Skip to content

Commit

Permalink
Merge remote-tracking branch 'upstream/main' into jabrefonline
Browse files Browse the repository at this point in the history
* upstream/main: (181 commits)
  Add of ADRs 22 and 23 (#8256)
  [Bot] Update CSL styles (#8245)
  Replace styfle/[email protected] by GitHub's "concurrency" feature (#8243)
  Bump gittools/actions from 0.9.10 to 0.9.11 (#8248)
  Bump commons-cli from 1.4 to 1.5.0 (#8250)
  Bump byte-buddy-parent from 1.12.0 to 1.12.1 (#8249)
  Bump antlr4 from 4.9.2 to 4.9.3 (#8251)
  Bump archunit-junit5-api from 0.21.0 to 0.22.0 (#8252)
  Fix search: NOT binds more than AND (#8241)
  New Crowdin updates (#8240)
  Make PdfGrobiImporterTest as FetcherTest
  Oobranch g : add actions (#7792)
  Fix mixed CRLF / CR (#8238)
  Fix "Library has changed externally" with CRLF markers (#8239)
  Fix for issue 8198, 8133 (#8229)
  Added more unit tests in AuthorTest (#8214)
  Add confirmation dialog for empty entries in JabRef (#8218)
  Fix entry editor column visibility (#8232)
  Use regexp to remove non-ASCII characters from DOI and inform user when data for valid DOI does not exist #8127 (#8228)
  Fix exception for search flags (#8237)
  ...
  • Loading branch information
Siedlerchr committed Nov 19, 2021
2 parents 567a378 + 578c106 commit 6aad7f2
Show file tree
Hide file tree
Showing 315 changed files with 17,255 additions and 4,352 deletions.
7 changes: 5 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ body:
options:
- Windows
- GNU / Linux
- mac OS
- macOS
- Other (please describe below)
validations:
required: true
Expand All @@ -36,7 +36,7 @@ body:
attributes:
label: Details on version and operating system
description: OS Version, distribution, desktop environment, older JabRef version etc.
placeholder: Ubuntu 21.04 with Plasma 5.22 / Windows 10 21H1 / Mac OS 10.14
placeholder: Ubuntu 21.04 with Plasma 5.22 / Windows 10 21H1 / macOS 10.14
validations:
required: false

Expand Down Expand Up @@ -70,10 +70,13 @@ body:
value: |
...
<details>
<summary>Log File</summary>
```
Paste an excerpt of your log file here
```
</details>
validations:
required: false
1 change: 1 addition & 0 deletions .github/workflows/check-links.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ on:
schedule:
# Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
- cron: "0 9 1 * *"
workflow_dispatch:

jobs:
markdown-link-check:
Expand Down
16 changes: 8 additions & 8 deletions .github/workflows/deployment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,10 @@ env:
GRADLE_OPTS: -Xmx4g -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
JAVA_OPTS: -Xmx4g

concurrency:
group: ${{ github.head_ref }}
cancel-in-progress: true

jobs:
build:
strategy:
Expand All @@ -45,21 +49,17 @@ jobs:
runs-on: ${{ matrix.os }}
name: Create installer and portable version for ${{ matrix.displayName }}
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- name: Fetch all history for all tags and branches
uses: actions/checkout@v2
with:
fetch-depth: 0
- name: Install GitVersion
uses: gittools/actions/gitversion/[email protected].10
uses: gittools/actions/gitversion/[email protected].11
with:
versionSpec: "5.x"
- name: Run GitVersion
id: gitversion
uses: gittools/actions/gitversion/[email protected].10
uses: gittools/actions/gitversion/[email protected].11
- name: Set up JDK
uses: actions/setup-java@v2
with:
Expand Down Expand Up @@ -155,12 +155,12 @@ jobs:
- name: Fetch all history for all tags and branches
run: git fetch --prune --unshallow
- name: Install GitVersion
uses: gittools/actions/gitversion/[email protected].10
uses: gittools/actions/gitversion/[email protected].11
with:
versionSpec: '5.x'
- name: Run GitVersion
id: gitversion
uses: gittools/actions/gitversion/[email protected].10
uses: gittools/actions/gitversion/[email protected].11
- name: Get linux binaries
uses: actions/download-artifact@master
with:
Expand Down
1 change: 1 addition & 0 deletions .github/workflows/gource.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ on:
- gource
schedule:
- cron: '15 3 1 1,4,7,10 *'
workflow_dispatch:

jobs:
action:
Expand Down
4 changes: 4 additions & 0 deletions .github/workflows/snap.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@ on:
# run on each day
- cron: "33 4 * * *"

concurrency:
group: snap-${{ github.head_ref }}
cancel-in-progress: true

jobs:
build:
runs-on: ubuntu-latest
Expand Down
5 changes: 5 additions & 0 deletions .github/workflows/tests-fetchers.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,17 @@ on:
schedule:
# run on each Wednesday
- cron: '2 3 * * 3'
workflow_dispatch:

env:
SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}

concurrency:
group: fetcher-tests-${{ github.head_ref }}
cancel-in-progress: true

jobs:
fetchertests:
name: Fetcher tests
Expand Down
14 changes: 8 additions & 6 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,11 @@ name: Tests
on:
push:
branches:
- master
- main
- main-release
pull_request:
# always run on pull requests
workflow_dispatch:

env:
SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
Expand All @@ -14,15 +16,15 @@ env:
GRADLE_OPTS: -Xmx4g
JAVA_OPTS: -Xmx4g

concurrency:
group: tests-${{ github.head_ref }}
cancel-in-progress: true

jobs:
checkstyle:
name: Checkstyle
runs-on: ubuntu-latest
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- name: Checkout source
uses: actions/checkout@v2
- name: Set up JDK
Expand All @@ -41,7 +43,7 @@ jobs:
- name: Run markdown-lint
uses: avto-dev/markdown-lint@v1
with:
args: CHANGELOG.md CONTRIBUTING.md README.md docs/
args: CHANGELOG.md CONTRIBUTING.md README.md
config: '.markdownlint.yml'
tests:
name: Unit tests
Expand Down
18 changes: 1 addition & 17 deletions .markdownlint.yml
Original file line number Diff line number Diff line change
@@ -1,24 +1,8 @@
default: true

# Using h2 has side effects in GitBook's toc. Thus, we sometimes switch from h1 to h3
MD001: false

MD012:
# 2 are required, because GitBook adss two blank lines at the end of a file
maximum: 2

# allow arbitrary line length
MD013: false

# The FAQs state questions - we allow them
MD026:
punctuation: ".,;:!"

# not supported by gitbook
MD031: false

MD033:
# we have <a> tags with ids and superscript
allowed_elements: ['a', 'kbd', 'sup']

# seems to be unsupported by gitbook anymore
MD045: false
23 changes: 21 additions & 2 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve

### Added

- We added confirmation dialog when user wants to close a library where any empty entires are detected. [#8096](https://github.com/JabRef/jabref/issues/8096)
- We added import support for CFF files. [#7945](https://github.com/JabRef/jabref/issues/7945)
- We added the option to copy the DOI of an entry directly from the context menu copy submenu. [#7826](https://github.com/JabRef/jabref/issues/7826)
- We added a fulltext search feature. [#2838](https://github.com/JabRef/jabref/pull/2838)
Expand All @@ -23,9 +24,13 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We readded the possibility to keep the search string when switching tabs. It is implemented by a toggle button. [#4096](https://github.com/JabRef/jabref/issues/4096#issuecomment-575986882)
- We allowed the user to also preview the available citation styles in the preferences besides the selected ones [#8108](https://github.com/JabRef/jabref/issues/8108)
- We added an option to search the available citation styles by name in the preferences [#8108](https://github.com/JabRef/jabref/issues/8108)
- We added an option to generate bib-entries from ID through a popover in the toolbar. [#4183](https://github.com/JabRef/jabref/issues/4183)

### Changed

- Local library settings may overwrite the setting "Search and store files relative to library file location" [#8179](https://github.com/JabRef/jabref/issues/8179)
- The option "Fit table horizontally on screen" in the "Entry table" preferences is now disabled by default [#8148](https://github.com/JabRef/jabref/pull/8148)
- We improved the preferences and descriptions in the "Linked files" preferences tab [#8148](https://github.com/JabRef/jabref/pull/8148)
- We slightly changed the layout of the Journal tab in the preferences for ui consistency. [#7937](https://github.com/JabRef/jabref/pull/7937)
- The JabRefHost on Windows now writes a temporary file and calls `-importToOpen` instead of passing the bibtex via `-importBibtex`. [#7374](https://github.com/JabRef/jabref/issues/7374), [JabRef Browser Ext #274](https://github.com/JabRef/JabRef-Browser-Extension/issues/274)
- We reordered some entries in the right-click menu of the main table. [#6099](https://github.com/JabRef/jabref/issues/6099)
Expand All @@ -35,10 +40,19 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- The metadata-to-pdf actions now also embeds the bibfile to the PDF. [#8037](https://github.com/JabRef/jabref/pull/8037)
- The snap was updated to use the core20 base and to use lzo compression for better startup performance [#8109](https://github.com/JabRef/jabref/pull/8109)
- We improved the Drag and Drop behavior in the "Customize Entry Types" Dialog [#6338](https://github.com/JabRef/jabref/issues/6338)
- When determining the URL of an ArXiV eprint, the URL now points to the version [#8149](https://github.com/JabRef/jabref/pull/8149)
- We Included all standard fields with citation key when exporting to Old OpenOffice/LibreOffice Calc Format [#8176](https://github.com/JabRef/jabref/pull/8176)
- In case the database is encoded with `UTF8`, the `% Encoding` marker is not written anymore
- The written `.bib` file has the same line endings [#390](https://github.com/koppor/jabref/issues/390)
- The written `.bib` file always has a final line break
- The written `.bib` file keeps the newline separator of the loaded `.bib` file
- We present options to manually enter an article or return to the New Entry menu when the fetcher DOI fails to find an entry for an ID [#7870](https://github.com/JabRef/jabref/issues/7870)
- We trim white space and non-ASCII characters from DOI [#8127](https://github.com/JabRef/jabref/issues/8127)
- The duplicate checker now inspects other fields in case no difference in the required and optional fields are found.

### Fixed

- We fixed an issue where an exception ocurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
- We fixed an issue where an exception occurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
- We fixed an issue when checking for a new version when JabRef is used behind a corporate proxy. [#7884](https://github.com/JabRef/jabref/issues/7884)
- We fixed some icons that were drawn in the wrong color when JabRef used a custom theme. [#7853](https://github.com/JabRef/jabref/issues/7853)
- We fixed an issue where the `Aux file` on `Edit group` doesn't support relative sub-directories path to import. [#7719](https://github.com/JabRef/jabref/issues/7719).
Expand All @@ -47,10 +61,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where the icons in the search bar had the same color, toggled as well as untoggled. [#8014](https://github.com/JabRef/jabref/pull/8014)
- We fixed an issue where typing an invalid UNC path into the "Main file directory" text field caused an error. [#8107](https://github.com/JabRef/jabref/issues/8107)
- We fixed an issue where "Open Folder" didn't select the file on macOS in Finder [#8130](https://github.com/JabRef/jabref/issues/8130)
- We fixed an issue where importing PDFs resulted in an uncaught exception [#8143](https://github.com/JabRef/jabref/issues/8143)
- We fixed "The library has been modified by another program" showing up when line breaks change [#4877](https://github.com/JabRef/jabref/issues/4877)
- The default directory of the "LaTeX Citations" tab is now the directory of the currently opened database (and not the directory chosen at the last open file dialog or the last database save) [koppor#538](https://github.com/koppor/jabref/issues/538)
- We fixed an issue where right-clicking on a tab and selecting close will close the focused tab even if it is not the tab we right-clicked [#8193](https://github.com/JabRef/jabref/pull/8193)
- We fixed an issue where selecting a citation style in the preferences would sometimes produce an exception [#7860](https://github.com/JabRef/jabref/issues/7860)

### Removed


- We removed two orphaned preferences options [#8164](https://github.com/JabRef/jabref/pull/8164)



Expand Down
1 change: 0 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -100,5 +100,4 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th

JabRef development is powered by YourKit Java Profiler [![YourKit Java Profiler](https://www.yourkit.com/images/yk_logo.png)](https://www.yourkit.com/java/profiler/)


[JabRef]: https://www.jabref.org
40 changes: 20 additions & 20 deletions build.gradle
Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,11 @@ plugins {

id 'org.openjfx.javafxplugin' version '0.0.10'

id 'org.beryx.jlink' version '2.24.2'
id 'org.beryx.jlink' version '2.24.4'

// nicer test outputs during running and completion
// Homepage: https://github.com/radarsh/gradle-test-logger-plugin
id 'com.adarshr.test-logger' version '3.0.0'
id 'com.adarshr.test-logger' version '3.1.0'

id 'jacoco'

Expand Down Expand Up @@ -110,7 +110,7 @@ configurations {
}

javafx {
version = "17.0.0.1"
version = "17.0.1"
modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
}

Expand All @@ -130,19 +130,19 @@ dependencies {
// required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
implementation 'org.bouncycastle:bcprov-jdk15on:1.69'

implementation 'commons-cli:commons-cli:1.4'
implementation 'commons-cli:commons-cli:1.5.0'

implementation 'org.libreoffice:libreoffice:7.2.1'
implementation 'org.libreoffice:unoloader:7.2.0'
implementation 'org.libreoffice:libreoffice:7.2.2'
implementation 'org.libreoffice:unoloader:7.2.2'

implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
implementation 'info.debatty:java-string-similarity:2.0.0'

antlr3 'org.antlr:antlr:3.5.2'
implementation 'org.antlr:antlr-runtime:3.5.2'

antlr4 'org.antlr:antlr4:4.9.2'
implementation 'org.antlr:antlr4-runtime:4.9.2'
antlr4 'org.antlr:antlr4:4.9.3'
implementation 'org.antlr:antlr4-runtime:4.9.3'

implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.13.0.202109080827-r'

Expand All @@ -158,7 +158,7 @@ dependencies {
exclude module: 'oraclepki'
}

implementation ('com.google.guava:guava:31.0-jre') {
implementation ('com.google.guava:guava:31.0.1-jre') {
// TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
exclude module: "jsr305"
}
Expand All @@ -171,14 +171,14 @@ dependencies {
implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
implementation 'de.saxsys:mvvmfx:1.8.0'
implementation 'com.tobiasdiez:easybind:2.2'
implementation 'org.fxmisc.flowless:flowless:0.6.6'
implementation 'org.fxmisc.richtext:richtextfx:0.10.6'
implementation 'org.fxmisc.flowless:flowless:0.6.7'
implementation 'org.fxmisc.richtext:richtextfx:0.10.7'
implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
implementation 'com.jfoenix:jfoenix:9.0.10'
implementation 'org.controlsfx:controlsfx:11.1.0'

implementation 'org.jsoup:jsoup:1.14.2'
implementation 'com.konghq:unirest-java:3.13.0'
implementation 'org.jsoup:jsoup:1.14.3'
implementation 'com.konghq:unirest-java:3.13.3'

implementation 'org.slf4j:slf4j-api:2.0.0-alpha5'
implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
Expand Down Expand Up @@ -209,18 +209,18 @@ dependencies {

implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'

testImplementation 'io.github.classgraph:classgraph:4.8.121'
testImplementation 'io.github.classgraph:classgraph:4.8.130'
testImplementation 'org.junit.jupiter:junit-jupiter:5.8.1'
testImplementation 'org.junit.platform:junit-platform-launcher:1.8.1'

testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.18'
testImplementation 'net.bytebuddy:byte-buddy-parent:1.12.1'
testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
testImplementation 'org.mockito:mockito-core:3.12.4'
testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.21.0'
testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.21.0'
testImplementation 'org.mockito:mockito-core:4.0.0'
testImplementation 'org.xmlunit:xmlunit-core:2.8.3'
testImplementation 'org.xmlunit:xmlunit-matchers:2.8.3'
testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.22.0'
testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.22.0'
testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
testImplementation "org.hamcrest:hamcrest-library:2.2"
Expand Down
2 changes: 1 addition & 1 deletion buildres/csl/csl-locales/.github/workflows/merge.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ jobs:
if: github.event_name == 'workflow_dispatch' || (github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true'))
uses: ruby/setup-ruby@v1
with:
ruby-version: 3.0.0
ruby-version: 3.0.2
- name: but use cache to speed that up
if: github.event_name == 'workflow_dispatch' || (github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true'))
uses: actions/cache@v2
Expand Down
2 changes: 1 addition & 1 deletion buildres/csl/csl-locales/.github/workflows/sheldon.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ jobs:
- name: Set up Ruby
uses: ruby/setup-ruby@v1
with:
ruby-version: 3.0.0
ruby-version: 3.0.2
- name: but use cache to speed that up
uses: actions/cache@v2
with:
Expand Down
2 changes: 1 addition & 1 deletion buildres/csl/csl-locales/Gemfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
ruby '3.0.0'
ruby '3.0.2'
source 'https://rubygems.org'

gem 'rake'
Expand Down
Loading

0 comments on commit 6aad7f2

Please sign in to comment.