Merge pull request #41 from dwhswenson/wizard

Simulation Setup Wizard

Author: dwhswenson

.coveragerc

@@ -7,3 +7,4 @@ exclude_lines =
     no-cov
     def __repr__
     raise NotImplementedError
+    __name__ == "__main__":

.github/workflows/test-suite.yml

@@ -28,16 +28,25 @@ jobs:
           - 3.8
           - 3.7
           - 3.6
+        INTEGRATIONS: [""]
+        include:
+          - CONDA_PY: 3.9
+            INTEGRATIONS: 'all-optionals'
 
     steps:
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
       - uses: actions/setup-python@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: ${{ matrix.CONDA_PY }}
       - name: "Install testing tools"
         run: python -m pip install -r ./devtools/tests_require.txt
+      - name: "Install integrations"
+        if: matrix.INTEGRATIONS == 'all-optionals'
+        run: conda install -c conda-forge -y openmm openmmtools mdtraj
       - name: "Install"
         run: |
           conda install pip
@@ -57,6 +66,8 @@ jobs:
           fi
           python autorelease_check.py --branch $BRANCH --even ${EVENT}
       - name: "Unit tests"
+        env:
+          PY_COLORS: "1"
         run: |
           python -c "import paths_cli"
           py.test -vv --cov --cov-report xml:cov.xml

docs/index.rst

@@ -60,6 +60,7 @@ wrappers around well-tested OPS code.
    plugins
    parameters
    workflows
+   wizard
    full_cli
    api/index
 

docs/wizard.rst

@@ -0,0 +1,8 @@
+.. _wizard:
+
+Writing tools for the Wizard
+============================
+
+The Wizard API is still rapidly in flux, and we don't recommend developing
+custom Wizard tools at this time. However, once its API is more stable, the
+Wizard will be extendable by outside developers.

paths_cli/commands/wizard.py

@@ -0,0 +1,12 @@
+import click
+from paths_cli.wizard.two_state_tps import TWO_STATE_TPS_WIZARD
+
+@click.command(
+    'wizard',
+    short_help="run wizard for setting up simulations",
+)
+def wizard():  # no-cov
+    TWO_STATE_TPS_WIZARD.run_wizard()
+
+CLI = wizard
+SECTION = "Simulation setup"

paths_cli/parsing/tools.py

@@ -0,0 +1,45 @@
+import numpy as np
+
+def custom_eval(obj, named_objs=None):
+    """Parse user input to allow simple math.
+
+    This allows certain user input to be treated as a simplified subset of
+    Python. In particular, this is intended to allow simple arithmetic. It
+    allows use of the modules numpy (as ``np``) and math, which provide
+    potentially useful functions (e.g., ``cos``) as well as constants (e.g.,
+    ``pi``).
+    """
+    string = str(obj)
+    # TODO: check that the only attribute access comes from a whitelist
+    # (parse the AST for that)
+    namespace = {
+        'np': __import__('numpy'),
+        'math': __import__('math'),
+    }
+    return eval(string, namespace)
+
+
+class UnknownAtomsError(RuntimeError):
+    pass
+
+def mdtraj_parse_atomlist(inp_str, n_atoms, topology=None):
+    """
+    n_atoms: int
+        number of atoms expected
+    """
+    # TODO: change n_atoms to the shape desired?
+    # TODO: enable the parsing of either string-like atom labels or numeric
+    indices = custom_eval(inp_str)
+
+    arr = np.array(indices)
+    if arr.dtype != int:
+        raise TypeError("Input is not integers")
+    if arr.shape != (1, n_atoms):
+        # try to clean it up
+        if len(arr.shape) == 1 and arr.shape[0] ==  n_atoms:
+            arr.shape = (1, n_atoms)
+        else:
+            raise TypeError(f"Invalid input. Requires {n_atoms} "
+                            "atoms.")
+
+    return arr

paths_cli/tests/parsing/test_tools.py

@@ -0,0 +1,18 @@
+import pytest
+import numpy.testing as npt
+import numpy as np
+import math
+
+from paths_cli.parsing.tools import *
+
+@pytest.mark.parametrize('expr,expected', [
+    ('1+1', 2),
+    ('np.pi / 2', np.pi / 2),
+    ('math.cos(1.5)', math.cos(1.5)),
+])
+def test_custom_eval(expr, expected):
+    npt.assert_allclose(custom_eval(expr), expected)
+
+def test_mdtraj_parse_atomlist_bad_input():
+    with pytest.raises(TypeError, match="not integers"):
+        mdtraj_parse_atomlist("['a', 'b']", n_atoms=2)

paths_cli/tests/test_parameters.py

@@ -42,7 +42,6 @@ def undo_monkey_patch(stored_functions):
     importlib.reload(paths)
 
 
-
 class ParameterTest(object):
     def test_parameter(self):
         # this is just a smoke test to contrast with the ValueError case

paths_cli/tests/utils.py

@@ -0,0 +1,18 @@
+import urllib.request
+
+try:
+    urllib.request.urlopen('https://www.google.com')
+except:
+    HAS_INTERNET = False
+else:
+    HAS_INTERNET = True
+
+def assert_url(url):
+    if not HAS_INTERNET:
+        pytest.skip("Internet connection seems faulty")
+
+    # TODO: On a 404 this will raise a urllib.error.HTTPError. It would be
+    # nice to give some better output to the user here.
+    resp = urllib.request.urlopen(url)
+    assert resp.status == 200
+