Merge branch 'release/22.0.0'

Author: felliott

.github/workflows/test-build.yml

@@ -0,0 +1,63 @@
+name: mfr_ci_testing
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-20.04
+    env:
+      GHA_DISTRO: ubuntu-20.04
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    strategy:
+      matrix:
+        python-version: [3.6]
+    steps:
+      - name: Git checkout
+        uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache Build Requirements
+        id: pip-cache-step
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.GHA_DISTRO }}-${{ env.pythonLocation }}-${{ hashFiles('requirements.txt', 'dev-requirements.txt') }}
+      - name: install dependencies
+        if: steps.pip-cache-step.outputs.cache-hit != 'true'
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r dev-requirements.txt
+
+  runtests:
+    name: Run unit tests
+    needs: build
+    runs-on: ubuntu-20.04
+    env:
+      GHA_DISTRO: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+      - name: Cache pip
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.GHA_DISTRO }}-${{ env.pythonLocation }}-${{ hashFiles('requirements.txt', 'dev-requirements.txt') }}
+      - name: run syntax checks
+        run: |
+          flake8 .
+      - name: build plugins
+        run: |
+          python setup.py develop
+      - name: run unit tests
+        run: |
+          py.test --cov-report term-missing --cov mfr tests
+      - name: Upload coverage data to coveralls.io
+        run: coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.travis.yml

@@ -2,6 +2,16 @@
 ChangeLog
 *********
 
+22.0.0 (2022-05-27)
+===================
+- Feature: Improve Hypothes.is annotations by allowing the parent frame to pass in its url when
+turning on the annotator.
+- Feature: Enable syntax highlighting for .boa files (https://boa.cs.iastate.edu/) and bump Pygments
+dep to 2.12.0.
+- Code: Upgrade MFR's Dockerfile to be based off python3.6 and Debian buster.  Remove manual gosu
+installation and fetch from apt-get instead.  python3.6 is now the only supported python version.
+- Code: Migrate CI from TravisCI to Github Actions.
+
 20.0.1 (2020-10-21)
 ===================
 - Feature: Add flags to toggle logging of MFR events to specific Keen collections.

CHANGELOG

@@ -23,8 +23,8 @@ Clone the repo:
 Configure development environment and install the development dependencies.
 
 .. note::
-    Python 3.5 or greater, `R`_, and `pspp`_ are required.
-    Python 3.6 is reccomended. It's recommended that a python version manager such as `pyenv`_ is used and that you use a virtual environment such as `pyenv-virtualenv`_ during development.
+    Python 3.6 or greater, `R`_, and `pspp`_ are required.
+    It's recommended that a python version manager such as `pyenv`_ is used and that you use a virtual environment such as `pyenv-virtualenv`_ during development.
 
 .. _R: https://www.r-project.org/
 .. _pspp: https://www.gnu.org/software/pspp/

CONTRIBUTING.rst

@@ -1,4 +1,4 @@
-FROM python:3.5-slim-buster
+FROM python:3.6-slim-buster
 
 # ensure unoconv can locate the uno library
 ENV PYTHONPATH /usr/lib/python3/dist-packages
@@ -25,49 +25,32 @@ RUN usermod -d /home www-data \
         libxml2-dev \
         libxslt1-dev \
         zlib1g-dev \
+        gnupg2 \
         # convert .step to jsc3d-compatible format
         freecad \
         # pspp dependencies
         pspp \
         # unoconv dependencies
         libreoffice \
-        # gosu dependencies
-        curl \
-        gnupg2 \
-    # gosu
-    && export GOSU_VERSION='1.10' \
-    && mkdir ~/.gnupg && chmod 600 ~/.gnupg && echo "disable-ipv6" >> ~/.gnupg/dirmngr.conf \
-    && for server in hkp://ipv4.pool.sks-keyservers.net:80 \
-                     hkp://ha.pool.sks-keyservers.net:80 \
-                     hkp://pgp.mit.edu:80 \
-                     hkp://keyserver.pgp.com:80 \
-    ; do \
-      gpg --keyserver "$server" --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4 && break || echo "Trying new server..." \
-    ; done \
-    && curl -o /usr/local/bin/gosu -SL "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture)" \
-  	&& curl -o /usr/local/bin/gosu.asc -SL "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture).asc" \
-  	&& gpg --verify /usr/local/bin/gosu.asc \
-  	&& rm /usr/local/bin/gosu.asc \
-  	&& chmod +x /usr/local/bin/gosu \
-    # /gosu
+        # grab gosu for easy step-down from root
+        gosu \
     && apt-get clean \
     && apt-get autoremove -y \
-        curl \
-        gnupg2 \
-    && rm -rf /var/lib/apt/lists/* \
-    && pip install -U pip \
-    && pip install setuptools==37.0.0 \
-    && mkdir -p /code \
-    && pip install unoconv==0.8.2
+    && rm -rf /var/lib/apt/lists/*
 
+RUN mkdir -p /code
 WORKDIR /code
 
-COPY ./requirements.txt ./
+RUN pip install -U pip==18.1
+RUN pip install setuptools==37.0.0
+RUN pip install unoconv==0.8.2
+
+COPY ./requirements.txt /code/
 
 RUN pip install --no-cache-dir -r ./requirements.txt
 
 # Copy the rest of the code over
-COPY ./ ./
+COPY ./ /code/
 
 ARG GIT_COMMIT=
 ENV GIT_COMMIT ${GIT_COMMIT}

Dockerfile

@@ -1,24 +1,22 @@
 # MFR (Modular File Renderer)
 
-`master` Build Status: [![Build Status](https://travis-ci.org/CenterForOpenScience/modular-file-renderer.svg?branch=master)](https://travis-ci.org/CenterForOpenScience/modular-file-renderer)
+`master` Build Status: ![Build Status](https://github.com/CenterForOpenScience/modular-file-renderer/actions/workflows/test-build.yml/badge.svg?branch=master)[![Coverage Status](https://coveralls.io/repos/github/CenterForOpenScience/modular-file-renderer/badge.svg?branch=master)](https://coveralls.io/github/CenterForOpenScience/modular-file-renderer?branch=master)
 
-`develop` Build Status: [![Build Status](https://travis-ci.org/CenterForOpenScience/modular-file-renderer.svg?branch=develop)](https://travis-ci.org/CenterForOpenScience/modular-file-renderer)
-
-[![Coverage Status](https://coveralls.io/repos/github/CenterForOpenScience/modular-file-renderer/badge.svg)](https://coveralls.io/github/CenterForOpenScience/modular-file-renderer)
+`develop` Build Status: ![Build Status](https://github.com/CenterForOpenScience/modular-file-renderer/actions/workflows/test-build.yml/badge.svg?branch=develop)[![Coverage Status](https://coveralls.io/repos/github/CenterForOpenScience/modular-file-renderer/badge.svg?branch=develop)](https://coveralls.io/github/CenterForOpenScience/modular-file-renderer?branch=develop)
 
 A Python package for rendering files to HTML via an embeddable iframe.
 
 ### Compatibility
 
-MFR is compatible with Python 3.5 (tested up to 3.5.3) and 3.6.
+MFR is compatible with Python 3.6.
 
 ### Documentation
 
 Documentation available at: http://modular-file-renderer.readthedocs.io/en/latest/
 
 ### Setting up
 
-Install the latest version of python3.5.
+Install the latest version of python3.6.
 
 For MacOSX users:
 
@@ -35,12 +33,12 @@ apt-get install python3
 apt-get install pspp unoconv
 ```
 
-After installing python3.5, create the virtual environment with the following commands:
+After installing python3.6, create the virtual environment with the following commands:
 
 ```bash
 pip install virtualenv
 pip install virtualenvwrapper
-mkvirtualenv --python=`which python3.5` mfr
+mkvirtualenv --python=`which python3.6` mfr
 
 pip install setuptools==37.0.0
 pip install invoke==0.13.0
@@ -100,7 +98,7 @@ Interested in adding support for a new provider or file format? Check out the CO
 
 ### License
 
-Copyright 2013-2018 Center for Open Science
+Copyright 2013-2022 Center for Open Science
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

README.md

@@ -5,12 +5,12 @@
 
 beautifulsoup4
 colorlog==2.5.0
+coveralls
 flake8==3.0.4
 ipdb
 mccabe
 pydevd==0.0.6
 pyflakes
 pytest==2.8.2
 pytest-cov==2.2.0
-python-coveralls==2.9.1
 pyzmq==14.4.1

dev-requirements.txt

@@ -1,4 +1,5 @@
 import os
+import logging
 
 import chardet
 from humanfriendly import format_size
@@ -13,6 +14,8 @@
 from mfr.extensions.codepygments import settings
 from mfr.extensions.codepygments import exceptions
 
+logger = logging.getLogger(__name__)
+
 
 class CodePygmentsRenderer(extension.BaseRenderer):
 
@@ -98,9 +101,12 @@ def _render_html(self, fp, ext, *args, **kwargs):
             # check if there is a lexer available for more obscure file types
             if ext in settings.lexer_lib.keys():
                 lexer = pygments.lexers.get_lexer_by_name(settings.lexer_lib[ext])
+                logger.debug('found pygments lexer by name')
             else:
                 lexer = pygments.lexers.guess_lexer_for_filename(ext, content)
+                logger.debug('found pygments lexer by guessing')
         except ClassNotFound:
+            logger.debug('pygments lexer class not found! using default')
             self.metrics.add('default_lexer', True)
             lexer = self.DEFAULT_LEXER()
 

mfr/extensions/codepygments/render.py

@@ -2,15 +2,23 @@
     'use strict';
 
     var hypothesisLoaded = false;
+    var parentWindowUrl = undefined;
+
+    window.pymChild.onMessage('setParentUrl', setParentWindowUrl);
 
     window.pymChild.onMessage('startHypothesis', startHypothesis);
 
     window.addEventListener('message', function(event) {
-        if (event.data === 'startHypothesis') {
+        if (event.data.type === 'startHypothesis') {
+            setParentWindowUrl(event.data.parentUrl);
             startHypothesis(event);
         }
     });
 
+    function setParentWindowUrl(parentUrl) {
+        parentWindowUrl = parentUrl;
+    }
+
     function startHypothesis(event) {
         if (hypothesisLoaded) {
             return;
@@ -53,7 +61,7 @@
             // point to the export/download url, meaning the annotations could never be viewed in
             // context.  By linking to the referrer, the annotations can be viewed in the context of
             // the preprint.
-            window.PDFViewerApplication.url = document.referrer;
+            window.PDFViewerApplication.url = parentWindowUrl;
 
             // Load the hypothes.is client
             var script = window.document.createElement('script');

mfr/server/static/js/mfr.child.hypothesis.js

@@ -112,6 +112,7 @@
         };
 
         self.startHypothesis = function() {
+            self.pymParent.sendMessage('setParentUrl', window.location.toString());
             self.pymParent.sendMessage('startHypothesis');
         };