Merge pull request #161 from Autodesk/intro_experience

Test coverage and bug fixes

.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
+

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:

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

codeship-services.yml

@@ -23,7 +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
@@ -37,7 +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
@@ -51,7 +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
@@ -65,7 +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

@@ -60,22 +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
 
 - name: publish
   service: publisher
   # 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
+  command: deployment/publish.sh
 

deployment/codeship_runtests.sh

@@ -1,18 +1,18 @@
 #!/usr/bin/env bash
-# this script expects to run from the moldesign/_tests directory
+# this script expects to run from the root of the repository
 
 # fail immediately if any command fails:
 set -e
 
 VERSION="${TESTENV}.py${PYVERSION}"
 PYTESTFLAGS="-n 6 --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=1800"
 if [ "${VERSION}" == "complete.py3" ]; then
-       PYTESTFLAGS="--cov .. --cov-config=./.coveragerc ${PYTESTFLAGS}"
+       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}"
 }
 
 
@@ -54,6 +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]}
 

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/requirements.txt

@@ -1,7 +1,9 @@
 # Python dependencies for the build/test environment
 coveralls
+nbformat
 pathlib ; python_version < '3.5'
 PyGithub
 pytest-cov
 pytest-xdist != 1.17.0
 pytest-timeout
+

moldesign/HISTORY.rst

@@ -1,12 +1,13 @@
 0.8 - WIP
 =========
 Changes:
+  - Simultaneous Python 2/3 compatibility
   - To make installation easier, we've removed all Jupyter-specific functionality to the
-     ``Autodesk/mdtwidgets`` project (formerly known as ``nbolviz``), which vastly simplifies
-     MDT's dependencies. To use the notebook visualization utilities, run `pip install mdtwidgets`
+     which vastly simplifies
+     MDT's dependencies. To use the notebook visualization utilities, run `pip install nbmolviz`
 
 NEW MODELING FEATURES
-  - QM/MM
+  - NWChem QM
 
 
 0.7.3 - October 17, 2016

moldesign/__init__.py

@@ -43,6 +43,7 @@
 from . import molecules
 from . import tools
 from . import widgets
+from .widgets import configure, about
 
 # Populate the top-level namespace (imports everything from each <submodule>.__all__ variable)
 from .exceptions import *