dir and run it from a Unix bash shell: sh test_build_samples.sh
+#
+#  WARNING: this is primarily intended to be used by core developers when testing a new release.
+#            It will create new directories in /user_projects
+#
+#  Based on the following:
+#
+# $ make list-projects
+# Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample
+#                  celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample
+#                  worm-sample interaction-sample mechano-sample rules-sample physimess-sample
+#
+#  Note that it does not currently test building the intracellular projects:
+# Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample
+#                  cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion
+#
+#
+#  After running the script, you can :
+#    1) confirm all executables were created
+# $ ls -l template_sample biorobots cancer_biorobots cancer_immune_3D celltypes3 heterogeneity pred_prey virus_sample worm interaction_demo mechano_sample rules_sample physimess_sample 
+#   and then:
+#    2) confirm the user_projects were created; delete them
+# $ cd user_projects
+# $ ls
+# $ rm -rf template biorobots cancer_biorobots cancer_immune celltypes3 hetero pred_prey virus_mac worm interaction mechano rules physimess
+
+make reset
+make template
+make 
+mv project template_sample
+make save PROJ=template
+#
+echo "\n-----------------------------------------"
+make reset
+make biorobots-sample 
+make
+make save PROJ=biorobots
+#
+echo "\n-----------------------------------------"
+make reset
+make cancer-biorobots-sample
+make
+make save PROJ=cancer_biorobots
+#
+echo "\n-----------------------------------------"
+make reset
+make cancer-immune-sample
+make
+make save PROJ=cancer_immune
+#
+echo "\n-----------------------------------------"
+make reset
+make celltypes3-sample
+make
+make save PROJ=celltypes3
+#
+echo "\n-----------------------------------------"
+make reset
+make heterogeneity-sample
+make
+make save PROJ=hetero
+#
+echo "\n-----------------------------------------"
+make reset
+make  pred-prey-farmer
+make
+make save PROJ=pred_prey
+#
+echo "\n-----------------------------------------"
+make reset
+make  virus-macrophage-sample
+make
+make save PROJ=virus_mac
+#
+echo "\n-----------------------------------------"
+make reset
+make worm-sample
+make
+make save PROJ=worm
+#
+echo "\n-----------------------------------------"
+make reset
+make interaction-sample
+make
+make save PROJ=interaction
+#
+echo "\n-----------------------------------------"
+make reset
+make mechano-sample
+make
+mv project mechano_sample
+make save PROJ=mechano
+#
+echo "\n-----------------------------------------"
+make reset
+make rules-sample
+make
+mv project rules_sample
+make save PROJ=rules
+#
+echo "\n-----------------------------------------"
+make reset
+make physimess-sample
+make
+mv project physimess_sample
+make save PROJ=physimess

beta/test_run_samples.py

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+#  Copy this Python script to the root dir and run it to:
+#     - load each sample project (from user_projects)
+#     - compile it
+#     - modify each project's .xml:  max_time, # threads, output folder
+#     - run it
+#
+#  WARNING: this is primarily intended to be used by core developers when testing a new release.
+#            It will create new output directories  ("output_<proj>")
+#
+#  Reminder:
+# $ ls user_projects/
+# biorobots/		hetero/			pred_prey/		worm/
+# cancer_biorobots/	interaction/		rules/
+# cancer_immune/		mechano/		template/
+# celltypes3/		physimess/		virus_mac/
+
+# Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample
+#                  celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample
+#                  worm-sample interaction-sample mechano-sample rules-sample physimess-sample
+#
+#  It does not currently test running the intracellular projects:
+# Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample
+#                  cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion
+#
+#
+#   If you want to cleanup the created execs:
+# $ rm -rf template biorobots cancer_biorobots cancer_immune celltypes3 hetero pred_prey virus_mac worm interaction mechano rules physimess
+
+import subprocess
+import xml.etree.ElementTree as ET
+import os
+import time
+
+# skip over the 3D cancer_immune_sample for now
+user_proj = ["template", "biorobots", "cancer_biorobots", "celltypes3", "hetero", "pred_prey", "virus_mac", "worm", "interaction", "mechano", "rules", "physimess"]  # 
+model_execs = ["project", "biorobots", "cancer_biorobots", "celltypes3", "heterogeneity", "pred_prey", "virus-sample", "worm", "interaction_demo", "project", "project", "project"]
+
+# using dummy values of 99; users can change
+max_times = [120, 10, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99]
+
+for (uproj, myexec, max_time) in zip(user_proj, model_execs, max_times):
+    print("\n\n------------   ",uproj,myexec, "   ----------------------------------")
+    subprocess.run(["make","reset"])
+    # make load PROJ=template
+    s= "PROJ=" + uproj
+    print("\n ---- doing: make load ",s)
+    subprocess.run(["make","load",s])
+    subprocess.run(["make"])
+
+    # update max_time and omp_num_threads (=1)
+    tree = ET.parse('config/PhysiCell_settings.xml')
+    root = tree.getroot()
+    root.find(".//max_time").text = str(max_time)
+    root.find(".//omp_num_threads").text = "1"
+    new_output_dir = "output_" + uproj
+    root.find(".//save//folder").text = new_output_dir
+    tree.write('config/PhysiCell_settings.xml')
+    try:
+        os.makedirs(new_output_dir)
+    except:
+        pass
+    time.sleep(1)
+
+    subprocess.run([myexec])