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updates in methodology chapter #14

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merged 4 commits into from
Sep 5, 2024
Merged

updates in methodology chapter #14

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50c760d
update Zotero references from a.cli #11
prudhomm Sep 5, 2024
e6b521f
add reframe section #13
prudhomm Sep 5, 2024
355d19c
add spack ref and guix-hpc refs
prudhomm Sep 5, 2024
c1d5d4f
add basic section for guix-hpc
prudhomm Sep 5, 2024
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128 changes: 104 additions & 24 deletions a.cli
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Original file line number Diff line number Diff line change
Expand Up @@ -3,23 +3,62 @@
# 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="5582837"
DEFAULT_BIBTEX_FILE="references.bib"

# 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}

# 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
}

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."
# 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 checkout
git checkout

if ! test -f .git/gitHeadInfo.gin; then
cp .git/gitHeadInfo.gin gitHeadLocal.gin
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
git add gitHeadLocal.gin
git commit -m "Created gitHeadLocal.gin for initial setup"
fi
}

# Function to create a release
Expand All @@ -31,26 +70,25 @@ 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 Down Expand Up @@ -83,12 +121,44 @@ 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=bibtex"
else
URL="https://api.zotero.org/groups/$ZOTERO_GROUP_ID/items?format=bibtex"
fi

# Fetch and save BibTeX entries
curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" "$URL" > "$BIBTEX_FILE"

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

# Main script logic
parse_args "$@"

case "$1" in
setup)
setup
Expand All @@ -102,13 +172,23 @@ case "$1" in
delete)
delete_release "$2"
;;
update-bibtex)
update_bibtex
;;
*)
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 " 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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