Add initial infrastructure

.autorc

@@ -6,11 +6,8 @@
     "first-time-contributor",
     "released"
   ],
-  "release": {
-    "prerelease": true
-  },
   "owner": "physiopy",
-  "repo": "phys2bids",
+  "repo": "phys2denoise",
   "name": "Stefano Moia",
   "email": "s.moia@bcbl.eu",
   "labels": [
@@ -19,68 +16,78 @@
       "changelogTitle": "💥 Breaking Change",
       "description": "This PR breaks compatibility, and increments the major version (+1.0.0)",
       "releaseType": "major",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#05246d"
     },
     {
       "name": "Minormod",
       "changelogTitle": "🚀 Enhancement",
       "description": "This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0)",
       "releaseType": "minor",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#05246d"
     },
     {
       "name": "Minormod-breaking",
       "changelogTitle": "💥 Breaking Change during development",
       "description": "For development only, this PR increments the minor version (0.+1.0) but breaks compatibility",
       "releaseType": "minor",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#05246d"
     },
     {
       "name": "BugFIX",
       "changelogTitle": "🐛 Bug Fix",
       "description": "This PR generally closes a `Bug` issue, and increments the patch version (0.0.+1)",
       "releaseType": "patch",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#d73a4a"
     },
     {
       "name": "Documentation",
       "changelogTitle": "📝 Documentation",
       "description": "This issue or PR is about the documentation ",
       "releaseType": "none",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#1D70CF"
     },
     {
       "name": "Testing",
       "changelogTitle": "⚠️ Tests",
       "description": "This is for testing features, writing tests or producing testing code",
       "releaseType": "none",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#ffb5b4"
     },
     {
       "name": "Internal",
       "changelogTitle": "🏠 Internal",
       "description": "Changes affect the internal API. It doesn't increase the version, but produces a changelog",
       "releaseType": "none",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#ffffff"
     },
     {
       "name": "Outreach",
       "changelogTitle": "🖋️  Outreach",
       "description": "Issue about outreaching of any form",
       "releaseType": "none",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#0e8a16"
     },
     {
       "name": "Skip release",
       "description": "This PR preserves the current version when merged, and doesn't appear in the changelog",
       "releaseType": "skip",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#ffffff"
     },
     {
       "name": "Release",
       "description": "For PR only, trigger a release at the merge",
       "releaseType": "release",
-      "overwrite": true
+      "overwrite": true,
+      "color": "#FFFFFF"
     }
   ]
 }

.circleci/artifact_path

@@ -0,0 +1 @@
+0/tmp/src/phys2denoise/docs/_build/html/index.html

.circleci/config.yml

@@ -0,0 +1,216 @@
+# Python CircleCI 2.1 configuration file
+#
+#
+#
+version: 2.1
+orbs:
+  codecov: codecov/codecov@1.0.5
+jobs:
+
+  makeenv_37:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/phys2denoise
+    steps:
+      - checkout
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/phys2denoise
+      - restore_cache:
+          key: conda-py37-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Generate environment
+          command: |
+            if [[ -e /opt/conda/envs/py36_env ]]; then
+              echo "Restoring environment from cache"
+                source activate phys2denoise_py37
+            else
+              conda create -yq -n phys2denoise_py37 python=3.7
+              source activate phys2denoise_py37
+              pip install -e ".[test,doc]"
+            fi
+      - save_cache:
+          key: conda-py37-v1-{{ checksum "setup.cfg" }}
+          paths:
+              - /opt/conda/envs/phys2denoise_py37
+
+  unittest_36:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/phys2denoise
+    steps:
+      - checkout
+      - restore_cache:
+          key: conda-py36-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Generate environment
+          command: |
+            apt-get install -yqq make
+            if [ ! -d /opt/conda/envs/phys2denoise_py36 ]; then
+              conda create -yq -n phys2denoise_py36 python=3.6
+              source activate phys2denoise_py36
+              pip install -e ".[test]"
+            fi
+      - run:
+          name: Running unit tests
+          command: |
+            source activate phys2denoise_py36
+            make unittest
+            mkdir /tmp/src/coverage
+            mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.py36
+      - save_cache:
+          key: conda-py36-v1-{{ checksum "setup.cfg" }}
+          paths:
+              - /opt/conda/envs/phys2denoise_py36
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.py36
+
+  unittest_37:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/phys2denoise
+    steps:
+      - checkout
+      - restore_cache:
+          key: conda-py37-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Running unit tests
+          command: |
+            apt-get install -y make
+            source activate phys2denoise_py37  # depends on makeenv_37
+            make unittest
+            mkdir /tmp/src/coverage
+            mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.py37
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.py37
+
+  integrationtest_36:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/phys2denoise
+    steps:
+      - checkout
+      - restore_cache:
+          key: conda-py36-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Generate environment
+          command: |
+            apt-get install -yqq make
+            if [ ! -d /opt/conda/envs/phys2denoise_py36 ]; then
+              conda create -yq -n phys2denoise_py36 python=3.6
+              source activate phys2denoise_py36
+              pip install -e ".[test]"
+            fi
+      - run:
+          name: Run integration tests
+          no_output_timeout: 10m
+          command: |
+            source activate phys2denoise_py36
+            make integration
+            mkdir /tmp/src/coverage
+            mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.integration36
+      - store_artifacts:
+          path: /tmp/data
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.integration36
+
+  integrationtest_37:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/phys2denoise
+    steps:
+      - checkout
+      - restore_cache:
+          key: conda-py37-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Run integration tests
+          no_output_timeout: 10m
+          command: |
+            apt-get install -yqq make
+            source activate phys2denoise_py37  # depends on makeenv_37
+            make integration
+            mkdir /tmp/src/coverage
+            mv /tmp/src/phys2denoise/.coverage /tmp/src/coverage/.coverage.integration37
+      - store_artifacts:
+          path: /tmp/data
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.integration37
+
+  style_check:
+    docker:
+      - image: continuumio/miniconda3
+    working_directory: /tmp/src/phys2denoise
+    steps:
+      - checkout
+      - restore_cache:
+          key: conda-py37-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Style check
+          command: |
+            apt-get install -yqq make
+            source activate phys2denoise_py37  # depends on makeenv37
+            make lint
+      - store_artifacts:
+          path: /tmp/data/lint
+
+  build_docs:
+    working_directory: /tmp/src/phys2denoise
+    docker:
+      - image: continuumio/miniconda3
+    steps:
+      - attach_workspace:  # get phys2denoise
+          at: /tmp
+      - restore_cache:  # load environment
+          key: conda-py37-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Build documentation
+          command: |
+            apt-get install -yqq make
+            source activate phys2denoise_py37  # depends on makeenv_37
+            make -C docs html
+      - store_artifacts:
+          path: /tmp/src/phys2denoise/docs/_build/html
+
+  merge_coverage:
+    working_directory: /tmp/src/phys2denoise
+    docker:
+      - image: continuumio/miniconda3
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - checkout
+      - restore_cache:
+          key: conda-py37-v1-{{ checksum "setup.cfg" }}
+      - run:
+          name: Merge coverage files
+          command: |
+            apt-get install -yqq curl
+            source activate phys2denoise_py37  # depends on makeenv37
+            cd /tmp/src/coverage/
+            coverage combine
+            coverage xml
+      - store_artifacts:
+          path: /tmp/src/coverage
+      - codecov/upload:
+          file: /tmp/src/coverage/coverage.xml
+
+workflows:
+  version: 2.1
+  build_test:
+    jobs:
+      - makeenv_37
+      - style_check:
+          requires:
+            - makeenv_37
+      - merge_coverage:
+          requires:
+            - style_check

.github/workflows/auto-release.yml

@@ -0,0 +1,43 @@
+# This workflows will create a release using auto when a PR is merged in master.
+
+name: Auto-release on PR merge
+
+on:
+  # ATM, this is the closest trigger to a PR merging
+  push:
+    branches:
+      - master
+
+jobs:
+  auto-release:
+    runs-on: ubuntu-18.04
+    # Set skip ci to avoid loops
+    if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
+    # Set bash as default shell for jobs
+    defaults:
+      run:
+        shell: bash
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v2
+      with:
+        # Fetch all history for all branches and tags
+        fetch-depth: 0
+        # Use token with write access to the repo
+        token: ${{ secrets.GH_TOKEN }}
+    - name: Download and install latest auto
+      env:
+        # OS can be linux, macos, or win
+        OS: linux
+        # Retrieve URL of latest auto, download it, unzip it, and give exec permissions.
+      run: |
+        curl -vkL -o - $( curl -s https://api.github.com/repos/intuit/auto/releases/latest \
+        | grep browser_download_url | grep ${OS} | awk -F'"' '{print $4}') \
+        | gunzip > ~/auto
+        chmod a+x ~/auto
+    - name: Create release without version prefix
+      env:
+        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
+        # Run auto release, don't use 'v' prefix, and be verbose
+      run: |
+        ~/auto shipit --no-version-prefix -v

.readthedocs.yml

@@ -0,0 +1,19 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
+  system_packages: true

.requires.yml

@@ -1,6 +1,7 @@
 version: 1.0
 requirements:
   - requirements.txt
+  - setup.cfg
   - setup.py
   - tox.ini
   - path: /requirements.txt