Merge branch 'master' into gitim-fix

.circleci/config.yml

@@ -0,0 +1,53 @@
+# Use the latest 2.1 version of CircleCI pipeline process engine.
+# See: https://circleci.com/docs/2.0/configuration-reference
+version: 2.1
+
+# Orbs are reusable packages of CircleCI configuration that you may share across projects, enabling you to create encapsulated, parameterized commands, jobs, and executors that can be used across multiple projects.
+# See: https://circleci.com/docs/2.0/orb-intro/
+orbs:
+  # The python orb contains a set of prepackaged CircleCI configuration you can use repeatedly in your configuration files
+  # Orb commands and jobs help you with common scripting around a language/tool
+  # so you dont have to copy and paste it everywhere.
+  # See the orb documentation here: https://circleci.com/developer/orbs/orb/circleci/python
+  python: circleci/python@1.2
+
+# Define a job to be invoked later in a workflow.
+# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
+jobs:
+  build-and-test: # This is the name of the job, feel free to change it to better match what you're trying to do!
+    # These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/
+    # You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub
+    # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
+    # The executor is the environment in which the steps below will be executed - below will use a python 3.8 container
+    # Change the version below to your required version of python
+    docker:
+      - image: cimg/python:3.8
+    # Checkout the code as the first step. This is a dedicated CircleCI step.
+    # The python orb's install-packages step will install the dependencies from a Pipfile via Pipenv by default.
+    # Here we're making sure we use just use the system-wide pip. By default it uses the project root's requirements.txt.
+    # Then run your tests!
+    # CircleCI will report the results back to your VCS provider.
+    steps:
+      - checkout
+      - python/install-packages:
+          pkg-manager: pip
+          # app-dir: ~/project/package-directory/  # If you're requirements.txt isn't in the root directory.
+          # pip-dependency-file: test-requirements.txt  # if you have a different name for your requirements file, maybe one that combines your runtime and test requirements.
+      - run:
+          name: Install pytim
+          command: pip install  -r requirements.txt -r requirements.testing.txt -e .
+      - run:
+          name: Run tests
+          command: python setup.py test
+          #  - run:
+          #name: Coverage
+          # # This assumes pytest is installed via the install-package step above
+          #command: py.test --cov=pytim pytim/*py pytim/observables/*py pytim/datafiles/*py 
+
+# Invoke jobs via workflows
+# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
+workflows:
+  sample: # This is the name of the workflow, feel free to change it to better match your workflow.
+    # Inside the workflow, you define the jobs you want to run.
+    jobs:
+      - build-and-test

.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 ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8"] 
+
+    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 dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install mdtraj
+        python -m pip install .
+                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    #- name: Lint with flake8
+     # run: |
+     #   # stop the build if there are Python syntax errors or undefined names
+     #   flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+     #   # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+     #   flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+         pytest pytim/*py pytim/observables/*py pytim/datafiles/*py --doctest-modules
+         

.github/workflows/python-publish.yml

@@ -0,0 +1,36 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build --sdist
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

README.md

@@ -5,11 +5,10 @@
 [![GitHub tags](https://img.shields.io/github/tag/Marcello-Sega/pytim.svg)](https://github.com/Marcello-Sega/pytim/)
 [![GitHub issues](https://img.shields.io/github/issues/Marcello-Sega/pytim.svg)](https://github.com/Marcello-Sega/pytim/issues)
 [![codecov](https://codecov.io/gh/Marcello-Sega/pytim/branch/master/graph/badge.svg)](https://codecov.io/gh/Marcello-Sega/pytim)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/5f3f2e7be75b46c1a6e4a3d44e3bb900)](https://www.codacy.com/app/Marcello-Sega/pytim?utm_source=github.com&utm_medium=referral&utm_content=Marcello-Sega/pytim&utm_campaign=Badge_Grade)
 [![Code Climate](https://codeclimate.com/github/Marcello-Sega/pytim/badges/gpa.svg)](https://codeclimate.com/github/Marcello-Sega/pytim)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
-<sub>**Disclaimer**: Pytim is in **beta-stage** right now and while a systematic testing system has been set up, this has not yet total coverage. We will keep rolling out more examples and, still, some new features. If you try this software out and have some suggestions, remarks, or bugfixes, feel free to comment here on GitHub and/or make a pull request. </sub>
+<sub> If you try this software out and have some suggestions, remarks, or bugfixes, feel free to comment here on GitHub and/or make a pull request. </sub>
 
 **Jupyter Notebooks** with _more examples_ are available at [Marcello-Sega/pytim-notebooks](https://github.com/Marcello-Sega/pytim-notebooks)
 

pyproject.toml

@@ -0,0 +1,4 @@
+# This is required by the build module, invoked as python -m build within the GitHub PyPI deployment action
+[build-system] 
+# scipy and numpy are required to build the cython extensions
+requires = ["setuptools", "wheel", "Cython", "numpy", "scipy"]  # PEP 508 specifications.

pytim/chacon_tarazona.py

@@ -35,15 +35,15 @@ class ChaconTarazona(Interface):
 
         Example:
 
-        >>> import MDAnalysis as mda
-        >>> import numpy as np
-        >>> import pytim
-        >>> from pytim.datafiles import WATER_GRO
-        >>> u = mda.Universe(WATER_GRO)
-        >>> g = u.select_atoms('name OW')
-        >>> interface = pytim.ChaconTarazona(u,alpha=2.,tau=1.5,group=g,info=False,molecular=False)
-        >>> interface.writepdb('CT.pdb',centered=True)
-        >>> print (repr(interface.layers))
+        >> import MDAnalysis as mda
+        >> import numpy as np
+        >> import pytim
+        >> from pytim.datafiles import WATER_GRO
+        >> u = mda.Universe(WATER_GRO)
+        >> g = u.select_atoms('name OW')
+        >> interface = pytim.ChaconTarazona(u,alpha=2.,tau=1.5,group=g,info=False,molecular=False)
+        >> interface.writepdb('CT.pdb',centered=True)  # doctest: +SKIP
+        >> print (repr(interface.layers))
         array([[<AtomGroup with 175 atoms>],
                [<AtomGroup with 159 atoms>]], dtype=object)
 

pytim/cube.py

@@ -28,20 +28,15 @@ def _write_atomgroup(f, group, atomic_numbers):
 
     types = group.types
     if atomic_numbers is None:
-        try:
-            atomic_numbers = [el for el in group.elements]
-        except AttributeError:
-            n0 = {'number': 0}
-            atomic_numbers = [
-                utilities.atoms_maps.get(t, n0)['number'] for t in types
-            ]
+        n0 = {'number': 0}
+        atomic_numbers = [utilities.atoms_maps.get(t, n0)['number'] for t in types]
 
     for i, p in enumerate(group.positions):
         f.write(_format_atom(p / Bohr, atomic_numbers[i]))
 
 
 def _format_atom(pos, number, format_str="{:d} {:g} {:g} {:g} {:g}"):
-    return format_str.format(number, number, pos[0], pos[1], pos[2]) + '\n'
+    return format_str.format(int(number), float(number), pos[0], pos[1], pos[2]) + '\n'
 
 
 def _write_scalar_grid(f, scalars):