refactor upload to codecov

poldracklab · Nov 19, 2020 · 6ac620b · 6ac620b
1 parent 703aadb
commit 6ac620b
Showing 1 changed file with 27 additions and 76 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -131,17 +131,6 @@ jobs:
       - restore_cache:
           keys:
             - docker-v0-{{ .Branch }}-{{ .Revision }}
-      - restore_cache:
-          keys:
-            - ds003-v0-{{ .Branch }}-
-            - ds003-v0-master-
-            - ds003-v0-
-      - run:
-          name: Install coverage and codecov
-          command: |
-              pyenv install 3.6.3
-              pyenv local 3.6.3
-              python -m pip install -U "coverage<5" codecov
       - run:
           name: Load Docker image layer cache
           no_output_timeout: 30m
@@ -153,58 +142,24 @@ jobs:
               pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
               docker images
             fi
-      - run:
-          name: Install coverage and codecov
-          command: |
-              pyenv install 3.6.3
-              pyenv local 3.6.3
-              python -m pip install -U "coverage<5" codecov
       - run:
           name: Run pytest
           no_output_timeout: 2h
           command: |
-            mkdir -p /tmp/ds003/work
-            chmod 777 /tmp/ds003/work
+            mkdir -p /tmp/pytestcov
             docker run --rm \
-                -v /tmp/ds003/work:/scratch \
+                -v /tmp/pytestcov:/scratch \
                 -e COVERAGE_FILE=/scratch/.coverage.pytest \
                 --entrypoint="/neurodocker/startup.sh" \
                 poldracklab/fitlins:latest \
-                bash -c '\
-                export PATH=/opt/miniconda-latest/envs/neuro/bin:$PATH \
-                && pip install pytest \
-                && coverage run --rcfile /src/fitlins/docker/multiproc.coveragerc `which pytest` /src/fitlins'
-
+                pytest --cov=fitlins --cov-report xml:/scratch/cov_pytest.xml /src/fitlins
       - run:
-          name: Combine coverage and submit
+          name: Submit pytest coverage
           command: |
-              pyenv local 3.6.3
-              python -m coverage combine \
-                --rcfile /tmp/src/fitlins/docker/multiproc.coveragerc \
-                /tmp/ds003/work/.coverage.* 
-              sed -i -e 's/.opt.miniconda-latest.envs.neuro.lib.python3.6.site-packages/\/tmp\/src\/fitlins/g' .coverage
-              python -m coverage xml
-              python -m codecov --file coverage.xml --flags pytest -e CIRCLE_JOB
-      - store_artifacts:
-          path: /tmp/ds003
-          command: |
-            mkdir -p /tmp/pytestcov
-            chmod 777 /tmp/pytestcov
-            docker run -v /tmp/pytestcov:/scratch \
-              -e COVERAGE_FILE=/scratch/.coverage.pytest \
-              --entrypoint="/neurodocker/startup.sh" \
-              poldracklab/fitlins:latest \
-              pytest --cov=fitlins /src/fitlins
-      - run:
-          name: Combine coverage and submit
-          command: |
-              pyenv local 3.6.3
-              python -m coverage combine \
-                --rcfile /tmp/src/fitlins/docker/multiproc.coveragerc \
-                /tmp/pytestcov/.coverage*
-              sed -i -e 's/\/src\/fitlins/\/tmp\/src\/fitlins/g' .coverage
-              python -m coverage xml
-              python -m codecov --file coverage.xml --flags pytest -e CIRCLE_JOB
+              bash <(curl --retry 5 -s https://codecov.io/bash) \
+                -f /tmp/pytestcov/cov_pytest.xml \
+                -F pytest \
+                -e CIRCLE_JOB
 
   test_ds003:
     parameters:
@@ -235,12 +190,6 @@ jobs:
               pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
               docker images
             fi
-      - run:
-          name: Install coverage and codecov
-          command: |
-              pyenv install 3.6.3
-              pyenv local 3.6.3
-              python -m pip install -U "coverage<5" codecov
       - run:
           name: Run FitLins
           no_output_timeout: 2h
@@ -305,15 +254,24 @@ jobs:
       - run:
           name: Combine coverage and submit
           command: |
-              pyenv local 3.6.3
-              python -m coverage combine \
-                --rcfile /tmp/src/fitlins/docker/multiproc.coveragerc \
-                /tmp/ds003/work/.coverage.* \
-                /tmp/ds003/work_dbf*/.coverage.* \
-
-              sed -i -e 's/.opt.miniconda-latest.envs.neuro.lib.python3.6.site-packages/\/tmp\/src\/fitlins/g' .coverage
-              python -m coverage xml
-              python -m codecov --file coverage.xml --flags << parameters.estimator >> -e CIRCLE_JOB
+              # combine coverage
+              docker run --rm \
+                -v /tmp/ds003/work:/scratch0 \
+                -v /work_dbf:/scratch1 \
+                -v /tmp/ds003/work_dbf2:/scratch2 \
+                -w /scratch0 \
+                --entrypoint="/neurodocker/startup.sh" \
+                poldracklab/fitlins:latest \
+                bash -c "coverage combine \
+                          /scratch0/.coverage* \
+                          /scratch1/.coverage* \
+                          /scratch2/.coverage* \
+                         && coverage xml"
+              # submit coverage
+              bash <(curl --retry 5 -s https://codecov.io/bash) \
+                -f /tmp/ds003/work/coverage.xml \
+                -F << parameters.estimator >> \
+                -e CIRCLE_JOB
       - store_artifacts:
           path: /tmp/ds003
 
@@ -480,7 +438,7 @@ workflows:
           filters:
             tags:
               only: /.*/
-      - test_pytest:
+      - run_pytest:
           requires:
             - build
           filters:
@@ -501,13 +459,6 @@ workflows:
           filters:
             tags:
               only: /.*/
-      - run_pytest:
-          requires:
-            - build
-            - cache_test_data
-          filters:
-            tags:
-              only: /.*/
       - deploy_master:
           requires:
             - test_ds003_nistats