Clean up project root and MDT image layers

DockerMakefiles/Moldesign.yml

@@ -4,19 +4,26 @@ moldesign_requirements:
   build: |
     RUN conda install -qy -c omnia parmed biopython
 
-moldesign:
+moldesign_minimal:
  description: Base installation of the MDT library. Built from the current directory.
  requires:
   - moldesign_requirements
  build_directory: ../
  build: |
-  COPY requirements.txt /opt/mdtreqs.txt
+  COPY requirements.txt /tmp/mdtreqs.txt
   RUN apt-get update \
    && apt-get install -y gcc \
-   && pip install -r /opt/mdtreqs.txt
+   && pip install -r /tmp/mdtreqs.txt
   COPY . /opt/molecular-design-toolkit
   RUN pip install -e /opt/molecular-design-toolkit
 
+
+moldesign_complete:
+  description: An image with moldesign and all python dependencies
+  requires:
+   - chem_python
+   - moldesign_minimal
+
 moldesign_notebook:
  description: A production-ready, fully outfitted jupyter server container
  requires:
@@ -28,12 +35,6 @@ moldesign_notebook:
   RUN jupyter nbextension enable --python --sys-prefix widgetsnbextension \
    && jupyter nbextension enable --python --sys-prefix nbmolviz
 
-moldesign_complete:
-  description: An image with moldesign and all python dependencies
-  requires:
-   - chem_python
-   - moldesign
-
 
 moldesign_standalone:
   description: |
@@ -47,14 +48,3 @@ moldesign_standalone:
   build: |
     RUN mkdir -p ~/.moldesign \
      && echo "engine_type: subprocess" > ~/.moldesign/moldesign.yml
-
-moldesign_minimal:
-   description: |
-      Same as moldesign_notebook, but *without* any dependencies (OpenBabel, OpenMM etc.).
-      Used for testing remote execution environment
-   requires:
-    - notebook
-    - moldesign
-   build: |
-     ENTRYPOINT []
-     CMD ''

codeship-services.yml

@@ -1,26 +1,27 @@
 docker_make:
   build:
     context: .
-    dockerfile: ./buildfiles/build-env.dockerfile
+    dockerfile: ./deployment/build-env.dockerfile
   volumes:
     - ./tmp/makefiles:/makefiles
   add_docker: true
   cached: true
 
 publisher:
-  encrypted_env_file: tokens.crypt
+  encrypted_env_file: deployment/tokens.crypt
   build:
     context: .
-    dockerfile: ./buildfiles/build-env.dockerfile
+    dockerfile: ./deployment/build-env.dockerfile
   add_docker: true
   volumes:
   - ./tmp/reports:/opt/reports
 
 test_moldesign_minimal:
+  encrypted_env_file: deployment/tokens.crypt
   build:
-    context: ./buildfiles
+    context: ./deployment
     dockerfile: moldesign-minimal-cache.dockerfile
-  cached: true
+  cached: false  # do not cache this! It gets built before the cache is triggered
   working_dir: /opt/molecular-design-toolkit/moldesign/_tests
   add_docker: true
   environment:
@@ -29,10 +30,11 @@ test_moldesign_minimal:
     - ./tmp/reports:/opt/reports
 
 test_moldesign_complete:
+  encrypted_env_file: deployment/tokens.crypt
   build:
-    context: ./buildfiles
+    context: ./deployment
     dockerfile: moldesign-complete-cache.dockerfile
-  cached: true
+  cached: false  # do not cache this! It gets built before the cache is triggered
   working_dir: /opt/molecular-design-toolkit/moldesign/_tests
   add_docker: true
   environment:

codeship-steps.yml

@@ -46,7 +46,7 @@
       name: symmol
   - type: serial
     steps:
-    - command: docker-make --tag dev pyscf_build
+    - command: docker-make --tag dev pyscf
       name: pyscf
     - command: docker-make --tag dev moldesign_complete
       name: mdt_complete
@@ -63,7 +63,7 @@
     - test_moldesign_minimal
     - test_moldesign_complete
   steps:  # we test 2 environments: one without tools locally installed, and one with
-    - command: ../../buildfiles/codeship_runtests.sh
+    - command: ../../deployment/codeship_runtests.sh
 
 # TODO: test the merged versions of PRs; test additional environments sometimes
 

buildfiles/codeship_runtests.sh → deployment/codeship_runtests.sh

@@ -8,6 +8,6 @@ statline="$(tail -n1 /opt/reports/pytest.${TESTENV}.log)"
 echo 'Test status:'
 echo ${statline}
 
-python ../../buildfiles/send_test_status.py ${exitstat} "${statline}"
+python ../../deployment/send_test_status.py ${exitstat} "${statline}"
 
 exit ${exitstat}

deployment/tokens.crypt

@@ -0,0 +1 @@
+PGMZqKq9Cqk+45rl14lfqLk3lOHBQdF6us36dluCvADGhpfTNnOrzI1aE+QkotYLFDkskUQTOQQbysHBts/jLxg7RzDYheY3rIakpFbqsxruChwHqibbf05xI+uHp6XGLPNptflO5/fq9NJqwTIV+w7OVLhxJP8PdA7XmXHey8eYp38=