Get tests up and running in CI

DockerMakefiles/requirements.txt

@@ -1 +1,2 @@
-DockerMake >= 0.6.1a1
+DockerMake >= 0.6.1a2
+shyaml

codeship-services.yml

@@ -1,4 +1,4 @@
-build_base: &build-base
+image_builder:
   build:
     context: .
     dockerfile: ./deployment/build-env.dockerfile
@@ -8,37 +8,19 @@ build_base: &build-base
   cached: true
   environment:
     chemdocker_tag: 0.9.0rc5
-
-python_builder:
-  <<: *build-base
-  working_dir: /opt/molecular-design-toolkit
-
-image_builder:
-  <<: *build-base
-  working_dir: /opt/molecular-design-toolkit/DockerMakefiles
-
-
-publisher:
-  <<: *build-base
-  working_dir: /opt/molecular-design-toolkit
-  encrypted_env_file: deployment/tokens.crypt
-  add_docker: true
   working_dir: /opt/molecular-design-toolkit
-  volumes:
-  - ./tmp/reports:/opt/reports
 
 
-test_base: &test-base
-  image: dummy
+test_moldesign_minimal: &test-base
   working_dir: /opt/molecular-design-toolkit/
   add_docker: true
   volumes:
     - ./tmp/reports:/opt/reports
-
-
-test_moldesign_minimal:
-  <<: *test-base
-  image: moldesign_minimal:dev
+  build: &test-build-base
+    context: ./
+    dockerfile: deployment/test-env.dockerfile
+    args:
+      baseimage: moldesign_minimal
   environment:
     TESTENV: minimal
     PYVERSION: 3
@@ -47,7 +29,10 @@ test_moldesign_minimal:
 
 test_moldesign_minimal_py2:
   <<: *test-base
-  image: moldesign_minimal_py2:dev
+  build:
+    <<: *test-build-base
+    args:
+      baseimage: moldesign_minimal_py2
   environment:
     TESTENV: minimal
     PYVERSION: 2
@@ -56,7 +41,10 @@ test_moldesign_minimal_py2:
 
 test_moldesign_complete:
   <<: *test-base
-  image: moldesign_complete:dev
+  build:
+    <<: *test-build-base
+    args:
+      baseimage: moldesign_complete
   environment:
     TESTENV: complete
     PYVERSION: 3
@@ -65,7 +53,10 @@ test_moldesign_complete:
 
 test_moldesign_complete_py2:
   <<: *test-base
-  image: moldesign_complete_py2:dev
+  build:
+    <<: *test-build-base
+    args:
+      baseimage: moldesign_complete_py2
   environment:
     TESTENV: complete
     PYVERSION: 2

codeship-steps.yml

@@ -1,66 +1,56 @@
 - name: pull-cache
   service: image_builder
-  command: ../deployment/pull-cache.sh
+  command: deployment/pull-cache.sh
 
 - name: build-sdist
   service: image_builder
-  command: docker-make --tag dev moldesign_py_build
+  command: docker-make moldesign_py_build
+            --keep-build-tags
+            -f DockerMakefiles/DockerMake.yml --tag dev
 
 - name: build_and_pull_images
   service: image_builder
   type: parallel
   steps:
   - name: pull-dependent-images
-    command: ../deployment/pull-chemdocker.sh
-  - type: serial
-    steps:
-      - name: build_py3
-        command:
-             docker-make moldesign_minimal moldesign_complete
-             --tag dev --keep-build-tags
-             --cache-repo moldesign --cache-tag cache
-    steps:
-      - name: build_py2
-        command:
-          docker-make moldesign_minimal_py2 moldesign_complete_py2
-             --tag dev --keep-build-tags
-             --cache-repo moldesign --cache-tag cache
+    command: deployment/pull-chemdocker.sh
+  - name: build_py3
+    command:
+         docker-make moldesign_minimal moldesign_complete moldesign_notebook
+          -f DockerMakefiles/DockerMake.yml
+          --tag dev --keep-build-tags
+          --cache-repo moldesign --cache-tag cache
+  - name: build_py2
+    command:
+        docker-make moldesign_minimal_py2 moldesign_complete_py2
+         -f DockerMakefiles/DockerMake.yml
+         --tag dev --keep-build-tags
+         --cache-repo moldesign --cache-tag cache
+
+- name: push_images
+  service: image_builder
+  command: deployment/push.sh
 
 - name: print_environments
-  type: parallel
+  type: serial
+  services:
+    - test_moldesign_complete
+    - test_moldesign_complete_py2
+    - test_moldesign_minimal
+    - test_moldesign_minimal_py2
+  steps:
+   - command: deployment/print_environment.sh
+
+- name: run_tests
   services:
    - test_moldesign_complete
    - test_moldesign_complete_py2
-   - test_moldesign_minimal
    - test_moldesign_minimal_py2
+   - test_moldesign_minimal
   steps:
-   - command: ../deployment/print_environment.sh
-
-- service: test_moldesign_complete
-  name: test_moldesign_complete
-  command: deployment/codeship_runtests.sh
-
-- service: test_moldesign_complete_py2
-  name: test_moldesign_complete_py2
-  command: deployment/codeship_runtests.sh
-
-- service: test_moldesign_minimal
-  name: test_moldesign_minimal
-  command: deployment/codeship_runtests.sh
-
-- service: test_moldesign_minimal_py2
-  name: test_moldesign_minimal_py2
-  command: deployment/codeship_runtests.sh
-
-- service: image_builder
-  command: docker-make --tag dev moldesign_notebook --cache-repo moldesign --cache-tag cache
-  name: build-notebook
-
-- name: push
-  service: publisher
-  command: deployment/push.sh
+   - command: deployment/codeship_runtests.sh
 
-- name: publish
+- name: publish_python
   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*))?$'

deployment/codeship_runtests.sh

@@ -1,9 +1,7 @@
 #!/usr/bin/env bash
-# this script expects to run from the root of the repository
 
 set -e  # fail immediately if any command fails
 
-
 VERSION="${TESTENV}.py${PYVERSION}"
 PYTESTFLAGS="-n 3 --spec  --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=3600 --tb=short"
 if [ "${VERSION}" == "complete.py3" ]; then
@@ -59,7 +57,8 @@ function run_tests(){
     echo "py.test ${PYTESTFLAGS}"
     echo
 
-    py.test ${PYTESTFLAGS} | tee /opt/reports/pytest.${VERSION}.log
+    cd tests && \
+        py.test ${PYTESTFLAGS} | tee /opt/reports/pytest.${VERSION}.log
     exitstat=${PIPESTATUS[0]}
 
     statline="$(tail -n1 /opt/reports/pytest.${VERSION}.log)"

deployment/print_environment.sh

@@ -7,22 +7,12 @@ echo " * Python interpreter: $(python -c "import sys; print(sys.version)")"
 echo
 echo " * Conda version: $(conda --version 2>/dev/null || echo 'not installed')"
 echo
-echo " * Missing optional interfaces:"
 
 # This will print logging messages about optional interfaces
-plats=$(python -c "import moldesign;
-if not moldesign.interfaces.openmm.force_remote: print(moldesign.interfaces.openmm.list_openmmplatforms())"
-)
-
-if [ "$?" != "0" ]; then
-  plats="None (OpenMM not installed)"
-fi
-
-echo
-echo " * OpenMM platforms:"
-echo ${plats}
+python -c "import moldesign; moldesign.compute.packages.print_env()"
 echo
 echo " * Conda environment: $(conda list 2>/dev/null || echo "not installed")"
 echo
 echo " * Installed python packages: "
 pip freeze
+

deployment/pull-cache.sh

@@ -32,7 +32,7 @@ function run-pull(){
 }
 
 # we copy binaries out of this one for our build
-echocmd docker pull chemdocker/pyscf-build-1.3.1:0.9.0rc5:${chemdocker_tag}
+echocmd docker pull chemdocker/pyscf-build-1.3.1:${chemdocker_tag} | tee -a pull.log | egrep -i 'pull|already';
 
 for img in moldesign_minimal       \
            moldesign_minimal_py2   \

deployment/push.sh

@@ -2,7 +2,12 @@
 
 if [ -z ${CI_BRANCH} ]; then
   echo "\$CI_BRANCH" var not set.
-  exit 10
+  exit 1
+fi
+
+if [ -z ${DOCKERHUB_USER} ] || [ -z ${DOCKERHUB_PASSWORD} ]; then
+    echo "Dockerhub credentials not provided. Skipping push ..."
+    exit 0
 fi
 
 function echocmd() {
@@ -15,7 +20,7 @@ imgs=$(cat DockerMakefiles/DockerMake.yml | shyaml get-values _ALL_)
 docker login -u ${DOCKERHUB_USER} -p ${DOCKERHUB_PASSWORD}
 
 for img in ${imgs}; do
-    remote_img=autodesk/moldesign:${img}-${CI_BRANCH}
+    remote_img=autodesk/moldesign:${img}-${CI_BRANCH}-devbuild
 
     echocmd docker tag ${img}:dev ${remote_img}
     echocmd docker push ${remote_img} | tee -a push.log | egrep -i 'push|already';

deployment/test-env.dockerfile

@@ -0,0 +1,7 @@
+# For building test images
+ARG baseimage
+FROM ${baseimage}:dev
+ADD ./deployment /opt/molecular-design-toolkit/deployment
+ADD ./moldesign/_tests /opt/molecular-design-toolkit/tests
+RUN pip install -r /opt/molecular-design-toolkit/deployment/requirements.txt
+WORKDIR /opt/molecular-design-toolkit

moldesign/compute/packages.py

@@ -238,7 +238,7 @@ def installed_version(self):
             return None
 
     def is_installed(self):
-        if self.path is None:
+        if not self.path:
             return False
 
         return os.path.exists(self.path)
@@ -279,4 +279,19 @@ def _getimage(name):
 executables = [nwchem, opsin, nab, symmol, tleap, antechamber]
 
 
+def print_env():
+    print(' * Interfaces: ')
+    for pkg in packages:
+        if pkg.is_installed():
+            print('     %s: installed' % pkg.name)
+        else:
+            print('     %s: not found' % pkg.name)
+
+    print('\n * Executables:')
+    for exe in executables:
+        if exe.is_installed():
+            print('     %s: installed' % exe.name)
+        else:
+            print('     %s: not found' % exe.name)
+
 __all__ = [x.name for x in packages + executables]