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resolves 28: add script to update the zotero references #30

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merged 5 commits into from
Oct 24, 2024
Merged

resolves 28: add script to update the zotero references #30

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cd1356e
add script to update the zotero references #28
prudhomm Oct 24, 2024
2132ab3
update workflow to automate bibtex references update
prudhomm Oct 24, 2024
87ad40b
up doc authors
prudhomm Oct 24, 2024
6351396
Merge branch 'main' into 28-add-script-to-update-the-zotero-references
prudhomm Oct 24, 2024
b59875a
fix typos in document
thomas-saigre Oct 24, 2024
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34 changes: 30 additions & 4 deletions .github/workflows/latex.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ jobs:
id: texlive_runner
run: |
if ! [ -z "$GH_TOKEN" ]; then
runners=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" /orgs/feelpp/actions/runners)
runners=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" /orgs/${{ github.repository_owner }}/actions/runners)
texlive=$(echo $runners | jq --arg label "self-texlive" '[.runners[] | any(.labels[]; .name == $label) and .status == "online"] | any')
if [ "$texlive" = "false" ]; then
echo "runner=ubuntu-latest" >> "$GITHUB_OUTPUT"
Expand Down Expand Up @@ -60,16 +60,35 @@ jobs:
name: Build LaTeX Artifact
env:
VERSION: ${{ github.ref_name }}
ZOTERO_API_KEY: ${{ secrets.ZOTERO_API_KEY }}
steps:
- name: Set up Git repository
uses: actions/checkout@v4
with:
clean: true

- name: Install hooks
- name: Install hooks
run: |
bash ./a.cli setup

- name: Update BibTeX references
if: ${{ github.ref != 'refs/heads/main' }}
run: |
bash ./a.cli update-bibtex

- name: Commit new references.bib
if: ${{ github.ref != 'refs/heads/main' }}
run: |
git config --local user.email "${{ github.actor }}@users.noreply.github.com"
git config --local user.name "${{ github.actor }}"
git add references.bib
if ! git diff --cached --quiet; then
git commit -m "Update references.bib from Zotero"
git push
else
echo "No changes in references.bib to commit."
fi

- name: Compile LaTeX document
uses: xu-cheng/latex-action@v3
if: ${{ needs.workflow-setup.outputs.runner == 'ubuntu-latest' }}
Expand Down Expand Up @@ -97,10 +116,18 @@ jobs:
./*.bbl
./${{ needs.workflow-setup.outputs.pdf }}
./README.adoc
./hooks*
./img*
./dat*
./*.png
./a.cli
./*.sty
./chapters*
./software*
./exclude.txt
./sections*
./litterature*
./graphics*
!./.git*
!./.github*
!./.vscode*
Expand Down Expand Up @@ -152,13 +179,12 @@ jobs:
- name: Archive Article
run: |
temp_dir=$(mktemp -d)
# tar -czvf "${temp_dir}/${{ needs.workflow-setup.outputs.prefixwithref }}.tar.gz" -C artifact ./
# mv "${temp_dir}/${{ needs.workflow-setup.outputs.prefixwithref }}.tar.gz" ./
cd artifact
zip -r "${temp_dir}/${{ needs.workflow-setup.outputs.prefixwithref }}.zip" ./
cd ..
mv "${temp_dir}/${{ needs.workflow-setup.outputs.prefixwithref }}.zip" ./
rm -rf "$temp_dir"
rm -rf "$temp_dir"

- name: Create Release
id: create_release
Expand Down
7 changes: 5 additions & 2 deletions CITATION.cff
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,13 @@ authors:
- family-names: "Prud'homme"
given-names: "Christophe"
orcid: https://orcid.org/0000-0003-2287-2961
- family-names: "Saigre"
given-names: "Thomas"
orcid: https://orcid.org/0009-0009-5763-4956
title: "Template article repository"
version: 1.7.0
version: 1.8.0
identifiers:
- type: doi
value: 10.5281/zenodo.12760235
date-released: 2024-08-17
date-released: 2024-10-24
url: "https://github.com/feelpp/article.template"
223 changes: 198 additions & 25 deletions a.cli
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Original file line number Diff line number Diff line change
Expand Up @@ -3,23 +3,63 @@
# Exit immediately if a command exits with a non-zero status
set -e

# setup hooks
setup() {
# Default values
DEFAULT_ZOTERO_USER_ID=""
DEFAULT_ZOTERO_API_KEY=""
DEFAULT_ZOTERO_GROUP_ID="4678293"
DEFAULT_BIBTEX_FILE="references.bib"
COLLECTION_ID=""

for i in commit checkout merge; do
cp hooks/post-commit .git/hooks/post-$i
chmod +x .git/hooks/post-$i
done
echo "Hooks setup successfully."
# Read environment variables or set defaults
ZOTERO_USER_ID=${ZOTERO_USER_ID:-$DEFAULT_ZOTERO_USER_ID}
ZOTERO_API_KEY=${ZOTERO_API_KEY:-$DEFAULT_ZOTERO_API_KEY}
ZOTERO_GROUP_ID=${ZOTERO_GROUP_ID:-$DEFAULT_ZOTERO_GROUP_ID}
BIBTEX_FILE=${BIBTEX_FILE:-$DEFAULT_BIBTEX_FILE}

git checkout
# Function to parse command-line arguments
parse_args() {
while [[ "$#" -gt 0 ]]; do
case $1 in
--zotero-user-id) ZOTERO_USER_ID="$2"; shift ;;
--zotero-api-key) ZOTERO_API_KEY="$2"; shift ;;
--zotero-group-id) ZOTERO_GROUP_ID="$2"; shift ;;
--bibtex-file) BIBTEX_FILE="$2"; shift ;;
--help)
echo "Usage: $0 [options] {setup|create|list|delete|update-bibtex} [version]"
echo "Options:"
echo " --zotero-user-id Zotero User ID"
echo " --zotero-api-key Zotero API Key"
echo " --zotero-group-id Zotero Group ID (optional, omit if using user library)"
echo " --bibtex-file Path to the BibTeX file (default: your_bibtex_file.bib)"
echo "Commands:"
echo " setup : Setup hooks for commit, checkout, and merge"
echo " create : Create a new release with the provided version"
echo " list : List all existing releases"
echo " delete : Delete the release with the provided version"
echo " update-bibtex : Fetch and update the BibTeX file from Zotero"
echo " version : Optional argument specifying the version for create and delete commands"
exit 0 ;;
esac
shift
done
}

if ! test -f .git/gitHeadInfo.gin; then
cp .git/gitHeadInfo.gin gitHeadLocal.gin
# Function to setup hooks
setup() {
for i in commit checkout merge; do
cp hooks/post-commit .git/hooks/post-$i
chmod +x .git/hooks/post-$i
done
echo "Hooks setup successfully."

git add gitHeadLocal.gin
git commit -m "Created gitHeadLocal.gin for initial setup"
fi
git checkout

if ! test -f .git/gitHeadInfo.gin; then
cp .git/gitHeadInfo.gin gitHeadLocal.gin

git add gitHeadLocal.gin
git commit -m "Created gitHeadLocal.gin for initial setup"
fi
}

# Function to create a release
Expand All @@ -31,26 +71,25 @@ create_release() {
exit 1
fi

# check if the tag already exists
# Check if the tag already exists
if git rev-parse "$VERSION" >/dev/null 2>&1; then
echo "Error: Tag $VERSION already exists."
exit 1
fi

# check the format of the version number
# Check the format of the version number
if [[ ! "$VERSION" =~ ^v[0-9]+\.[0-9]+\.[0-9]+(-[a-z]+\.[0-9]+)?$ ]]; then
echo "Error: Version number should be in the format vx.y.z or vx.y.z-pre.a."
exit 1
fi


# Tag the repository with the provided version
git tag -a "$VERSION" -m "Release $VERSION"

# Checkout the tag to trigger post-commit hook to update gitinfo2 info file
git checkout

# show the reltag line of .git/gitHeadInfo.gin
# Show the reltag line of .git/gitHeadInfo.gin
grep reltag .git/gitHeadInfo.gin

cp .git/gitHeadInfo.gin gitHeadLocal.gin
Expand All @@ -60,7 +99,7 @@ create_release() {
git tag -f -a "$VERSION" -m "Release $VERSION"

# Push the changes and the tags
git push origin main --follow-tags
git push origin --follow-tags

echo "Release $VERSION created and pushed successfully."
}
Expand All @@ -70,6 +109,11 @@ list_releases() {
git tag --sort=-creatordate | head -n $1
}

# Function to clean latex build files
clean() {
# clean latex build files
rm -f *.aux *.bbl *.blg *.log *.out *.pyg *.fls *.synctex* *.toc *.fdb_latexmk *.fls *.idx *.ilg *.ind *.chl *.lof *.lot *.pdf
}
# Function to delete a release
delete_release() {
VERSION=$1
Expand All @@ -83,16 +127,134 @@ delete_release() {
git tag -d "$VERSION"

# Delete the tag remotely
#git push origin --delete "$VERSION"
# git push origin --delete "$VERSION"

echo "Release $VERSION deleted successfully."
}

# Function to fetch and update BibTeX file from Zotero
update_bibtex() {
if [ -z "$ZOTERO_GROUP_ID" ]; then
if [ -z "$ZOTERO_USER_ID" ]; then
echo "Zotero group ID and user ID are not set, one of them is required."
echo "If Group ID is set, User ID is not required."
exit 1
fi
fi

if [ -z "$ZOTERO_API_KEY" ]; then
echo "Zotero API key is not set."
exit 1
fi

echo "Fetching BibTeX entries from Zotero..."

# Define the URL to fetch BibTeX
if [ -z "$ZOTERO_GROUP_ID" ]; then
URL="https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=biblatex"
else
URL="https://api.zotero.org/groups/$ZOTERO_GROUP_ID/items?format=biblatex"
fi
start=0
limit=100
has_more=true
echo "" > "$BIBTEX_FILE"
while $has_more; do
response=$(curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" "$URL&start=$start&limit=$limit")

if [ -z "$response" ]; then
echo "No more items to fetch."
has_more=false
break
fi

echo "$response" >> "$BIBTEX_FILE"

# Check if we need to fetch more items
num_items=$(echo "$response" | grep -c "@") # Counting the number of BibTeX entries
if [ "$num_items" -lt "$limit" ]; then
has_more=false
else
start=$((start + limit))
fi
done

echo "BibTeX entries updated successfully in $BIBTEX_FILE."
}

update_bibtex2() {
if [ -z "$ZOTERO_GROUP_ID" ]; then
if [ -z "$ZOTERO_USER_ID" ]; then
echo "Zotero group ID and user ID are not set, one of them is required."
echo "If Group ID is set, User ID is not required."
exit 1
fi
fi

if [ -z "$ZOTERO_API_KEY" ]; then
echo "Zotero API key is not set."
exit 1
fi

echo "Fetching BibTeX entries from Zotero..."

# Define the URL to fetch BibTeX
if [ -z "$ZOTERO_GROUP_ID" ]; then
URL="https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=bibtex"
else
URL="https://api.zotero.org/groups/$ZOTERO_GROUP_ID/items?format=bibtex"
fi

start=0
limit=100
has_more=true # Initialize the loop control variable
echo "" > "$BIBTEX_FILE"

while $has_more; do
# Send the request
response=$(curl -s -w "%{http_code}" -H "Zotero-API-Key: $ZOTERO_API_KEY" "$URL&start=$start&limit=$limit")

# Separate the response content and the status code
http_code=$(echo "$response" | tail -n1)
content=$(echo "$response" | sed '$d') # Everything except the last line (status code)

# Check if the request was successful (status code 200)
if [ "$http_code" -ne 200 ]; then
echo "Error fetching data: HTTP status $http_code"
exit 1
fi
if [ -z "$content" ]; then
echo "No more items to fetch."
has_more=false
break
fi
# Append the content to the BibTeX file
echo "$content" >> "$BIBTEX_FILE"

# Check if there are more items by inspecting the Link header or counting the items
num_items=$(echo "$content" | grep -c "@") # Counting BibTeX entries
echo "downloaded $num_items items"
if [ "$num_items" = "0" ]; then
has_more=false
else
start=$((start + limit))
fi
echo "start=$start, has_more=$has_more"
done

echo "BibTeX entries updated successfully in $BIBTEX_FILE."
}

# Main script logic
parse_args "$@"

case "$1" in
setup)
setup
;;
clean)
clean
;;
create)
create_release "$2"
;;
Expand All @@ -102,13 +264,24 @@ case "$1" in
delete)
delete_release "$2"
;;
update-bibtex)
update_bibtex2
;;
*)
echo "Usage: $0 {setup|create|list|delete} [version]"
echo " setup : Setup hooks for commit, checkout, and merge"
echo " create : Create a new release with the provided version"
echo " list : List all existing releases"
echo " delete : Delete the release with the provided version"
echo " version : Optional argument specifying the version for create and delete commands"
echo "Usage: $0 [options] {setup|create|list|delete|update-bibtex} [version]"
echo "Options:"
echo " --zotero-user-id Zotero User ID (optional, omit if using group id given)"
echo " --zotero-api-key Zotero API Key"
echo " --zotero-group-id Zotero Group ID (optional, omit if using user id given)"
echo " --bibtex-file Path to the BibTeX file (default: your_bibtex_file.bib)"
echo "Commands:"
echo " setup : Setup hooks for commit, checkout, and merge"
echo " clean : Clean latex build files"
echo " create : Create a new release with the provided version"
echo " list : List all existing releases"
echo " delete : Delete the release with the provided version"
echo " update-bibtex : Fetch and update the BibTeX file from Zotero"
echo " version : Optional argument specifying the version for create and delete commands"
exit 1
;;
esac
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