girder 3.2.4.dev9__tar.gz → 5.0.0a3.dev2__tar.gz

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/.circleci/Dockerfile

@@ -13,7 +13,7 @@ RUN apt-get update \
     automake \
   && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN curl -sL https://deb.nodesource.com/setup_14.x | bash - \
+RUN curl -sL https://deb.nodesource.com/setup_16.x | bash - \
   && apt-get install -y nodejs \
   && find / -xdev -name __pycache__ -type d -exec rm -r {} \+ \
   && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
@@ -22,6 +22,8 @@ RUN curl -sL https://deb.nodesource.com/setup_14.x | bash - \
 RUN apt-get update \
   && apt-get install --assume-yes \
     cmake \
+    automake \
+    nodejs \
   # Note: universal-ctags is installed for use in the public_names CI job.
   && git clone "https://github.com/universal-ctags/ctags.git" "./ctags" \
   && cd ./ctags \

girder-5.0.0a3.dev2/.circleci/build_plugins.py

@@ -0,0 +1,19 @@
+from pathlib import Path
+import subprocess
+import sys
+
+plugins_dir = Path(sys.argv[1])
+
+for plugin_dir in plugins_dir.iterdir():
+    if plugin_dir.is_dir():
+        plugin_web_client = plugin_dir / f'girder_{plugin_dir.name}' / 'web_client'
+
+        if plugin_web_client.exists() and (plugin_web_client / 'package-lock.json').exists():
+            subprocess.run(
+                'npm ci && npm run build',
+                check=True,
+                shell=True,
+                stdout=sys.stdout,
+                stderr=sys.stderr,
+                cwd=plugin_web_client
+            )

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/.circleci/config.yml

@@ -5,11 +5,11 @@ executors:
   py3:
     docker:
       # This image uses the newest version of many dependencies
-      - image: girder/girder_test:py38-node14
+      - image: girder/girder_test:py38-node16
     working_directory: /home/circleci/project
   py3-mongo:
     docker:
-      - image: girder/girder_test:py38-node14
+      - image: girder/girder_test:latest
       # Use the oldest supported MongoDB
       # This is equivalent to the deprecated circleci/mongo:<version>-ram image
       - image: mongo:3.6
@@ -24,11 +24,11 @@ commands:
   install-girder:
     description: "Install Girder in a virtualenv and configure CTest"
     steps:
-      - run:
-          name: Generate python environment checksum file
-          command: ./girder/.circleci/generatePyEnvChecksum.sh > girder/py-env-checksum
-      - restore_cache:
-          key: venv-py3.8-{{ arch }}-{{ checksum "girder/py-env-checksum" }}-4
+      #- run:
+      #    name: Generate python environment checksum file
+      #    command: ./girder/.circleci/generatePyEnvChecksum.sh > girder/py-env-checksum
+      #- restore_cache:
+      #    key: venv-py3.8-{{ arch }}-{{ checksum "girder/py-env-checksum" }}
       - run:
           name: Create virtual environment (if necessary)
           command: if [ ! -d girder_env ]; then python3 -m venv girder_env; fi
@@ -49,10 +49,10 @@ commands:
             --editable clients/python
             --requirement requirements-dev.txt
           working_directory: girder
-      - save_cache:
-          paths:
-            - girder_env
-          key: venv-py3.8-{{ arch }}-{{ checksum "girder/py-env-checksum" }}-4
+      #- save_cache:
+      #    paths:
+      #      - girder_env
+      #    key: venv-py3.8-{{ arch }}-{{ checksum "girder/py-env-checksum" }}
 
 jobs:
   server-lint-test:
@@ -64,10 +64,10 @@ jobs:
           name: Run server linting tests
           command: tox -e lint
           working_directory: girder
-      - run:
-          name: Test public symbols
-          command: tox -e public_names
-          working_directory: girder
+      #- run:
+      #    name: Test public symbols
+      #    command: tox -e public_names
+      #    working_directory: girder
       - run:
           name: Test building docs
           command: tox -e docs
@@ -136,30 +136,28 @@ jobs:
           path: girder
       - install-girder
       - run:
-          name: Build Girder web client
-          command: girder build --dev | cat
+          name: Install and build @girder/core
+          command: |
+            npm ci
+            npm run build
+          working_directory: girder/girder/web
       - run:
-          name: Create Girder build directory
-          command: mkdir girder_build
+          name: Install and build all plugins
+          command: python girder/.circleci/build_plugins.py girder/plugins
       - run:
-          name: Run CTest
-          command: >-
-            ctest
-            --extra-verbose
-            --script "$CIRCLE_WORKING_DIRECTORY/girder/.circleci/ci_test.cmake"
-          environment:
-            TEST_GROUP: browser
-            PYTHON_VERSION: 3.8
-            PYTHON_EXECUTABLE: /home/circleci/project/girder_env/bin/python
-            JASMINE_TIMEOUT: 15000
-          working_directory: girder_build
+          name: Install playwright browser dependencies
+          command: npm run install-browsers
+          working_directory: girder/girder/web
+      - run:
+          name: Test @girder/core
+          command: npm run test
+          working_directory: girder/girder/web
       - store_artifacts:
-          # Failure screenshots from web tests
-          path: girder/build/test/artifacts
-      - persist_to_workspace:
-          root: /home/circleci/project
-          paths:
-            - girder/build/test/coverage
+          path: girder/girder/web/coverage/report
+          destination: coverage
+      - store_artifacts:
+          path: girder/girder/web/test-results
+          destination: test-results
 
   integration-test:
     executor: machine
@@ -167,14 +165,14 @@ jobs:
       - checkout:
           path: girder
       - run:
-          name: Install NodeJS 14
+          name: Install NodeJS 16
           # CircleCI resets the Bash environment between every step, so any steps using node or npm
           # must first:
           #   source $NVM_DIR/nvm.sh
           command: |
             source $NVM_DIR/nvm.sh
-            nvm install v14
-            nvm alias default v14
+            nvm install v16
+            nvm alias default v16
             NODE_DIR=$(dirname $(which node))
             echo "export PATH=$NODE_DIR:\$PATH" >> $BASH_ENV
       - run:
@@ -220,11 +218,11 @@ jobs:
           command: sudo apt-get install -y libldap2-dev libsasl2-dev
       - install-girder
       - run:
-          name: Build Girder web client
+          name: Install and build @girder/core
           command: |
-            npm --version
-            node --version
-            girder build --dev | cat
+            npm ci
+            npm run build
+          working_directory: girder/girder/web
       - run:
           name: Create Girder build directory
           command: mkdir girder_build
@@ -269,17 +267,6 @@ jobs:
           name: Generate Python coverage report
           command: tox -e coverage
           working_directory: girder
-      - run:
-          name: Install Javascript utilities
-          command: npm ci
-          working_directory: girder
-      - run:
-          name: Generate web coverage report
-          command: npm run coverage
-          working_directory: girder
-      - store_artifacts:
-          # Human-readable coverage reports
-          path: girder/build/test/artifacts
       - run:
           name: Install Codecov client
           command: |
@@ -291,29 +278,6 @@ jobs:
           command: ./codecov --disable search pycov gcov --root girder --required --file build/test/coverage/py_coverage.xml build/test/coverage/cobertura-coverage.xml
           working_directory: girder
 
-  ansible-test:
-    docker:
-      - image: cimg/python:3.8
-    working_directory: ~/project
-    steps:
-      - run:
-          name: Install packages needed for ansible
-          command: |
-            sudo apt-get update
-            sudo apt-get install -y rsync
-      - checkout:
-          path: girder
-      - setup_remote_docker:
-          docker_layer_caching: true
-          version: 20.10.12
-      - run:
-          name: Install tox
-          command: pip install tox
-      - run:
-          name: Run Ansible tests
-          command: tox -e ansible
-          working_directory: girder
-
   dockers:
     machine:
         image: ubuntu-2004:202111-02
@@ -327,7 +291,7 @@ jobs:
           name: Build the Girder test docker
           command: |
             cd .circleci
-            docker build --force-rm -t girder/girder_test:py38-node14 .
+            docker build --force-rm -t girder/girder_test:py38-node16 .
 
   publish-dockers:
     machine:
@@ -342,7 +306,7 @@ jobs:
           name: Build the Girder test docker
           command: |
             cd .circleci
-            docker build --force-rm -t girder/girder_test:py38-node14 .
+            docker build --force-rm -t girder/girder_test:py38-node16 .
       - run:
           name: Publish the images to Docker Hub
           command: |
@@ -356,11 +320,11 @@ jobs:
               docker tag girder/girder:latest "girder/girder:${CIRCLE_TAG}-py3"
               docker push "girder/girder:${CIRCLE_TAG}-py3"
               fi
-              docker push girder/girder_test:py38-node14
+              docker push girder/girder_test:py38-node16
 
   publish:
     docker:
-      - image: cimg/python:3.8
+      - image: girder/girder_test:py38-node16
     working_directory: ~/project
     steps:
       - checkout:
@@ -372,10 +336,6 @@ jobs:
           name: Publish Python packages
           command: tox -e publish
           working_directory: girder
-      # - deploy:
-      #     name: Publish Ansible role
-      #     command: tox -e release_ansible
-      #     working_directory: girder
 
   publish-release:
     executor: py3
@@ -424,10 +384,6 @@ workflows:
           filters:
             tags:
               only: /^v[0-9]+.*/
-      # - ansible-test:
-      #     filters:
-      #       tags:
-      #         only: /^v[0-9]+.*/
       - dockers:
           filters:
             tags:
@@ -437,18 +393,18 @@ workflows:
             - server-lint-test
             - web-lint-test
             - coverage
-            # - ansible-test
           filters:
             tags:
               only: /^v[0-9]+.*/
             branches:
-              only: master
+              only:
+                - master
+                - v4-integration
       - publish-release:
           requires:
             - server-lint-test
             - web-lint-test
             - coverage
-            # - ansible-test
           filters:
             tags:
               only: /^v[0-9]+.*/

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/.circleci/publish_npm.sh

@@ -6,12 +6,9 @@ set -e
 readonly GIT_VERSION=$(git describe --tags)
 readonly PUBLISHED_NPM_PACKAGES=(
   # Published Fontello is used by all builds, and is critical to publish
-  girder/web_client/fontello
-  # These lint configs are used by downstream plugins
-  girder/web_client/eslint-config
-  girder/web_client/pug-lint-config
+  girder/web/fontello
   # The raw JS source is used by some downstream 'external builds'
-  girder/web_client/src
+  girder/web/src
   # These plugins were published to support downstream external builds, and should be kept updated
   plugins/jobs/girder_jobs/web_client
   plugins/oauth/girder_oauth/web_client

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/.circleci/publish_pypi.sh

@@ -1,7 +1,14 @@
 #!/bin/bash
 set -e
 
-# Build and publish sdist's for all Python packages in this repo
+pushd girder/web
+npm ci
+npm run build
+popd
+
+python .circleci/build_plugins.py plugins/
+
+# Build and publish all Python packages in this repo
 readonly PUBLISHED_PYTHON_PACKAGES=(
   .
   plugins/*
@@ -11,7 +18,7 @@ readonly PUBLISHED_PYTHON_PACKAGES=(
 for directory in "${PUBLISHED_PYTHON_PACKAGES[@]}"; do
     pushd "$directory"
     rm -fr dist
-    python setup.py sdist
+    python -m build
+    twine upload --skip-existing dist/*
     popd
-    twine upload --skip-existing "$directory/dist/*"
 done

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/.editorconfig

@@ -26,9 +26,6 @@ indent_size = 2
 indent_size = 4
 max_line_length = 100
 
-[{*.rb,Vagrantfile}]
-indent_size = 2
-
 [{*.sh,*.bat}]
 indent_size = 4
 

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/.gitignore

@@ -11,7 +11,6 @@ node_modules/
 __pycache__
 .eslintcache
 /npm-debug.log
-.vagrant
 *.py[cod]
 **/*.retry
 
@@ -22,3 +21,6 @@ __pycache__
 .vscode/
 .*.swo
 .*.swp
+
+# Generated during CI
+/py-env-checksum

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/.readthedocs.yml

@@ -10,7 +10,6 @@ sphinx:
 
 python:
   install:
-    - requirements: docs/requirements-docs.txt
     - method: pip
       path: .
     - method: pip

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/CMakeLists.txt

@@ -14,7 +14,6 @@ set(PYTHON_VERSION "3.8" CACHE STRING "Python version used for testing")
 
 find_package(PythonInterp ${PYTHON_VERSION} REQUIRED)
 
-option(BUILD_JAVASCRIPT_TESTS "Build Javascript tests" ON)
 option(RUN_CORE_TESTS "Whether to run the core tests" ON)
 set(TEST_PLUGINS "" CACHE STRING "List of plugins to test. Leave empty to test all plugins")
 
@@ -24,6 +23,5 @@ if(BUILD_TESTING)
   include(tests/TestData.cmake)
   include(tests/TestCommon.cmake)
   include(tests/PythonTests.cmake)
-  include(tests/JavascriptTests.cmake)
   add_subdirectory(tests)
 endif()

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/Dockerfile

@@ -24,31 +24,15 @@ RUN apt-get update && apt-get install -qy \
 RUN curl -LJ https://github.com/krallin/tini/releases/download/v0.19.0/tini -o /sbin/tini && \
     chmod +x /sbin/tini
 
-# Use nvm to install node
-RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash
-
-# Default node version
-RUN . ~/.bashrc && \
-    nvm install 14 && \
-    nvm alias default 14 && \
-    nvm use default && \
-    ln -s $(dirname `which npm`) /usr/local/node
-
-ENV PATH="/usr/local/node:$PATH"
+RUN curl -sL https://deb.nodesource.com/setup_18.x | bash - && \
+    apt-get install -qy nodejs
 
 RUN mkdir /girder
-WORKDIR /girder
 COPY . /girder/
 
-# Build girder wheel file, and install it
-RUN python3 setup.py bdist_wheel \
- && cd dist && python3 -m pip install --no-cache-dir girder && cd .. \
- && rm -rf build dist
+RUN cd /girder/girder/web && npm i && npm run build
 
-RUN girder build && \
-    rm --recursive --force \
-    /root/.npm \
-    /usr/local/lib/python*/site-packages/girder/web_client/node_modules
+RUN pip install -e /girder
 
 EXPOSE 8080
 

girder-5.0.0a3.dev2/MANIFEST.in

@@ -0,0 +1,19 @@
+include LICENSE
+include setup.py
+include README.rst
+graft girder
+prune plugins
+prune test
+prune tests
+prune girder/web/fontello
+prune girder/web/node_modules
+prune girder/web/public
+prune girder/web/src
+exclude girder/web/index.html
+exclude girder/web/package-lock.json
+exclude girder/web/package.json
+exclude girder/web/tsconfig.app.json
+exclude girder/web/tsconfig.json
+exclude girder/web/tsconfig.node.json
+exclude girder/web/vite.config.ts
+global-exclude *.pyc *.pyo *.cmake __pycache__

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: girder
-Version: 3.2.4.dev9
+Version: 5.0.0a3.dev2
 Summary: Web-based data management platform
 Home-page: https://girder.readthedocs.org
 Author: Kitware, Inc.

girder-5.0.0a3.dev2/docker-compose.yml

@@ -0,0 +1,24 @@
+version: '3.8'
+
+services:
+  mongodb:
+    image: mongo:4.4
+    ports:
+      - "27017:27017"
+    volumes:
+      - mongodb_data:/data/db
+
+  girder:
+    build: .
+    ports:
+      - "8080:8080"
+    depends_on:
+      - mongodb
+    command: --host 0.0.0.0 --database mongodb://mongodb:27017/girder
+    volumes:
+      - ".:/girder"
+      - assetstore:/assetstore
+
+volumes:
+  mongodb_data:
+  assetstore:

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/docs/admin-docs.rst

@@ -8,4 +8,3 @@ Administrator Documentation
    configuration
    mount
    sftp
-   deployment-alternatives

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/docs/api-docs.rst

@@ -181,9 +181,6 @@ Utility
 .. automodule:: girder.utility.filesystem_assetstore_adapter
    :members:
 
-.. automodule:: girder.utility.gridfs_assetstore_adapter
-   :members:
-
 .. automodule:: girder.utility.mail_utils
    :members:
 

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/docs/conf.py

@@ -3,7 +3,7 @@ import pkg_resources
 import sphinx_rtd_theme
 from sphinx.domains.python import PythonDomain
 
-# needs_sphinx = '1.6'
+needs_sphinx = '1.6'
 
 # Get package imports and version
 # The 'girder' and "girder_client" packages must be installed at this point
@@ -46,7 +46,6 @@ extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.intersphinx',
     'sphinx.ext.viewcode',
-    'sphinxcontrib.jquery',
 ]
 
 autodoc_mock_imports = list(_girder_imports)

girder-5.0.0a3.dev2/docs/configuration.rst

@@ -0,0 +1,54 @@
+Configuration
+=============
+
+.. _configuration:
+
+In many cases, Girder will work with default configuration whether installed via
+pip or from a source checkout or tarball. That said, the Girder config file can
+be set at the following locations (ordered by precedent):
+
+#. The path specified by the environment variable ``GIRDER_CONFIG``.
+#. ~/.girder/girder.cfg
+#. /etc/girder.cfg
+
+Settings
+--------
+
+Girder settings are specific key-value pairs that control system behavior.
+There are two ways to change Girder settings.
+
+Via the Web API / front-end web site
+....................................
+
+System settings can be set and retrieved using the web API endpoint at ``/api/v1/system/setting``.
+Most of them are exposed via the web UI under **Admin console** -> **System configuration**.
+When setting the values through the web API endpoint, they will be interpreted as JSON.
+
+.. note:: Modifying setting values via the web API is officially deprecated, as it violates the
+   `Twelve-Factor App <https://12factor.net/>`_  principle of storing configuration in the
+   environment. Setting values should instead be set via environment variables as documented below.
+
+
+
+.. _configuration_via_env:
+
+Via the environment
+...................
+
+Any system setting can be controlled via environment variables as well. To do so, find the
+key of the setting and apply the following transformation:
+
+* transform all ``.`` characters in the key to ``_``
+* convert it to uppercase
+* prefix it with ``GIRDER_SETTING_``
+
+Whatever value you set for that environment variable will be parsed as JSON and used at runtime.
+If the value cannot be parsed as JSON, its raw string value will be used instead. For example, to set
+the setting named ``"core.brand_name"``, you'd use ``GIRDER_SETTING_CORE_BRAND_NAME='My brand name'``
+
+Settings set through environment variables will override any setting value that is set in the database
+via the web API.
+
+The full list of system settings available in Girder core can be seen in the file
+``girder/girder/settings.py``, under the ``SettingKey`` class. Plugins may add additional settings
+within their own packages.

{girder-3.2.4.dev9 → girder-5.0.0a3.dev2}/docs/dependencies.rst

@@ -11,7 +11,7 @@ Installation of Girder's server has the following system dependencies:
           of dependencies. The Girder development team can only provide bugfixes and support
           for this environment.
 
-* `Ubuntu <https://releases.ubuntu.com/>`_ 18.04
+* `Ubuntu <https://releases.ubuntu.com/>`_ 20.04
 
   * Girder interacts with some system libraries (particularly
     `OpenSSL <https://packages.ubuntu.com/bionic/openssl>`_) at a very low level, so other

girder-5.0.0a3.dev2/docs/deployment.rst

@@ -0,0 +1,52 @@
+.. _deployment:
+
+Deployment
+==========
+
+Girder exposes a well-behaved WSGI application at ``girder.wsgi:app``, so it can be deployed behind
+any WSGI server. There are many servers and managed cloud offerings that will run WSGI applications,
+and we won't attempt to enumerate them all. We like ``gunicorn``, so we provide an example of a
+simple invocation that serves Girder: ::
+
+    gunicorn girder.wsgi:app --bind=localhost:8080 --workers=4 --preload
+
+Because deployment requirements are very specific to each application, we consider configuration
+and tuning of the WSGI server to be out of scope of Girder's documentation.
+
+A note on reverse proxy configuration
+-------------------------------------
+
+Typically, one would serve Girder behind a reverse proxy that manages things like TLS termination.
+If you're setting up your own proxy rather than using a managed cloud offering, you will need to
+configure it to support Girder's behaviors, in particular for large file uploads and downloads.
+We provide an example nginx configuration block to show the settings that are necessary for Girder
+to work properly behind nginx:
+
+.. code-block:: nginx
+
+    location / {
+        proxy_set_header Host $proxy_host;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_set_header X-Forwarded-Host $host;
+        proxy_set_header X-Forwarded-Proto $scheme;
+        proxy_pass http://localhost:8080/;
+        # Must set the following for SSE notifications to work
+        proxy_buffering off;
+        proxy_cache off;
+        proxy_set_header Connection '';
+        proxy_http_version 1.1;
+        chunked_transfer_encoding off;
+        proxy_read_timeout 600s;
+        proxy_send_timeout 600s;
+        # proxy_request_buffering option only works on nginx >= 1.7.11
+        # but is necessary to support streaming requests
+        proxy_request_buffering off;
+    }
+
+And under the containing ``server`` block, make sure to add the following rule:
+
+.. code-block:: nginx
+
+    server {
+        client_max_body_size 500M;
+    }

girder-5.0.0a3.dev2/docs/dev-installation.rst

@@ -0,0 +1,11 @@
+Developer Installation
+======================
+
+It is recommended to use ``docker-compose up`` to run Girder in development.
+
+If you wish to run Girder natively, you'll need to run your own ``mongod``, and run: ::
+
+    girder serve
+
+This command runs a local development server on port 8080, but is not suitable
+for production deployments.