From e5aecf7a5f845d30c8c0315d2a6c157b36fb9ea8 Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 17:54:12 -0500 Subject: [PATCH 1/8] Adjusts makefile --- Makefile | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 4ad309fd7..155bb507d 100644 --- a/Makefile +++ b/Makefile @@ -15,5 +15,9 @@ lint: unittest: @py.test --skipintegration --cov-append --cov-report term-missing --cov=tedana tedana/ -integration: - @py.test --cov-append --cov-report term-missing --cov=tedana tedana/tests/test_integration.py +three-echo: + @py.test --cov-append --cov-report term-missing --cov=tedana -k test_three_echo tedana/tests/test_integration.py + +five-echo: + @py.test --cov-append --cov-report term-missing --cov=tedana -k test_five_echo tedana/tests/test_integration.py + From 88a997c0a5436b85295aacb56e8a1192aa84115c Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 23:17:55 -0500 Subject: [PATCH 2/8] Adjusts CircleCI config --- .circleci/config.yml | 39 +++++++++++++++++++++++++++++++++------ 1 file changed, 33 insertions(+), 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 6c834a581..ee1df2ecf 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -149,7 +149,7 @@ jobs: - store_artifacts: path: /tmp/docs - integration: + three-echo: docker: - image: continuumio/miniconda3 working_directory: /tmp/src/tedana @@ -163,15 +163,38 @@ jobs: command: | apt-get install -yqq make source activate tedana_py37 # depends on makeenv_37 - make integration + make three-echo mkdir /tmp/src/coverage - mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.integration + mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.three-echo - store_artifacts: path: /tmp/data - persist_to_workspace: root: /tmp paths: - - src/coverage/.coverage.integration + - src/coverage/.coverage.three-echo + five-echo: + docker: + - image: continuumio/miniconda3 + working_directory: /tmp/src/tedana + steps: + - checkout + - restore_cache: + key: conda-py37-v1-{{ checksum "dev_requirements.txt" }} + - run: + name: Run integration tests + no_output_timeout: 40m + command: | + apt-get install -yqq make + source activate tedana_py37 # depends on makeenv_37 + make five-echo + mkdir /tmp/src/coverage + mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.five-echo + - store_artifacts: + path: /tmp/data + - persist_to_workspace: + root: /tmp + paths: + - src/coverage/.coverage.five-echo merge_coverage: working_directory: /tmp/src/tedana @@ -209,7 +232,10 @@ workflows: - style_check: requires: - makeenv_37 - - integration: + - three-echo: + requires: + - makeenv_37 + - five-echo: requires: - makeenv_37 - build_docs: @@ -220,4 +246,5 @@ workflows: - unittest_35 - unittest_36 - unittest_37 - - integration + - three-echo + - five-echo From 568084bf07a007ab97b5a3a9f9d07ba53e49a23c Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 23:23:25 -0500 Subject: [PATCH 3/8] Attempts to correct Makefile --- Makefile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 155bb507d..955bf5476 100644 --- a/Makefile +++ b/Makefile @@ -1,12 +1,13 @@ .PHONY: all lint -all_tests: lint unittest integration +all_tests: lint unittest three-echo five-echo help: @echo "Please use 'make ' where is one of:" @echo " lint to run flake8 on all Python files" @echo " unittest to run unit tests on tedana" - @echo " integration to run integration tests on tedana" + @echo " three-echo to run the three-echo test set on tedana" + @echo " five-echo to run the five-echo test set on tedana" @echo " all_tests to run 'lint', 'unittest', and 'integration'" lint: From 76cf831afe3c13b182493a5e351e31aa51a70fba Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 23:31:40 -0500 Subject: [PATCH 4/8] Attempt again to fix tests --- dev_tools/run_tests.sh | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/dev_tools/run_tests.sh b/dev_tools/run_tests.sh index a6fd7625b..6d1181097 100644 --- a/dev_tools/run_tests.sh +++ b/dev_tools/run_tests.sh @@ -17,14 +17,22 @@ cprint() { } -run_integration_tests() { +run_three_echo_test() { # - # Runs tedana integration tests + # Runs tedana three-echo test # - cprint "RUNNING INTEGRATION TESTS" - make integration - cprint "INTEGRATION TESTS PASSED !" + cprint "RUNNING THREE-ECHO TEST" + make three-echo + cprint "THREE-ECHO TEST PASSED !" +} + +run_five_echo_test() { + # + # Runs tedana five-echo test + cprint "RUNNING FIVE-ECHO TEST" + make five-echo + cprint "FIVE-ECHO TEST PASSED !" } @@ -57,7 +65,8 @@ run_all_tests() { run_lint_tests run_unit_tests - run_integration_tests + run_three_echo_test + run_five_echo_test cprint "FINISHED RUNNING ALL TESTS -- GREAT SUCCESS !" } From 29b37fbe40dce41156103f74794aadb29360a271 Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 23:34:05 -0500 Subject: [PATCH 5/8] :-( --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 955bf5476..315092612 100644 --- a/Makefile +++ b/Makefile @@ -17,7 +17,7 @@ unittest: @py.test --skipintegration --cov-append --cov-report term-missing --cov=tedana tedana/ three-echo: - @py.test --cov-append --cov-report term-missing --cov=tedana -k test_three_echo tedana/tests/test_integration.py + @py.test -k test_three_echo tedana/tests/test_integration.py five-echo: @py.test --cov-append --cov-report term-missing --cov=tedana -k test_five_echo tedana/tests/test_integration.py From 5c51b72ad9b614b7a855418d9c752485a3243969 Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 23:39:57 -0500 Subject: [PATCH 6/8] Correct test names --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 315092612..1f9383515 100644 --- a/Makefile +++ b/Makefile @@ -17,8 +17,8 @@ unittest: @py.test --skipintegration --cov-append --cov-report term-missing --cov=tedana tedana/ three-echo: - @py.test -k test_three_echo tedana/tests/test_integration.py + @py.test -k test_integration_three_echo tedana/tests/test_integration.py five-echo: - @py.test --cov-append --cov-report term-missing --cov=tedana -k test_five_echo tedana/tests/test_integration.py + @py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_five_echo tedana/tests/test_integration.py From 43cd08892b0182650683cf7597fe1b3f4457dd0f Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 23:43:47 -0500 Subject: [PATCH 7/8] Add back in converage for three-echo dataset --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 1f9383515..ad706eac5 100644 --- a/Makefile +++ b/Makefile @@ -17,7 +17,7 @@ unittest: @py.test --skipintegration --cov-append --cov-report term-missing --cov=tedana tedana/ three-echo: - @py.test -k test_integration_three_echo tedana/tests/test_integration.py + @py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_three_echo tedana/tests/test_integration.py five-echo: @py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_five_echo tedana/tests/test_integration.py From a82bb3f3e5b2bb6abfa43b385b52c0e4ab2a2a13 Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Sun, 10 Nov 2019 16:37:34 -0500 Subject: [PATCH 8/8] Removes doc-building from CircleCI --- .circleci/config.yml | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index ee1df2ecf..d4bcd86a5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -130,25 +130,6 @@ jobs: source activate tedana_py37 # depends on makeenv37 make lint - build_docs: - docker: - - image: continuumio/miniconda3 - working_directory: /tmp/src/tedana - steps: - - checkout - - restore_cache: - key: conda-py37-v1-{{ checksum "dev_requirements.txt" }} - - run: - name: Build docs - command: | - apt-get install -yqq make - source activate tedana_py37 # depends on makeenv37 - cd docs && make html doctest - mkdir /tmp/docs - mv /tmp/src/tedana/docs/_build/* /tmp/docs/ - - store_artifacts: - path: /tmp/docs - three-echo: docker: - image: continuumio/miniconda3 @@ -238,9 +219,6 @@ workflows: - five-echo: requires: - makeenv_37 - - build_docs: - requires: - - makeenv_37 - merge_coverage: requires: - unittest_35