Small text fixes, update to requirements version. (#4)

* Update to requirements version.
* Adding makefile for test data, remove large test data files.
* A few small changes to tests
* Add media gitignore
* Update readme to include instructions for building test data.

README.md

@@ -20,3 +20,18 @@ $ python ~/projects/gromppery/client/gromppery_client.py \
 ```
 
 This command will connect to a gromppery running at `localhost:43443`, download a work unit from the project called `lambda-repressor`, run it in a directory like `~/sim/YEAR-MONTH-DAY-HASH`, and return it. Because the `--iterations` flag is 2, it will then repeat this process again. If `--iterations` is not specified, it will run until terminated.
+
+## Running the Tests
+
+First, you need to build some of the test data.
+
+```bash
+cd testdata/
+make
+```
+
+Then, you'll be able to run the tests normally
+
+```bash
+./manage.py test
+```

client/test_client.py

@@ -18,27 +18,32 @@ def setUp(self):
             os.path.join(settings.BASE_DIR, 'testdata'),
             os.path.join(settings.MEDIA_ROOT, 'testdata'))
 
-        short_mdp = os.path.join(settings.MEDIA_ROOT, 'testdata', 'short.mdp')
-        with open(short_mdp, 'w') as mdp:
-            with open('testdata/plcg_sh2_wt.mdp', 'r') as f:
-                for line in f.readlines():
-                    if 'nsteps' in line.split():
-                        mdp.write('nsteps = 500 ; .01 ns')
-                    elif 'nstxtcout' in line.split():
-                        mdp.write('nstxtcout = 25   ; 10 ps')
-                    elif 'nstenergy' in line.split():
-                        mdp.write('nstenergy = 25   ; 10 ps')
-                    else:
-                        mdp.write(line)
-
-        self.project = Project.objects.create(
-            name='plcg_sh2_wt',
-            gro='testdata/plcg_sh2_wt.gro',
-            mdp=short_mdp,
-            top='testdata/plcg_sh2_wt.top'
+        try:
+            short_mdp = os.path.join(settings.MEDIA_ROOT, 'testdata',
+                                     'short.mdp')
+            with open(short_mdp, 'w') as mdp:
+                with open('testdata/plcg_sh2_wt.mdp', 'r') as f:
+                    for line in f.readlines():
+                        if 'nsteps' in line.split():
+                            mdp.write('nsteps = 500 ; .01 ns')
+                        elif 'nstxtcout' in line.split():
+                            mdp.write('nstxtcout = 25   ; 10 ps')
+                        elif 'nstenergy' in line.split():
+                            mdp.write('nstenergy = 25   ; 10 ps')
+                        else:
+                            mdp.write(line)
+
+            self.project = Project.objects.create(
+                name='plcg_sh2_wt',
+                gro='testdata/plcg_sh2_wt.gro',
+                mdp=short_mdp,
+                top='testdata/plcg_sh2_wt.top'
             )
 
-        self.scratchpath = tempfile.mkdtemp()
+            self.scratchpath = tempfile.mkdtemp()
+        except:
+            self.tearDown()
+            raise
 
     def tearDown(self):
         shutil.rmtree(settings.MEDIA_ROOT)

gromppery.sublime-project

@@ -14,9 +14,6 @@
 			"folder_exclude_patterns": ["__pycache__"],
 			"path": "."
 		},
-		{
-			"path": "../gromppery-pyramid"
-		},
 		{
 			"folder_exclude_patterns": ["__pycache__"],
 			"path": "../armoir/"

media/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

requirements.txt

@@ -1,4 +1,4 @@
 Django==1.10.6
 djangorestframework==3.6.2
 Markdown==2.6.8
-requests==2.13.0
+requests==2.20.0

testdata/.gitignore

@@ -0,0 +1,2 @@
+mdout.mdp
+plcg_sh2_wt.tpr

testdata/Makefile

@@ -0,0 +1,8 @@
+.PHONY : submission
+submission : submission/plcg_sh2_wt.log
+
+submission/plcg_sh2_wt.log : plcg_sh2_wt.tpr
+	bash -c "cd submission; gmx mdrun -s ../plcg_sh2_wt.tpr -deffnm plcg_sh2_wt"
+
+plcg_sh2_wt.tpr : plcg_sh2_wt.gro plcg_sh2_wt.mdp plcg_sh2_wt.top
+	gmx grompp -f plcg_sh2_wt.mdp -c plcg_sh2_wt.gro -p plcg_sh2_wt.top -o plcg_sh2_wt.tpr -maxwarn 1; rm mdout.mdp

testdata/submission/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+plcg_sh2_wt*
+# Except this file
+!.gitignore

tprs/test_projects.py

@@ -98,7 +98,7 @@ def test_create_project(self):
                                      'testdata/plcg_sh2_wt.top'), 'rb'),
             'gro': open(os.path.join(settings.MEDIA_ROOT,
                                      'testdata/plcg_sh2_wt.gro'), 'rb'),
-            }
+        }
 
         response = self.client.post(url, data, format='multipart')
 
@@ -108,7 +108,7 @@ def test_create_project(self):
         self.assertEqual(Project.objects.first().name, 'plcg_sh2_wt')
 
         response = self.client.get(reverse('project-list'))
-        self.assertEqual(len(response.data), 1)
+        self.assertEqual(len(response.data['results']), 1)
 
         tprdata = Project.objects.first().grompp()
         self.assertGreater(len(tprdata.read()), 100)

tprs/test_submission.py

@@ -20,23 +20,27 @@ def setUp(self):
             os.path.join(settings.BASE_DIR, 'testdata'),
             os.path.join(settings.MEDIA_ROOT, 'testdata'))
 
-        self.project = Project.objects.create(
-            name='plcg_sh2_wt',
-            gro='testdata/plcg_sh2_wt.gro',
-            mdp='testdata/plcg_sh2_wt.mdp',
-            top='testdata/plcg_sh2_wt.top'
+        try:
+            self.project = Project.objects.create(
+                name='plcg_sh2_wt',
+                gro='testdata/plcg_sh2_wt.gro',
+                mdp='testdata/plcg_sh2_wt.mdp',
+                top='testdata/plcg_sh2_wt.top'
             )
 
-        self.good_data = {
-            'hostname': 'debug01',
-            'xtc': open(self.filepath('plcg_sh2_wt.xtc'), 'rb'),
-            'log': open(self.filepath('plcg_sh2_wt.log'), 'rb'),
-            'edr': open(self.filepath('plcg_sh2_wt.edr'), 'rb'),
-            'gro': open(self.filepath('plcg_sh2_wt.gro'), 'rb'),
-            'cpt': open(self.filepath('plcg_sh2_wt.cpt'), 'rb'),
-            'tpr': open(os.path.join(settings.MEDIA_ROOT,
-                                     'testdata/plcg_sh2_wt.tpr'), 'rb'),
-        }
+            self.good_data = {
+                'hostname': 'debug01',
+                'xtc': open(self.filepath('plcg_sh2_wt.xtc'), 'rb'),
+                'log': open(self.filepath('plcg_sh2_wt.log'), 'rb'),
+                'edr': open(self.filepath('plcg_sh2_wt.edr'), 'rb'),
+                'gro': open(self.filepath('plcg_sh2_wt.gro'), 'rb'),
+                'cpt': open(self.filepath('plcg_sh2_wt.cpt'), 'rb'),
+                'tpr': open(os.path.join(settings.MEDIA_ROOT,
+                                         'testdata/plcg_sh2_wt.tpr'), 'rb'),
+            }
+        except:
+            self.tearDown()
+            raise
 
     def tearDown(self):
         shutil.rmtree(settings.MEDIA_ROOT)