Merge branch 'master' into jupyter_telemetry

Author: kiendang

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,69 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+# ******** NOTE ********
+
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ '*' ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '25 18 * * 4'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more...
+        # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+        queries: security-and-quality
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/main.yml

@@ -6,17 +6,15 @@ on:
     branches: '*'
 jobs:
   build:
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}-latest
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [ '3.5', '3.6', '3.7', '3.8' ]
+        os: [ubuntu, macos, windows]
+        python-version: [ '3.6', '3.7', '3.8', '3.9', 'pypy3' ]
         exclude:
-          - os: windows-latest
-            python-version: '3.5'
-          - os: windows-latest
-            python-version: '3.6'
+        - os: windows
+          python-version: pypy3
     steps:
     - name: Checkout
       uses: actions/checkout@v1
@@ -25,9 +23,37 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         architecture: 'x64'
+    - name: Upgrade packaging dependencies
+      run: |
+        pip install --upgrade pip setuptools wheel --user
+    - name: Get pip cache dir
+      id: pip-cache
+      run: |
+        echo "::set-output name=dir::$(pip cache dir)"
+    - name: Cache pip
+      uses: actions/cache@v1
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-${{ matrix.python-version }}-
+          ${{ runner.os }}-pip-
     - name: Install the Python dependencies
       run: |
-        pip install -e .[test]
+        pip install -e .[test] codecov
+    - name: List installed packages
+      run: |
+        pip freeze
+        pip check
     - name: Run the tests
       run: |
-        pytest
+        pytest -vv --cov jupyter_server --cov-branch --cov-report term-missing:skip-covered
+    - name: Install the Python dependencies for the examples
+      run: |
+        cd examples/simple && pip install -e .
+    - name: Run the tests for the examples
+      run: |
+        pytest examples/simple/tests/test_handlers.py
+    - name: Coverage
+      run: |
+        codecov

.gitignore

@@ -19,7 +19,7 @@ __pycache__
 .DS_Store
 \#*#
 .#*
-.coverage
+.coverage*
 .pytest_cache
 src
 

CHANGELOG.md

@@ -7,6 +7,70 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.1.0] - 2020-12-11
+
+[Full Changelog](https://github.com/jupyter-server/jupyter_server/compare/1.0.10...1.1.0)
+
+**Merged pull requests:**
+
+- Restore pytest plugin from pytest-jupyter [\#360](https://github.com/jupyter-server/jupyter_server/pull/360) ([kevin-bates](https://github.com/kevin-bates))
+- Fix upgrade packaging dependencies build step [\#354](https://github.com/jupyter-server/jupyter_server/pull/354) ([mwakaba2](https://github.com/mwakaba2))
+- Await \_connect and inline read\_messages callback to \_connect [\#350](https://github.com/jupyter-server/jupyter_server/pull/350) ([ricklamers](https://github.com/ricklamers))
+- Update release instructions and dev version [\#348](https://github.com/jupyter-server/jupyter_server/pull/348) ([kevin-bates](https://github.com/kevin-bates))
+- Fix test\_trailing\_slash  [\#346](https://github.com/jupyter-server/jupyter_server/pull/346) ([kevin-bates](https://github.com/kevin-bates))
+- Apply security advisory fix to master [\#345](https://github.com/jupyter-server/jupyter_server/pull/345) ([kevin-bates](https://github.com/kevin-bates))
+- Allow toggling auth for prometheus metrics [\#344](https://github.com/jupyter-server/jupyter_server/pull/344) ([yuvipanda](https://github.com/yuvipanda))
+- Port Notebook PRs 5565 and 5588 - terminal shell heuristics [\#343](https://github.com/jupyter-server/jupyter_server/pull/343) ([kevin-bates](https://github.com/kevin-bates))
+- Port gateway updates from notebook \(PRs 5317 and 5484\) [\#341](https://github.com/jupyter-server/jupyter_server/pull/341) ([kevin-bates](https://github.com/kevin-bates))
+- add check\_origin handler to gateway WebSocketChannelsHandler [\#340](https://github.com/jupyter-server/jupyter_server/pull/340) ([ricklamers](https://github.com/ricklamers))
+- Remove pytest11 entrypoint and plugin, require tornado 6.1, remove asyncio patch, CI work [\#339](https://github.com/jupyter-server/jupyter_server/pull/339) ([bollwyvl](https://github.com/bollwyvl))
+- Switch fixtures to use those in pytest-jupyter to avoid collisions [\#335](https://github.com/jupyter-server/jupyter_server/pull/335) ([kevin-bates](https://github.com/kevin-bates))
+- Enable CodeQL runs on all pushed branches [\#333](https://github.com/jupyter-server/jupyter_server/pull/333) ([kevin-bates](https://github.com/kevin-bates))
+- Asynchronous Contents API [\#324](https://github.com/jupyter-server/jupyter_server/pull/324) ([mwakaba2](https://github.com/mwakaba2))
+
+
+
+## [1.0.6] - 2020-11-18
+
+1.0.6 is a security release, fixing one vulnerability:
+
+### Changed
+
+- Fix open redirect vulnerability GHSA-grfj-wjv9-4f9v (CVE-2020-26232)
+
+
+## [1.0] - 2020-9-18
+
+### Added.
+
+* Added a basic, styled `login.html` template. ([220](https://github.com/jupyter/jupyter_server/pull/220), [295](https://github.com/jupyter/jupyter_server/pull/295))
+* Added new extension manager API for handling server extensions. ([248](https://github.com/jupyter/jupyter_server/pull/248), [265](https://github.com/jupyter/jupyter_server/pull/265), [275](https://github.com/jupyter/jupyter_server/pull/275), [303](https://github.com/jupyter/jupyter_server/pull/303))
+* The favicon and Jupyter logo are now available under jupyter_server's static namespace. ([284](https://github.com/jupyter/jupyter_server/pull/284))
+
+### Changed.
+
+* `load_jupyter_server_extension` should be renamed to `_load_jupyter_server_extension` in server extensions. Server now throws a warning when the old name is used. ([213](https://github.com/jupyter/jupyter_server/pull/213))
+* Docs for server extensions now recommend using `authenticated` decorator for handlers. ([219](https://github.com/jupyter/jupyter_server/pull/219))
+* `_load_jupyter_server_paths` should be renamed to `_load_jupyter_server_points` in server extensions. ([277](https://github.com/jupyter/jupyter_server/pull/277))
+* `static_url_prefix` in ExtensionApps is now a configurable trait. ([289](https://github.com/jupyter/jupyter_server/pull/289))
+* `extension_name` trait was removed in favor of `name`. ([232](https://github.com/jupyter/jupyter_server/pull/232))
+* Dropped support for Python 3.5. ([296](https://github.com/jupyter/jupyter_server/pull/296))
+* Made the `config_dir_name` trait configurable in `ConfigManager`. ([297](https://github.com/jupyter/jupyter_server/pull/297))
+
+### Removed for now removed features.
+
+* Removed ipykernel as a dependency of jupyter_server. ([255](https://github.com/jupyter/jupyter_server/pull/255))
+
+### Fixed for any bug fixes.
+* Prevent a re-definition of prometheus metrics if `notebook` package already imports them. ([#210](https://github.com/jupyter/jupyter_server/pull/210))
+* Fixed `terminals` REST API unit tests that weren't shutting down properly. ([221](https://github.com/jupyter/jupyter_server/pull/221))
+* Fixed jupyter_server on Windows for Python < 3.7. Added patch to handle subprocess cleanup. ([240](https://github.com/jupyter/jupyter_server/pull/240))
+* `base_url` was being duplicated when getting a url path from the `ServerApp`. ([280](https://github.com/jupyter/jupyter_server/pull/280))
+* Extension URLs are now properly prefixed with `base_url`. Previously, all `static` paths were not. ([285](https://github.com/jupyter/jupyter_server/pull/285))
+* Changed ExtensionApp mixin to inherit from `HasTraits`. This broke in traitlets 5.0 ([294](https://github.com/jupyter/jupyter_server/pull/294))
+* Replaces `urlparse` with `url_path_join` to prevent URL squashing issues. ([304](https://github.com/jupyter/jupyter_server/pull/304))
+
+
 ## [0.3] - 2020-4-22
 
 ### Added
@@ -74,4 +138,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
     - [Batch 8](https://github.com/jupyter/jupyter_server/pull/106)
 
 ### Security
-- Added a "secure_write to function for cookie/token saves ([#77](https://github.com/jupyter/jupyter_server/pull/77))
+- Added a "secure_write to function for cookie/token saves ([#77](https://github.com/jupyter/jupyter_server/pull/77))

MANIFEST.in

@@ -1,9 +1,12 @@
 include COPYING.md
 include CONTRIBUTING.rst
 include README.md
+include RELEASE.md
+include CHANGELOG.md
 include setupbase.py
-include Dockerfile
-graft tools
+
+# include everything in package_data
+recursive-include jupyter_server *
 
 # Event Schemas
 graft jupyter_server/event-schemas
@@ -26,3 +29,5 @@ global-exclude *.pyc
 global-exclude *.pyo
 global-exclude .git
 global-exclude .ipynb_checkpoints
+global-exclude .pytest_cache
+global-exclude .coverage

README.md

@@ -14,13 +14,7 @@ To install the latest release locally, make sure you have
 
     $ pip install jupyter_server
 
-Jupyter Server currently supports the following Python versions:
-
-Platform | Python
---- | ---
-Linux | >=3.5
-OSX | >=3.5
-Windows | >=3.7
+Jupyter Server currently supports Python>=3.5 on Linux, OSX and Windows.
 
 ### Versioning and Branches
 
@@ -45,12 +39,8 @@ If you are interested in contributing to the project, see [`CONTRIBUTING.rst`](C
 
 ## Team Meetings and Roadmap
 
-When: Thursdays [8:00am, Pacific time](https://www.thetimezoneconverter.com/?t=8%3A00%20am&tz=San%20Francisco&)
-Where: [calpoly/jupyter Zoom](https://zoom.us/my/jovyan)
-What: [Meeting notes](https://github.com/jupyter/jupyter_server/issues/126)
-
 * When: Thursdays [8:00am, Pacific time](https://www.thetimezoneconverter.com/?t=8%3A00%20am&tz=San%20Francisco&)
-* Where: [Jupyter Zoom](https://calpoly.zoom.us/my/jupyter)
+* Where: [Jovyan Zoom](https://zoom.us/my/jovyan?pwd=c0JZTHlNdS9Sek9vdzR3aTJ4SzFTQT09)
 * What: [Meeting notes](https://github.com/jupyter/jupyter_server/issues/126)
 
 See our tentative [roadmap here](https://github.com/jupyter/jupyter_server/issues/127).

RELEASE.md

@@ -0,0 +1,41 @@
+# Making a Jupyter Server Release
+To create a release, perform the following steps...
+
+## Remove untracked files
+```
+git clean -dffx
+```
+
+## Update the version and apply the tag
+```
+vim jupyter_server/_version.py
+export script_version=`python setup.py --version 2>/dev/null`
+git commit -a -m "Release $script_version"
+git tag $script_version
+```
+
+## Build the artifacts
+```
+rm -rf dist
+python setup.py sdist
+python setup.py bdist_wheel
+```
+
+## Update the version back to dev
+```
+vim jupyter_server/_version.py
+git commit -a -m "Back to dev version"
+```
+
+## Push the commits and tag
+```
+git push --all
+git push --tags
+```
+
+## Publish the artifacts to pypi
+```
+pip install twine
+twine check dist/* 
+twine upload dist/*
+```

docs/README.md

@@ -0,0 +1,3 @@
+# Jupyter Server Docs Sources
+
+Read [this page](https://jupyter-server.readthedocs.io/en/latest/contributors/contributing.html#building-the-docs) to build the docs.

docs/source/developers/contents.rst

@@ -192,19 +192,19 @@ methods:
    ContentsManager.is_hidden
 
 You may be required to specify a Checkpoints object, as the default one,
-``FileCheckpoints``, could be incompatible with your custom 
+``FileCheckpoints``, could be incompatible with your custom
 ContentsManager.
 
 Customizing Checkpoints
 -----------------------
 .. currentmodule:: jupyter_server.services.contents.checkpoints
 
-Customized Checkpoint definitions allows behavior to be 
+Customized Checkpoint definitions allows behavior to be
 altered and extended.
 
 The ``Checkpoints`` and ``GenericCheckpointsMixin`` classes
 (from :mod:`jupyter_server.services.contents.checkpoints`)
-have reusable code and are intended to be used together, 
+have reusable code and are intended to be used together,
 but require the following methods to be implemented.
 
 .. autosummary::
@@ -220,7 +220,7 @@ No-op example
 ~~~~~~~~~~~~~
 
 Here is an example of a no-op checkpoints object - note the mixin
-comes first. The docstrings indicate what each method should do or 
+comes first. The docstrings indicate what each method should do or
 return for a more complete implementation.
 
 .. code-block:: python
@@ -238,7 +238,7 @@ return for a more complete implementation.
         def delete_checkpoint(self, checkpoint_id, path):
             """deletes a checkpoint for a file"""
         def list_checkpoints(self, path):
-            """returns a list of checkpoint models for a given file, 
+            """returns a list of checkpoint models for a given file,
             default just does one per file
             """
             return []
@@ -267,3 +267,24 @@ ContentsManager.
 .. _NBFormat: https://nbformat.readthedocs.io/en/latest/index.html
 .. _PGContents: https://github.com/quantopian/pgcontents
 .. _PostgreSQL: https://www.postgresql.org/
+
+Asynchronous Support
+--------------------
+
+An asynchronous version of the Contents API is available to run slow IO processes concurrently.
+
+- :class:`~manager.AsyncContentsManager`
+- :class:`~filemanager.AsyncFileContentsManager`
+- :class:`~largefilemanager.AsyncLargeFileManager`
+- :class:`~checkpoints.AsyncCheckpoints`
+- :class:`~checkpoints.AsyncGenericCheckpointsMixin`
+
+.. note::
+
+   .. _contentfree:
+
+   In most cases, the non-asynchronous Contents API is performant for local filesystems.
+   However, if the Jupyter Notebook web application is interacting with a high-latent virtual filesystem, you may see performance gains by using the asynchronous version.
+   For example, if you're experiencing terminal lag in the web application due to the slow and blocking file operations, the asynchronous version can reduce the lag.
+   Before opting in, comparing both non-async and async options' performances is recommended.
+