Merge pull request #150 from poldracklab/rel/0.4.0

REL: 0.4.0
poldracklab · May 10, 2019 · 6691058 · 6691058
2 parents 224db12 + ce2addf
commit 6691058
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Showing 16 changed files with 201 additions and 139 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -23,6 +23,8 @@ jobs:
             THISVERSION=$( python3 -c 'import fitlins; print(fitlins.__version__)' )
             echo "Building version ${CIRCLE_TAG:-$THISVERSION}"
             docker build \
+              --cache-from=poldracklab/fitlins \
+              --rm=false \
               --tag poldracklab/fitlins:latest \
               --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
               --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
@@ -33,7 +35,13 @@ jobs:
       - run:
           name: Check version
           command: |
-              docker run --rm -it poldracklab/fitlins:latest --version
+            THISVERSION=$( python3 -c 'import fitlins; print(fitlins.__version__)' )
+            THISVERSION="${CIRCLE_TAG:-$THISVERSION}"
+            DOCKERVERSION=$(docker run --rm -it poldracklab/fitlins:latest --version \
+                           | tail -n 1 | sed -e 's/.*fit/fit/' -e 's/[\r\n]//g')
+            echo "$THISVERSION"
+            echo "$DOCKERVERSION"
+            test "$DOCKERVERSION" = "fitlins v$THISVERSION"
       - run:
           name: Docker save
           no_output_timeout: 40m
@@ -44,8 +52,11 @@ jobs:
       - persist_to_workspace:
           root: /tmp
           paths:
-            - cache/docker.tar.gz
             - src/fitlins
+      - save_cache:
+          key: docker-v0-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
+          paths:
+            - /tmp/cache/docker.tar.gz
 
   cache_test_data:
     docker:
@@ -106,6 +117,9 @@ jobs:
     steps:
       - attach_workspace:
           at: /tmp
+      - restore_cache:
+          keys:
+            - docker-v0-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
             - ds003-v0-{{ .Branch }}-
@@ -161,36 +175,93 @@ jobs:
       - store_artifacts:
           path: /tmp/ds003
 
-  deploy_test:
-    machine:
-      image: circleci/classic:201711-01
+  test_packaging:
+    docker:
+      - image: python:latest
     working_directory: /tmp/src/fitlins
     steps:
-      - attach_workspace:
-          at: /tmp
       - run:
-          name: Check Docker credentials
-          no_output_timeout: 40m
+          name: Check Python version and upgrade pip
           command: |
-            if [[ -n "$DOCKER_PASS" ]]; then
-              docker login -u $DOCKER_USER -p $DOCKER_PASS
-            fi
+            python --version
+            python -m pip install -U pip setuptools virtualenv twine
+      - checkout
       - run:
-          name: Build and check Python packages
+          name: Build FitLins
           command: |
-            pip install "setuptools>=27.0" twine
-            echo "${CIRCLE_TAG}" > fitlins/VERSION
+            virtualenv --python=python /tmp/venv/build
+            source /tmp/venv/build/bin/activate
+            pip install --upgrade "pip>=19.1" setuptools wheel
             python setup.py sdist
             pip wheel --no-deps -w dist/ .
-            twine check dist/*
+      - store_artifacts:
+          path: /tmp/src/fitlins/dist
+      - run:
+          name: Check sdist distribution
+          command: |
+            THISVERSION=$( python -c 'import fitlins; print(fitlins.__version__)' )
+            THISVERSION="${CIRCLE_TAG:-$THISVERSION}"
+            twine check dist/fitlins*.tar.gz
+            virtualenv --python=python /tmp/venv/sdist
+            source /tmp/venv/sdist/bin/activate
+            pip install --upgrade "pip>=19.1" setuptools wheel
+            pip install dist/fitlins*.tar.gz
+            which fitlins | grep sdist\\/bin
+            INSTALLED_VERSION=$(fitlins --version)
+            echo "VERSION: \"$THISVERSION\""
+            echo "INSTALLED: \"$INSTALLED_VERSION\""
+            test "$INSTALLED_VERSION" = "fitlins v$THISVERSION"
+      - run:
+          name: Check wheel distribution
+          command: |
+            THISVERSION=$( python -c 'import fitlins; print(fitlins.__version__)' )
+            THISVERSION="${CIRCLE_TAG:-$THISVERSION}"
+            twine check dist/fitlins*.tar.gz
+            virtualenv --python=python /tmp/venv/wheel
+            source /tmp/venv/wheel/bin/activate
+            pip install --upgrade "pip>=19.1" setuptools wheel
+            pip install dist/fitlins*.whl
+            which fitlins | grep wheel\\/bin
+            INSTALLED_VERSION=$(fitlins --version)
+            echo "VERSION: \"$THISVERSION\""
+            echo "INSTALLED: \"$INSTALLED_VERSION\""
+            test "$INSTALLED_VERSION" = "fitlins v$THISVERSION"
+
+  deploy_pypi:
+    docker:
+      - image: python:latest
+    working_directory: /tmp/src/fitlins
+    steps:
+      - run:
+          name: Check Python version and upgrade pip
+          command: |
+            python --version
+            python -m pip install -U pip setuptools virtualenv twine
+      - checkout
+      - run:
+          name: Build FitLins
+          command: |
+            virtualenv --python=python /tmp/venv/build
+            source /tmp/venv/build/bin/activate
+            pip install --upgrade "pip>=19.1" setuptools wheel
+            python setup.py sdist
+            pip wheel --no-deps -w dist/ .
+      - store_artifacts:
+          path: /tmp/src/fitlins/dist
+      - run:
+          name: Upload packages to PyPI
+          command: |
+            twine check dist/fitlins*
+            twine upload dist/fitlins*
 
   deploy_master:
     machine:
       image: circleci/classic:201711-01
     working_directory: /tmp/src/fitlins
     steps:
-      - attach_workspace:
-          at: /tmp
+      - restore_cache:
+          keys:
+            - docker-v0-{{ .Branch }}-{{ .Revision }}
       - run:
           name: Load Docker image layer cache
           no_output_timeout: 30m
@@ -211,13 +282,14 @@ jobs:
               docker push poldracklab/fitlins:master
             fi
 
-  deploy:
+  deploy_docker:
     machine:
       image: circleci/classic:201711-01
     working_directory: /tmp/src/fitlins
     steps:
-      - attach_workspace:
-          at: /tmp
+      - restore_cache:
+          keys:
+            - docker-v0-{{ .Branch }}-{{ .Revision }}
       - run:
           name: Load Docker image layer cache
           no_output_timeout: 30m
@@ -238,15 +310,13 @@ jobs:
               docker tag poldracklab/fitlins poldracklab/fitlins:$CIRCLE_TAG
               docker push poldracklab/fitlins:$CIRCLE_TAG
             fi
-      - run:
-          name: Deploy to PyPi
-          command: |
-            pip install "setuptools>=27.0" twine
-            echo "${CIRCLE_TAG}" > fitlins/VERSION
-            python setup.py sdist
-            pip wheel --no-deps -w dist/ .
-            twine check dist/*
-            twine upload dist/*
+
+  deployable:
+    docker:
+      - image: busybox:latest
+    steps:
+      - run: echo Deploying!
+
 
 workflows:
   version: 2
@@ -275,24 +345,30 @@ workflows:
           filters:
             tags:
               only: /.*/
+      - test_packaging:
+          filters:
+            tags:
+              only: /.*/
       - deploy_master:
           requires:
             - test_ds003
           filters:
             branches:
               only: master
-      - deploy_test:
+      - deploy_docker:
           requires:
-            - build
+            - test_ds003
+            - build_docs
           filters:
             branches:
-              only: /rel\/[\d\.]+/
-            tags:
               ignore: /.*/
-      - deploy:
+            tags:
+              only: /.*/
+      - deploy_pypi:
           requires:
             - test_ds003
             - build_docs
+            - test_packaging
           filters:
             branches:
               ignore: /.*/

diff --git a/.codecov.yml b/.codecov.yml
@@ -1,2 +1,2 @@
-fixes:
-  - "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages::"
+ignore:
+  - "fitlins/_version.py"
diff --git a/.dockerignore b/.dockerignore
@@ -7,3 +7,5 @@ data
 *.md
 *.egg-info/
 .circleci/
+docs/
+examples/
diff --git a/.neurodocker.json b/.neurodocker.json
@@ -63,16 +63,6 @@
       "user",
       "root"
     ],
-    [
-      "arg",
-      {
-        "VERSION": ""
-      }
-    ],
-    [
-      "run",
-      "echo \"$VERSION\" > /src/fitlins/fitlins/VERSION"
-    ],
     [
       "run",
       "mkdir /work && chown -R neuro /src /work && chmod a+w /work"
@@ -82,21 +72,23 @@
       "neuro"
     ],
     [
-      "miniconda",
+      "arg",
       {
-        "use_env": "neuro",
-        "pip_opts": "-r",
-        "pip_install": [
-          "/src/fitlins/requirements.txt"
-        ]
+        "VERSION": ""
       }
     ],
+    [
+      "run",
+      "echo \"$VERSION\" > /src/fitlins/VERSION"
+    ],
     [
       "miniconda",
       {
         "use_env": "neuro",
+        "pip_opts": "-r",
         "pip_install": [
-          "/src/fitlins[all,test]"
+          "/src/fitlins/requirements.txt",
+          "/src/fitlins[all]"
         ],
         "activate": true
       }

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,25 @@
+0.4.0 (May 10, 2019)
+====================
+
+This release produces effect, variance, statistic (t or F), Z-score, and p-value
+maps at every level, and enables smoothing at higher levels if preferred.
+
+Additionally, documentation has been added at https://fitlins.readthedocs.io and
+versioning/packaging issues have been resolved.
+
+* FIX: Do not install FitLins as editable in Docker (https://github.com/poldracklab/fitlins/pull/137)
+* ENH: Save design matrix as TSV to output directory (https://github.com/poldracklab/fitlins/pull/143)
+* ENH: Enable smoothing at any analysis level (https://github.com/poldracklab/fitlins/pull/135)
+* ENH: Produce all available statistical maps from each analysis unit (https://github.com/poldracklab/fitlins/pull/131)
+* ENH: Add version to non-release Docker images. (https://github.com/poldracklab/fitlins/pull/136)
+* DOC: Flesh out documentation (https://github.com/poldracklab/fitlins/pull/147)
+* DOC: Build API docs on RTD (https://github.com/poldracklab/fitlins/pull/146)
+* DOC: Create Sphinx documentation with API autodocs (https://github.com/poldracklab/fitlins/pull/145)
+* MAINT: Drop Python 3.5 support (https://github.com/poldracklab/fitlins/pull/140)
+* CI: Run FitLins with coverage (https://github.com/poldracklab/fitlins/pull/144)
+* CI: Test FitLins on OpenNeuro DS000003, preprocessed with fMRIPrep 1.3.2 (https://github.com/poldracklab/fitlins/pull/141)
+
+
 0.3.0 (April 19, 2019)
 ======================