From 86ee5fc1e2a5ed52ce3210d7f4f4444c9e19655c Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Mon, 20 Nov 2017 16:55:06 -0800
Subject: [PATCH 01/18] Use correct docker image names for releases

---
 codeship-services.yml      |  6 +++++
 codeship-steps.yml         | 46 +++++++++++++++++++++++++++-----------
 deployment/README.md       |  6 ++++-
 deployment/publish.sh      | 10 +++++++++
 deployment/pull-cache.sh   |  3 ++-
 deployment/push.sh         |  5 +++--
 deployment/run-ci-tests.sh | 27 +++++++++++++++++++---
 7 files changed, 83 insertions(+), 20 deletions(-)

diff --git a/codeship-services.yml b/codeship-services.yml
index ab5f69b..c5417bb 100644
--- a/codeship-services.yml
+++ b/codeship-services.yml
@@ -7,6 +7,8 @@ image_builder: &build-base
   add_docker: true
   cached: true
   working_dir: /opt/molecular-design-toolkit
+  environment: &repo
+    REPO: "docker.io/autodesk/moldesign:"
 
 
 publisher:
@@ -26,6 +28,7 @@ test_moldesign_minimal: &test-base
     args:
       baseimage: moldesign_minimal
   environment:
+    <<: *repo
     TESTENV: minimal
     PYVERSION: 3
     OPENMM_CPU_THREADS: 1
@@ -38,6 +41,7 @@ test_moldesign_minimal_py2:
     args:
       baseimage: moldesign_minimal_py2
   environment:
+    <<: *repo
     TESTENV: minimal
     PYVERSION: 2
     OPENMM_CPU_THREADS: 1
@@ -50,6 +54,7 @@ test_moldesign_complete:
     args:
       baseimage: moldesign_complete
   environment:
+    <<: *repo
     TESTENV: complete
     PYVERSION: 3
     OPENMM_CPU_THREADS: 1
@@ -62,6 +67,7 @@ test_moldesign_complete_py2:
     args:
       baseimage: moldesign_complete_py2
   environment:
+    <<: *repo
     TESTENV: complete
     PYVERSION: 2
     OPENMM_CPU_THREADS: 1
diff --git a/codeship-steps.yml b/codeship-steps.yml
index a6b8fa1..d4bfed8 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -1,13 +1,21 @@
+# Pull previous builds from DockerHub to use as a cache.
+# These images are tagged as [imagename]-cache
 - name: pull-cache
   service: image_builder
   command: deployment/pull-cache.sh
 
+# Build the python package to be tested (and uploaded to PyPI if this is a release)
+# The package is built in the "autodesk/moldesign:moldesign_py_build-[branch name]" image
 - name: build-sdist
   service: image_builder
-  command: docker-make moldesign_py_build
+  command: bash -c "docker-make moldesign_py_build
+            --repo ${REPO} --tag ${CI_BRANCH}
             --keep-build-tags
-            -f DockerMakefiles/DockerMake.yml --tag dev
+            -f DockerMakefiles/DockerMake.yml"
 
+# Build docker images for all test environments. They will be tagged as
+# autodesk/moldesign:[imagename]-[branchname]
+# (For the sake of parallelism, we also download other images that the tests depend on)
 - name: build-and-pull-images
   service: image_builder
   type: parallel
@@ -15,23 +23,28 @@
   - name: pull-dependent-images
     command: deployment/pull-chemdocker.sh
   - name: build_py3
-    command:
-         docker-make moldesign_minimal moldesign_complete
+    command: bash -c
+          "docker-make moldesign_minimal moldesign_complete
           -f DockerMakefiles/DockerMake.yml
-          --tag dev --keep-build-tags
-          --cache-repo moldesign --cache-tag cache
+          --repo ${REPO} --tag ${CI_BRANCH}
+           --keep-build-tags
+          --cache-repo moldesign --cache-tag cache"
   - name: build_py2
-    command:
-        docker-make moldesign_minimal_py2 moldesign_complete_py2
+    command: bash -c
+         "docker-make moldesign_minimal_py2 moldesign_complete_py2
          -f DockerMakefiles/DockerMake.yml
-         --tag dev --keep-build-tags
-         --cache-repo moldesign --cache-tag cache
+         --repo ${REPO} --tag ${CI_BRANCH}
+         --keep-build-tags
+         --cache-repo moldesign --cache-tag cache"
 
+
+# Push build artifacts to Dockerhub.
+# These are tagged as autodesk/moldesign:[imagename]-[branchame]-devbuild
 - name: push-images
   type: parallel
   steps:
     - name: push-artifacts
-      command: deployment/push.sh moldesign_minimal moldesign_py2
+      command: deployment/push.sh moldesign_minimal moldesign_py2 moldesign_py_build
                                   moldesign_complete moldesign_complete_py2
       service: publisher
     - type: serial
@@ -39,14 +52,17 @@
       steps:
         - name: build-notebook
           service: image_builder
-          command: docker-make moldesign_notebook
+          command: bash -c
+              "docker-make moldesign_notebook
               -f DockerMakefiles/DockerMake.yml
-              --tag dev --cache-repo moldesign --cache-tag cache
+              --repo ${REPO} --tag ${CI_BRANCH}
+              --cache-tag cache"
         - name: push-notebook
           service: publisher
           command: deployment/push.sh moldesign_notebook
 
 
+# Prints out internal information about the test environments
 - name: print-environments
   type: parallel
   services:
@@ -58,6 +74,7 @@
    - command: deployment/print-environment.sh
      name: env-report
 
+# Run the tests in each environment.
 - name: run-tests
   type: serial
   services:
@@ -69,6 +86,9 @@
    - command: deployment/run-ci-tests.sh
      name: testrunner
 
+# If this build is tagged with a PEP440-compliant version number AND the tests have passed,
+# upload the package to PyPI, and push the docker images to dockerhub as
+# autodesk/moldesign:[imagename]-[version-number]
 - name: publish-python
   service: publisher
   # matches tags that are valid PEP440 versions
diff --git a/deployment/README.md b/deployment/README.md
index 0602eb8..44507d8 100644
--- a/deployment/README.md
+++ b/deployment/README.md
@@ -1 +1,5 @@
-Files in this directory are for use with our Codeship CI/CD setup, and aren't generally useful outside of that context.
\ No newline at end of file
+Files in this directory are for use with our Codeship CI/CD setup,
+and aren't generally useful outside of that context.
+
+
+The build process is annotated in ../codeship-steps.yml
\ No newline at end of file
diff --git a/deployment/publish.sh b/deployment/publish.sh
index 8756aaa..b10de52 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -18,6 +18,16 @@ else
 fi
 
 
+# Push images
+for img in moldesign_minimal       \
+           moldesign_minimal_py2   \
+           moldesign_complete      \
+           moldesign_complete_py2  \
+           moldesign_notebook; do
+   docker push ${REPO}{$img}-${CI_BRANCH} | tee -a push.log | egrep -i 'pull|already'
+done
+
+
 # Copy build artifacts
 sdist=moldesign-${pyversion}.tar.gz
 docker run moldesign_py_build:dev -v ./tmp/dists:/hostdists  cp dist/${sdist} /hostdists
diff --git a/deployment/pull-cache.sh b/deployment/pull-cache.sh
index 737a51c..7c35b4c 100755
--- a/deployment/pull-cache.sh
+++ b/deployment/pull-cache.sh
@@ -14,7 +14,7 @@ function run-pull(){
     # pull an image. If successful, retags the image with the "cache" tag
     img=$1
     tag=$2
-    imgpath="autodesk/moldesign:${img}-${tag}"
+    imgpath="${REPO}${img}-${tag}"
 
     echocmd docker pull ${imgpath} | tee -a pull.log | egrep -i 'pull|already';
 
@@ -34,6 +34,7 @@ for img in moldesign_minimal       \
            moldesign_minimal_py2   \
            moldesign_complete      \
            moldesign_complete_py2  \
+           moldesign_py_build      \
            moldesign_notebook; do
    run-pull ${img} ${CI_BRANCH}-devbuild || run-pull ${img} master || \
    echo " --> Failed to pull cache for ${img}"
diff --git a/deployment/push.sh b/deployment/push.sh
index 53a54e4..79bbbbb 100755
--- a/deployment/push.sh
+++ b/deployment/push.sh
@@ -18,8 +18,9 @@ function echocmd() {
 docker login -u ${DOCKERHUB_USER} -p ${DOCKERHUB_PASSWORD}
 
 for img in $@; do
-    remote_img=autodesk/moldesign:${img}-${CI_BRANCH}-devbuild
+    local_img=${REPO}${img}-${CI_BRANCH}
+    remote_img=${local_img}-devbuild
 
-    echocmd docker tag ${img}:dev ${remote_img}
+    echocmd docker tag ${local_img} ${remote_img}
     echocmd docker push ${remote_img} | tee -a push.log | egrep -i 'push|already';
 done
\ No newline at end of file
diff --git a/deployment/run-ci-tests.sh b/deployment/run-ci-tests.sh
index be6d0f3..de341a1 100755
--- a/deployment/run-ci-tests.sh
+++ b/deployment/run-ci-tests.sh
@@ -1,7 +1,19 @@
 #!/usr/bin/env bash
+# Drives tests for our CI system. This looks for the following environment variables:
+# Defined by codeship
+# - CI_BRANCH
+# - CI_COMMIT_MESSAGE
+# Defined in ../codeship-services.yml
+# - TESTENV
+# - PYVERSION
 
 set -e  # fail immediately if any command fails
 
+if [ -z "${CI_BRANCH}" ]; then
+   echo "FAILURE: Variable \$CI_BRANCH not defined."
+   exit 1
+fi
+
 install_location=$(python -c "import moldesign, os; print(moldesign.__path__[0])")
 test_location=$(dirname "${install_location}")
 
@@ -19,22 +31,31 @@ function send_status_update(){
 
 function check_if_tests_should_run(){
    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 [[ "${CI_BRANCH}" =~ ^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$ ]]
+   then
+       echo "YES: this is a release version: \"${CI_BRANCH}\""
+       return 0
+   else  # otherwise, point to the appropriate docker image tag
+       mkdir -p ~/.moldesign
+       echo "default_version_tag: ${CI_BRANCH}" >> ~/.moldesign/moldesign.yml
+   fi
+
+
    if [ "${TESTENV}" == "complete" ]; then
-       runthem=true
        echo "YES: always run in 'complete' environment"
+       return 0
    fi
 
    case "${CI_BRANCH}" in
        master|deploy|dev)
-       runthem=true
        echo "YES: always run in branch \"${CI_BRANCH}\""
+       return 0
        ;;
    esac
 

From 7417a0a4a433487b772831d542d97d35760a1a88 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 21 Nov 2017 11:36:11 -0800
Subject: [PATCH 02/18] Better docker tag handling

---
 codeship-steps.yml                      | 26 ++++++++++++++-----------
 deployment/pull-cache.sh                |  2 +-
 deployment/{push.sh => push-and-tag.sh} | 10 ++++++----
 3 files changed, 22 insertions(+), 16 deletions(-)
 rename deployment/{push.sh => push-and-tag.sh} (55%)

diff --git a/codeship-steps.yml b/codeship-steps.yml
index d4bfed8..d94ba79 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -14,7 +14,7 @@
             -f DockerMakefiles/DockerMake.yml"
 
 # Build docker images for all test environments. They will be tagged as
-# autodesk/moldesign:[imagename]-[branchname]
+# [imagename]-dev
 # (For the sake of parallelism, we also download other images that the tests depend on)
 - name: build-and-pull-images
   service: image_builder
@@ -26,26 +26,30 @@
     command: bash -c
           "docker-make moldesign_minimal moldesign_complete
           -f DockerMakefiles/DockerMake.yml
-          --repo ${REPO} --tag ${CI_BRANCH}
-           --keep-build-tags
-          --cache-repo moldesign --cache-tag cache"
+          --tag dev
+          --keep-build-tags
+          --cache-tag cache"
   - name: build_py2
     command: bash -c
          "docker-make moldesign_minimal_py2 moldesign_complete_py2
          -f DockerMakefiles/DockerMake.yml
-         --repo ${REPO} --tag ${CI_BRANCH}
+         --tag dev
          --keep-build-tags
-         --cache-repo moldesign --cache-tag cache"
+         --cache-tag cache"
 
 
 # Push build artifacts to Dockerhub.
 # These are tagged as autodesk/moldesign:[imagename]-[branchame]-devbuild
-- name: push-images
+# For testing purposes, they are also tagged as
+# autodesk/moldesign:[imagename]-[branchname] (this is the tag that will be pushed
+# to dockerhub for successful releases)
+- name: tag-and-push-images
   type: parallel
   steps:
     - name: push-artifacts
-      command: deployment/push.sh moldesign_minimal moldesign_py2 moldesign_py_build
-                                  moldesign_complete moldesign_complete_py2
+      command: deployment/push-and-tag.sh
+          moldesign_minimal moldesign_py2 moldesign_py_build
+          moldesign_complete moldesign_complete_py2
       service: publisher
     - type: serial
       name: make-notebook
@@ -55,11 +59,11 @@
           command: bash -c
               "docker-make moldesign_notebook
               -f DockerMakefiles/DockerMake.yml
-              --repo ${REPO} --tag ${CI_BRANCH}
+              --tag dev
               --cache-tag cache"
         - name: push-notebook
           service: publisher
-          command: deployment/push.sh moldesign_notebook
+          command: deployment/push-and-tag.sh moldesign_notebook
 
 
 # Prints out internal information about the test environments
diff --git a/deployment/pull-cache.sh b/deployment/pull-cache.sh
index 7c35b4c..362aa1a 100755
--- a/deployment/pull-cache.sh
+++ b/deployment/pull-cache.sh
@@ -22,7 +22,7 @@ function run-pull(){
     if [ "$success" -ne 0 ]; then
        return ${success};
     else
-       docker tag ${imgpath} moldesign/${img}:cache
+       docker tag ${imgpath} ${img}:cache
     fi
 }
 
diff --git a/deployment/push.sh b/deployment/push-and-tag.sh
similarity index 55%
rename from deployment/push.sh
rename to deployment/push-and-tag.sh
index 79bbbbb..9046c4e 100755
--- a/deployment/push.sh
+++ b/deployment/push-and-tag.sh
@@ -18,9 +18,11 @@ function echocmd() {
 docker login -u ${DOCKERHUB_USER} -p ${DOCKERHUB_PASSWORD}
 
 for img in $@; do
-    local_img=${REPO}${img}-${CI_BRANCH}
-    remote_img=${local_img}-devbuild
+    build_img=${img}:dev
+    release_tag=${REPO}${img}-${CI_BRANCH}
+    artifact_tag=${release_tag}-devbuild
 
-    echocmd docker tag ${local_img} ${remote_img}
-    echocmd docker push ${remote_img} | tee -a push.log | egrep -i 'push|already';
+    echocmd docker tag ${build_img} ${release_tag}
+    echocmd docker tag ${build_img} ${artifact_tag}
+    echocmd docker push ${artifact_tag} | tee -a push.log | egrep -i 'push|already';
 done
\ No newline at end of file

From f4b797ecc70f4de02903dce3b386abbd82142ef9 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 21 Nov 2017 13:56:46 -0800
Subject: [PATCH 03/18] Better handling of the PyPI deploy archive

---
 codeship-services.yml             |  2 --
 codeship-steps.yml                | 15 +++++++++++++--
 deployment/publish.sh             | 18 +++++-------------
 deployment/run-ci-tests.sh        |  1 +
 deployment/test-version-number.sh | 22 ++++++++++++++++++++++
 5 files changed, 41 insertions(+), 17 deletions(-)
 create mode 100755 deployment/test-version-number.sh

diff --git a/codeship-services.yml b/codeship-services.yml
index c5417bb..6a110cb 100644
--- a/codeship-services.yml
+++ b/codeship-services.yml
@@ -2,8 +2,6 @@ image_builder: &build-base
   build:
     context: .
     dockerfile: ./deployment/build-env.dockerfile
-  volumes:
-    - ./tmp/dist:/opt/molecular-design-toolkit/dist
   add_docker: true
   cached: true
   working_dir: /opt/molecular-design-toolkit
diff --git a/codeship-steps.yml b/codeship-steps.yml
index d94ba79..c9d2400 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -90,12 +90,23 @@
    - command: deployment/run-ci-tests.sh
      name: testrunner
 
+
 # If this build is tagged with a PEP440-compliant version number AND the tests have passed,
 # upload the package to PyPI, and push the docker images to dockerhub as
 # autodesk/moldesign:[imagename]-[version-number]
-- name: publish-python
+- name: release
   service: publisher
   # matches tags that are valid PEP440 versions
+  type: serial
   tag: '^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$'
-  command: deployment/publish.sh
+  steps:
+   - type: parallel
+     services:
+       - test_moldesign_complete
+       - test_moldesign_complete_py2
+     steps:
+     - command: deployment/test-version-number.sh
+   - name: upload
+     command: deployment/publish.sh
+     service: publisher
 
diff --git a/deployment/publish.sh b/deployment/publish.sh
index b10de52..d2c40c9 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -8,17 +8,11 @@
 # 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 '${CI_BRANCH}'"
-  exit 1
-fi
-
+# Copy python package out of the docker image
+sdist=moldesign-${pyversion}.tar.gz
+docker run moldesign_py_build:dev -v ./tmp/dist:/hostdists  cp dist/${sdist} /hostdists
 
-# Push images
+# Push images to dockerhub
 for img in moldesign_minimal       \
            moldesign_minimal_py2   \
            moldesign_complete      \
@@ -28,8 +22,6 @@ for img in moldesign_minimal       \
 done
 
 
-# Copy build artifacts
-sdist=moldesign-${pyversion}.tar.gz
-docker run moldesign_py_build:dev -v ./tmp/dists:/hostdists  cp dist/${sdist} /hostdists
+# Push python package to PyPI
 echo "Uploading version ${CI_BRANCH} to PyPI:"
 twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ./tmp/dists/moldesign-${pyversion}.tar.gz
diff --git a/deployment/run-ci-tests.sh b/deployment/run-ci-tests.sh
index de341a1..e0c8cb3 100755
--- a/deployment/run-ci-tests.sh
+++ b/deployment/run-ci-tests.sh
@@ -3,6 +3,7 @@
 # Defined by codeship
 # - CI_BRANCH
 # - CI_COMMIT_MESSAGE
+# - PROJECT_ID
 # Defined in ../codeship-services.yml
 # - TESTENV
 # - PYVERSION
diff --git a/deployment/test-version-number.sh b/deployment/test-version-number.sh
new file mode 100755
index 0000000..2505562
--- /dev/null
+++ b/deployment/test-version-number.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+set -e
+
+if [ -z "${CI_BRANCH}" ]; then
+  echo "Error: env var CI_BRANCH not set"
+  exit 1
+fi
+
+
+pyversion=$(python -m moldesign version | tail -n 1)
+
+echo "Expecting moldesign==${pyversion}"
+echo "Found moldesign==${pyversion}"
+
+
+if [ "${pyversion}" == "${CI_BRANCH}" ]; then
+  echo "All good"
+  exit 0
+else
+  echo "Error: moldesign package version '${pyversion}' differs from its Git tag '${CI_BRANCH}'"
+  exit 1
+fi

From b7054d3bf7b15ec9cbf1e88de7ec70a246a12a01 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 21 Nov 2017 14:01:56 -0800
Subject: [PATCH 04/18] Fix yml typo

---
 codeship-steps.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/codeship-steps.yml b/codeship-steps.yml
index c9d2400..2908acc 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -91,11 +91,12 @@
      name: testrunner
 
 
+
+
 # If this build is tagged with a PEP440-compliant version number AND the tests have passed,
 # upload the package to PyPI, and push the docker images to dockerhub as
 # autodesk/moldesign:[imagename]-[version-number]
 - name: release
-  service: publisher
   # matches tags that are valid PEP440 versions
   type: serial
   tag: '^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$'

From f6fbb72ff7749dc4bfc072984b0649bc78135f7b Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Mon, 27 Nov 2017 14:29:36 -0800
Subject: [PATCH 05/18] Build python package from complete git repo to keep
 version clean

---
 DockerMakefiles/Moldesign.yml     | 1 -
 deployment/test-version-number.sh | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/DockerMakefiles/Moldesign.yml b/DockerMakefiles/Moldesign.yml
index 2d40dbc..8b3c51c 100644
--- a/DockerMakefiles/Moldesign.yml
+++ b/DockerMakefiles/Moldesign.yml
@@ -5,7 +5,6 @@ moldesign_py_build:
   requires:
    - python_deploy
   build_directory: ..
-  ignorefile: buildfiles/moldesign/moldesign.dockerignore
   build: |
     COPY . /opt/molecular-design-toolkit
     WORKDIR /opt/molecular-design-toolkit
diff --git a/deployment/test-version-number.sh b/deployment/test-version-number.sh
index 2505562..73ad170 100755
--- a/deployment/test-version-number.sh
+++ b/deployment/test-version-number.sh
@@ -9,7 +9,7 @@ fi
 
 pyversion=$(python -m moldesign version | tail -n 1)
 
-echo "Expecting moldesign==${pyversion}"
+echo "Expecting moldesign==${CI_BRANCH}"
 echo "Found moldesign==${pyversion}"
 
 

From c41061884f4d40ecd82267bbd3bc8424809dd3ab Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 28 Nov 2017 11:18:43 -0800
Subject: [PATCH 06/18] Fix mdt-py-build tag

---
 codeship-steps.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/codeship-steps.yml b/codeship-steps.yml
index 2908acc..7eec4b4 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -9,7 +9,7 @@
 - name: build-sdist
   service: image_builder
   command: bash -c "docker-make moldesign_py_build
-            --repo ${REPO} --tag ${CI_BRANCH}
+            --tag dev
             --keep-build-tags
             -f DockerMakefiles/DockerMake.yml"
 

From 1326783d650a33a0f52968d324991e6e9026c541 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 28 Nov 2017 15:56:14 -0800
Subject: [PATCH 07/18] Fix commands in publish script

---
 codeship-services.yml | 1 +
 deployment/publish.sh | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/codeship-services.yml b/codeship-services.yml
index 6a110cb..719f777 100644
--- a/codeship-services.yml
+++ b/codeship-services.yml
@@ -11,6 +11,7 @@ image_builder: &build-base
 
 publisher:
    <<: *build-base
+   cached: false
    encrypted_env_file: ./deployment/deploy-tokens.crypt
 
 
diff --git a/deployment/publish.sh b/deployment/publish.sh
index d2c40c9..6cb4db5 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -8,9 +8,11 @@
 # fail immediately if any command fails:
 set -e
 
+echo "Now deploying moldesign-${pyversion}"
+
 # Copy python package out of the docker image
 sdist=moldesign-${pyversion}.tar.gz
-docker run moldesign_py_build:dev -v ./tmp/dist:/hostdists  cp dist/${sdist} /hostdists
+docker run -v ${PWD}/tmp/dist:/hostdists moldesign_py_build:dev cp dist/${sdist} /hostdists
 
 # Push images to dockerhub
 for img in moldesign_minimal       \

From 70c794b179b055ea2f45b7cd8ffb65e453d71fc2 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 28 Nov 2017 23:21:28 -0800
Subject: [PATCH 08/18] Fix publish version determination

---
 deployment/publish.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/deployment/publish.sh b/deployment/publish.sh
index 6cb4db5..1119b02 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -8,10 +8,10 @@
 # fail immediately if any command fails:
 set -e
 
-echo "Now deploying moldesign-${pyversion}"
+echo "Now deploying moldesign-${CI_BRANCH}"
 
 # Copy python package out of the docker image
-sdist=moldesign-${pyversion}.tar.gz
+sdist=moldesign-${CI_BRANCH}.tar.gz
 docker run -v ${PWD}/tmp/dist:/hostdists moldesign_py_build:dev cp dist/${sdist} /hostdists
 
 # Push images to dockerhub
@@ -26,4 +26,4 @@ done
 
 # Push python package to PyPI
 echo "Uploading version ${CI_BRANCH} to PyPI:"
-twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ./tmp/dists/moldesign-${pyversion}.tar.gz
+twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ./tmp/dists/moldesign-${CI_BRANCH}.tar.gz

From d7e619b72a20acec686305593227597e3e4a7b0f Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 28 Nov 2017 23:22:11 -0800
Subject: [PATCH 09/18] Combine coverage from all environments

---
 .coveragerc                     |  2 +-
 codeship-services.yml           |  8 ++++++++
 codeship-steps.yml              | 22 ++++++++--------------
 deployment/build-env.dockerfile |  5 +++--
 deployment/push-coverage.sh     | 11 +++++++++++
 deployment/run-ci-tests.sh      | 23 +++++++++--------------
 6 files changed, 40 insertions(+), 31 deletions(-)
 create mode 100755 deployment/push-coverage.sh

diff --git a/.coveragerc b/.coveragerc
index 2d586d5..f5572e2 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,7 +1,7 @@
 [paths]
 source =
   moldesign
-
+  */moldesign
 
 [run]
 source = moldesign
diff --git a/codeship-services.yml b/codeship-services.yml
index 719f777..dc731cd 100644
--- a/codeship-services.yml
+++ b/codeship-services.yml
@@ -9,6 +9,14 @@ image_builder: &build-base
     REPO: "docker.io/autodesk/moldesign:"
 
 
+coverage_pusher:
+   <<: *build-base
+   cached: false
+   encrypted_env_file: ./deployment/test-tokens.crypt
+   volumes:
+    - ./tmp/reports:/opt/reports
+
+
 publisher:
    <<: *build-base
    cached: false
diff --git a/codeship-steps.yml b/codeship-steps.yml
index 7eec4b4..7bac42a 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -66,19 +66,7 @@
           command: deployment/push-and-tag.sh moldesign_notebook
 
 
-# Prints out internal information about the test environments
-- name: print-environments
-  type: parallel
-  services:
-    - test_moldesign_complete
-    - test_moldesign_complete_py2
-    - test_moldesign_minimal
-    - test_moldesign_minimal_py2
-  steps:
-   - command: deployment/print-environment.sh
-     name: env-report
-
-# Run the tests in each environment.
+# Run the tests in each environment
 - name: run-tests
   type: serial
   services:
@@ -87,10 +75,16 @@
    - test_moldesign_minimal_py2
    - test_moldesign_minimal
   steps:
+   - command: deployment/print-environment.sh
+     name: environment
    - command: deployment/run-ci-tests.sh
-     name: testrunner
+     name: tests
 
 
+# Upload coverage results
+- name: push-coverage
+  service: coverage_pusher
+  command: deployment/push-coverage.sh
 
 
 # If this build is tagged with a PEP440-compliant version number AND the tests have passed,
diff --git a/deployment/build-env.dockerfile b/deployment/build-env.dockerfile
index 9f0a20f..467efb0 100644
--- a/deployment/build-env.dockerfile
+++ b/deployment/build-env.dockerfile
@@ -10,6 +10,7 @@ RUN curl -fsSLO https://get.docker.com/builds/Linux/x86_64/docker-17.04.0-ce.tgz
   && mv docker/docker /usr/local/bin \
   && rm -r docker docker-17.04.0-ce.tgz
 
-ADD . /opt/molecular-design-toolkit
-RUN pip install -r /opt/molecular-design-toolkit/DockerMakefiles/requirements.txt
+ADD ./DockerMakefiles/requirements.txt /tmp/reqs.txt
+RUN pip install -r /tmp/reqs.txt && pip install coveralls
 
+ADD . /opt/molecular-design-toolkit
diff --git a/deployment/push-coverage.sh b/deployment/push-coverage.sh
new file mode 100755
index 0000000..05de8e8
--- /dev/null
+++ b/deployment/push-coverage.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+# combines coverage from all test environments and pushes it to coveralls.io
+
+set -e
+
+mkdir -p /opt/reports/env-coverage
+cp /opt/reports/env-coverage/coverage.* /opt/reports/
+
+coverage combine /opt/reports/coverage.*              \
+  && coveralls                                        \
+  || echo "Failed to upload coverage to coveralls.io"
\ No newline at end of file
diff --git a/deployment/run-ci-tests.sh b/deployment/run-ci-tests.sh
index e0c8cb3..33f7fd4 100755
--- a/deployment/run-ci-tests.sh
+++ b/deployment/run-ci-tests.sh
@@ -19,10 +19,9 @@ install_location=$(python -c "import moldesign, os; print(moldesign.__path__[0])
 test_location=$(dirname "${install_location}")
 
 VERSION="${TESTENV}.py${PYVERSION}"
-PYTESTFLAGS="moldesign/_tests/ -n 2 --spec  --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=3600 --tb=short"
-if [ "${VERSION}" == "complete.py3" ]; then
-       PYTESTFLAGS="${PYTESTFLAGS} --cov moldesign --cov-config /opt/molecular-design-toolkit/.coveragerc"
-fi
+PYTESTFLAGS="moldesign/_tests/ -n 2 --spec  --durations=20
+        --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=3600 --tb=short
+        --cov moldesign --cov-config /opt/molecular-design-toolkit/.coveragerc"
 
 
 function send_status_update(){
@@ -78,29 +77,25 @@ function run_tests(){
     send_status_update "na" "Starting tests for ${VERSION}"
     cd ${test_location}
 
+
     echo
     echo "Test command running in working dir '$(pwd)':"
     echo "py.test ${PYTESTFLAGS}"
     echo
 
-    py.test ${PYTESTFLAGS} | tee /opt/reports/pytest.${VERSION}.log
+    py.test ${PYTESTFLAGS} -k test_bond_alignment_on_axis | tee /opt/reports/pytest.${VERSION}.log
     exitstat=${PIPESTATUS[0]}
-
     statline="$(tail -n1 /opt/reports/pytest.${VERSION}.log)"
 
+    # Make a copy of the coverage report
+    mkdir -p /opt/reports/env-coverage/
+    cp .coverage /opt/reports/env-coverage/coverage.${VERSION}
+
     echo 'Test status:'
     echo ${statline}
 
     send_status_update "${exitstat}" "${statline}"
 
-    if [ "${VERSION}" == "complete.py3" ]; then
-       if [[ ${exitstat} == 0 && "$CI_BRANCH" != "" ]]; then
-          coveralls || echo "Failed to upload code coverage stats"
-       else
-          echo "Skipping coveralls upload: tests not passing or \$CI_COMMIT not set."
-       fi
-    fi
-
     exit ${exitstat}
 }
 

From 422ed256cabf8a91cba1c1968a87631bf920c280 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Fri, 1 Dec 2017 10:44:22 -0800
Subject: [PATCH 10/18] Fix dumb typos

---
 deployment/publish.sh      | 2 +-
 deployment/run-ci-tests.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/deployment/publish.sh b/deployment/publish.sh
index 1119b02..4f16ee6 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -20,7 +20,7 @@ for img in moldesign_minimal       \
            moldesign_complete      \
            moldesign_complete_py2  \
            moldesign_notebook; do
-   docker push ${REPO}{$img}-${CI_BRANCH} | tee -a push.log | egrep -i 'pull|already'
+   docker push ${REPO}${img}-${CI_BRANCH} | tee -a push.log | egrep -i 'pull|already'
 done
 
 
diff --git a/deployment/run-ci-tests.sh b/deployment/run-ci-tests.sh
index 33f7fd4..aa7a01e 100755
--- a/deployment/run-ci-tests.sh
+++ b/deployment/run-ci-tests.sh
@@ -83,7 +83,7 @@ function run_tests(){
     echo "py.test ${PYTESTFLAGS}"
     echo
 
-    py.test ${PYTESTFLAGS} -k test_bond_alignment_on_axis | tee /opt/reports/pytest.${VERSION}.log
+    py.test ${PYTESTFLAGS} | tee /opt/reports/pytest.${VERSION}.log
     exitstat=${PIPESTATUS[0]}
     statline="$(tail -n1 /opt/reports/pytest.${VERSION}.log)"
 

From 926b7e1a24dc68c47bc07a6205e507e6d253eb2c Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Fri, 1 Dec 2017 15:18:19 -0800
Subject: [PATCH 11/18] Add dockerhub auth

---
 deployment/publish.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/deployment/publish.sh b/deployment/publish.sh
index 4f16ee6..98625d4 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -10,6 +10,9 @@ set -e
 
 echo "Now deploying moldesign-${CI_BRANCH}"
 
+docker login -u ${DOCKERHUB_USER} -p ${DOCKERHUB_PASSWORD}
+
+
 # Copy python package out of the docker image
 sdist=moldesign-${CI_BRANCH}.tar.gz
 docker run -v ${PWD}/tmp/dist:/hostdists moldesign_py_build:dev cp dist/${sdist} /hostdists

From 43baaf3298c036b06607133639d05427827492a5 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Mon, 4 Dec 2017 10:04:44 -0800
Subject: [PATCH 12/18] Add missing tag

---
 codeship-steps.yml         | 2 +-
 deployment/push-and-tag.sh | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/codeship-steps.yml b/codeship-steps.yml
index 7bac42a..8cb5feb 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -48,7 +48,7 @@
   steps:
     - name: push-artifacts
       command: deployment/push-and-tag.sh
-          moldesign_minimal moldesign_py2 moldesign_py_build
+          moldesign_minimal moldesign_minimal_py2 moldesign_py_build
           moldesign_complete moldesign_complete_py2
       service: publisher
     - type: serial
diff --git a/deployment/push-and-tag.sh b/deployment/push-and-tag.sh
index 9046c4e..9655ec6 100755
--- a/deployment/push-and-tag.sh
+++ b/deployment/push-and-tag.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -e
+
 if [ -z ${CI_BRANCH} ]; then
   echo "\$CI_BRANCH" var not set.
   exit 1

From e30a97508499c16584a4e20a1b29d8530c4bf2a7 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Mon, 4 Dec 2017 10:51:14 -0800
Subject: [PATCH 13/18] Install twine, add option for skipping tests

--skip-ci-tests
---
 deployment/build-env.dockerfile | 3 ++-
 deployment/run-ci-tests.sh      | 5 +++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/deployment/build-env.dockerfile b/deployment/build-env.dockerfile
index 467efb0..9252040 100644
--- a/deployment/build-env.dockerfile
+++ b/deployment/build-env.dockerfile
@@ -11,6 +11,7 @@ RUN curl -fsSLO https://get.docker.com/builds/Linux/x86_64/docker-17.04.0-ce.tgz
   && rm -r docker docker-17.04.0-ce.tgz
 
 ADD ./DockerMakefiles/requirements.txt /tmp/reqs.txt
-RUN pip install -r /tmp/reqs.txt && pip install coveralls
+RUN pip install -r /tmp/reqs.txt \
+ && pip install coveralls twine
 
 ADD . /opt/molecular-design-toolkit
diff --git a/deployment/run-ci-tests.sh b/deployment/run-ci-tests.sh
index aa7a01e..f0e8668 100755
--- a/deployment/run-ci-tests.sh
+++ b/deployment/run-ci-tests.sh
@@ -32,6 +32,11 @@ function send_status_update(){
 function check_if_tests_should_run(){
    echo "Should I run the tests in this environment?"
 
+   if [[ "${CI_COMMIT_MESSAGE}" == *"--skip-ci-tests"* ]];  then
+       echo "NO: found \"--skip-ci-tests\" flag in commit message; will not run any test suites"
+       exit 0
+   fi
+
    if [[ "${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

From 32c238f58fbb908442780da2d01dc12da27876f8 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Mon, 4 Dec 2017 15:20:24 -0800
Subject: [PATCH 14/18] Ignore missing coverage files if tests skipped

---
 deployment/push-coverage.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/deployment/push-coverage.sh b/deployment/push-coverage.sh
index 05de8e8..14202fe 100755
--- a/deployment/push-coverage.sh
+++ b/deployment/push-coverage.sh
@@ -6,6 +6,8 @@ set -e
 mkdir -p /opt/reports/env-coverage
 cp /opt/reports/env-coverage/coverage.* /opt/reports/
 
-coverage combine /opt/reports/coverage.*              \
-  && coveralls                                        \
-  || echo "Failed to upload coverage to coveralls.io"
\ No newline at end of file
+if $(coverage combine /opt/reports/coverage.*); then
+  coveralls || echo "Failed to upload coverage to coveralls.io"
+else
+   echo "No coverage files found, skipping coveralls upload"
+fi

From bc2826dd1fb44611c8ffb3f1bc1934b86c906d8a Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Mon, 4 Dec 2017 16:04:44 -0800
Subject: [PATCH 15/18] Correct leaks in sanity

--skip-ci-tests
---
 deployment/publish.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deployment/publish.sh b/deployment/publish.sh
index 98625d4..7841dc8 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -29,4 +29,4 @@ done
 
 # Push python package to PyPI
 echo "Uploading version ${CI_BRANCH} to PyPI:"
-twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ./tmp/dists/moldesign-${CI_BRANCH}.tar.gz
+twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ./tmp/dist/moldesign-${CI_BRANCH}.tar.gz

From 3ce8e27ba6ec5b1f33e4239262f32c6a737ee7f6 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Mon, 4 Dec 2017 16:08:58 -0800
Subject: [PATCH 16/18] Rename commit message flags to avoid clashes

---
 deployment/run-ci-tests.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/deployment/run-ci-tests.sh b/deployment/run-ci-tests.sh
index f0e8668..a832708 100755
--- a/deployment/run-ci-tests.sh
+++ b/deployment/run-ci-tests.sh
@@ -32,12 +32,12 @@ function send_status_update(){
 function check_if_tests_should_run(){
    echo "Should I run the tests in this environment?"
 
-   if [[ "${CI_COMMIT_MESSAGE}" == *"--skip-ci-tests"* ]];  then
+   if [[ "${CI_COMMIT_MESSAGE}" == *"--no-tests"* ]];  then
        echo "NO: found \"--skip-ci-tests\" flag in commit message; will not run any test suites"
        exit 0
    fi
 
-   if [[ "${CI_COMMIT_MESSAGE}" == *"--fast-ci-tests"* && "${VERSION}" != "complete.py3" ]];  then
+   if [[ "${CI_COMMIT_MESSAGE}" == *"--fast-tests"* && "${VERSION}" != "complete.py3" ]];  then
        echo "NO: found \"--fast-ci-tests\" flag in commit message; run complete.py3 only"
        exit 0
    fi

From 37e6035665fdba5ab4ef78ef3179394ebdfc800c Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 5 Dec 2017 18:08:32 -0800
Subject: [PATCH 17/18] Fix coverage pusher better

---
 deployment/push-coverage.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/deployment/push-coverage.sh b/deployment/push-coverage.sh
index 14202fe..214da24 100755
--- a/deployment/push-coverage.sh
+++ b/deployment/push-coverage.sh
@@ -4,9 +4,8 @@
 set -e
 
 mkdir -p /opt/reports/env-coverage
-cp /opt/reports/env-coverage/coverage.* /opt/reports/
-
-if $(coverage combine /opt/reports/coverage.*); then
+if $(cp /opt/reports/env-coverage/coverage.* /opt/reports/); then
+  coverage combine /opt/reports/coverage.*
   coveralls || echo "Failed to upload coverage to coveralls.io"
 else
    echo "No coverage files found, skipping coveralls upload"

From fd2b0f0f7230424474365f46291b21570ac01981 Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 5 Dec 2017 19:07:02 -0800
Subject: [PATCH 18/18] Really copy the sdist correctly

---
 codeship-services.yml | 2 ++
 deployment/publish.sh | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/codeship-services.yml b/codeship-services.yml
index dc731cd..62dc1d5 100644
--- a/codeship-services.yml
+++ b/codeship-services.yml
@@ -21,6 +21,8 @@ publisher:
    <<: *build-base
    cached: false
    encrypted_env_file: ./deployment/deploy-tokens.crypt
+   volumes:
+    - ./tmp/dist:/opt/dist
 
 
 test_moldesign_minimal: &test-base
diff --git a/deployment/publish.sh b/deployment/publish.sh
index 7841dc8..85ba9f8 100755
--- a/deployment/publish.sh
+++ b/deployment/publish.sh
@@ -15,7 +15,7 @@ docker login -u ${DOCKERHUB_USER} -p ${DOCKERHUB_PASSWORD}
 
 # Copy python package out of the docker image
 sdist=moldesign-${CI_BRANCH}.tar.gz
-docker run -v ${PWD}/tmp/dist:/hostdists moldesign_py_build:dev cp dist/${sdist} /hostdists
+docker run moldesign_py_build:dev cat dist/${sdist} > /opt/dist/${sdist}
 
 # Push images to dockerhub
 for img in moldesign_minimal       \
@@ -29,4 +29,4 @@ done
 
 # Push python package to PyPI
 echo "Uploading version ${CI_BRANCH} to PyPI:"
-twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ./tmp/dist/moldesign-${CI_BRANCH}.tar.gz
+twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} /opt/dist/${sdist}