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Merge remote-tracking branch 'upstream/main' into tryToCreateMergedTr…
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…ustStore

* upstream/main:
  Introduces test http server (#9748)
  Generate journal-list.mv on build (#10298)

# Conflicts:
#	src/main/java/org/jabref/logic/net/ssl/TrustStoreManager.java
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Siedlerchr committed Sep 4, 2023
2 parents 4cf9020 + 2518f7b commit 58e8c6c
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2 changes: 2 additions & 0 deletions .gitattributes
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Expand Up @@ -12,6 +12,8 @@ gradlew text eol=lf

# .bib files have to be written using OS specific line endings to enable our tests working
*.bib text !eol
# Exception: The files used for the http server test - they should have linux line endings
src/test/resources/org/jabref/http/server/*.bib text eol=lf

# Citavi needs to be LF line ending
# This overwrites the setting of "*.bib"
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2 changes: 1 addition & 1 deletion .github/workflows/automerge.yml
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Expand Up @@ -8,7 +8,7 @@ permissions:
jobs:
dependabot:
runs-on: ubuntu-latest
if: ${{ github.actor == 'dependabot[bot]' }}
if: ${{ (github.actor == 'dependabot[bot]') || (github.actor == 'koppor' && startsWith(github.event.pull_request.title, '[Bot]')) }}
steps:
- name: Approve PR
run: gh pr review --approve "$PR_URL"
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2 changes: 2 additions & 0 deletions .github/workflows/check-links.yaml
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Expand Up @@ -11,6 +11,8 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
show-progress: 'false'
- uses: gaurav-nelson/github-action-markdown-link-check@v1
with:
use-quiet-mode: 'yes'
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2 changes: 2 additions & 0 deletions .github/workflows/deployment-arm64.yml
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Expand Up @@ -49,6 +49,8 @@ jobs:
uses: actions/checkout@v3
with:
fetch-depth: 0
submodules: 'true'
show-progress: 'false'
- name: Install GitVersion
uses: gittools/actions/gitversion/[email protected]
with:
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11 changes: 8 additions & 3 deletions .github/workflows/deployment.yml
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Expand Up @@ -74,6 +74,8 @@ jobs:
uses: actions/checkout@v3
with:
fetch-depth: 0
submodules: 'true'
show-progress: 'false'
- name: Install pigz and cache (linux)
if: (matrix.os == 'ubuntu-latest')
uses: awalsh128/cache-apt-pkgs-action@latest
Expand Down Expand Up @@ -273,6 +275,8 @@ jobs:
uses: actions/checkout@v3
with:
fetch-depth: 0
submodules: 'true'
show-progress: 'false'
- name: Install GitVersion
if: steps.checksecrets.outputs.secretspresent == 'YES'
uses: gittools/actions/gitversion/[email protected]
Expand Down Expand Up @@ -334,9 +338,10 @@ jobs:
- name: Checkout source
if: steps.checksecrets.outputs.secretspresent == 'YES'
uses: actions/checkout@v3
- name: Fetch all history for all tags and branches
if: steps.checksecrets.outputs.secretspresent == 'YES'
run: git fetch --prune --unshallow
with:
fetch-depth: 0
submodules: 'true'
show-progress: 'false'
- name: Install GitVersion
if: steps.checksecrets.outputs.secretspresent == 'YES'
uses: gittools/actions/gitversion/[email protected]
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3 changes: 2 additions & 1 deletion .github/workflows/gource.yml
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Expand Up @@ -12,7 +12,7 @@ on:
concurrency:
group: gource
cancel-in-progress: true

jobs:
action:
runs-on: ubuntu-latest
Expand All @@ -21,6 +21,7 @@ jobs:
uses: actions/checkout@v3
with:
fetch-depth: 0
show-progress: 'false'
- name: 'Development history of current build'
uses: BoundfoxStudios/action-gource@v2
with:
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2 changes: 2 additions & 0 deletions .github/workflows/pages.yml
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Expand Up @@ -28,6 +28,8 @@ jobs:
steps:
- name: Checkout
uses: actions/checkout@v3
with:
show-progress: 'false'
- name: Setup Ruby
uses: ruby/setup-ruby@v1
with:
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31 changes: 16 additions & 15 deletions .github/workflows/refresh-csl-subtrees.yml
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Expand Up @@ -2,7 +2,6 @@ name: Refresh Citation Style Language Files

on:
schedule:
# run on 1st and 15th of each month
- cron: '1 2 1,15 * *'
workflow_dispatch:

Expand All @@ -21,34 +20,36 @@ jobs:
- uses: actions/checkout@v3
with:
persist-credentials: true
ref: main
fetch-depth: 0
submodules: 'true'
show-progress: 'false'
- name: Initialize git
run: |
git checkout main
git config --local core.editor /usr/bin/cat
git config user.name 'github-actions[bot]'
git config user.email 'github-actions[bot]@users.noreply.github.com'
- name: Add csl-styles remote
run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
- name: Update csl-styles
- name: Update buildres/csl/csl-styles
run: |
git subtree pull --prefix buildres/csl/csl-styles csl-styles master --squash || true
cd buildres/csl/csl-styles
git checkout master
git pull
cd ..
cd ..
cd ..
cp buildres/csl/csl-styles/acm-siggraph.csl src/main/resources/csl-styles/
cp buildres/csl/csl-styles/apa.csl src/main/resources/csl-styles/
cp buildres/csl/csl-styles/ieee.csl src/main/resources/csl-styles/
cp buildres/csl/csl-styles/turabian-author-date.csl src/main/resources/csl-styles/
git add .
git commit -m"Refresh example styles" || true
- name: Add csl-locales remote
run: git remote add -f csl-locales https://github.com/citation-style-language/locales.git
- name: Update csl-locales
- name: Update buildres/csl/csl-locales
run: |
git subtree pull --prefix buildres/csl/csl-locales csl-locales master --squash || true
cd buildres/csl/csl-locales
git checkout master
git pull
cd ..
cd ..
cd ..
cp buildres/csl/csl-locales/locales.json src/main/resources/csl-locales/
cp buildres/csl/csl-locales/locales-en-US.xml src/main/resources/csl-locales/
git add .
git commit -m"Refresh example styles" || true
- uses: peter-evans/create-pull-request@v5
with:
token: ${{ secrets.GITHUB_TOKEN }}
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55 changes: 20 additions & 35 deletions .github/workflows/refresh-journal-lists.yml
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@@ -1,65 +1,50 @@
name: Refresh Journal Lists

on:
push:
paths:
- '.github/workflows/refresh-journal-lists.yml'
- 'buildSrc/build.gradle'
- 'buildSrc/src/main/java/**'
- 'src/main/java/org/jabref/logic/journals/**'
schedule:
- cron: '1 2 2,16 * *'
workflow_dispatch:

permissions:
contents: read

jobs:
publish:
name: Refresh Journal List Files
runs-on: ubuntu-latest
permissions:
contents: write # for peter-evans/create-pull-request to create branch
pull-requests: write # for peter-evans/create-pull-request to create a PR
name: Refresh Journal List Files
runs-on: ubuntu-latest
if: (github.repository == 'JabRef/jabref' || github.repository == 'koppor/jabref')
steps:
- uses: actions/checkout@v3
with:
persist-credentials: true
fetch-depth: 0
submodules: 'true'
show-progress: 'false'
- name: Initialize git
run: |
git config --local core.editor /usr/bin/cat
git config user.name 'github-actions[bot]'
git config user.email 'github-actions[bot]@users.noreply.github.com'
- name: Update buildres/abbrv.jabref.org
run: |
cd buildres/abbrv.jabref.org
git checkout main
git pull
- name: Set up JDK
uses: actions/setup-java@v3
with:
java-version: 20
distribution: 'temurin'
cache: 'gradle'
- name: Update journal lists
- name: Check whether journal-list.mv can be generated (the "real" generation is done inside JabRef's build process)
run: |
set +o pipefail
# prepare journal lists
cd /tmp
git clone --depth=1 https://github.com/JabRef/abbrv.jabref.org.git
cd abbrv.jabref.org/journals
# remove all lists without dot in them
# we use abbreviation lists containing dots in them only (to be consistent)
rm journal_abbreviations_entrez.csv
rm journal_abbreviations_medicus.csv
rm journal_abbreviations_webofscience-dotless.csv
# we currently do not have good support for BibTeX strings
rm journal_abbreviations_ieee_strings.csv
# prepare building
mkdir -p $GITHUB_WORKSPACE/build/journals
cp * $GITHUB_WORKSPACE/build/journals/
# ensure that the .java classes are the most recent ones
cp $GITHUB_WORKSPACE/src/main/java/org/jabref/logic/journals/* $GITHUB_WORKSPACE/buildSrc/src/main/java/org/jabref/logic/journals
# create .mv file
cd $GITHUB_WORKSPACE
./gradlew generateJournalAbbreviationList
- uses: peter-evans/create-pull-request@v5
with:
token: ${{ secrets.GITHUB_TOKEN }}
branch: update-journallist
branch: update-journal-lists
title: "[Bot] Update journal abbreviation lists"
commit-message: Update journal abbreviation lists
3 changes: 3 additions & 0 deletions .github/workflows/tests-fetchers.yml
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Expand Up @@ -42,6 +42,9 @@ jobs:
steps:
- name: Checkout source
uses: actions/checkout@v3
with:
submodules: 'true'
show-progress: 'false'
- name: Set up JDK
uses: actions/setup-java@v3
with:
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19 changes: 19 additions & 0 deletions .github/workflows/tests.yml
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Expand Up @@ -29,6 +29,9 @@ jobs:
steps:
- name: Checkout source
uses: actions/checkout@v3
with:
submodules: 'false'
show-progress: 'false'
- name: Set up JDK
uses: actions/setup-java@v3
with:
Expand Down Expand Up @@ -77,6 +80,9 @@ jobs:
steps:
- name: Checkout source
uses: actions/checkout@v3
with:
submodules: 'true'
show-progress: 'false'
- name: Set up JDK
uses: actions/setup-java@v3
with:
Expand Down Expand Up @@ -109,6 +115,9 @@ jobs:
steps:
- name: Checkout source
uses: actions/checkout@v3
with:
submodules: 'true'
show-progress: 'false'
- name: Set up JDK
uses: actions/setup-java@v3
with:
Expand Down Expand Up @@ -143,6 +152,9 @@ jobs:
steps:
- name: Checkout source
uses: actions/checkout@v3
with:
submodules: 'true'
show-progress: 'false'
- name: Set up JDK
uses: actions/setup-java@v3
with:
Expand Down Expand Up @@ -181,6 +193,9 @@ jobs:
SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
- name: Checkout source
uses: actions/checkout@v3
with:
submodules: 'true'
show-progress: 'false'
- name: Set up JDK
uses: actions/setup-java@v3
with:
Expand All @@ -201,12 +216,16 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
show-progress: 'false'
- uses: gradle/wrapper-validation-action@v1
# This ensures that no git merge conflict markers (<<<, ...) are contained
merge_conflict_job:
name: Find merge conflicts
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
show-progress: 'false'
- name: Merge Conflict finder
uses: olivernybroe/[email protected]
9 changes: 9 additions & 0 deletions .gitmodules
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@@ -0,0 +1,9 @@
[submodule "buildres/abbrv.jabref.org"]
path = buildres/abbrv.jabref.org
url = https://github.com/JabRef/abbrv.jabref.org.git
[submodule "buildres/csl-styles"]
path = buildres/csl/csl-styles
url = https://github.com/citation-style-language/styles.git
[submodule "buildres/csl-locales"]
path = buildres/csl/csl-locales
url = https://github.com/citation-style-language/locales.git
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