Merge pull request #469 from oesteban/maint/fix-coverage-collection

MAINT: Revise code coverage collection

Author: oesteban

.circleci/config.yml

@@ -219,14 +219,15 @@ jobs:
             mkdir -p $PWD/artifacts $PWD/summaries
             sudo setfacl -d -m group:ubuntu:rwx $PWD
             sudo setfacl -m group:ubuntu:rwx $PWD
-            docker run -u $( id -u ) -it --rm=false \
+            docker run -u $( id -u ) -it --rm=false -w /src/niworkflows \
+              -e COVERAGE_FILE=/tmp/summaries/.pytest.coverage \
               -e TEST_DATA_HOME=/data -v /tmp/data:/data \
               -v ${PWD}:/tmp niworkflows:py3 \
               pytest --junit-xml=/tmp/summaries/pytest.xml \
                      --cov niworkflows --cov-report xml:/tmp/summaries/unittests.xml \
-                     --ignore=/src/niworkflows/niworkflows/tests/ \
-                     --ignore=/src/niworkflows/niworkflows/func/tests/ \
-                     /src/niworkflows/niworkflows
+                     --ignore=niworkflows/tests/ \
+                     --ignore=niworkflows/func/tests/ \
+                     niworkflows/
 
       - run:
           name: Submit unit test coverage
@@ -239,14 +240,15 @@ jobs:
           name: Run reportlet tests
           no_output_timeout: 2h
           command: |
-            docker run -u $( id -u ) -it --rm=false \
+            docker run -u $( id -u ) -it --rm=false -w /src/niworkflows \
+              -e COVERAGE_FILE=/tmp/summaries/.reportlets.coverage \
               -e SAVE_CIRCLE_ARTIFACTS="/tmp/artifacts/" \
               -e TEST_DATA_HOME=/data -v /tmp/data:/data \
               -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
               -v ${PWD}:/tmp niworkflows:py3 \
               pytest -n auto --junit-xml=/tmp/summaries/reportlets.xml \
                      --cov niworkflows --cov-report xml:/tmp/summaries/reportlets.xml \
-                     /src/niworkflows/niworkflows/tests/
+                     niworkflows/tests/
       - run:
           name: Submit reportlet test coverage
           command: |
@@ -309,15 +311,16 @@ jobs:
           no_output_timeout: 2h
           command: |
             mkdir -p /tmp/masks/reports && \
-            docker run -ti --rm=false \
+            docker run -ti --rm=false  -w /src/niworkflows \
+              -e COVERAGE_FILE=/tmp/masks/.coverage \
               -v /tmp/data:/tmp/data -v /tmp/masks:/tmp/masks \
               -e FMRIPREP_REGRESSION_SOURCE=/tmp/data/fmriprep_bold_truncated \
               -e FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
               -e FMRIPREP_REGRESSION_REPORTS=/tmp/masks/reports \
               niworkflows:py3 \
               pytest --junit-xml=/tmp/masks/regression.xml \
                      --cov niworkflows --cov-report xml:/tmp/masks/coverage.xml \
-                     /src/niworkflows/niworkflows/func/tests/
+                     niworkflows/func/tests/
 
       - run:
           name: Submit masks test coverage
@@ -424,6 +427,24 @@ jobs:
           command: make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html
       - store_artifacts:
           path: ./docs/_build/no_version_html
+      - run:
+          name: Install niworkflows
+          command: |
+            pip install --no-cache-dir codecov
+            pip install --no-cache-dir -e .[all]
+      - run:
+          name: Build only this commit with coverage collection
+          command: |
+            make -C docs/ clean
+            export COVERAGE_FILE=/tmp/.coverage
+            coverage run --source=niworkflows $( which sphinx-build ) \
+                -b html -W -d docs/_build/no_version_doctrees ./docs/ docs/_build/no_version_html
+            coverage xml -o /tmp/documentation.xml
+            python -m codecov --file /tmp/documentation.xml --flags documentation -e CIRCLE_JOB
+      - run:
+          name: Uninstall NiWorkflows
+          command: |
+            pip uninstall -y niworkflows
       - run:
           name: Generate Versioned Docs
           command: |
@@ -434,6 +455,7 @@ jobs:
               echo "Not a tag or master branch - skipping versioned docs."
               circleci step halt
             else
+              make -C docs/ clean
               make -f ./docs/Makefile versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH}
             fi
       - save_cache:

.codecov.yml

@@ -18,6 +18,8 @@ src/
 .git/
 .github/
 .gitignore
+.gitattributes
+.gitmodules
 
 # ci
 .circleci/

.dockerignore

@@ -47,7 +47,7 @@ before_install:
   - python -m pip --version
   - |
     if [ "$INSTALL_TYPE" == "pip" ]; then
-        PACKAGE="."
+        PACKAGE="-e ."
     elif [ "$INSTALL_TYPE" == "sdist" ]; then
         python setup.py sdist
         PACKAGE="$( ls dist/*.tar.gz )"
@@ -93,4 +93,4 @@ script:
 
 after_script:
   - python -m pip install codecov
-  - codecov
+  - python -m codecov --flags travis --file cov.xml -e $TRAVIS_JOB_NUMBER

.gitmodules

@@ -150,7 +150,7 @@ RUN python -c "from matplotlib import font_manager" && \
 WORKDIR /src/
 COPY requirements.txt requirements.txt
 RUN pip install --no-cache-dir -r requirements.txt && \
-    rm -rf $HOME/.cache/pip
+    rm -rf $HOME/.cache/pip requirements.txt
 
 # Precaching atlases
 RUN python -c "from templateflow import api as tfapi; \
@@ -161,7 +161,8 @@ RUN python -c "from templateflow import api as tfapi; \
                tfapi.get(['OASIS30ANTs', 'NKI'], resolution=1, desc='BrainCerebellumRegistration', suffix='mask'); "
 
 COPY . niworkflows/
-RUN pip install --no-cache-dir /src/niworkflows[all] && \
+WORKDIR /src/niworkflows/
+RUN pip install --no-cache-dir -e .[all] && \
     rm -rf $HOME/.cache/pip
 
 # Cleanup and ensure perms.

.travis.yml

@@ -40,10 +40,10 @@ install_requires =
     transforms3d
     templateflow >= 0.4.2
 test_requires =
+    coverage < 5
     pytest >= 4.4
-    pytest-xdist >= 1.28
     pytest-cov
-    coverage
+    pytest-xdist >= 1.28
 packages = find:
 include_package_data = True
 
@@ -62,9 +62,9 @@ exclude =
 
 [options.extras_require]
 doc =
-    sphinx >= 2.1.2
     pydot >= 1.2.3
     pydotplus
+    sphinx >= 2.1.2
     sphinx_rtd_theme
     sphinxcontrib-apidoc ~= 0.3.0
     sphinxcontrib-napoleon
@@ -78,10 +78,10 @@ pointclouds =
 style =
     flake8 >= 3.7.0
 test =
+    coverage < 5
     pytest >= 4.4
-    pytest-xdist >= 1.28
     pytest-cov
-    coverage
+    pytest-xdist >= 1.28
 tests =
     %(test)s
 all =