Merge pull request #329 from girder/girder-3

Refactor and convert to Girder 3.

.circleci/config.yml

@@ -1,77 +1,60 @@
 version: 2
 jobs:
-  py35:
-    machine: true
-    working_directory: /home/circleci/project
+  build:
+    working_directory: ~/project
+    docker:
+      - image: zachmullen/tox-and-node
+      - image: memcached
+      - image: circleci/mongo:4.0-ram
+      - image: rabbitmq
     steps:
       - checkout
       - run:
-          name: upgrade pip
-          command: |
-            pip install --upgrade pip
+          name: Preinstall phantomjs to work around an npm permission issue
+          command: npm install -g phantomjs-prebuilt --unsafe-perm
       - run:
-          name: Install Docker Compose
-          command: |
-            pip install docker-compose
+          name: Run tests via tox
+          # Piping through cat does less buffering of the output but can
+          # consume the exit code
+          command: tox | cat; test ${PIPESTATUS[0]} -eq 0
       - run:
-          name: Get the environment up and running
-          command: |
-            cd devops/mapnik_py35 && docker-compose build && docker-compose up -d
-      - run:
-          name: upgrade pip
-          command: |
-            docker exec large-image-mapnik-python35 pip3 install --upgrade pip
+          name: Install Codecov client
+          command: pip install codecov
       - run:
-          name: Install large image plugin
-          command: |
-            docker exec large-image-mapnik-python35 sed -i 's/PY2_ONLY/PY3_ONLY/g' /large_image/plugin.cmake
-            docker exec large-image-mapnik-python35 pip3 install -e /large_image[mapnik]
-            docker exec large-image-mapnik-python35 girder-install plugin -s /large_image
-
-      - run:
-          name: Run the tests
-          command: |
-            docker exec large-image-mapnik-python35 cmake -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 girder
-            docker exec large-image-mapnik-python35 make -j 5
-            docker exec large-image-mapnik-python35 ctest -R mapnik -V
-  py36:
-    machine: true
-    working_directory: /home/circleci/project
+          name: Upload coverage
+          # Retry as codecov can be flaky
+          command: for i in $(seq 1 10); do [ %i -gt 1 ] && echo "retrying $i" && sleep 5; codecov --required --disable search pycov gcov --root project --file build/test/coverage/py_coverage.xml build/test/coverage/cobertura-coverage.xml && s=0 && break || s=$?; done; (exit $s)
+  release:
+    docker:
+      - image: circleci/python:3.7
     steps:
       - checkout
       - run:
-          name: upgrade pip
+          name: Setup virtual environment
           command: |
-            pip install --upgrade pip
+            if [ ! -d env ]; then python -m virtualenv env || python -m venv env; fi
+            echo ". $CIRCLE_WORKING_DIRECTORY/env/bin/activate" >> $BASH_ENV
       - run:
-          name: Install Docker Compose
-          command: |
-            pip install docker-compose
-      - run:
-          name: Get the environment up and running
-          command: |
-            cd devops/mapnik_py36 && docker-compose build && docker-compose up -d
-      - run:
-          name: upgrade pip
-          command: |
-            docker exec large-image-mapnik-python36 pip3 install --upgrade pip
+          name: Install python packages
+          command: pip install setuptools_scm twine
       - run:
-          name: Install large image plugin
-          command: |
-            docker exec large-image-mapnik-python36 sed -i 's/PY2_ONLY/PY3_ONLY/g' /large_image/plugin.cmake
-            docker exec large-image-mapnik-python36 pip3 install -e /large_image[mapnik]
-            docker exec large-image-mapnik-python36 girder-install plugin -s /large_image
-
-      - run:
-          name: Run the tests
-          command: |
-            docker exec large-image-mapnik-python36 cmake -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 girder
-            docker exec large-image-mapnik-python36 make -j 5
-            docker exec large-image-mapnik-python36 ctest -R mapnik -V
+          name: Release to PyPi
+          command: ./.circleci/release_pypi.sh
 
 workflows:
   version: 2
-  test_all:
+  ci:
     jobs:
-      - py35
-      - py36
+      - build:
+          filters:
+            tags:
+              only: /^v.*/
+      - release:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              only: girder-3
+# Change to master branch when girder-3 becomes the master

.circleci/release_pypi.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+set -e
+
+ROOTPATH=`pwd`
+
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/girder"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/girder_annotation"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/tasks"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/dummy"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/mapnik"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/openslide"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/ometiff"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/pil"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/test"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/tiff"
+python setup.py sdist
+twine upload --verbose dist/*
+

.editorconfig

@@ -0,0 +1,36 @@
+root = true
+
+[*]
+indent_style = space
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+
+[*.js]
+indent_size = 4
+
+[{*.json}]
+indent_size = 4
+
+[Makefile]
+indent_style = tab
+
+[*.pug]
+indent_size = 2
+
+[*.py]
+indent_size = 4
+max_line_length = 100
+
+[{*.rb,Vagrantfile}]
+indent_size = 2
+
+[{*.sh,*.bat}]
+indent_size = 4
+
+[*.styl]
+indent_size = 2
+
+[*.yml]
+indent_size = 2

.gitignore

@@ -1,9 +1,58 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
 *.py[cod]
-node_modules
-_build
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# pyenv
+.python-version
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+node_modules/
+
 .*.swp
 .*.swo
-env
-dist
-build
-large_image.egg-info
+*.aux.xml
+
+.eslintcache