Merge pull request #247 from rheiland/new-build-test

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
+#
+#  This script is intended to serve as a first step in a two-step process. The second step is
+#  to run the beta/test_run_samples.py Python script (see its header for instructions).
+#
+#
+#  This test_build_samples.sh script is 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_diffs_svg.py

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+# compare diffs between .svg files in different runs
+#  e.g.,
+# python beta/test_diffs_svg.py ~/git/new-build-test/samples_test ~/git/fix_constants/samples_test
+
+
+import os
+import sys
+from pathlib import Path
+import glob
+
+# print(len(sys.argv))
+if (len(sys.argv) < 3):
+  usage_str = "Usage: %s <dir1> <dir2>" % (sys.argv[0])
+  print(usage_str)
+  print("e.g.:  python test_diffs_svg.py ~/blah1 ~/blah2")
+  exit(1)
+else:
+   dir1 = sys.argv[1]
+   dir2 = sys.argv[2]
+
+
+# svg_files = Path(dir1).glob(f'{dir1}/out_heterog/snap*.svg')
+#print("svg_files=",svg_files)
+
+
+#for filename in glob.iglob(f'{dir1}/snap*.svg'):
+
+# output_biorobots/		output_interaction/		output_template/
+# output_cancer_biorobots/	output_mechano/			output_virus_mac/
+# output_cancer_immune/		output_physimess/		output_worm/
+# output_celltypes3/		output_pred_prey/
+# output_hetero/			output_rules/
+
+# note that we omit 'output_physimess' only because, currently, it fails the recursive copy of
+# additional files needed in config/subdirs (until the Makefiles and "make load PROJ" is updated)
+for out_dir in ['output_template','output_biorobots','output_cancer_biorobots','output_celltypes3','output_heterog','output_interaction','output_mechano','output_pred_prey','output_virus_mac','output_worm','output_rules','output_cancer_immune']:
+#for out_dir in ['out_template']:
+    print("----------  processing ",out_dir)
+    svg_files = glob.glob(f'{dir1}/{out_dir}/snap*.svg')
+    svg_files.sort()
+    for filename in svg_files:
+        f = os.path.basename(filename)
+        f1 = os.path.join(dir1,out_dir,f)
+        f2 = os.path.join(dir2,out_dir,f)
+        # print(f1,f2)
+        # cmd =  f"diff {f1} {f2} | wc -l"
+        cmd =  f"diff {f1} {f2} | wc -l > diff_result.txt"
+        print(cmd)
+        os.system(cmd)
+        with open('diff_result.txt') as f:
+            vstr = f.readline()
+            print(vstr)
+            # Note: a "diff" will almost certainly return 4 lines, showing different run times
+            # 1340c1340
+            # <    0 days, 0 hours, 1 minutes, and 12.1327 seconds
+            # ---
+            # >    0 days, 0 hours, 1 minutes, and 12.4215 seconds
+            if (int(vstr) == 0):   
+                print("======---------------->  WOW: exact match! (same sim time)")
+                # userinput = input("\nPress Enter to skip remaining files for this sample:")
+                # break
+            elif (int(vstr) != 4):   # hard-coded "4"
+                print("======---------------->  Warning: not a match!")
+                userinput = input("\nPress Enter to skip remaining files for this sample:")
+                # print("Username is: " + username)
+                break
+                # sys.exit(1)
+
+# for fname in os.listdir(dir1):
+#     fname1 = os.path.join(dir1, fname)
+#     fname2 = os.path.join(dir2, fname)
+#     # checking if it is a file
+#     if os.path.isfile(f):
+#         print(f)
+
+#             cmd =  "diff " + dir1 + "out_heterog" + " > " + log_file + " " + background_str
+#             print("----- cmd = ",cmd)
+# #            os.system(cmd)   # <------ Execute the simulation

beta/test_run_samples.py

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+#
+#  This Python script assumes you have run the beta/test_build_sample.sh script first.
+#  See its header for instructions.
+#
+#  Copy this Python script from /beta to the root dir (in case you want to edit it), then run it
+#  It will do the following:
+#     - load each sample project (from user_projects; created by test_build_sample.sh)
+#     - 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>")
+#
+#    Run via:
+#  $ python beta/test_run_samples.py 
+#    or, pipe the terminal output to a file:
+#  $ python beta/test_run_samples.py > test_run_samples.out
+#
+#  Any serious error should show up in your terminal output. Some "errors" may be benign, e.g.,
+#   "Error: Could not find <cell_rules> section of XML config file"
+#
+#  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_3D celltypes3 hetero pred_prey virus_mac worm interaction mechano rules physimess
+
+import subprocess
+import xml.etree.ElementTree as ET
+import os
+import time
+
+user_proj = ["template", "biorobots", "cancer_biorobots", "celltypes3", "hetero", "pred_prey", "virus_mac", "worm", "interaction", "mechano", "rules", "physimess", "cancer_immune"] 
+
+model_execs = ["project", "biorobots", "cancer_biorobots", "celltypes3", "heterogeneity", "pred_prey", "virus-sample", "worm", "interaction_demo", "project", "project", "project", "cancer_immune_3D"]
+
+# Using dummy max_time values of 99 for many projects; 61 for the more time-consuming cancer_immune_3D. 
+# Users can change them as they wish.
+max_times = [120, 10, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 61]
+
+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])