[FIX, TST] Fix the failing tests (#518)

* Change requirements. * Change env checksums. * Improve documentation for debugging.
ME-ICA · Jan 16, 2020 · 97a4ca4 · 97a4ca4
1 parent ca177d5
commit 97a4ca4
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Showing 8 changed files with 106 additions and 68 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -14,7 +14,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Generate environment
           command: |
@@ -24,7 +24,7 @@ jobs:
               pip install -r dev_requirements.txt
             fi
       - save_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
           paths:
               - /opt/conda/envs/tedana_py37
 
@@ -35,7 +35,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py35-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py35-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Generate environment
           command: |
@@ -53,7 +53,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py35
       - save_cache:
-          key: conda-py35-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py35-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
           paths:
               - /opt/conda/envs/tedana_py35
       - persist_to_workspace:
@@ -68,7 +68,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py36-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py36-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Generate environment
           command: |
@@ -86,7 +86,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py36
       - save_cache:
-          key: conda-py36-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py36-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
           paths:
               - /opt/conda/envs/tedana_py36
       - persist_to_workspace:
@@ -101,7 +101,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Running unit tests
           command: |
@@ -122,7 +122,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Style check
           command: |
@@ -137,7 +137,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -161,7 +161,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -185,7 +185,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -211,7 +211,7 @@ jobs:
           at: /tmp
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
+          key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}-{{ checksum "requirements.txt" }}
       - run:
           name: Merge coverage files
           command: |

diff --git a/dev_requirements.txt b/dev_requirements.txt
@@ -2,7 +2,7 @@
 sphinx
 sphinx-argparse
 sphinx_rtd_theme
-coverage
+coverage<5.0
 flake8>=3.7
 numpydoc
 pytest

diff --git a/requirements.txt b/requirements.txt
@@ -1,8 +1,8 @@
 duecredit
 matplotlib
-nibabel>=2.1.0
-nilearn
-numpy>=1.14
+nibabel>=2.5.1
+nilearn>=0.5.2
+numpy>=1.15
 pandas
-scikit-learn
-scipy
+scikit-learn>=0.22
+scipy>=1.3.3
diff --git a/tedana/metrics/kundu_fit.py b/tedana/metrics/kundu_fit.py
@@ -91,7 +91,7 @@ def dependence_metrics(catd, tsoc, mmix, t2s, tes, ref_img,
                              't2s ({1})'.format(catd.shape[2], t2s.shape[1]))
 
     RepLGR.info("A series of TE-dependence metrics were calculated for "
-                "each ICA component, including Kappa, Rho, and variance "
+                "each component, including Kappa, Rho, and variance "
                 "explained.")
 
     # mask everything we can

diff --git a/tedana/tests/data/cornell_three_echo_outputs.txt b/tedana/tests/data/cornell_three_echo_outputs.txt
@@ -40,6 +40,42 @@ figures/comp_032.png
 figures/comp_033.png
 figures/comp_034.png
 figures/comp_035.png
+figures/comp_036.png
+figures/comp_037.png
+figures/comp_038.png
+figures/comp_039.png
+figures/comp_040.png
+figures/comp_041.png
+figures/comp_042.png
+figures/comp_043.png
+figures/comp_044.png
+figures/comp_045.png
+figures/comp_046.png
+figures/comp_047.png
+figures/comp_048.png
+figures/comp_049.png
+figures/comp_050.png
+figures/comp_051.png
+figures/comp_052.png
+figures/comp_053.png
+figures/comp_054.png
+figures/comp_055.png
+figures/comp_056.png
+figures/comp_057.png
+figures/comp_058.png
+figures/comp_059.png
+figures/comp_060.png
+figures/comp_061.png
+figures/comp_062.png
+figures/comp_063.png
+figures/comp_064.png
+figures/comp_065.png
+figures/comp_066.png
+figures/comp_067.png
+figures/comp_068.png
+figures/comp_069.png
+figures/comp_070.png
+figures/comp_071.png
 dn_ts_OC.nii.gz
 feats_OC2.nii.gz
 figures

diff --git a/tedana/tests/data/fiu_four_echo_outputs.txt b/tedana/tests/data/fiu_four_echo_outputs.txt
@@ -1,22 +1,46 @@
+T1gs.nii.gz
 adaptive_mask.nii.gz
 betas_OC.nii.gz
-betas_hik_OC.nii.gz
+betas_hik_OC_T1c.nii.gz
 dn_ts_OC.nii.gz
-feats_OC2.nii.gz
-figures
-hik_ts_OC.nii.gz
+dn_ts_OC_T1c.nii.gz
+dn_ts_e1.nii.gz
+dn_ts_e2.nii.gz
+dn_ts_e3.nii.gz
+dn_ts_e4.nii.gz
+glsig.1D
+hik_ts_OC_T1c.nii.gz
 ica_components.nii.gz
 ica_decomposition.json
 ica_mixing.tsv
-ica_orth_mixing.tsv
 lowk_ts_OC.nii.gz
+lowk_ts_e1.nii.gz
+lowk_ts_e2.nii.gz
+lowk_ts_e3.nii.gz
+lowk_ts_e4.nii.gz
+meica_R2_pred.nii.gz
+meica_S0_pred.nii.gz
+meica_betas_catd.nii.gz
+meica_metric_weights.nii.gz
+meica_mix_T1c.1D
+mepca_R2_pred.nii.gz
+mepca_S0_pred.nii.gz
+mepca_betas_catd.nii.gz
+mepca_metric_weights.nii.gz
 pca_components.nii.gz
 pca_decomposition.json
 pca_mixing.tsv
 report.txt
 s0v.nii.gz
+s0vG.nii.gz
+sphis_hik.nii.gz
 t2sv.nii.gz
+t2svG.nii.gz
 ts_OC.nii.gz
+ts_OC_whitened.nii.gz
+tsoc_nogs.nii.gz
+tsoc_orig.nii.gz
+figures
 figures/Component_Overview.png
 figures/Kappa_vs_Rho_Scatter.png
 figures/Kappa_Rho_Scree_plot.png
@@ -41,27 +65,3 @@ figures/comp_017.png
 figures/comp_018.png
 figures/comp_019.png
 figures/comp_020.png
-figures/comp_021.png
-figures/comp_022.png
-figures/comp_023.png
-figures/comp_024.png
-figures/comp_025.png
-figures/comp_026.png
-figures/comp_027.png
-figures/comp_028.png
-figures/comp_029.png
-figures/comp_030.png
-figures/comp_031.png
-figures/comp_032.png
-figures/comp_033.png
-figures/comp_034.png
-figures/comp_035.png
-figures/comp_036.png
-figures/comp_037.png
-figures/comp_038.png
-figures/comp_039.png
-figures/comp_040.png
-figures/comp_041.png
-figures/comp_042.png
-figures/comp_043.png
-figures/comp_044.png
diff --git a/tedana/tests/data/nih_five_echo_outputs_verbose.txt b/tedana/tests/data/nih_five_echo_outputs_verbose.txt
@@ -1,19 +1,14 @@
-T1gs.nii.gz
 adaptive_mask.nii.gz
 betas_OC.nii.gz
 betas_hik_OC.nii.gz
-betas_hik_OC_T1c.nii.gz
 dn_ts_OC.nii.gz
-dn_ts_OC_T1c.nii.gz
 dn_ts_e1.nii.gz
 dn_ts_e2.nii.gz
 dn_ts_e3.nii.gz
 dn_ts_e4.nii.gz
 dn_ts_e5.nii.gz
 feats_OC2.nii.gz
-glsig.1D
 hik_ts_OC.nii.gz
-hik_ts_OC_T1c.nii.gz
 hik_ts_e1.nii.gz
 hik_ts_e2.nii.gz
 hik_ts_e3.nii.gz
@@ -22,6 +17,7 @@ hik_ts_e5.nii.gz
 ica_components.nii.gz
 ica_decomposition.json
 ica_mixing.tsv
+ica_orth_mixing.tsv
 lowk_ts_OC.nii.gz
 lowk_ts_e1.nii.gz
 lowk_ts_e2.nii.gz
@@ -32,7 +28,6 @@ meica_R2_pred.nii.gz
 meica_S0_pred.nii.gz
 meica_betas_catd.nii.gz
 meica_metric_weights.nii.gz
-meica_mix_T1c.1D
 mepca_R2_pred.nii.gz
 mepca_S0_pred.nii.gz
 mepca_betas_catd.nii.gz
@@ -43,13 +38,10 @@ pca_mixing.tsv
 report.txt
 s0v.nii.gz
 s0vG.nii.gz
-sphis_hik.nii.gz
 t2sv.nii.gz
 t2svG.nii.gz
 ts_OC.nii.gz
 ts_OC_whitened.nii.gz
-tsoc_nogs.nii.gz
-tsoc_orig.nii.gz
 figures
 figures/Component_Overview.png
 figures/Kappa_vs_Rho_Scatter.png
@@ -117,3 +109,11 @@ figures/comp_059.png
 figures/comp_060.png
 figures/comp_061.png
 figures/comp_062.png
+figures/comp_063.png
+figures/comp_064.png
+figures/comp_065.png
+figures/comp_066.png
+figures/comp_067.png
+figures/comp_068.png
+figures/comp_069.png
+figures/comp_070.png
diff --git a/tedana/tests/test_integration.py b/tedana/tests/test_integration.py
@@ -90,10 +90,9 @@ def test_integration_five_echo(skip_integration):
         data=datalist,
         tes=[15.4, 29.7, 44.0, 58.3, 72.6],
         out_dir=out_dir,
-        tedpca='mdl',
-        gscontrol=['gsr', 't1c'],
-        png_cmap='bone',
-        debug=True,
+        tedpca='aic',
+        fittype='curvefit',
+        tedort=True,
         verbose=True)
 
     # Just a check on the component table pending a unit test of load_comptable
@@ -124,12 +123,15 @@ def test_integration_four_echo(skip_integration):
     prepend += 'sub-PILOT_ses-01_task-localizerDetection_run-01_echo-'
     suffix = '_space-sbref_desc-preproc_bold+orig.HEAD'
     datalist = [prepend + str(i + 1) + suffix for i in range(4)]
-    tedana_workflow(data=datalist,
-                    tes=[11.8, 28.04, 44.28, 60.52],
-                    out_dir=out_dir,
-                    tedpca='aic',
-                    fittype='curvefit',
-                    tedort=True)
+    tedana_workflow(
+        data=datalist,
+        tes=[11.8, 28.04, 44.28, 60.52],
+        out_dir=out_dir,
+        tedpca='kundu-stabilize',
+        gscontrol=['gsr', 't1c'],
+        png_cmap='bone',
+        debug=True,
+        verbose=True)
 
     # compare the generated output files
     fn = resource_filename('tedana', 'tests/data/fiu_four_echo_outputs.txt')
@@ -155,7 +157,7 @@ def test_integration_three_echo(skip_integration):
         tes=[14.5, 38.5, 62.5],
         out_dir=out_dir,
         low_mem=True,
-        tedpca='kundu-stabilize')
+        tedpca='mdl')
 
     # test rerunning the workflow
     tedana_workflow(