Merge 71dfcff into 23cbf9d

.gitignore

@@ -23,9 +23,13 @@ env
 */_markdown
 */visualizations
 
+*.c
+*.html
+*.so
+*.egg-info
 data/example_dataset/metaclustering/*output*.csv
 data/example_dataset/metaclustering/example_manually_adjust_metaclusters.ipynb
 Pipfile
 Pipfile.lock
 .coverage
-.python-version
+.python-version

.travis.yml

@@ -24,6 +24,7 @@ cache: pip
 
 # command to run tests
 script:
+  - python -m pip install --editable .
   - python -m pytest --cov=ark --pycodestyle ark
 
 jobs:
@@ -43,8 +44,11 @@ jobs:
         - "travis_wait 120 sleep 7200 &"
         - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
         # Tag the image with a version such as vX.Y.Z,
-        - docker build -t "$TRAVIS_REPO_SLUG":"$TRAVIS_TAG" . 1> /dev/null
+        - docker build -t "$TRAVIS_REPO_SLUG":"$TRAVIS_TAG" . 1> out.log
         - docker push --all-tags "$TRAVIS_REPO_SLUG"
 
+after_failure:
+  - cat out.log
+
 after_success:
   - coveralls

Dockerfile

@@ -23,8 +23,6 @@ RUN apt-get install -y gcc r-base
 # install cmake (needed for nloptr)
 RUN apt-get install -y cmake
 
-WORKDIR /scripts
-
 # Install R dependency packages
 RUN R -e "install.packages('arrow')"
 RUN R -e "install.packages('data.table')"
@@ -37,14 +35,17 @@ RUN R -e "BiocManager::install('ConsensusClusterPlus')"
 
 # Install ark-analysis
 # copy over the requirements.txt, install dependencies, and README
-COPY setup.py requirements.txt README.md /opt/ark-analysis/
-RUN pip install -r /opt/ark-analysis/requirements.txt
+COPY setup.py pyproject.toml requirements.txt README.md /opt/ark-analysis/
+RUN python -m pip install -r /opt/ark-analysis/requirements.txt
 
 # copy the scripts over
+# this should catch changes to the scripts from updates
 COPY ark /opt/ark-analysis/ark
 
 # Install the package via setup.py
-RUN pip install /opt/ark-analysis
+RUN cd /opt/ark-analysis && python -m pip install .
+
+WORKDIR /scripts
 
 # jupyter lab
 CMD jupyter lab --ip=0.0.0.0 --allow-root --no-browser --port=$JUPYTER_PORT --notebook-dir=/$JUPYTER_DIR