Merge master commit '939ed29769f971374982a0663dcd3ab22d5f74a4' into n…

…wchem_qmmm

# Conflicts:
#	moldesign/_tests/helpers.py
#	moldesign/_tests/test_qm_xfaces.py
#	moldesign/compute/compute.py
#	moldesign/fileio.py
#	moldesign/orbitals/wfn.py

.coveragerc

@@ -0,0 +1,33 @@
+[paths]
+source =
+  moldesign
+  */site-packages/moldesign
+  */dist-packages/moldesign
+
+
+[run]
+source = moldesign
+omit =
+   moldesign/_notebooks/*
+   moldesign/_tests/*
+   moldesign/_static_data/*
+   moldesign/_version.py
+   moldesign/external/*
+   moldesign/widgets.py
+   moldesign/interfaces/nbo_interface.py
+   moldesign/utils/_deadfunctions.py
+   moldesign/utils/docparsers/google.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    def __str__
+    def _repr_markdown_
+    raise AssertionError
+    raise NotImplementedError
+    if PY2
+    if future.utils.PY2
+    def show
+    def unshow
+

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,16 @@
+<!-- Delete the text below if you're not filing a bug report -->
+## Bug report
+#### Description
+<!-- A quick description of what's going wrong -->
+
+#### Steps to reproduce
+<!-- If possible, show us how to reproduce the bug, INCLUDING any error messages you receive -->
+
+```python
+### code to reproduce the bug goes here ###
+```
+
+#### Environment
+  - Operating system: <!-- e.g., "MacOS 10.12.3" or "Debian 8.8"-->
+  - `python --version` output: <!-- e.g., "2.7.13" or "Python 3.5.2 :: Continuum Analytics, Inc."-->
+  - `pip show moldesign nbmolviz | grep -B1 Version` output:

DEVELOPMENT.md

@@ -1,32 +1,33 @@
 # DEVELOPING MDT
 
 ### Setting up a dev environment
-(WIP)
+(still under construction)
 
-### Install prerequisites (first time only)
-To make these instructions reasonably cross-platform, we'll use pyenv as the python environment manager. 
+### Install prequisites (first time only)
+You need to install docker, and an environment manager for Python 3 (Miniconda 3). Here's one way to do that:
 1. Install docker: [link]
 2. Install pyenv and pyenv-venv: [link]
-3. Install miniconda2 by running: `pyenv install miniconda2-latest`
-4. Switch to miniconda environment by running: `pyenv shell miniconda2-latest`
+3. Install miniconda3 by running: `pyenv install miniconda3-latest`
+4. Switch to miniconda environment by running: `pyenv shell miniconda3-latest`
 
 ### Set up your environment (first time only)
-1. Change directory to the base of the `molecular-design-toolkit` repository
+1. Get MDT: `git clone http://github.com/Autodesk/molecular-design-toolkit`
+1. `cd molecular-design-toolkit`
 1. Create conda environment (optional but recommended) by running: [command to create conda env]
-2. Activate the environment: `pyenv shell [environment name???]`
-1. Install dev dependencies: `pip install -r requirements.txt DockerMakefiles/requirements.txt moldesign/_tests/requirements.txt`
+2. Activate the environment: `pyenv activate [environment name???]`
+1. Install dev dependencies: `pip install -r requirements.txt DockerMakefiles/requirements.txt deployment/requirements.txt`
 2. Set up for local dev mode (this tells MDT to use your local docker containers):
 ```bash
 mkdir ~/.moldesign
 echo "devmode: true" > ~/.moldesign/moldesign.yml
 ```
-8. Link your installation within your environment
+8. Install MDT in "development mode": 
 ```
 pip install -e molecular-design-toolkit
 ```
 
 ### To activate environment (in any new shell)
-1. Run `pyenv shell [environment name???]`
+1. Run `pyenv activate [environment name???]`
 
 ### To rebuild docker images (first time and after changes that affect dockerized code)
 5. Build development versions of all docker images:
@@ -87,9 +88,18 @@ are considered "stable".
 
 ### Releases
 
-1. Decide on the new version number (using [semantic versioning](http://semver.org/)). For our purposes here, we'll pretend it's `0.9.3`.
+1. Decide on the new version number (see below). For our purposes here, we'll pretend it's `0.9.3`.
 1. Tag the relevant commit (the build must be passing) with a release candidate version number, e.g., `0.9.3rc1`.
-1. Codeship will automatically deploy the updated release to PyPI and DockerHub (still WIP 5/17)
+1. Codeship will automatically deploy the updated release to PyPI and DockerHub
+1. Manually test the example notebooks against this pre-release version.
+1. If succesful, tag the relevant commit with the official release version `0.9.3`
+
+### Versioning
+For now, we're using a subset [PEP 440](https://www.python.org/dev/peps/pep-0440/):
+1. Every release should be of the form MAJOR.MINOR.PATCH, e.g. `0.1.2`
+2. Pre-releases should be numbered consecutively, and may be alpha, beta, or "release candidate", e.g. `1.0.1rc3` or `0.5.3a1`
+3. Our deployment infrastructure uses this regular expression to accept version strings:
+`^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$`
 
 ### Maintainers: updating the documentation
 

DockerMakefiles/Moldesign.yml

@@ -17,7 +17,8 @@ moldesign_minimal_requirements:
    && apt-get install -y gcc \
    && pip install -r /tmp/mdtreqs.txt
   COPY . /opt/molecular-design-toolkit
-  RUN pip install -e /opt/molecular-design-toolkit
+  WORKDIR /opt/molecular-design-toolkit
+  RUN python setup.py sdist && pip install `ls -t dist/*.tar.gz | head -n1`
 
 moldesign_minimal:
   requires:

DockerMakefiles/requirements.txt

@@ -1 +1 @@
-DockerMake >= 0.5.3
+DockerMake >= 0.5.6

MANIFEST.in

@@ -7,6 +7,7 @@ include CONTRIBUTING.md
 include DEVELOPMENT.md
 include NOTICES
 include moldesign/HISTORY.rst
+include .coveragerc
 recursive-include moldesign/_static_data *.*
 recursive-include moldesign/_notebooks *.*
 global-exclude *.py[cod] __pycache__ *~ *.bak

README.md

@@ -1,10 +1,11 @@
 <img src="moldesign/_notebooks/img/Header.png">
 
-[![PyPI version](https://badge.fury.io/py/moldesign.svg)](https://badge.fury.io/py/moldesign)
-[![GitHub version](https://badge.fury.io/gh/autodesk%2Fmolecular-design-toolkit.svg)](https://badge.fury.io/gh/autodesk%2Fmolecular-design-toolkit)
-<a href="https://github.com/autodesk/molecular-design-toolkit/blob/master/LICENSE" style="font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; background-color: rgb(70, 61, 84);"><img src="https://img.shields.io/badge/license-Apache%202-blue.svg"> </a>
-[ ![Codeship Status for Autodesk/molecular-design-toolkit](https://app.codeship.com/projects/5ed079f0-08f6-0135-3493-3696d72919a3/status?branch=master)](https://app.codeship.com/projects/214515)
-[![Coverage Status](https://coveralls.io/repos/github/Autodesk/molecular-design-toolkit/badge.svg?branch=master)](https://coveralls.io/github/Autodesk/molecular-design-toolkit?branch=master)
+[![PyPI version](https://img.shields.io/pypi/v/moldesign.svg?label=dev)](https://pypi.python.org/pypi/moldesign)
+[![github release tag](https://img.shields.io/github/release/autodesk/molecular-design-toolkit.svg?label=stable)](https://pypi.python.org/pypi/moldesign)
+![Python versions](https://img.shields.io/pypi/pyversions/moldesign.svg)
+[![License](https://img.shields.io/pypi/l/moldesign.svg)](LICENSE.md)
+[ ![Codeship Status for Autodesk/molecular-design-toolkit](https://img.shields.io/codeship/5ed079f0-08f6-0135-3493-3696d72919a3/master.svg)](https://app.codeship.com/projects/214515)
+[![Coverage Status](https://img.shields.io/coveralls/Autodesk/molecular-design-toolkit/master.svg)](https://coveralls.io/github/Autodesk/molecular-design-toolkit?branch=master)
 
 **Try it now:** [![Binder](http://mybinder.org/badge.svg)](http://mybinder.org:/repo/avirshup/mdt-gallery-test)
 

codeship-services.yml

@@ -10,9 +10,10 @@ docker_make:
 publisher:
   encrypted_env_file: deployment/tokens.crypt
   build:
-    context: .
-    dockerfile: ./deployment/build-env.dockerfile
+    context: ./deployment
+    dockerfile: ./moldesign-complete-cache.dockerfile
   add_docker: true
+  working_dir: /opt/molecular-design-toolkit
   volumes:
   - ./tmp/reports:/opt/reports
 
@@ -22,7 +23,7 @@ test_moldesign_minimal:
     context: ./deployment
     dockerfile: moldesign-minimal-cache.dockerfile
   cached: false  # do not cache this! It gets built before the cache is triggered
-  working_dir: /opt/molecular-design-toolkit/moldesign/_tests
+  working_dir: /opt/molecular-design-toolkit/
   add_docker: true
   environment:
     TESTENV: minimal
@@ -36,7 +37,7 @@ test_moldesign_minimal_py2:
     context: ./deployment
     dockerfile: moldesign-minimal-py2-cache.dockerfile
   cached: false  # do not cache this! It gets built before the cache is triggered
-  working_dir: /opt/molecular-design-toolkit/moldesign/_tests
+  working_dir: /opt/molecular-design-toolkit/
   add_docker: true
   environment:
     TESTENV: minimal
@@ -50,7 +51,7 @@ test_moldesign_complete:
     context: ./deployment
     dockerfile: moldesign-complete-cache.dockerfile
   cached: false  # do not cache this! It gets built before the cache is triggered
-  working_dir: /opt/molecular-design-toolkit/moldesign/_tests
+  working_dir: /opt/molecular-design-toolkit/
   add_docker: true
   environment:
     TESTENV: complete
@@ -64,7 +65,7 @@ test_moldesign_complete_py2:
     context: ./deployment
     dockerfile: moldesign-complete-py2-cache.dockerfile
   cached: false  # do not cache this! It gets built before the cache is triggered
-  working_dir: /opt/molecular-design-toolkit/moldesign/_tests
+  working_dir: /opt/molecular-design-toolkit/
   add_docker: true
   environment:
     TESTENV: complete

codeship-steps.yml

@@ -60,36 +60,22 @@
   service: docker_make
   command: docker-make --all --tag dev
 
-- command: ../../deployment/codeship_runtests.sh
+- command: deployment/codeship_runtests.sh
   service: test_moldesign_complete
   name: complete_test_py3
-- command: ../../deployment/codeship_runtests.sh
+- command: deployment/codeship_runtests.sh
   service: test_moldesign_minimal
   name: minimal_test_py3
-- command: ../../deployment/codeship_runtests.sh
+- command: deployment/codeship_runtests.sh
   service: test_moldesign_complete_py2
   name: complete_test_py2
-- command: ../../deployment/codeship_runtests.sh
+- command: deployment/codeship_runtests.sh
   service: test_moldesign_minimal_py2
   name: minimal_test_py2
 
-# TODO: test the merged versions of PRs; test additional environments sometimes
-
-#- name: code_coverage
-#  service: test_moldesign_complete
-#  command: cd /opt/molecular-design-toolkit/ && coveralls
-
 - name: publish
   service: publisher
-  # matches tags that are valid semantic versions
-  tag: '^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(-(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(\.(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*)?(\+[0-9a-zA-Z-]+(\.[0-9a-zA-Z-]+)*)?$'
-  type: serial
-  steps:
-    - command: exit 1 # test that the code has the right version (and test that it's a good semver?)
-      name: verify_version
-    - command: build any additional images for deployment (moldesign_notebook, at least?)
-      tag: build_notebook
-    - command: tag and push docker images
-      name: docker_deploy
-    - command: upload package to pypi
-      name: pypi_deploy
+  # matches tags that are valid PEP440 versions
+  tag: '^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$'
+  command: deployment/publish.sh
+

deployment/codeship_runtests.sh

@@ -1,21 +1,29 @@
 #!/usr/bin/env bash
+# this script expects to run from the root of the repository
 
-# this script expects to run from the moldesign/_tests directory
+# fail immediately if any command fails:
+set -e
 
 VERSION="${TESTENV}.py${PYVERSION}"
-PYTESTFLAGS="-n 6 --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=1800"
-if [ "${TESTENV}" == "complete" ]; then
-       PYTESTFLAGS="--cov .. --cov-config=./.coveragerc ${PYTESTFLAGS}"
+PYTESTFLAGS="-n 5 --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=1800 --tb=short"
+if [ "${VERSION}" == "complete.py3" ]; then
+       PYTESTFLAGS="--cov moldesign ${PYTESTFLAGS}"
 fi
 
 
 function send_status_update(){
-     python ../../deployment/send_test_status.py "${1}" "${2}"
+     python deployment/send_test_status.py "${1}" "${2}"
 }
 
 
 function check_if_tests_should_run(){
-    echo "Should I run the tests in this environment?"
+   echo "Should I run the tests in this environment?"
+   runthem=false
+
+   if [[ "${CI_COMMIT_MESSAGE}" == *"--fast-ci-tests"* && "${VERSION}" != "complete.py3" ]];  then
+       echo "NO: found \"--fast-ci-tests\" flag in commit message; run complete.py3 only"
+       exit 0
+   fi
 
    if [ "${TESTENV}" == "complete" ]; then
        runthem=true
@@ -38,7 +46,6 @@ function check_if_tests_should_run(){
      echo "SKIPPING tests in this environment."
      echo "To run these tests, add \"--testall\" to your commit message"
      echo "(or work in the dev or deploy branches)"
-     send_status_update 0 "Skipped (dev/deploy branches only)"
      exit 0
    fi
 }
@@ -47,6 +54,11 @@ function check_if_tests_should_run(){
 function run_tests(){
     send_status_update "na" "Starting tests for ${VERSION}"
 
+    echo
+    echo "Test command running in working dir '$(pwd)':"
+    echo "py.test ${PYTESTFLAGS}"
+    echo
+
     py.test ${PYTESTFLAGS} | tee /opt/reports/pytest.${VERSION}.log
     exitstat=${PIPESTATUS[0]}
 
@@ -57,7 +69,7 @@ function run_tests(){
 
     send_status_update "${exitstat}" "${statline}"
 
-    if [ "${TESTENV}" == "complete" ]; then
+    if [ "${VERSION}" == "complete.py3" ]; then
        if [[ ${exitstat} == 0 && "$CI_BRANCH" != "" ]]; then
           coveralls || echo "Failed to upload code coverage stats"
        else

deployment/moldesign-complete-cache.dockerfile

@@ -1,3 +1,6 @@
 FROM moldesign_complete:dev
 ADD requirements.txt provision_testrunner_image.sh /tmp/
 RUN cd /tmp && ./provision_testrunner_image.sh
+RUN pip install twine
+WORKDIR /opt/molecular-design-toolkit
+RUN pip install -r DockerMakefiles/requirements.txt

deployment/provision_testrunner_image.sh

@@ -1,5 +1,8 @@
 #!/usr/bin/env bash
+# Gets image ready to run tests
 
-mkdir -p ~/.moldesign \
- && echo devmode: true >> ~/.moldesign/moldesign.yml \
- && pip install -r ./requirements.txt
+set -e
+
+mkdir -p ~/.moldesign
+echo devmode: true >> ~/.moldesign/moldesign.yml
+pip install -r ./requirements.txt

deployment/publish.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# Publish a new release (triggered by a git tag that conforms to a PEP440 release)
+# Exit 1 if there's a mismatch between the git tag and the package's version
+# Expects to run in base directory
+
+# fail immediately if any command fails:
+set -e
+
+pyversion=$(python -m moldesign version | tail -n 1)
+
+if [ "${pyversion}" == "${CI_BRANCH}" ]; then
+  echo "Deploying version ${CI_BRANCH}"
+else
+  echo "Can't publish - moldesign package version '${pyversion}' differs from its Git tag '${CI_BRANCH}'"
+  exit 1
+fi
+
+docker-make -f DockerMakefiles/DockerMake.yml \
+            --repo docker.io/autodesk/moldesign: \
+            --tag ${pyversion} \
+            --all \
+            --push --user ${DOCKERHUB_USER} --token ${DOCKERHUB_PASSWORD}
+
+twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} dist/moldesign-${pyversion}.tar.gz

deployment/requirements.txt

@@ -1,6 +1,9 @@
 # Python dependencies for the build/test environment
+coveralls
+nbformat
+pathlib ; python_version < '3.5'
 PyGithub
 pytest-cov
-pytest-xdist
+pytest-xdist != 1.17.0
 pytest-timeout
-coveralls
+