Merge pull request #29 from eirrgang/release-0.0.5

Release 0.0.5

.travis.yml

@@ -30,6 +30,11 @@ matrix:
       - gmxapi_DIR=$HOME/gromacs
       - GROMACS_DIR=$HOME/gromacs
 
+# It is clearly a bad idea to have the development branch of a project requiring the development branch
+# of another project in the primary build recipe. We either need to build and test development and master
+# branches distinctly in a build matrix, only build off of tagged releases or the master branch of the
+# dependency, or otherwise find a better solution that allows the master branch to be entirely included in
+# the develop branch.
 before_install:
   - uname -a
   - apt list --installed
@@ -46,7 +51,7 @@ install:
   - make -j4 install
   - popd
   - popd
-  # pip 10 appears to be broken
+  # pip 10.0.0 appears to be broken
   - python -m pip install --upgrade pip==9 --user
   - python -m pip install --upgrade setuptools --user
   - python -m pip install virtualenv --user

CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_minimum_required(VERSION 3.4.3)
 #list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 # Sets the PROJECT_VERSION variable, as well...
-project(gmxpy VERSION 0.0.4)
+project(gmxpy VERSION 0.0.5)
 
 add_subdirectory(pybind11)
 

RELEASE.txt

@@ -0,0 +1,18 @@
+Future release notes go here...
+
+When a new release is about to be tagged, version and release information needs to be updated in a few places.
+
+Once the required features in gromacs-gmxapi have been merged to its master branch, update the several lines in
+.travis.yml to reference the gromacs-gmxapi release archive instead of master or a development branch.
+
+Similarly, update the `gromacs_url` embedded in setup.py
+
+After merging the gmxapi development branch to master and before tagging the release, 
+update setup.py so that it writes a version.py file with `release = True`.
+
+Once the release is tagged and any last-minute essentials are cherry-picked to the refreshed development branch,
+bump the version in the development branch in CMakeLists.txt _and_ in setup.py. If / when feature branches
+require new libgmxapi features, `find_package(gmxapi...` can be updated in `src/gmx/core/CMakeLists.txt`. While
+we have the package version check set to REQUIRED, this is probably an immediate update. Sometime after 0.1.0,
+though, we hope we can have some backwards compatibility and leave the libgmxapi version more flexible.
+

docker/Dockerfile

@@ -0,0 +1,32 @@
+# Build container for gmxapi/gmxapi:<tag>
+# Initially we will use a tmpi libgromacs and openmpi mpi4py
+
+FROM gmxapi/gromacs-gmxapi:0.0.5
+
+# Allow build for an arbitrary branch or tag, but default to the tip of `master`
+ARG BRANCH=master
+
+RUN conda install pytest tox cmake
+
+# At least one conda release does not leave tox executable...
+# However, tox doesn't seem to be helping us here...
+# RUN chmod a+x /opt/conda/bin/tox
+
+# Note default for the base image at this point is Python3
+RUN pip install --upgrade pip && \
+    pip install sphinx mpi4py
+
+RUN pip install --upgrade setuptools --user
+
+#ADD --chown=1000:100 gmxpy /home/jovyan/gmxpy
+
+RUN wget https://github.com/kassonlab/gmxapi/archive/$BRANCH.zip && \
+    unzip $BRANCH.zip && \
+    mv gmxapi-$BRANCH /home/jovyan/gmxpy && \
+    rm $BRANCH.zip
+
+RUN (cd /home/jovyan/gmxpy && \
+    gmxapi_DIR=/home/jovyan/install/gromacs pip install . --upgrade --verbose)
+
+# Test with
+#    docker run --cpus 2 --rm -ti gmxapi/gmxapi bash -c "cd gmxpy && mpiexec -n 2 python -m mpi4py -m pytest  --log-cli-level=DEBUG --pyargs gmx -s --verbose"

docs/components/plugins.rst

@@ -1,7 +1,10 @@
 ====================
 Simulation internals
 ====================
+.. toctree::
+    :hidden:
 
+    ../examples/externalForce
 
 The applied_forces facility implemented for the electric field module has become
 the starting point for discussions on API requirements to allow less tightly
@@ -17,6 +20,8 @@ an interface that prevents misuse, provides the minimal access, and hides the
 implementation sufficiently that external or higher-level code cannot invalidate
 assumptions made for optimizations in the core code.
 
+Simulation plugins are further discussed in :doc:`../examples/externalForce`
+
 Simulation loop
 ===============
 

docs/developerguide.rst

@@ -5,6 +5,7 @@ Developer Guide
 
 .. toctree::
 
+    intro
     projectstructure
     design
     components

docs/index.rst

@@ -9,9 +9,8 @@ based on a GROMACS fork hosted at https://bitbucket.org/kassonlab/gromacs
     :maxdepth: 2
     :caption: Documentation sections
 
-    intro
-    guides
-    reference
+    userguide
+    developerguide
     changelog
 
 ..