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shnizzedyshnizzedy
authored
Fix/check s3 (#2282)
2 parents c72d516 + 855e83a commit 2544523

34 files changed

+518
-379
lines changed

‎.github/scripts/autoversioning.sh‎

Lines changed: 163 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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#!/bin/bash
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#!/usr/bin/env bash
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3-
# Copyright (C) 2024 C-PAC Developers
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# Copyright (C) 2024-2025 C-PAC Developers
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# This file is part of C-PAC.
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@@ -17,54 +17,174 @@
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# You should have received a copy of the GNU Lesser General Public
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# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
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20-
# Update version comment strings
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function wait_for_git_lock() {
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while [ -f "./.git/index.lock" ]; do
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echo "Waiting for the git lock file to be removed..."
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sleep 1
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done
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set -euo pipefail
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trap 'echo "❌ Script failed at line $LINENO with exit code $?"' ERR
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# -------------------------------------------------------------------------
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# Helpers
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# -------------------------------------------------------------------------
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git_add_with_retry() {
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local file=$1
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local attempts=0
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local max_attempts=10
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while ! git add "$file"; do
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attempts=$((attempts+1))
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echo "Git add failed for $file (attempt $attempts), retrying..."
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sleep 1
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if [[ $attempts -ge $max_attempts ]]; then
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echo "❌ Failed to git add $file after $max_attempts attempts"
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exit 1
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fi
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done
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}
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update_file_if_changed() {
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# Run a regex replacement or copy on a file and stage it if it changed
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local expr=$1
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local src=$2
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local dest=${3:-$src}
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local changed=0
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if [[ -n "$expr" ]]; then
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tmp=$(mktemp)
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sed -E "$expr" "$src" > "$tmp"
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if ! cmp -s "$tmp" "$dest"; then
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mv "$tmp" "$dest"
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git_add_with_retry "$dest"
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changed=1
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else
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rm "$tmp"
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fi
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else
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if [[ ! -f "$dest" ]] || ! cmp -s "$src" "$dest"; then
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cp "$src" "$dest"
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git_add_with_retry "$dest"
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changed=1
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fi
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fi
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return $changed
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}
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28-
cd CPAC || exit 1
29-
VERSION=$(python -c "from info import __version__; print(('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__).split('+', 1)[0])")
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cd ..
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echo "v${VERSION}" > version
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export _SED_COMMAND="s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g"
33-
if [[ "$OSTYPE" == "darwin"* ]]; then
34-
# Mac OSX
35-
find ./CPAC/resources/configs -name "*.yml" -exec sed -i '' -E "${_SED_COMMAND}" {} \;
70+
log_info() {
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echo "=== $* ==="
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}
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# -------------------------------------------------------------------------
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# Main
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# -------------------------------------------------------------------------
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START_DIR=$(pwd)
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SCRIPT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
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REPO_ROOT="$(realpath "$SCRIPT_DIR/../..")"
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# -------------------------------------------------------------------------
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# Fetch version
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# -------------------------------------------------------------------------
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log_info "Fetching version"
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VERSION=$(python -c "import sys; sys.path.insert(0, '$REPO_ROOT/CPAC'); from info import __version__; print(__version__.split('+', 1)[0])")
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VERSION_FILE="$REPO_ROOT/version"
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if [[ -f "$VERSION_FILE" ]]; then
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cd "$REPO_ROOT"
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OLD_VERSION=$(git show "$(git log --pretty=format:'%h' -n 1 -- version | tail -n 1)":version)
91+
cd "$START_DIR"
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else
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# Linux and others
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find ./CPAC/resources/configs -name "*.yml" -exec sed -i'' -r "${_SED_COMMAND}" {} \;
93+
OLD_VERSION="<none>"
3994
fi
40-
wait_for_git_lock && git add version
41-
VERSIONS=( `git show $(git log --pretty=format:'%h' -n 1 version | tail -n 1):version` `cat version` )
42-
export PATTERN="(declare|typeset) -a"
43-
if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]]
44-
then
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for DOCKERFILE in $(find ./.github/Dockerfiles -name "*.Dockerfile")
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do
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export IFS=""
48-
for LINE in $(grep "FROM ghcr\.io/fcp\-indi/c\-pac/.*\-${VERSIONS[0]}" ${DOCKERFILE})
49-
do
50-
echo "Updating stage tags in ${DOCKERFILE}"
95+
echo "v${VERSION}" > "$VERSION_FILE"
96+
97+
# -------------------------------------------------------------------------
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# Write version file and stage it
99+
# -------------------------------------------------------------------------
100+
log_info "Updating version file"
101+
if update_file_if_changed "" <(echo "v${VERSION}") "$VERSION_FILE"; then
102+
git_add_with_retry "$VERSION_FILE"
103+
fi
104+
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# -------------------------------------------------------------------------
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# Update YAML config files
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# -------------------------------------------------------------------------
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log_info "Updating YAML config files"
109+
VERSION_EXPR="s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g"
110+
for YAML_FILE in "$REPO_ROOT"/CPAC/resources/configs/{*.yml,*.yaml,test_configs/*.yml,test_configs/*.yaml}; do
111+
[[ -e "$YAML_FILE" ]] || continue
112+
113+
echo "Processing ${YAML_FILE}"
114+
echo "Applying regex: ${VERSION_EXPR}"
115+
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# Run sed safely
117+
tmp=$(mktemp)
118+
if ! sed -E "$VERSION_EXPR" "$YAML_FILE" > "$tmp"; then
119+
echo "❌ sed failed on $YAML_FILE"
120+
rm "$tmp"
121+
exit 1
122+
fi
123+
124+
if ! cmp -s "$tmp" "$YAML_FILE"; then
125+
mv "$tmp" "$YAML_FILE"
126+
echo "Updated $YAML_FILE"
127+
git_add_with_retry "$YAML_FILE"
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else
129+
rm "$tmp"
130+
echo "No changes needed for $YAML_FILE"
131+
fi
132+
done
133+
134+
# -------------------------------------------------------------------------
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# Update Dockerfiles (only C-PAC tags)
136+
# -------------------------------------------------------------------------
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log_info "Updating Dockerfiles"
138+
NEW_VERSION=$(<"$VERSION_FILE")
139+
140+
if [[ "$OLD_VERSION" != "$NEW_VERSION" ]]; then
141+
for DOCKERFILE in "$REPO_ROOT"/.github/Dockerfiles/*.Dockerfile; do
142+
if grep -q "FROM ghcr\.io/fcp-indi/c-pac/.*-${OLD_VERSION}" "$DOCKERFILE"; then
143+
echo "Updating C-PAC version in ${DOCKERFILE} from ${OLD_VERSION} to ${NEW_VERSION}"
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51145
if [[ "$OSTYPE" == "darwin"* ]]; then
52-
# Mac OSX
53-
sed -i "" "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
146+
# macOS sed
147+
sed -i "" "s/-${OLD_VERSION}/-${NEW_VERSION}/g" "$DOCKERFILE"
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else
55-
# Linux and others
56-
sed -i "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
149+
# Linux sed
150+
sed -i -E "s/-${OLD_VERSION}/-${NEW_VERSION}/g" "$DOCKERFILE"
57151
fi
58-
done
152+
153+
git_add_with_retry "$DOCKERFILE"
154+
fi
59155
done
60-
unset IFS
61156
fi
62-
wait_for_git_lock && git add CPAC/resources/configs .github/Dockerfiles
63-
64-
# Overwrite top-level Dockerfiles with the CI Dockerfiles
65-
wait_for_git_lock && cp .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile Dockerfile
66-
wait_for_git_lock && cp .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile variant-lite.Dockerfile
67-
for DOCKERFILE in $(ls *Dockerfile)
68-
do
69-
wait_for_git_lock && git add $DOCKERFILE
157+
158+
# -------------------------------------------------------------------------
159+
# Overwrite top-level Dockerfiles
160+
# -------------------------------------------------------------------------
161+
log_info "Updating top-level Dockerfiles"
162+
TOP_DOCKERFILES=(
163+
".github/Dockerfiles/C-PAC.develop-jammy.Dockerfile:Dockerfile"
164+
".github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile:variant-lite.Dockerfile"
165+
)
166+
for SRC_DST in "${TOP_DOCKERFILES[@]}"; do
167+
# Split SRC_DST by colon safely
168+
SRC="${SRC_DST%%:*}"
169+
DST="${SRC_DST##*:}"
170+
171+
FULL_SRC="$REPO_ROOT/$SRC"
172+
FULL_DST="$REPO_ROOT/$DST"
173+
174+
if [[ ! -f "$FULL_SRC" ]]; then
175+
echo "⚠️ Source Dockerfile does not exist: $FULL_SRC"
176+
continue
177+
fi
178+
echo "Updating top-level Dockerfile: $FULL_DST from $FULL_SRC"
179+
cp "$FULL_SRC" "$FULL_DST" && git_add_with_retry "$FULL_DST"
70180
done
181+
182+
# Return to original directory
183+
cd "$START_DIR"
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185+
# -------------------------------------------------------------------------
186+
# Summary
187+
# -------------------------------------------------------------------------
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echo
189+
echo "Version changed: (from ${OLD_VERSION} to ${NEW_VERSION})"
190+
echo "======================"

‎.pre-commit-config.yaml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ repos:
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name: Update Dockerfiles and version comments
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entry: .github/scripts/autoversioning.sh
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language: script
72-
files: '.*Dockerfile$|.*\.yaml$|^CPAC/info\.py$'
72+
files: '(^CPAC/info\.py$|.*Dockerfile$|.*\.ya?ml$)'
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- id: update-yaml-comments
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name: Update YAML comments
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entry: CPAC/utils/configuration/yaml_template.py

‎.ruff.toml‎

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Original file line numberDiff line numberDiff line change
@@ -20,7 +20,6 @@ external = ["T20"] # Don't autoremove 'noqa` comments for these rules
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"nibabel" = "nib"
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"nipype.interfaces.io" = "nio"
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"networkx" = "nx"
23-
"pkg_resources" = "p"
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"CPAC.pipeline.nipype_pipeline_engine" = "pe"
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[lint.isort]

‎CHANGELOG.md‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -59,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Removed broken support for native-space masking.
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- Introduced a new `template_space_func_masking` section in the pipeline config for template-space-only methods.
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- Moved `Anatomical_Resampled` masking method from `func_masking` to the `template_space_func_masking`.
62+
- Upgraded resource retrieval to `importlib.resources`.
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- Turned `On` boundary_based_registration for abcd-options preconfig.
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- Refactored `transform_timeseries_to_T1template_abcd` nodeblock removing unnecessary nodes, changing `desc-preproc_T1w` inputs as reference to `desc-head_T1w`.
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- Appended `T1w to Template` FOV match transform to the XFM.

‎CPAC/__init__.py‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -35,10 +35,14 @@ def _docs_prefix() -> str:
3535
return DOCS_URL_PREFIX
3636

3737

38-
license_notice = f"""Copyright (C) 2022-2024 C-PAC Developers.
38+
def license_notice() -> str:
39+
"""Get the license notice for this version."""
40+
return f"""Copyright (C) 2022-2024 C-PAC Developers.
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4042
This program comes with ABSOLUTELY NO WARRANTY. This is free software,
4143
and you are welcome to redistribute it under certain conditions. For
4244
details, see {_docs_prefix()}/license or the COPYING and
4345
COPYING.LESSER files included in the source code."""
46+
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4448
__all__ = ["license_notice", "version", "__version__"]

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