Refresh tests (mdtraj#1266)

* Re-work tests

* Remove get_fn

* Modify examples to not use get_fn

* Switch to relative imports

* Remove redundant DelayImportError

* Use `is` to compare to None

* Relative imports

* Relative imports

* Use `is` to compare to None

* Error checking

* Relative imports

* Topology hash

* Trajectory updates

 - initialize traces
 - add .dtr file format

* Remove package data

* fix test_xtc

* Spruce up shiftx2 wrapper

* Whoops ... revert skip logic for shiftx2

* No crazy recipe

* Latest numpy

* update doc building requirements

* Bump appveyor matrix

* Logic to skip openmm notebook where applicable

* py2 special logic for comparing longs

* skip shiftx2 test on travis

Author: mpharrigan

.travis.yml

@@ -24,18 +24,18 @@ os:
 
 env:
   - CONDA_PY=2.7 CONDA_NPY=1.7
-  - CONDA_PY=2.7 CONDA_NPY=1.11
-  - CONDA_PY=3.4 CONDA_NPY=1.10
+  - CONDA_PY=2.7
   - CONDA_PY=3.5 CONDA_NPY=1.11
+  - CONDA_PY=3.6
 
 # Do include/exclude to add "DOCDEPLOY" to one matrix entry.
 matrix:
   exclude:
     - os: linux
-      env: CONDA_PY=3.5 CONDA_NPY=1.11
+      env: CONDA_PY=3.6
   include:
     - os: linux
-      env: CONDA_PY=3.5 CONDA_NPY=1.11 DOCDEPLOY=YES
+      env: CONDA_PY=3.6 DOCDEPLOY=YES
 
 deploy:
   - provider: s3

appveyor.yml

@@ -8,18 +8,14 @@ environment:
 
   matrix:
     - PYTHON: "C:\\Miniconda3"
-      CONDA_PY: "35"
-      CONDA_NPY: "1.10"
+      CONDA_PY: "36"
     - PYTHON: "C:\\Miniconda3"
       CONDA_PY: "27"
-      CONDA_NPY: "1.10"
     - PYTHON: "C:\\Miniconda3-x64"
       CONDA_PY: "27"
-      CONDA_NPY: "1.10"
       ARCH: "64"
     - PYTHON: "C:\\Miniconda3-x64"
-      CONDA_PY: "35"
-      CONDA_NPY: "1.10"
+      CONDA_PY: "36"
       ARCH: "64"
 
 install:

devtools/conda-recipe/meta.yaml

@@ -15,41 +15,52 @@ build:
 requirements:
   build:
     - python
-    - cython
-    - numpy x.x
-    - msinttypes #  [win and py2k]
     - setuptools
-    - zlib
+    - cython
+    - numpy
+    - zlib 1.2.8
+    - msinttypes  # [win and py27]
 
   run:
     - python
     - setuptools
-    - numpy x.x
-    - pandas
+    - numpy
     - scipy
+    - pandas
     - pytables
 
 test:
   requires:
-    - nose
-    - scripttest
+    - pytest
     - networkx
     - matplotlib
-    - pandas
     - openmm  # [not (win32 or (win and py2k))]
-    - shiftx2 # [linux]
+    - shiftx2  # [linux and py2k]
     - nbformat
     - ipykernel
     - scikit-learn
 
   source_files:
     - examples/*
+    - pytest.ini
+    - tests/*
+
+  imports:
+    - mdtraj
 
   commands:
-    - nosetests mdtraj -v -s
-    - cd examples && nosetests test_examples.py -v -s # [not (win32 or (win and py2k))]
+    - pytest
 
 about:
-  home: http://mdtraj.org
-  license: GNU Lesser General Public License v2 or later (LGPLv2+)
-  summary: A modern, open library for the analysis of molecular dynamics trajectories (development snapshot)
+  home: https://github.com/mdtraj/mdtraj
+  license: LGPL-2.1
+  summary: "A modern, open library for the analysis of molecular dynamics trajectories"
+  description: |
+    MDTraj is a python library that allows users to manipulate molecular dynamics
+    (MD) trajectories and perform a variety of analyses, including fast RMSD,
+    solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
+    is the wide variety of molecular dynamics trajectory file formats which are
+    supported, including RCSB pdb, GROMACS xtc, tng, and trr, CHARMM / NAMD dcd, AMBER
+    binpos, AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5.
+  doc_url: http://mdtraj.org/
+  dev_url: https://github.com/mdtraj/mdtraj

docs/requirements.txt

@@ -1,6 +1,6 @@
 sphinx
 matplotlib
-ipython-notebook
+jupyter
 jinja2
 runipy
 openmm

mdtraj/testing/reference/frame0.h5 renamed to examples/data/frame0.h5

@@ -3,9 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from __future__ import print_function\n",
@@ -37,13 +35,10 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "import mdtraj.testing\n",
-    "traj_filename = mdtraj.testing.get_fn('frame0.h5')"
+    "traj_filename = 'data/frame0.h5'"
    ]
   },
   {
@@ -58,9 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "first_frame = md.load_frame(traj_filename, 0)\n",
@@ -69,9 +62,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "source": [
     "Using `md.iterload`, you can iterate through chunks\n",
     "of the trajectory. If you don't retain a reference to the chunk\n",
@@ -82,9 +73,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "rmsds = []\n",
@@ -104,9 +93,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "rmsds = np.concatenate(rmsds)\n",
@@ -118,7 +105,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python",
    "language": "python",
    "name": "python3"
   },
@@ -132,9 +119,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.1"
+   "version": "3.5.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }

mdtraj/testing/reference/frame0.xtc renamed to examples/data/frame0.xtc

@@ -3,9 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
@@ -17,29 +15,23 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Find two files that are distributed with MDTraj for testing purposes -- \n",
-    "we can us them to make our plot"
+    "Use two files that are distributed with MDTraj examples"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "import mdtraj.testing\n",
-    "crystal_fn = mdtraj.testing.get_fn('native.pdb')\n",
-    "trajectory_fn = mdtraj.testing.get_fn('frame0.xtc')"
+    "crystal_fn = 'data/native.pdb'\n",
+    "trajectory_fn = 'data/frame0.xtc'"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "crystal = md.load(crystal_fn)\n",
@@ -58,9 +50,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "rmsds_to_crystal = md.rmsd(trajectory, crystal, 0)\n",
@@ -71,20 +61,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "from matplotlib.pylab import *\n",
-    "\n",
-    "figure()\n",
-    "plot(trajectory.time, rmsds_to_crystal, 'r', label='all atom')\n",
-    "plot(trajectory.time, heavy_rmds_to_crystal, 'b', label='heavy atom')\n",
-    "legend()\n",
-    "title('RMSDs to crystal')\n",
-    "xlabel('simulation time (ps)')\n",
-    "ylabel('RMSD (nm)')"
+    "from matplotlib import pyplot as plt\n",
+    "plt.plot(trajectory.time, rmsds_to_crystal, 'r', label='all atom')\n",
+    "plt.plot(trajectory.time, heavy_rmds_to_crystal, 'b', label='heavy atom')\n",
+    "plt.legend()\n",
+    "plt.title('RMSDs to crystal')\n",
+    "plt.xlabel('simulation time (ps)')\n",
+    "plt.ylabel('RMSD (nm)')"
    ]
   }
  ],
@@ -104,9 +90,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.1"
+   "version": "3.5.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }