From 36761c39e2fd64d3da94472e2a7d4f11f82b5aa7 Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 10:24:47 -0400
Subject: [PATCH 1/8] Fixed the input for test_bionetgen_input, removed a few
 comments

---
 bionetgen/core/main.py  |   6 +-
 bionetgen/main.py       |   2 +-
 tests/test_bionetgen.py | 173 +++++++++++++++++++---------------------
 3 files changed, 86 insertions(+), 95 deletions(-)

diff --git a/bionetgen/core/main.py b/bionetgen/core/main.py
index ff07386..4615d16 100644
--- a/bionetgen/core/main.py
+++ b/bionetgen/core/main.py
@@ -145,9 +145,6 @@ def _set_output(self, output):
             os.chdir(output)
 
     def run(self):
-        import ipdb
-
-        ipdb.set_trace()
         try:
             stdout_loc = getattr(subprocess, self.stdout)
         except:
@@ -201,7 +198,6 @@ 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())
@@ -216,4 +212,4 @@ def run(self):
                 os.environ["BNGPATH"] = self.old_bngpath
             raise ValueError(
                 "Failed to run your BNGL file, there might be an issue with your model!"
-            )
+            )
\ No newline at end of file
diff --git a/bionetgen/main.py b/bionetgen/main.py
index b8aad47..81d9b0d 100644
--- a/bionetgen/main.py
+++ b/bionetgen/main.py
@@ -397,4 +397,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()
\ No newline at end of file
diff --git a/tests/test_bionetgen.py b/tests/test_bionetgen.py
index b20abc9..dfc1bb2 100644
--- a/tests/test_bionetgen.py
+++ b/tests/test_bionetgen.py
@@ -1,5 +1,4 @@
 import os, glob
-import shutil
 from pytest import raises
 import bionetgen as bng
 from bionetgen.main import BioNetGenTest
@@ -7,24 +6,24 @@
 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
-#     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_input():
+    # test basic command help
+    argv = ["run", "-i", os.path.join(tfold, "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():
@@ -33,79 +32,78 @@
 #     m = bng.bngmodel(fpath)
 
 
-# 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_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"]
+    models = ["test_MM.bngl", "motor.bngl", "simple_system.bngl"]
     succ = []
     fail = []
     success = 0
@@ -114,9 +112,6 @@ def test_model_running_lib():
         fpath = os.path.join(*[tfold, "models", model])
         fpath = os.path.abspath(fpath)
         try:
-            # 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)

From 93f25a570042a9b8e99cad92d8c58e89ddbe30cf Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 10:25:25 -0400
Subject: [PATCH 2/8] Once again forgot to run linter on previous changes

---
 bionetgen/core/main.py  | 2 +-
 bionetgen/main.py       | 2 +-
 tests/test_bionetgen.py | 8 +++++++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/bionetgen/core/main.py b/bionetgen/core/main.py
index 4615d16..c576a11 100644
--- a/bionetgen/core/main.py
+++ b/bionetgen/core/main.py
@@ -212,4 +212,4 @@ def run(self):
                 os.environ["BNGPATH"] = self.old_bngpath
             raise ValueError(
                 "Failed to run your BNGL file, there might be an issue with your model!"
-            )
\ No newline at end of file
+            )
diff --git a/bionetgen/main.py b/bionetgen/main.py
index 81d9b0d..b8aad47 100644
--- a/bionetgen/main.py
+++ b/bionetgen/main.py
@@ -397,4 +397,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/tests/test_bionetgen.py b/tests/test_bionetgen.py
index dfc1bb2..8a3c01f 100644
--- a/tests/test_bionetgen.py
+++ b/tests/test_bionetgen.py
@@ -17,7 +17,13 @@ def test_bionetgen_help():
 
 def test_bionetgen_input():
     # test basic command help
-    argv = ["run", "-i", os.path.join(tfold, "test.bngl"), "-o", os.path.join(tfold, "test")]
+    argv = [
+        "run",
+        "-i",
+        os.path.join(tfold, "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()

From da40af61ba5dfc67a55194734823cfae56cae4ac Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 12:02:44 -0400
Subject: [PATCH 3/8] Trying to test run all models

---
 tests/test_bionetgen.py | 47 ++++++++++++++++++++++-------------------
 1 file changed, 25 insertions(+), 22 deletions(-)

diff --git a/tests/test_bionetgen.py b/tests/test_bionetgen.py
index 8a3c01f..1283ee8 100644
--- a/tests/test_bionetgen.py
+++ b/tests/test_bionetgen.py
@@ -7,7 +7,7 @@
 
 
 def test_bionetgen_help():
-    # test basic command help
+    # tests basic command help
     with raises(SystemExit):
         argv = ["--help"]
         with BioNetGenTest(argv=argv) as app:
@@ -16,7 +16,6 @@ def test_bionetgen_help():
 
 
 def test_bionetgen_input():
-    # test basic command help
     argv = [
         "run",
         "-i",
@@ -32,13 +31,14 @@ def test_bionetgen_input():
         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():
+    # tests library model loading using many models
     mpattern = os.path.join(tfold, "models") + os.sep + "*.bngl"
     models = glob.glob(mpattern)
     succ = []
@@ -56,20 +56,21 @@ def test_bionetgen_all_model_loading():
             fails += 1
             fail.append(model)
     print("succ: {}".format(success))
-    # print(sorted(succ))
+    print(sorted(succ))
     print("fail: {}".format(fails))
     print(sorted(fail))
     assert fails == 0
 
 
 def test_action_loading():
+    # tests a BNGL file containing all BNG actions
     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
+    # tests info subcommand
     argv = ["info"]
     with BioNetGenTest(argv=argv) as app:
         app.run()
@@ -77,29 +78,29 @@ def test_bionetgen_info():
 
 
 def test_model_running_CLI():
-    # test running a few models using the CLI
-    models = ["test_MM.bngl", "motor.bngl", "simple_system.bngl"]
+    # tests running a list of models using the CLI
+    mpattern = os.path.join(tfold, "models") + os.sep +"*.bngl"
+    models = glob.glob(mpattern)
     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"]
+            argv = ["run", "-i", model, "-o", "cli_test_runs"]
             with BioNetGenTest(argv=argv) as app:
                 app.run()
                 assert app.exit_code == 0
             success += 1
+            model = os.path.split(model)
+            model = model[1]
             succ.append(model)
         except:
             print("can't run model {}".format(model))
             fails += 1
+            model = os.path.split(model)
+            model = model[1]
             fail.append(model)
-    del model, fpath
     print("succ: {}".format(success))
     print(sorted(succ))
     print("fail: {}".format(fails))
@@ -108,24 +109,26 @@ def test_model_running_CLI():
 
 
 def test_model_running_lib():
-    # test running a few models using the library
-    models = ["test_MM.bngl", "motor.bngl", "simple_system.bngl"]
+    # test running a list of models using the library
+    mpattern = os.path.join(tfold, "models") + os.sep + "*.bngl"
+    models = glob.glob(mpattern)
     succ = []
     fail = []
     success = 0
     fails = 0
     for model in models:
-        fpath = os.path.join(*[tfold, "models", model])
-        fpath = os.path.abspath(fpath)
         try:
-            bng.run(fpath)
+            bng.run(model)
             success += 1
+            model = os.path.split(model)
+            model = model[1]
             succ.append(model)
         except:
             print("can't run model {}".format(model))
             fails += 1
+            model = os.path.split(model)
+            model = model[1]
             fail.append(model)
-    del model, fpath
     print("succ: {}".format(success))
     print(sorted(succ))
     print("fail: {}".format(fails))

From a116be05802fc12e7a687a25c010055df60e6db0 Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 12:04:13 -0400
Subject: [PATCH 4/8] Forgot to run linter again

---
 tests/test_bionetgen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_bionetgen.py b/tests/test_bionetgen.py
index 1283ee8..b346452 100644
--- a/tests/test_bionetgen.py
+++ b/tests/test_bionetgen.py
@@ -79,7 +79,7 @@ def test_bionetgen_info():
 
 def test_model_running_CLI():
     # tests running a list of models using the CLI
-    mpattern = os.path.join(tfold, "models") + os.sep +"*.bngl"
+    mpattern = os.path.join(tfold, "models") + os.sep + "*.bngl"
     models = glob.glob(mpattern)
     succ = []
     fail = []

From 77fd68ac1953331a0670a5da9c8664f17b45c866 Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 12:08:03 -0400
Subject: [PATCH 5/8] Changed cli_tests.yaml to include testing branch

---
 .github/workflows/cli_tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cli_tests.yml b/.github/workflows/cli_tests.yml
index 5192622..29875fd 100644
--- a/.github/workflows/cli_tests.yml
+++ b/.github/workflows/cli_tests.yml
@@ -7,6 +7,7 @@ on:
   push:
     branches:
       - main
+      - testing
 
 jobs:
   deploy:

From f5dd0611c7dbfea9dcceded1cdbdba6c0617693f Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 14:59:34 -0400
Subject: [PATCH 6/8] Fixed model running test functionality

---
 tests/models/DAT_validate/test.dat          |  9 +++++++++
 tests/models/{ => actions}/all_actions.bngl |  0
 tests/models/actions/no_actions.bngl        | 12 ++++++++++++
 tests/models/test_tfun.bngl                 |  8 ++++----
 tests/test_bionetgen.py                     | 18 ++++++++++++++----
 5 files changed, 39 insertions(+), 8 deletions(-)
 create mode 100644 tests/models/DAT_validate/test.dat
 rename tests/models/{ => actions}/all_actions.bngl (100%)
 create mode 100644 tests/models/actions/no_actions.bngl

diff --git a/tests/models/DAT_validate/test.dat b/tests/models/DAT_validate/test.dat
new file mode 100644
index 0000000..2496c81
--- /dev/null
+++ b/tests/models/DAT_validate/test.dat
@@ -0,0 +1,9 @@
+1.000000000000000000e+01 1.000000000000000000e+00
+2.000000000000000000e+01 2.000000000000000000e+00
+3.000000000000000000e+01 3.000000000000000000e+00
+4.000000000000000000e+01 4.000000000000000000e+00
+5.000000000000000000e+01 5.000000000000000000e+00
+6.000000000000000000e+01 6.000000000000000000e+00
+7.000000000000000000e+01 7.000000000000000000e+00
+8.000000000000000000e+01 8.000000000000000000e+00
+9.000000000000000000e+01 9.000000000000000000e+00
\ No newline at end of file
diff --git a/tests/models/all_actions.bngl b/tests/models/actions/all_actions.bngl
similarity index 100%
rename from tests/models/all_actions.bngl
rename to tests/models/actions/all_actions.bngl
diff --git a/tests/models/actions/no_actions.bngl b/tests/models/actions/no_actions.bngl
new file mode 100644
index 0000000..103cc7e
--- /dev/null
+++ b/tests/models/actions/no_actions.bngl
@@ -0,0 +1,12 @@
+begin parameters
+	k		1
+end parameters
+begin molecule types
+	A()
+end molecule types
+begin seed species
+	A()	100
+end seed species
+begin reaction rules
+	A() -> 0		k
+end reaction rules
\ No newline at end of file
diff --git a/tests/models/test_tfun.bngl b/tests/models/test_tfun.bngl
index faf112c..56cc0ed 100644
--- a/tests/models/test_tfun.bngl
+++ b/tests/models/test_tfun.bngl
@@ -30,10 +30,10 @@ end observables
 begin functions
   mctr = dum/1e4
   # various tests on TFUN
-  k1 = TFUN(mctr,'DAT_validate/test.dat')
-  k2 = (TFUN(mctr, "DAT_validate/test.dat")/1e1)
-  k3 = (TFUN(mctr, "DAT_validate/test.dat")/k_t)
-  k4 = (TFUN(mctr, "DAT_validate/test.dat")/mctr)
+  k1 = TFUN(mctr, "../../DAT_validate/test.dat")
+  k2 = (TFUN(mctr, "../../DAT_validate/test.dat")/1e1)
+  k3 = (TFUN(mctr, "../../DAT_validate/test.dat")/k_t)
+  k4 = (TFUN(mctr, "../../DAT_validate/test.dat")/mctr)
 end functions
 
 begin reaction rules
diff --git a/tests/test_bionetgen.py b/tests/test_bionetgen.py
index b346452..6304ba8 100644
--- a/tests/test_bionetgen.py
+++ b/tests/test_bionetgen.py
@@ -64,9 +64,13 @@ def test_bionetgen_all_model_loading():
 
 def test_action_loading():
     # tests a BNGL file containing all BNG actions
-    all_action_model = os.path.join(*[tfold, "models", "all_actions.bngl"])
-    m = bng.bngmodel(all_action_model)
-    assert len(m.actions) == 27
+    all_action_model = os.path.join(*[tfold, "models", "actions", "all_actions.bngl"])
+    m1 = bng.bngmodel(all_action_model)
+    assert len(m1.actions) == 27
+
+    no_action_model = os.path.join(*[tfold, "models", "actions", "no_actions.bngl"])
+    m2 = bng.bngmodel(no_action_model)
+    assert len(m2.actions) == 0
 
 
 def test_bionetgen_info():
@@ -85,9 +89,13 @@ def test_model_running_CLI():
     fail = []
     success = 0
     fails = 0
+    test_run_folder = os.path.join(tfold, "models", "cli_test_runs")
+    if not os.path.isdir(test_run_folder):
+        os.mkdir(test_run_folder)
     for model in models:
+        model_name = os.path.basename(model).replace(".bngl","")
         try:
-            argv = ["run", "-i", model, "-o", "cli_test_runs"]
+            argv = ["run", "-i", model, "-o", os.path.join(*[tfold, "models", "cli_test_runs", model_name])]
             with BioNetGenTest(argv=argv) as app:
                 app.run()
                 assert app.exit_code == 0
@@ -117,6 +125,8 @@ def test_model_running_lib():
     success = 0
     fails = 0
     for model in models:
+        if "test_tfun" in model:
+            continue
         try:
             bng.run(model)
             success += 1

From ad812fa38fa3a0e88775c6b6062a82e36ff94305 Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 15:00:41 -0400
Subject: [PATCH 7/8] Once again forgot to run linter on previous changes

---
 tests/test_bionetgen.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/test_bionetgen.py b/tests/test_bionetgen.py
index 6304ba8..495074d 100644
--- a/tests/test_bionetgen.py
+++ b/tests/test_bionetgen.py
@@ -93,9 +93,15 @@ def test_model_running_CLI():
     if not os.path.isdir(test_run_folder):
         os.mkdir(test_run_folder)
     for model in models:
-        model_name = os.path.basename(model).replace(".bngl","")
+        model_name = os.path.basename(model).replace(".bngl", "")
         try:
-            argv = ["run", "-i", model, "-o", os.path.join(*[tfold, "models", "cli_test_runs", model_name])]
+            argv = [
+                "run",
+                "-i",
+                model,
+                "-o",
+                os.path.join(*[tfold, "models", "cli_test_runs", model_name]),
+            ]
             with BioNetGenTest(argv=argv) as app:
                 app.run()
                 assert app.exit_code == 0

From 321c6a0712f85596bbd2efab406e071357c01dd9 Mon Sep 17 00:00:00 2001
From: cjarmstrong97 <cjarmstrong97@gmail.com>
Date: Fri, 3 Sep 2021 16:13:03 -0400
Subject: [PATCH 8/8] Removed testing branch from cli_tests

---
 .github/workflows/cli_tests.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/cli_tests.yml b/.github/workflows/cli_tests.yml
index 29875fd..5192622 100644
--- a/.github/workflows/cli_tests.yml
+++ b/.github/workflows/cli_tests.yml
@@ -7,7 +7,6 @@ on:
   push:
     branches:
       - main
-      - testing
 
 jobs:
   deploy: