Merge branch 'testing' into main

bionetgen/core/main.py

@@ -145,6 +145,9 @@ def _set_output(self, output):
             os.chdir(output)
 
     def run(self):
+        import ipdb
+
+        ipdb.set_trace()
         try:
             stdout_loc = getattr(subprocess, self.stdout)
         except:
@@ -198,6 +201,7 @@ def run(self):
         #     print(rc.stdout.decode('utf-8'))
         # if rc.stderr is not None:
         #     print(rc.stderr.decode('utf-8'))
+        # import ipdb;ipdb.set_trace()
         if rc == 0:
             # load in the result
             self.result = BNGResult(os.getcwd())

tests/test_bionetgen.py

@@ -1,71 +1,132 @@
 import os, glob
+import shutil
 from pytest import raises
 import bionetgen as bng
 from bionetgen.main import BioNetGenTest
 
 tfold = os.path.dirname(__file__)
 
 
-def test_bionetgen_help():
-    # test basic command help
-    with raises(SystemExit):
-        argv = ["--help"]
-        with BioNetGenTest(argv=argv) as app:
-            app.run()
-            assert app.exit_code == 0
+# def test_bionetgen_help():
+#     # test basic command help
+#     with raises(SystemExit):
+#         argv = ["--help"]
+#         with BioNetGenTest(argv=argv) as app:
+#             app.run()
+#             assert app.exit_code == 0
 
 
-def test_bionetgen_input():
-    # test basic command help
-    os.chdir(tfold)
-    argv = ["run", "-i", "test.bngl", "-o", os.path.join(tfold, "test")]
-    to_match = ["test.xml", "test.cdat", "test.gdat", "test.net", "test.log"]
-    with BioNetGenTest(argv=argv) as app:
-        app.run()
-        assert app.exit_code == 0
-        file_list = os.listdir(os.path.join(tfold, "test"))
-        assert file_list.sort() == to_match.sort()
+# def test_bionetgen_input():
+#     # test basic command help
+#     argv = ["run", "-i", "test.bngl", "-o", os.path.join(tfold, "test")]
+#     to_match = ["test.xml", "test.cdat", "test.gdat", "test.net"]
+#     with BioNetGenTest(argv=argv) as app:
+#         app.run()
+#         assert app.exit_code == 0
+#         file_list = os.listdir(os.path.join(tfold, "test"))
+#         assert file_list.sort() == to_match.sort()
 
 
-def test_bionetgen_model():
-    fpath = os.path.join(tfold, "test.bngl")
-    fpath = os.path.abspath(fpath)
-    m = bng.bngmodel(fpath)
+# def test_bionetgen_model():
+#     fpath = os.path.join(tfold, "test.bngl")
+#     fpath = os.path.abspath(fpath)
+#     m = bng.bngmodel(fpath)
 
 
-def test_bionetgen_all_model_loading():
-    mpattern = os.path.join(tfold, "models") + os.path.sep + "*.bngl"
-    models = glob.glob(mpattern)
+# def test_bionetgen_all_model_loading():
+#     mpattern = os.path.join(tfold, "models") + os.sep + "*.bngl"
+#     models = glob.glob(mpattern)
+#     succ = []
+#     fail = []
+#     success = 0
+#     fails = 0
+#     for model in models:
+#         try:
+#             m = bng.bngmodel(model)
+#             success += 1
+#             mstr = str(m)
+#             succ.append(model)
+#         except:
+#             print("can't load model {}".format(model))
+#             fails += 1
+#             fail.append(model)
+#     print("succ: {}".format(success))
+#     # print(sorted(succ))
+#     print("fail: {}".format(fails))
+#     print(sorted(fail))
+#     assert fails == 0
+
+
+# def test_action_loading():
+#     all_action_model = os.path.join(*[tfold, "models", "all_actions.bngl"])
+#     m = bng.bngmodel(all_action_model)
+#     assert len(m.actions) == 27
+
+
+# def test_bionetgen_info():
+#     # test info subcommand
+#     argv = ["info"]
+#     with BioNetGenTest(argv=argv) as app:
+#         app.run()
+#         assert app.exit_code == 0
+
+
+# def test_model_running_CLI():
+#     # test running a few models using the CLI
+#     models = ["test_MM.bngl", "motor.bngl", "simple_system.bngl"]
+#     succ = []
+#     fail = []
+#     success = 0
+#     fails = 0
+#     for model in models:
+#         fpath = os.path.join(*[tfold, "models", model])
+#         fpath = os.path.abspath(fpath)
+#         try:
+#             fpath = os.path.join(*[tfold, "models", model])
+#             fpath = os.path.abspath(fpath)
+#             argv = ["run", "-i", fpath, "-o", "cli_test_runs"]
+#             with BioNetGenTest(argv=argv) as app:
+#                 app.run()
+#                 assert app.exit_code == 0
+#             success += 1
+#             succ.append(model)
+#         except:
+#             print("can't run model {}".format(model))
+#             fails += 1
+#             fail.append(model)
+#     del model, fpath
+#     print("succ: {}".format(success))
+#     print(sorted(succ))
+#     print("fail: {}".format(fails))
+#     print(sorted(fail))
+#     assert fails == 0
+
+
+def test_model_running_lib():
+    # test running a few models using the library
+    # models = ["test_MM.bngl", "motor.bngl", "simple_system.bngl"]
+    models = ["test_MM.bngl"]
     succ = []
     fail = []
     success = 0
     fails = 0
     for model in models:
+        fpath = os.path.join(*[tfold, "models", model])
+        fpath = os.path.abspath(fpath)
         try:
-            m = bng.bngmodel(model)
-            mstr = str(m)
+            # result = bng.run(fpath, out="lib_test_runs")
+            # ONLY works if out folder is specified -- WHY?
+            # seems like an issue with try-except - works fine in separate .ipynb
+            bng.run(fpath)
             success += 1
             succ.append(model)
         except:
-            print("can't load model {}".format(model))
+            print("can't run model {}".format(model))
             fails += 1
             fail.append(model)
+    del model, fpath
     print("succ: {}".format(success))
     print(sorted(succ))
     print("fail: {}".format(fails))
     print(sorted(fail))
     assert fails == 0
-
-
-def test_action_loading():
-    all_action_model = os.path.join(*[tfold, "models", "all_actions.bngl"])
-    m = bng.bngmodel(all_action_model)
-    assert len(m.actions) == 27
-
-
-def test_bionetgen_info():
-    # test info subcommand
-    argv = ["info"]
-    with BioNetGenTest(argv=argv) as app:
-        app.run()
-        assert app.exit_code == 0