roboneuro 0.1.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 3facccb4e09f68c233c0a386b6c9d35262ca140316c182026928c090a5a13e86
+  data.tar.gz: '00588aa4a555273fcb1bf62a78f0237167ab6c9d0e16d9b1c7ddeb4ee41eabb4'
+SHA512:
+  metadata.gz: 88571deda0ffdccffd7a65a0756a9446b3ad1b52bcf397a53156062173d8a707ae03d2950d8e1ca78120487c752ac56084e44074fc47544bd91e1c58f22fef20
+  data.tar.gz: b543ab1f0436e2625cce9553bef99a549bb8b622d5639aee6225c0f87328a047f05266e5561dab649f061b7f2305c2bb1ee2f31147eaeca3d036929baa624342

data/.env-example

@@ -0,0 +1,12 @@
+GH_TOKEN=xxxxxxxxxxxxxxxxxxxx
+WHEDON_SECRET=xxxxxxxxxxxxxxxxxxxx
+DOI_PREFIX = "10.xxxxx"
+PAPER_REPOSITORY = "joss-papers-example"
+REVIEW_REPOSITORY = "openjournals/joss-reviews-example"
+JOURNAL_URL = "http://example.theoj.org"
+JOURNAL_NAME = "Journal of Open Source Examples"
+JOURNAL_ALIAS = 'jose'
+JOURNAL_LAUNCH_DATE = '2016-05-05'
+CROSSREF_USERNAME="xxxxxxxxxxxxxxxxxxxx"
+CROSSREF_PASSWORD="xxxxxxxxxxxxxxxxxxxx"
+JOURNAL_ISSN="xxxxxxxxxxxxxx"

data/.env.test

@@ -0,0 +1,8 @@
+GH_TOKEN=FOO
+DOI_PREFIX = "10.21105"
+PAPER_REPOSITORY = "openjournals/joss-papers-testing"
+REVIEW_REPOSITORY = "openjournals/joss-reviews"
+JOURNAL_URL = "http://joss.theoj.org"
+JOURNAL_NAME = "Journal of Open Source Software"
+JOURNAL_ALIAS = "joss"
+JOURNAL_LAUNCH_DATE = "2016-05-05"

data/.github/workflows/docker-image.yml

@@ -0,0 +1,63 @@
+name: Build Images
+
+on:
+  # Build and publish when pushed to master
+  push:
+    branches:
+      - master
+  # Build, but don't push on pull requests
+  pull_request:
+
+env:
+  IMAGE_NAME: agahkarakuzu/paperdraft
+
+jobs:
+  # Build images and store them as tar archive
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Build image
+        run: |
+            docker build \
+              --tag $IMAGE_NAME \
+              -f paperdraft.Dockerfile \
+              .
+
+      - name: Save images to archive
+        run: docker save $IMAGE_NAME > image.tar
+
+      - name: Upload archive
+        uses: actions/upload-artifact@v1
+        with:
+          name: paperdraft
+          path: image.tar
+
+  # Push image to GitHub Packages.
+  push:
+    name: Push
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+    needs:
+      - build
+
+    steps:
+      - name: Download stored images
+        uses: actions/download-artifact@v1
+        with:
+          name: paperdraft
+
+      - name: Load images
+        run: |
+          docker load --input paperdraft/image.tar
+
+      - name: Log into registry
+        run: >-
+          echo "${{ secrets.DOCKER_HUB_TOKEN }}" |
+            docker login -u ${{ secrets.DOCKER_HUB_USERNAME }} --password-stdin
+
+      - name: Push core image
+        run: docker push $IMAGE_NAME

data/.github/workflows/tests.yml

@@ -0,0 +1,28 @@
+name: tests
+
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    continue-on-error: ${{ matrix.failure-allowed }}
+    strategy:
+      matrix:
+        ruby-version: ['2.6.3', '3.0.2']
+        failure-allowed: [false]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install Pandoc
+      run: |
+        curl -L https://github.com/jgm/pandoc/releases/download/2.9.1.1/pandoc-2.9.1.1-1-amd64.deb > pandoc.deb
+        dpkg -x pandoc.deb .
+        echo "pandoc downloaded and unpacked"
+        echo "$PWD/usr/bin" >> $GITHUB_PATH
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: ${{ matrix.ruby-version }}
+        bundler-cache: true
+    - name: Run specs
+      run: |
+        bundle exec ruby -v
+        bundle exec rake spec

data/.gitignore

@@ -0,0 +1,3 @@
+.env
+tmp
+roboneuro*.gem

data/Gemfile

@@ -0,0 +1,3 @@
+source "https://rubygems.org"
+
+gemspec

data/Gemfile.lock

@@ -0,0 +1,135 @@
+PATH
+  remote: .
+  specs:
+    roboneuro (0.1.1)
+      bibtex-ruby (~> 6.0.0)
+      dotenv
+      github-linguist (~> 5.3)
+      latex-decode
+      octokit (~> 4.20)
+      openjournals-nameable
+      redcarpet (~> 3.3)
+      rest-client (>= 1.8)
+      thor (~> 0.19)
+      tilt
+      unicode (~> 0.4.4)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
+    bibtex-ruby (6.0.0)
+      latex-decode (~> 0.0)
+    charlock_holmes (0.7.7)
+    coderay (1.1.3)
+    crack (0.4.5)
+      rexml
+    diff-lcs (1.4.4)
+    domain_name (0.5.20190701)
+      unf (>= 0.0.5, < 1.0.0)
+    dotenv (2.7.6)
+    escape_utils (1.1.1)
+    faraday (1.10.0)
+      faraday-em_http (~> 1.0)
+      faraday-em_synchrony (~> 1.0)
+      faraday-excon (~> 1.1)
+      faraday-httpclient (~> 1.0)
+      faraday-multipart (~> 1.0)
+      faraday-net_http (~> 1.0)
+      faraday-net_http_persistent (~> 1.0)
+      faraday-patron (~> 1.0)
+      faraday-rack (~> 1.0)
+      faraday-retry (~> 1.0)
+      ruby2_keywords (>= 0.0.4)
+    faraday-em_http (1.0.0)
+    faraday-em_synchrony (1.0.0)
+    faraday-excon (1.1.0)
+    faraday-httpclient (1.0.1)
+    faraday-multipart (1.0.3)
+      multipart-post (>= 1.2, < 3)
+    faraday-net_http (1.0.1)
+    faraday-net_http_persistent (1.2.0)
+    faraday-patron (1.0.0)
+    faraday-rack (1.0.0)
+    faraday-retry (1.0.3)
+    github-linguist (5.3.3)
+      charlock_holmes (~> 0.7.5)
+      escape_utils (~> 1.1.0)
+      mime-types (>= 1.19)
+      rugged (>= 0.25.1)
+    hashdiff (1.0.1)
+    http-accept (1.7.0)
+    http-cookie (1.0.4)
+      domain_name (~> 0.5)
+    latex-decode (0.3.2)
+    method_source (1.0.0)
+    mime-types (3.4.1)
+      mime-types-data (~> 3.2015)
+    mime-types-data (3.2022.0105)
+    mini_portile2 (2.4.0)
+    multipart-post (2.1.1)
+    netrc (0.11.0)
+    nokogiri (1.10.8)
+      mini_portile2 (~> 2.4.0)
+    octokit (4.22.0)
+      faraday (>= 0.9)
+      sawyer (~> 0.8.0, >= 0.5.3)
+    openjournals-nameable (1.1.7)
+    pry (0.13.1)
+      coderay (~> 1.1)
+      method_source (~> 1.0)
+    public_suffix (4.0.6)
+    rake (10.5.0)
+    redcarpet (3.5.1)
+    rest-client (2.1.0)
+      http-accept (>= 1.7.0, < 2.0)
+      http-cookie (>= 1.0.2, < 2.0)
+      mime-types (>= 1.16, < 4.0)
+      netrc (~> 0.8)
+    rexml (3.2.4)
+    rspec (3.10.0)
+      rspec-core (~> 3.10.0)
+      rspec-expectations (~> 3.10.0)
+      rspec-mocks (~> 3.10.0)
+    rspec-core (3.10.1)
+      rspec-support (~> 3.10.0)
+    rspec-expectations (3.10.1)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.10.0)
+    rspec-mocks (3.10.2)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.10.0)
+    rspec-support (3.10.2)
+    ruby2_keywords (0.0.5)
+    rugged (1.4.2)
+    sawyer (0.8.2)
+      addressable (>= 2.3.5)
+      faraday (> 0.8, < 2.0)
+    thor (0.20.3)
+    tilt (2.0.10)
+    unf (0.1.4)
+      unf_ext
+    unf_ext (0.0.8.1)
+    unicode (0.4.4.4)
+    vcr (6.0.0)
+    webmock (3.11.2)
+      addressable (>= 2.3.6)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler
+  nokogiri (= 1.10.8)
+  pry (~> 0.10)
+  rake (~> 10.0)
+  roboneuro!
+  rspec (~> 3.3)
+  vcr (~> 6.0)
+  webmock (~> 3.11.2)
+
+BUNDLED WITH
+   2.2.17

data/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 Open Journals
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

@@ -0,0 +1,190 @@
+# What is Whedon?
+
+Whedon is a collection of command-line utilities to manage JOSS submissions. Whedon is used by the [Whedon-API bot](https://github.com/openjournals/whedon-api) to interact with authors and reviewers during the review process on https://github.com/openjournals/joss-reviews
+
+## Setup
+
+Whedon uses [`dotenv`](https://github.com/bkeepers/dotenv) to manage local configuration. Take a look at `.env-example` (which needs renaming to `.env` to be picked up).
+
+Whedon requires a local installation of Pandoc 2 and Pandoc-Citeproc as well as a LaTeX (ideally [TeXLive](https://www.tug.org/texlive/)) installation. See [Pandoc's install instruction](http://pandoc.org/installing.html) for details.
+
+## Is it green?
+
+Hopefully...
+
+[![Build Status](https://github.com/openjournals/whedon/actions/workflows/tests.yml/badge.svg)](https://github.com/openjournals/whedon/actions/workflows/tests.yml)
+
+## Installation
+
+Depending on how Ruby is installed on your system there might slightly different steps be necessary. Note that Whedon is only tested for reasonably modern versions of Ruby (i.e. > 2.1) [Bundler](http://bundler.io/) is used to install dependencies.
+
+On macOS and with a Homebrew installed Ruby Bundler should be installable with
+
+```
+gem install bundler
+```
+
+On other Linux distros this might be a separate package or already installed.
+
+After cloning the `whedon` repository with
+
+```
+git clone https://github.com/openjournals/whedon.git
+```
+
+from within the `whedon` directory run the following command:
+
+```
+bundle install
+```
+
+or
+
+```
+bundle install --path vendor/bundle
+```
+
+Next, it's necessary to create a `.env` file based on the example
+[`.env.test`](https://github.com/openjournals/whedon/blob/master/.env.test).
+
+The `GH_TOKEN` can be created following the instructions from GitHub's
+[help pages](https://help.github.com/articles/creating-a-personal-access-token-for-the-command-line/).
+
+Once you have edited the `.env` file you can run the commands described below.
+It might be necessary to prefix the `whedon` command with `bundle exec` or
+give the full path to the executable, e.g. `./bin/whedon`.
+
+## Usage
+
+There are two main ways to use `Whedon`, 1) via the command-line utility or 2) using the Ruby API. If you want to see how the command line is implemented, take a look at the [executable](https://github.com/openjournals/whedon/blob/master/bin/whedon).
+
+### Currently implemented functionality
+
+List available commands:
+
+```
+$ bundle exec whedon # or just 'whedon' depending on whether you have built and installed the RubyGem locally
+
+Commands:
+  whedon compile         # Compile the paper and XML metadata
+  whedon deposit         # Deposit the metadata with the JOSS application and Crossref
+  whedon download        # Download the repo
+  whedon help [COMMAND]  # Describe available commands or one specific command
+  whedon open            # Open browser for review
+  whedon prepare         # Just prepare the PDF
+  whedon reviews         # Lists open reviews
+  whedon verify          # Check the key values in the review issue
+```
+
+**whedon reviews**
+
+List all open reviews in the GitHub review repository:
+
+```ruby
+$ whedon reviews
+
+# Ruby API equivalent
+>> require 'whedon'
+>> Whedon::Paper.list
+```
+
+**whedon verify**
+
+Verify the review issue body has key fields present:
+
+```ruby
+$ whedon verify {id}
+
+# Ruby API equivalent
+>> require 'whedon'
+>> Whedon::Paper.new(issue_id).audit
+```
+
+**whedon open**
+
+Open the browser at the review issue page
+
+```
+$ whedon open {id}
+```
+
+**whedon download**
+
+Download locally the repository linked to in the review issue (note this tries to do a simple `git clone` of the repository address which will fail for non-git repositories).
+
+```ruby
+$ whedon download {id}
+
+# Ruby API equivalent
+>> require 'whedon'
+>> Whedon::Paper.new(issue_id).download
+```
+
+**whedon prepare**
+
+Compile a downloaded paper locally to a PDF.
+
+This is the command that the `Whedon-API` bot uses to generate a preview of the paper PDF for sharing with reviewers and editors.
+
+```ruby
+$ whedon prepare {id}
+
+# Ruby API equivalent
+>> require 'whedon'
+>> review = Whedon::Review.new(issue_id)
+>> processor = Whedon::Processor.new(issue_id, review.issue_body)
+>> processor.set_paper(path_to_paper.md_file)
+>> processor.generate_pdf
+```
+
+Under the hood, the `prepare` method does the following:
+
+- Looks for the paper.md
+  - If more than one paper.md is found, asks the user to pick the correct one
+- Compiles the markdown to a custom PDF: `pandoc -o paper.pdf -V geometry:margin=1in --filter pandoc-citeproc paper.md --template latex.template`. See the actual [command here](https://github.com/openjournals/whedon/blob/25f9a1307a83b6b89080d6d934a3621f6a244035/lib/whedon/processor.rb#L101-L122).
+- Returns the filesystem location of the compiled PDF for inspection
+
+
+**whedon compile**
+
+```ruby
+$ whedon compile {id}
+
+# Ruby API equivalent
+>> require 'whedon'
+>> review = Whedon::Review.new(issue_id)
+>> processor = Whedon::Processor.new(issue_id, review.issue_body)
+>> processor.set_paper(path_to_paper.md_file)
+>> processor.compile
+```
+
+Under the hood, the `compile` method does the following:
+
+- Looks for the paper.md
+  - If more than one paper.md is found, asks the user to pick the correct one
+- Compiles the markdown to [four different outputs](https://github.com/openjournals/whedon/blob/25f9a1307a83b6b89080d6d934a3621f6a244035/lib/whedon/processor.rb#L82-L87):
+  - [The JOSS PDF](https://github.com/openjournals/whedon/blob/25f9a1307a83b6b89080d6d934a3621f6a244035/lib/whedon/processor.rb#L101-L122)
+  - A (currently un-used) [custom XML output](https://github.com/openjournals/whedon/blob/25f9a1307a83b6b89080d6d934a3621f6a244035/lib/whedon/processor.rb#L149-L167)
+  - An [HTML representation](https://github.com/openjournals/whedon/blob/25f9a1307a83b6b89080d6d934a3621f6a244035/lib/whedon/processor.rb#L169-L206) of the paper (deprecated)
+  - The [Crossref deposit metadata](https://github.com/openjournals/whedon/blob/25f9a1307a83b6b89080d6d934a3621f6a244035/lib/whedon/processor.rb#L208-L247)
+- Returns the filesystem location of the compiled PDF for inspection
+
+### Functionality under development
+
+Accept a paper into JOSS. This method currently returns the necessary metadata for the JOSS application (i.e. fields that need updating in the [JOSS database](https://github.com/openjournals/joss/blob/ce7722c2ec6d1ff306b13f465887e9747c76b3b1/db/schema.rb#L35-L55)) once a paper is accepted.
+
+In the future, this method should:
+
+- Update the database fields automatically on the JOSS application.
+- Deposit the Crossref XML to the Crossref API
+
+```ruby
+$ whedon deposit {id}
+
+# Ruby API equivalent
+>> require 'whedon'
+>> review = Whedon::Review.new(issue_id)
+>> processor = Whedon::Processor.new(issue_id, review.issue_body)
+>> processor.set_paper(path_to_paper.md_file)
+>> processor.deposit
+```

data/Rakefile

@@ -0,0 +1,13 @@
+require "bundler/gem_tasks"
+require 'rspec/core/rake_task'
+
+require 'dotenv'
+Dotenv.load(".env.test")
+
+require_relative './lib/whedon'
+
+desc "Run specs"
+RSpec::Core::RakeTask.new do |t|
+  t.pattern = 'spec/**/*_spec.rb'
+  t.rspec_opts = ["--order", "rand", "--color"]
+end

data/bin/whedon

@@ -0,0 +1,131 @@
+#!/usr/bin/env ruby
+require_relative "../lib/whedon"
+require 'thor'
+
+class WhedonCli < Thor
+  desc "reviews", "Lists open reviews"
+  def reviews
+    Whedon::Paper.list
+  end
+
+  desc "tags", "List tags for a paper"
+  def tags(issue_id)
+    review = Whedon::Review.new(issue_id)
+    processor = Whedon::Processor.new(issue_id, review.issue_body)
+
+    paper_paths = processor.find_paper_paths
+    tags = Whedon::Paper.new(issue_id, paper_paths.first).tags
+
+    if tags
+      puts tags.join(',')
+    else
+      puts ""
+    end
+  end
+
+  desc "open", "Open browser for review"
+  def open(issue_id)
+    `open https://github.com/#{ENV['REVIEW_REPOSITORY']}/issues/#{issue_id}`
+  end
+
+  desc "verify", "Check the key values in the review issue"
+  def verify(issue_id)
+    Whedon::Paper.new(issue_id).audit
+  end
+
+  desc "download", "Download the repo"
+  def download(issue_id, custom_path=nil, paper_path=nil)
+    Whedon::Paper.new(issue_id, custom_path, paper_path).download
+  end
+
+  desc "prepare", "Just prepare the PDF (optional second argument of custom git branch, optional third argument for custom path)"
+  def prepare(issue_id, custom_path=nil, custom_branch=nil)
+    review = Whedon::Review.new(issue_id)
+    processor = Whedon::Processor.new(issue_id, review.issue_body, custom_path)
+    processor.archive_doi = 'PENDING'
+
+    # Optionally set the path to work in
+    path = custom_path ? custom_path : "tmp/#{issue_id}"
+    
+    # Need to checkout the new branch before looking for the paper.
+    `cd #{path} && git checkout #{custom_branch} --quiet` if custom_branch
+
+    paper_paths = processor.find_paper_paths(path)
+
+    if paper_paths.empty?
+      abort("Can't find any papers to compile :-(")
+    elsif paper_paths.size == 1
+      processor.set_paper(paper_paths.first)
+      processor.generate_pdf(custom_branch)
+    else
+      puts "Looks like we found more than one possible paper:"
+      paper_paths.each_with_index { |path, index| puts "#{index+1}. #{path}"}
+      selected_paper = ask("Pick which paper you want:")
+      paper_path = paper_paths[selected_paper.to_i - 1]
+      puts "Setting paper_path to #{paper_paths}"
+      processor.set_paper(paper_path)
+      processor.generate_pdf(custom_branch)
+    end
+  end
+
+  desc "compile", "Compile the paper and XML metadata"
+  def compile(issue_id, custom_path=nil, custom_branch=nil)
+    review = Whedon::Review.new(issue_id)
+    processor = Whedon::Processor.new(issue_id, review.issue_body, custom_path)
+
+    # Optionally set the path to work in
+    path = custom_path ? custom_path : "tmp/#{issue_id}"
+    
+    # Need to checkout the new branch before looking for the paper.
+    `cd #{path} && git checkout #{custom_branch} --quiet` if custom_branch
+
+    paper_paths = processor.find_paper_paths(path)
+
+    if paper_paths.empty?
+      abort("Can't find any papers to compile :-(")
+    elsif paper_paths.size == 1
+      processor.set_paper(paper_paths.first)
+      processor.compile
+    else
+      puts "Looks like we found more than one possible paper:"
+      paper_paths.each_with_index { |path, index| puts "#{index+1}. #{path}"}
+      selected_paper = ask("Pick which paper you want:")
+      paper_path = paper_paths[selected_paper.to_i - 1]
+      puts "Setting paper_path to #{paper_paths}"
+      processor.set_paper(paper_path)
+      processor.compile
+    end
+  end
+
+  desc "deposit", "Deposit the metadata with the JOSS application and Crossref"
+  def deposit(issue_id, custom_path=nil, custom_branch=nil)
+    review = Whedon::Review.new(issue_id)
+    processor = Whedon::Processor.new(issue_id, review.issue_body, custom_path)
+    
+    # Optionally set the path to work in
+    path = custom_path ? custom_path : "tmp/#{issue_id}"
+
+    # Need to checkout the new branch before looking for the paper.
+    `cd #{path} && git checkout #{custom_branch} --quiet` if custom_branch
+    
+    paper_paths = processor.find_paper_paths(path)
+
+    if paper_paths.empty?
+      abort("Can't find any papers to process :-(")
+    elsif paper_paths.size == 1
+      puts "Setting paper_path to #{paper_paths.first}"
+      processor.set_paper(paper_paths.first)
+      processor.deposit
+    else
+      puts "Looks like we found more than one possible paper:"
+      paper_paths.each_with_index { |path, index| puts "#{index+1}. #{path}"}
+      selected_paper = ask("Pick which paper you want:")
+      paper_path = paper_paths[selected_paper.to_i - 1]
+      puts "Setting paper_path to #{paper_paths}"
+      processor.set_paper(paper_path)
+      processor.deposit
+    end
+  end
+end
+
+WhedonCli.start