[REF, BRK] Decision tree modularization

.circleci/config.yml

@@ -12,6 +12,10 @@ jobs:
       - image: continuumio/miniconda3
     working_directory: /tmp/src/tedana
     steps:
+      - run:
+          name: Install parallel gzip and Python 3
+          command: |
+            apk add --no-cache pigz python3
       - checkout
       - restore_cache:
           key: conda-py37-v1-{{ checksum "dev_requirements.txt" }}
@@ -111,7 +115,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py37
       - persist_to_workspace:
-          root: /tmp
+          root: ~/coverage
           paths:
               - src/coverage/.coverage.py37
 
@@ -150,7 +154,7 @@ jobs:
       - store_artifacts:
           path: /tmp/data
       - persist_to_workspace:
-          root: /tmp
+          root: ~/coverage
           paths:
               - src/coverage/.coverage.three-echo
   five-echo:
@@ -196,9 +200,9 @@ jobs:
             coverage combine
             coverage xml
       - store_artifacts:
-          path: /tmp/src/coverage
+          path: ~/coverage
       - codecov/upload:
-          file: /tmp/src/coverage/coverage.xml
+          file: ~/coverage/coverage.xml
 
 workflows:
   version: 2.1

.pytest_cache/v/cache/nodeids

@@ -0,0 +1,48 @@
+[
+  "tedana/tests/test_combine.py::test__combine_t2s",
+  "tedana/tests/test_combine.py::test__combine_paid",
+  "tedana/tests/test_combine.py::test_make_optcom",
+  "tedana/tests/test_decay.py::test_fit_decay",
+  "tedana/tests/test_decay.py::test_fit_decay_ts",
+  "tedana/tests/test_decay.py::test_smoke_fit_decay",
+  "tedana/tests/test_decay.py::test_smoke_fit_decay_curvefit",
+  "tedana/tests/test_decay.py::test_smoke_fit_decay_ts",
+  "tedana/tests/test_decay.py::test_smoke_fit_decay_curvefit_ts",
+  "tedana/tests/test_gscontrol.py::test_break_gscontrol_raw",
+  "tedana/tests/test_io.py::test_new_nii_like",
+  "tedana/tests/test_io.py::test_filewrite",
+  "tedana/tests/test_io.py::test_load_data",
+  "tedana/tests/test_io.py::test_smoke_split_ts",
+  "tedana/tests/test_io.py::test_smoke_write_split_ts",
+  "tedana/tests/test_io.py::test_smoke_writefeats",
+  "tedana/tests/test_io.py::test_smoke_filewrite",
+  "tedana/tests/test_io.py::test_smoke_load_data",
+  "tedana/tests/test_model_fit_dependence_metrics.py::test_break_dependence_metrics",
+  "tedana/tests/test_model_kundu_metrics.py::test_smoke_kundu_metrics",
+  "tedana/tests/test_selection.py::test_manual_selection",
+  "tedana/tests/test_stats_computefeats2.py::test_break_computefeats2",
+  "tedana/tests/test_stats_computefeats2.py::test_smoke_computefeats2",
+  "tedana/tests/test_stats_get_coeffs.py::test_get_coeffs",
+  "tedana/tests/test_stats_get_coeffs.py::test_break_get_coeffs",
+  "tedana/tests/test_stats_get_coeffs.py::test_smoke_get_coeffs",
+  "tedana/tests/test_stats_getfbounds.py::test_getfbounds",
+  "tedana/tests/test_stats_getfbounds.py::test_smoke_getfbounds",
+  "tedana/tests/test_t2smap.py::TestT2smap::test_basic_t2smap1",
+  "tedana/tests/test_t2smap.py::TestT2smap::test_basic_t2smap2",
+  "tedana/tests/test_t2smap.py::TestT2smap::test_basic_t2smap3",
+  "tedana/tests/test_t2smap.py::TestT2smap::test_basic_t2smap4",
+  "tedana/tests/test_utils.py::test_unmask",
+  "tedana/tests/test_utils.py::test_dice",
+  "tedana/tests/test_utils.py::test_andb",
+  "tedana/tests/test_utils.py::test_load_image",
+  "tedana/tests/test_utils.py::test_make_adaptive_mask",
+  "tedana/tests/test_utils.py::test_smoke_load_image",
+  "tedana/tests/test_utils.py::test_smoke_make_adaptive_mask",
+  "tedana/tests/test_utils.py::test_smoke_unmask",
+  "tedana/tests/test_utils.py::test_smoke_dice",
+  "tedana/tests/test_utils.py::test_smoke_andb",
+  "tedana/tests/test_utils.py::test_smoke_get_spectrum",
+  "tedana/tests/test_utils.py::test_smoke_threshold_map",
+  "tedana/tests/test_viz.py::test_smoke_trim_edge_zeros",
+  "tedana/tests/test_integration_three_echo.py::test_integration_three_echo"
+]

.pytest_cache/v/cache/stepwise

@@ -0,0 +1 @@
+[]

dev_tools/build_docker.sh

@@ -0,0 +1,58 @@
+#!/usr/bin/env bash
+
+update_dev_dockerfile() {
+    #
+    # Generates Dockerfile to build Docker image for local tedana testing
+    #
+
+    generate_ipython_config="
+        /opt/conda/envs/tedana_py36/bin/ipython profile create
+        && sed -i 's/#c.InteractiveShellApp.extensions = \[\]/c.InteractiveShellApp.extensions = \['\''autoreload'\''\]/g' /root/.ipython/profile_default/ipython_config.py"
+
+    call_dir=${PWD}
+    git_root=$( git rev-parse --show-toplevel ); cd "${git_root}"
+    docker run --rm kaczmarj/neurodocker:0.6.0 generate docker                 \
+      --base debian:latest                                                     \
+      --pkg-manager apt                                                        \
+      --env LANG=C.UTF-8 LC_ALL=C.UTF-8                                        \
+      --install curl git wget bzip2 ca-certificates sed openssh-client         \
+      --run "mkdir -p /tedana/dev_tools/envs"                                  \
+      --copy ./dev_tools/envs/py35_env.yml /tedana/dev_tools/envs/py35_env.yml \
+      --copy ./dev_tools/envs/py36_env.yml /tedana/dev_tools/envs/py36_env.yml \
+      --copy ./dev_tools/envs/py37_env.yml /tedana/dev_tools/envs/py37_env.yml \
+      --miniconda create_env=tedana_py35                                       \
+                  install_path=/opt/conda                                      \
+                  yaml_file=/tedana/dev_tools/envs/py35_env.yml                \
+                  activate_env=false                                           \
+      --miniconda create_env=tedana_py36                                       \
+                  install_path=/opt/conda                                      \
+                  yaml_file=/tedana/dev_tools/envs/py36_env.yml                \
+                  activate_env=true                                            \
+      --miniconda create_env=tedana_py37                                       \
+                  install_path=/opt/conda                                      \
+                  yaml_file=/tedana/dev_tools/envs/py37_env.yml                \
+                  activate_env=false                                           \
+      --run "${generate_ipython_config}"                                       \
+      --copy "./dev_tools" /tedana/dev_tools                                   \
+      --add-to-entrypoint "source activate tedana_py36"                        \
+      --add-to-entrypoint "source /tedana/dev_tools/run_tests.sh"              \
+      --workdir /tedana                                                        \
+      > ./Dockerfile_dev
+    cd "${call_dir}"
+}
+
+
+build_dev_image() {
+    #
+    # Recreates local Dockerfile and builds tedana/tedana-dev:local Docker image
+    #
+
+    if [ ! -z "${1}" ]; then
+        tag="${1}"
+    else
+        tag=local
+    fi
+
+    update_dev_dockerfile
+    docker build --tag tedana/tedana-dev:"${tag}" -f Dockerfile_dev .
+}

dev_tools/get_data.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+
+get_three_echo_test_data() {
+    mkdir -p /tmp/data/three-echo
+    curl -s -L -o /tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz https://osf.io/gfkw7/download
+}
+    # && curl -L -o TED.Cornell_processed_three_echo_dataset.tar.xz https://osf.io/u65sq/download
+    # && tar xf TED.Cornell_processed_three_echo_dataset.tar.xz --no-same-owner -C /data/test/three-echo/
+    # && rm -f TED.Cornell_processed_three_echo_dataset.tar.xz'
+
+
+get_five_echo_test_data() {
+    mkdir /tmp/data/five-echo
+    curl -s -L https://osf.io/h6bmw/download | tar xJf - -C /tmp/data/five-echo
+}
+    # && curl -L -o TED.p06.tar.xz https://osf.io/fr6mx/download
+    # && tar xf TED.p06.tar.xz --no-same-owner -C /data/test/five-echo/
+    # && rm -f TED.p06.tar.xz'
+
+
+download_data() {
+    for ds in three-echo five-echo; do
+        datadir=/tmp/data/${ds}
+        # if the data directory doesn't exist OR the data directory is empty
+        # then download the data for the specified dataset
+        if [ ! -d ${datadir} ] || [ ! "$( ls -A ${datadir} )" ]; then
+            printf "Downloading ${ds} data into ${datadir}\n"
+            get_${ds/-/_}_test_data
+        fi
+    done
+}

dev_tools/run_tests.sh

@@ -1,5 +1,11 @@
 #!/usr/bin/env bash
 
+<<<<<<< HEAD
+DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+source ${DIRECTORY}/get_data.sh
+
+=======
+>>>>>>> tsala/modularize-metrics
 cprint() {
     #
     # Prints all supplied arguments as a bold, green string
@@ -17,6 +23,32 @@ cprint() {
 }
 
 
+<<<<<<< HEAD
+run_integration_tests() {
+    #
+    # Runs tedana integration tests; passes any parameters to py.test
+    #
+
+    download_data
+    cprint "RUNNING INTEGRATION TESTS"
+    source activate tedana_py36
+    py.test "$@" --cov-append --cov-report term-missing --cov=tedana tedana/tests/test_integration.py
+}
+
+
+run_unit_test() {
+    #
+    # Runs tedana unit tests for provided Python environment
+    #
+    # Required argments:
+    #   pyenv           name of python environment to use for testing. should
+    #                   be one of [tedana_py35, tedana_py36, tedana_py37]
+    #
+
+    cprint "RUNNING UNIT TESTS FOR PYTHON ENVIRONMENT: ${1}"
+    source activate "${1}"
+    py.test --skipintegration --cov-append --cov-report term-missing --cov=tedana tedana
+=======
 run_three_echo_test() {
     #
     # Runs tedana three-echo test
@@ -44,6 +76,7 @@ run_unit_tests() {
     cprint "RUNNING UNIT TESTS"
     make unittest
     cprint "UNIT TESTS PASSED !"
+>>>>>>> tsala/modularize-metrics
 }
 
 
@@ -52,14 +85,32 @@ run_lint_tests() {
     # Lints the tedana codebase
     #
 
+<<<<<<< HEAD
+    cprint "RUNNING FLAKE8 ON TEDANA DIRECTORY"
+    source activate tedana_py36
+    flake8 tedana
+=======
     cprint "RUNNING FLAKE8 TO LINT CODEBASE"
     make lint
     cprint "CODEBASE LINTED SUCCESSFULLY !"
+>>>>>>> tsala/modularize-metrics
 }
 
 
 run_all_tests() {
     #
+<<<<<<< HEAD
+    # Runs tedana test suite excluding five-echo test by default
+    #
+
+    run_lint_tests
+    for pyenv in tedana_py3{5,6,7}; do
+        run_unit_test "${pyenv}"
+    done
+    run_integration_tests
+
+    cprint "FINISHED RUNNING ALL TESTS! GREAT SUCCESS"
+=======
     # Runs tedana test suite
     #
 
@@ -69,4 +120,5 @@ run_all_tests() {
     run_five_echo_test
 
     cprint "FINISHED RUNNING ALL TESTS -- GREAT SUCCESS !"
+>>>>>>> tsala/modularize-metrics
 }

docs/_templates/function.rst

@@ -10,3 +10,4 @@
 .. raw:: html
 
     <div class="clearer"></div>
+

docs/api.rst

@@ -120,6 +120,9 @@ API
    tedana.selection.manual_selection
    tedana.selection.kundu_selection_v2
 
+   :template: module.rst
+   tedana.selection.selection_nodes
+   tedana.selection.decision_tree_class
 
 .. _api_gscontrol_ref: