Merge pull request #47 from jag1g13/release/1.0.2

Release/1.0.2

.github/workflows/python-package.yml

@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+        os: [ubuntu-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install project and dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -r requirements.txt mdtraj
+        pip install pytest coverage
+
+    - name: Test with pytest
+      run: |
+        coverage run --source=pycgtool -m pytest
+        coverage report --skip-covered

.gitignore

@@ -1,14 +1,39 @@
+# Data
+/*.gro*
+/*.itp*
+/*.xtc*
+/fftest.ff/
+/gromacs/
+*.offsets
+
+# Dependencies and runtime
+/.venv/
+/env/
+/minenv/
+/venv/
 *.pyc
+poetry.toml
+
+# Development and Testing
+.cache
+.coverage
+.python-version
+.tox/
+/build/
+/cover/
+/dist/
+/docs/_build/
+/htmlcov/
+/pycgtool.egg-info/
+/tmp/
+
+# IDE files
 .idea/
+.vscode/
+settings.json
+
+# Misc
 .cache/
-/*.gro
-/*.itp
-/fftest.ff
-/env
-/minenv
-.coverage
-/cover
-/tmp
-/doc/build
-/nose2-junit.xml
+/notes/
 *.offsets
+*.pkl

pycgtool/frame.py

@@ -111,7 +111,7 @@ class Frame:
     """
     Hold Atom data separated into Residues
     """
-    def __init__(self, gro=None, xtc=None, itp=None, frame_start=0, xtc_reader="simpletraj"):
+    def __init__(self, gro=None, xtc=None, itp=None, frame_start=0, xtc_reader=None):
         """
         Return Frame instance having read Residues and Atoms from GRO if provided
 
@@ -132,7 +132,7 @@ def __init__(self, gro=None, xtc=None, itp=None, frame_start=0, xtc_reader="simp
 
         if gro is not None:
             from .framereader import get_frame_reader
-            self._trajreader = get_frame_reader(gro, traj=xtc, frame_start=frame_start)
+            self._trajreader = get_frame_reader(gro, traj=xtc, frame_start=frame_start, name=xtc_reader)
 
             self._trajreader.initialise_frame(self)
 

pycgtool/interface.py

@@ -227,7 +227,7 @@ def __init__(self, maxits, length=20, dowhile=None, quiet=False):
         self._dowhile = dowhile
         self._quiet = quiet
         self._its = -1
-        self._start_time = time.clock()
+        self._start_time = time.perf_counter()
 
     def __len__(self):
         """
@@ -298,13 +298,13 @@ def _bar(self):
 
     def _stop(self):
         if not self._quiet:
-            time_taken = int(time.clock() - self._start_time)
+            time_taken = int(time.perf_counter() - self._start_time)
             print(self._bar + " took {0}s".format(time_taken))
         raise StopIteration
 
     def _display(self):
         try:
-            time_remain = int((time.clock() - self._start_time) * ((self._maxits - self._its) / self._its))
+            time_remain = int((time.perf_counter() - self._start_time) * ((self._maxits - self._its) / self._its))
         except ZeroDivisionError:
             time_remain = "-"
         print(self._bar + " {0}s left".format(time_remain), end="\r")

pycgtool/util.py

@@ -270,11 +270,18 @@ def sliding(vals):
     """
     it = iter(vals)
     prev = None
-    current = next(it)
+
+    try:
+        current = next(it)
+
+    except StopIteration:
+        raise ValueError('Iterable contains no items')
+
     for nxt in it:
         yield (prev, current, nxt)
         prev = current
         current = nxt
+
     yield (prev, current, None)