Merge pull request #55 from jhprinz/tests

Tests
markovmodel · May 26, 2017 · 186ffa0 · 186ffa0
2 parents 446e6cb + 802be3b
commit 186ffa0
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# adaptive-sampling
+# adaptiveMD
 A Python framework to run adaptive Markov state model (MSM) simulation on HPC resources
 
 The generation of MSMs requires a huge amount of trajectory data to be analyzed. In most cases
@@ -91,6 +91,9 @@ python setup.py develop
 # see if it works
 python -c "import adaptivemd" || echo 'FAILED'
 
+# run the mongodb server if not running already
+mongod --dbpath={path_to_your_db_folder}
+
 # run a simple test
 cd adaptive/tests/
 python test_simple.py
@@ -99,7 +102,7 @@ python test_simple.py
 
 All of this must also be installed on the cluster, where you want to run your simulations.
 
-For allegro I suggest to use a miniconda installation. Note that you only need these packages if you want to use some of it on the cluster like run openmm or make computations using pyemma. Just for running, say `acemd` conda is not required!
+For allegro I suggest to use a miniconda installation. Note that you only need these packages if you want to use some of it on the cluster like run openmm or make computations using pyemma. Just for running, say `acemd`, conda is not required!
 
 That's it. Have fun running adaptive simulations.
 

diff --git a/adaptivemd/tests/test_simple.py b/adaptivemd/tests/test_simple.py
@@ -66,51 +66,55 @@
     pdb = md.load('../../examples/files/alanine/alanine.pdb')
     cwd = os.getcwd()
 
-    # this part fakes a running worker without starting the worker process
-    worker = WorkerScheduler(project.resource)
-    worker.enter(project)
+    # we are using only the scheduling and excution logic, not a real
+    # separate worker task
+    scheduler = WorkerScheduler(project.resource)
+    scheduler.enter(project)
 
-    worker.submit(task)
+    scheduler(task)
 
     assert(len(project.trajectories) == 0)
 
     while not task.is_done():
-        worker.advance()
+        scheduler.advance()
 
     assert(len(project.trajectories) == 1)
 
     traj_path = os.path.join(
-        worker.path,
-        'workers',
-        'worker.' + hex(task.__uuid__),
-        worker.replace_prefix(project.trajectories.one.url)
+        scheduler.path,
+        'projects',
+        'example-simple-1',
+        'trajs',
+        '00000000',
+        'output.dcd'
     )
 
     assert(os.path.exists(traj_path))
 
     # go back to the place where we ran the test
     traj = md.load(traj_path, top=pdb)
 
-    assert(len(traj) == 100)
+    # 100 simulation steps + initial one should be 101 frames long
+    assert(len(traj) == 101)
 
     # well, we have a 100 step trajectory which matches the size of the initial PDB
     # that is a good sign
 
     # extend the trajectory by 50
     task2 = task.extend(50)
 
-    worker.submit(task2)
+    scheduler.submit(task2)
 
     while not task2.is_done():
-        worker.advance()
+        scheduler.advance()
 
     # should still be one, since we have the same trajectory
     assert(len(project.trajectories) == 1)
 
     traj = md.load(traj_path, top=pdb)
 
-    assert (len(traj) == 150)
+    assert (len(traj) == 151)
 
-    # after extension it is 150 frames. Excellent
+    # after extension it is 101 + 50 = 151 frames. Excellent
 
     project.close()
diff --git a/examples/tutorial/1_example_setup_project.ipynb b/examples/tutorial/1_example_setup_project.ipynb
@@ -114,7 +114,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {
     "collapsed": false
    },
@@ -132,7 +132,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {
     "collapsed": false
    },
@@ -150,7 +150,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {
     "collapsed": false
    },
@@ -161,7 +161,7 @@
        "'$HOME/adaptivemd/'"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -197,7 +197,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false
    },
@@ -215,7 +215,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 9,
    "metadata": {
     "collapsed": true
    },
@@ -240,7 +240,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 10,
    "metadata": {
     "collapsed": false
    },
@@ -265,7 +265,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "metadata": {
     "collapsed": true
    },
@@ -283,11 +283,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'alanine.pdb'"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "pdb_file.load()"
    ]
@@ -320,7 +331,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 48,
+   "execution_count": 13,
    "metadata": {
     "collapsed": true
    },
@@ -345,7 +356,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 49,
+   "execution_count": 14,
    "metadata": {
     "collapsed": false
    },
@@ -370,7 +381,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 50,
+   "execution_count": 15,
    "metadata": {
     "collapsed": false
    },
@@ -381,7 +392,7 @@
        "'openmm'"
       ]
      },
-     "execution_count": 50,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -401,7 +412,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 51,
+   "execution_count": 16,
    "metadata": {
     "collapsed": false
    },
@@ -420,7 +431,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 52,
+   "execution_count": 17,
    "metadata": {
     "collapsed": true
    },
@@ -438,7 +449,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 53,
+   "execution_count": 18,
    "metadata": {
     "collapsed": false
    },
@@ -485,7 +496,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 54,
+   "execution_count": 19,
    "metadata": {
     "collapsed": false
    },
@@ -546,7 +557,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 56,
+   "execution_count": 20,
    "metadata": {
     "collapsed": false
    },
@@ -557,7 +568,7 @@
        "Trajectory('alanine.pdb' >> [0..100])"
       ]
      },
-     "execution_count": 56,
+     "execution_count": 20,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -596,7 +607,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 61,
+   "execution_count": 21,
    "metadata": {
     "collapsed": false
    },
@@ -622,7 +633,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 64,
+   "execution_count": 22,
    "metadata": {
     "collapsed": false
    },
@@ -631,7 +642,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Frame(sandbox:///{}/00000001/[20])\n"
+      "Frame(sandbox:///{}/00000000/[20])\n"
      ]
     }
    ],
@@ -648,7 +659,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 65,
+   "execution_count": 23,
    "metadata": {
     "collapsed": false
    },
@@ -657,7 +668,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "<adaptivemd.engine.engine.TrajectoryExtensionTask object at 0x110e6e210>\n"
+      "<adaptivemd.engine.engine.TrajectoryExtensionTask object at 0x112c757d0>\n"
      ]
     }
    ],
@@ -674,7 +685,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 66,
+   "execution_count": 24,
    "metadata": {
     "collapsed": false
    },
@@ -683,7 +694,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "<adaptivemd.engine.engine.TrajectoryGenerationTask object at 0x110dd46d0>\n"
+      "<adaptivemd.engine.engine.TrajectoryGenerationTask object at 0x112c75450>\n"
      ]
     }
    ],