Merge branch 'master' of https://github.com/ME-ICA/tedana

.all-contributorsrc

@@ -39,7 +39,9 @@
       "avatar_url": "https://avatars1.githubusercontent.com/u/7314358?v=4",
       "profile": "https://github.com/javiergcas",
       "contributions": [
-        "ideas"
+        "ideas",
+        "code",
+        "design"
       ]
     },
     {
@@ -100,7 +102,8 @@
         "projectManagement",
         "doc",
         "review",
-        "maintenance"
+        "maintenance",
+        "code"
       ]
     },
     {
@@ -142,6 +145,25 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "eurunuela",
+      "name": "Eneko Uruñuela",
+      "avatar_url": "https://avatars0.githubusercontent.com/u/13706448?v=4",
+      "profile": "https://github.com/eurunuela",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "CesarCaballeroGaudes",
+      "name": "Cesar Caballero Gaudes",
+      "avatar_url": "https://avatars1.githubusercontent.com/u/7611340?v=4",
+      "profile": "https://github.com/CesarCaballeroGaudes",
+      "contributions": [
+        "doc",
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 5,

.circleci/config.yml

@@ -130,7 +130,7 @@ jobs:
             source activate tedana_py37  # depends on makeenv37
             make lint
 
-  build_docs:
+  three-echo:
     docker:
       - image: continuumio/miniconda3
     working_directory: /tmp/src/tedana
@@ -139,17 +139,21 @@ jobs:
       - restore_cache:
           key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
       - run:
-          name: Build docs
+          name: Run integration tests
+          no_output_timeout: 40m
           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/
+            source activate tedana_py37  # depends on makeenv_37
+            make three-echo
+            mkdir /tmp/src/coverage
+            mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.three-echo
       - store_artifacts:
-          path: /tmp/docs
-
-  integration:
+          path: /tmp/data
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.three-echo
+  five-echo:
     docker:
       - image: continuumio/miniconda3
     working_directory: /tmp/src/tedana
@@ -163,15 +167,15 @@ jobs:
           command: |
             apt-get install -yqq make
             source activate tedana_py37  # depends on makeenv_37
-            make integration
+            make five-echo
             mkdir /tmp/src/coverage
-            mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.integration
+            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.integration
+              - src/coverage/.coverage.five-echo
 
   merge_coverage:
     working_directory: /tmp/src/tedana
@@ -209,15 +213,16 @@ workflows:
       - style_check:
           requires:
             - makeenv_37
-      - integration:
+      - three-echo:
           requires:
             - makeenv_37
-      - build_docs:
+      - five-echo:
           requires:
             - makeenv_37
       - merge_coverage:
           requires:
             - unittest_35
             - unittest_36
             - unittest_37
-            - integration
+            - three-echo
+            - five-echo

.gitignore

@@ -104,4 +104,4 @@ ENV/
 .mypy_cache/
 
 # vscode
-.vscode
+.vscode

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 <target>' where <target> 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:
@@ -15,5 +16,9 @@ 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_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
+

README.md

@@ -14,7 +14,7 @@ multi-echo functional magnetic resonance imaging (fMRI) data.
 [![Codecov](https://codecov.io/gh/me-ica/tedana/branch/master/graph/badge.svg)](https://codecov.io/gh/me-ica/tedana)
 [![Join the chat at https://gitter.im/ME-ICA/tedana](https://badges.gitter.im/ME-ICA/tedana.svg)](https://gitter.im/ME-ICA/tedana?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![Join our tinyletter mailing list](https://img.shields.io/badge/receive-our%20newsletter%20❤%EF%B8%8F-blueviolet.svg)](https://tinyletter.com/tedana-devs)
-[![All Contributors](https://img.shields.io/badge/all_contributors-12-orange.svg?style=flat-square)](#contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-14-orange.svg?style=flat-square)](#contributors)
 
 
 ## About
@@ -102,20 +102,22 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
   <tr>
     <td align="center"><a href="https://github.com/dowdlelt"><img src="https://avatars2.githubusercontent.com/u/15126366?v=4" width="100px;" alt="Logan Dowdle"/><br /><sub><b>Logan Dowdle</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=dowdlelt" title="Code">💻</a> <a href="#question-dowdlelt" title="Answering Questions">💬</a> <a href="#design-dowdlelt" title="Design">🎨</a> <a href="https://github.com/ME-ICA/tedana/issues?q=author%3Adowdlelt" title="Bug reports">🐛</a></td>
     <td align="center"><a href="http://emdupre.me"><img src="https://avatars3.githubusercontent.com/u/15017191?v=4" width="100px;" alt="Elizabeth DuPre"/><br /><sub><b>Elizabeth DuPre</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Code">💻</a> <a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Documentation">📖</a> <a href="#ideas-emdupre" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-emdupre" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#review-emdupre" title="Reviewed Pull Requests">👀</a> <a href="#example-emdupre" title="Examples">💡</a> <a href="https://github.com/ME-ICA/tedana/commits?author=emdupre" title="Tests">⚠️</a> <a href="#question-emdupre" title="Answering Questions">💬</a></td>
-    <td align="center"><a href="https://github.com/javiergcas"><img src="https://avatars1.githubusercontent.com/u/7314358?v=4" width="100px;" alt="Javier Gonzalez-Castillo"/><br /><sub><b>Javier Gonzalez-Castillo</b></sub></a><br /><a href="#ideas-javiergcas" title="Ideas, Planning, & Feedback">🤔</a></td>
+    <td align="center"><a href="https://github.com/javiergcas"><img src="https://avatars1.githubusercontent.com/u/7314358?v=4" width="100px;" alt="Javier Gonzalez-Castillo"/><br /><sub><b>Javier Gonzalez-Castillo</b></sub></a><br /><a href="#ideas-javiergcas" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/ME-ICA/tedana/commits?author=javiergcas" title="Code">💻</a> <a href="#design-javiergcas" title="Design">🎨</a></td>
     <td align="center"><a href="https://github.com/handwerkerd"><img src="https://avatars3.githubusercontent.com/u/7406227?v=4" width="100px;" alt="Dan Handwerker"/><br /><sub><b>Dan Handwerker</b></sub></a><br /><a href="#design-handwerkerd" title="Design">🎨</a> <a href="https://github.com/ME-ICA/tedana/commits?author=handwerkerd" title="Documentation">📖</a> <a href="#example-handwerkerd" title="Examples">💡</a> <a href="#review-handwerkerd" title="Reviewed Pull Requests">👀</a></td>
     <td align="center"><a href="https://github.com/prantikk"><img src="https://avatars0.githubusercontent.com/u/1636689?v=4" width="100px;" alt="Prantik Kundu"/><br /><sub><b>Prantik Kundu</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=prantikk" title="Code">💻</a> <a href="#ideas-prantikk" title="Ideas, Planning, & Feedback">🤔</a></td>
   </tr>
   <tr>
     <td align="center"><a href="http://rossmarkello.me"><img src="https://avatars0.githubusercontent.com/u/14265705?v=4" width="100px;" alt="Ross Markello"/><br /><sub><b>Ross Markello</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=rmarkello" title="Code">💻</a> <a href="#infra-rmarkello" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#question-rmarkello" title="Answering Questions">💬</a></td>
     <td align="center"><a href="http://tsalo.github.io"><img src="https://avatars3.githubusercontent.com/u/8228902?v=4" width="100px;" alt="Taylor Salo"/><br /><sub><b>Taylor Salo</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Code">💻</a> <a href="#ideas-tsalo" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Documentation">📖</a> <a href="#tutorial-tsalo" title="Tutorials">✅</a> <a href="#question-tsalo" title="Answering Questions">💬</a> <a href="https://github.com/ME-ICA/tedana/issues?q=author%3Atsalo" title="Bug reports">🐛</a> <a href="https://github.com/ME-ICA/tedana/commits?author=tsalo" title="Tests">⚠️</a> <a href="#review-tsalo" title="Reviewed Pull Requests">👀</a></td>
-    <td align="center"><a href="https://github.com/jbteves"><img src="https://avatars3.githubusercontent.com/u/26722533?v=4" width="100px;" alt="Joshua Teves"/><br /><sub><b>Joshua Teves</b></sub></a><br /><a href="#projectManagement-jbteves" title="Project Management">📆</a> <a href="https://github.com/ME-ICA/tedana/commits?author=jbteves" title="Documentation">📖</a> <a href="#review-jbteves" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-jbteves" title="Maintenance">🚧</a></td>
+    <td align="center"><a href="https://github.com/jbteves"><img src="https://avatars3.githubusercontent.com/u/26722533?v=4" width="100px;" alt="Joshua Teves"/><br /><sub><b>Joshua Teves</b></sub></a><br /><a href="#projectManagement-jbteves" title="Project Management">📆</a> <a href="https://github.com/ME-ICA/tedana/commits?author=jbteves" title="Documentation">📖</a> <a href="#review-jbteves" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-jbteves" title="Maintenance">🚧</a> <a href="https://github.com/ME-ICA/tedana/commits?author=jbteves" title="Code">💻</a></td>
     <td align="center"><a href="https://whitakerlab.github.io"><img src="https://avatars1.githubusercontent.com/u/3626306?v=4" width="100px;" alt="Kirstie Whitaker"/><br /><sub><b>Kirstie Whitaker</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=KirstieJane" title="Documentation">📖</a> <a href="#projectManagement-KirstieJane" title="Project Management">📆</a> <a href="#review-KirstieJane" title="Reviewed Pull Requests">👀</a> <a href="#talk-KirstieJane" title="Talks">📢</a></td>
     <td align="center"><a href="https://github.com/monicayao"><img src="https://avatars1.githubusercontent.com/u/35382166?v=4" width="100px;" alt="Monica Yao"/><br /><sub><b>Monica Yao</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=monicayao" title="Documentation">📖</a> <a href="https://github.com/ME-ICA/tedana/commits?author=monicayao" title="Tests">⚠️</a></td>
   </tr>
   <tr>
     <td align="center"><a href="http://www.fmrwhy.com/"><img src="https://avatars0.githubusercontent.com/u/10141237?v=4" width="100px;" alt="Stephan Heunis"/><br /><sub><b>Stephan Heunis</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=jsheunis" title="Documentation">📖</a></td>
     <td align="center"><a href="https://www.linkedin.com/in/benoit-beranger/"><img src="https://avatars0.githubusercontent.com/u/16976839?v=4" width="100px;" alt="Benoît Béranger"/><br /><sub><b>Benoît Béranger</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=benoitberanger" title="Code">💻</a></td>
+    <td align="center"><a href="https://github.com/eurunuela"><img src="https://avatars0.githubusercontent.com/u/13706448?v=4" width="100px;" alt="Eneko Uruñuela"/><br /><sub><b>Eneko Uruñuela</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=eurunuela" title="Code">💻</a></td>
+    <td align="center"><a href="https://github.com/CesarCaballeroGaudes"><img src="https://avatars1.githubusercontent.com/u/7611340?v=4" width="100px;" alt="Cesar Caballero Gaudes"/><br /><sub><b>Cesar Caballero Gaudes</b></sub></a><br /><a href="https://github.com/ME-ICA/tedana/commits?author=CesarCaballeroGaudes" title="Documentation">📖</a> <a href="https://github.com/ME-ICA/tedana/commits?author=CesarCaballeroGaudes" title="Code">💻</a></td>
   </tr>
 </table>
 

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 !"
 }