♻️ Fix autoversioning

.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile

@@ -14,7 +14,7 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.8.dev1
 LABEL org.opencontainers.image.description="Full C-PAC image"
 LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
@@ -42,7 +42,7 @@ RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
     && apt-get autoremove -y \
     && ldconfig \
     && chmod 777 / \
-    && chmod 777 $(ls / | grep -v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1 sys | grep -v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1 proc)
+    && chmod 777 $(ls / | grep -v sys | grep -v proc)
 ENV PYTHONUSERBASE=/home/c-pac_user/.local
 ENV PATH=$PATH:/home/c-pac_user/.local/bin \
     PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages \

.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile

@@ -14,7 +14,7 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev1
 LABEL org.opencontainers.image.description="Full C-PAC image without FreeSurfer"
 LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
@@ -43,7 +43,7 @@ RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
     && apt-get autoremove -y \
     && ldconfig \
     && chmod 777 / \
-    && chmod 777 $(ls / | grep -v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1 sys | grep -v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1 proc)
+    && chmod 777 $(ls / | grep -v sys | grep -v proc)
 ENV PYTHONUSERBASE=/home/c-pac_user/.local
 ENV PATH=$PATH:/home/c-pac_user/.local/bin \
     PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages \

.github/Dockerfiles/base-standard.Dockerfile

@@ -16,7 +16,7 @@
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy AS freesurfer
 
-FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1
+FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev1
 LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 Standard software dependencies for C-PAC standard images"
 LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
@@ -56,7 +56,7 @@ RUN apt-get autoremove -y \
     && rm -rf results.txt \
     && ldconfig \
     && chmod 777 / /home/c-pac_user \
-    && chmod 777 $(ls / | grep -v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1 sys | grep -v1.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev11.8.8.dev1 proc)
+    && chmod 777 $(ls / | grep -v sys | grep -v proc)
 
 # set user
 USER c-pac_user

.github/scripts/autoversioning.sh

@@ -1,6 +1,6 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
-# Copyright (C) 2024  C-PAC Developers
+# Copyright (C) 2024-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -17,54 +17,174 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 
-# Update version comment strings
-function wait_for_git_lock() {
-    while [ -f "./.git/index.lock" ]; do
-        echo "Waiting for the git lock file to be removed..."
-        sleep 1
-    done
+
+set -euo pipefail
+trap 'echo "❌ Script failed at line $LINENO with exit code $?"' ERR
+
+# -------------------------------------------------------------------------
+# Helpers
+# -------------------------------------------------------------------------
+
+git_add_with_retry() {
+  local file=$1
+  local attempts=0
+  local max_attempts=10
+  while ! git add "$file"; do
+    attempts=$((attempts+1))
+    echo "Git add failed for $file (attempt $attempts), retrying..."
+    sleep 1
+    if [[ $attempts -ge $max_attempts ]]; then
+      echo "❌ Failed to git add $file after $max_attempts attempts"
+      exit 1
+    fi
+  done
+}
+
+update_file_if_changed() {
+  # Run a regex replacement or copy on a file and stage it if it changed
+  local expr=$1
+  local src=$2
+  local dest=${3:-$src}
+
+  local changed=0
+  if [[ -n "$expr" ]]; then
+    tmp=$(mktemp)
+    sed -E "$expr" "$src" > "$tmp"
+    if ! cmp -s "$tmp" "$dest"; then
+      mv "$tmp" "$dest"
+      git_add_with_retry "$dest"
+      changed=1
+    else
+      rm "$tmp"
+    fi
+  else
+    if [[ ! -f "$dest" ]] || ! cmp -s "$src" "$dest"; then
+      cp "$src" "$dest"
+      git_add_with_retry "$dest"
+      changed=1
+    fi
+  fi
+  return $changed
 }
 
-cd CPAC || exit 1
-VERSION=$(python -c "from info import __version__; print(('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__).split('+', 1)[0])")
-cd ..
-echo "v${VERSION}" > version
-export _SED_COMMAND="s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g"
-if [[ "$OSTYPE" == "darwin"* ]]; then
-    # Mac OSX
-    find ./CPAC/resources/configs -name "*.yml" -exec sed -i '' -E "${_SED_COMMAND}" {} \;
+log_info() {
+  echo "=== $* ==="
+}
+
+# -------------------------------------------------------------------------
+# Main
+# -------------------------------------------------------------------------
+
+START_DIR=$(pwd)
+SCRIPT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+REPO_ROOT="$(realpath "$SCRIPT_DIR/../..")"
+
+# -------------------------------------------------------------------------
+# Fetch version
+# -------------------------------------------------------------------------
+log_info "Fetching version"
+VERSION=$(python -c "import sys; sys.path.insert(0, '$REPO_ROOT/CPAC'); from info import __version__; print(__version__.split('+', 1)[0])")
+VERSION_FILE="$REPO_ROOT/version"
+if [[ -f "$VERSION_FILE" ]]; then
+    cd "$REPO_ROOT"
+    OLD_VERSION=$(git show "$(git log --pretty=format:'%h' -n 1 -- version | tail -n 1)":version)
+    cd "$START_DIR"
 else
-    # Linux and others
-    find ./CPAC/resources/configs -name "*.yml" -exec sed -i'' -r "${_SED_COMMAND}" {} \;
+    OLD_VERSION="<none>"
 fi
-wait_for_git_lock && git add version
-VERSIONS=( `git show $(git log --pretty=format:'%h' -n 1 version | tail -n 1):version` `cat version` )
-export PATTERN="(declare|typeset) -a"
-if [[ "$(declare -p VERSIONS)" =~ $PATTERN ]]
-then
-  for DOCKERFILE in $(find ./.github/Dockerfiles -name "*.Dockerfile")
-  do
-    export IFS=""
-    for LINE in $(grep "FROM ghcr\.io/fcp\-indi/c\-pac/.*\-${VERSIONS[0]}" ${DOCKERFILE})
-    do
-      echo "Updating stage tags in ${DOCKERFILE}"
+echo "v${VERSION}" > "$VERSION_FILE"
+
+# -------------------------------------------------------------------------
+# Write version file and stage it
+# -------------------------------------------------------------------------
+log_info "Updating version file"
+if update_file_if_changed "" <(echo "v${VERSION}") "$VERSION_FILE"; then
+  git_add_with_retry "$VERSION_FILE"
+fi
+
+# -------------------------------------------------------------------------
+# Update YAML config files
+# -------------------------------------------------------------------------
+log_info "Updating YAML config files"
+VERSION_EXPR="s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g"
+for YAML_FILE in "$REPO_ROOT"/CPAC/resources/configs/{*.yml,*.yaml,test_configs/*.yml,test_configs/*.yaml}; do
+  [[ -e "$YAML_FILE" ]] || continue
+
+  echo "Processing ${YAML_FILE}"
+  echo "Applying regex: ${VERSION_EXPR}"
+
+  # Run sed safely
+  tmp=$(mktemp)
+  if ! sed -E "$VERSION_EXPR" "$YAML_FILE" > "$tmp"; then
+    echo "❌ sed failed on $YAML_FILE"
+    rm "$tmp"
+    exit 1
+  fi
+
+  if ! cmp -s "$tmp" "$YAML_FILE"; then
+    mv "$tmp" "$YAML_FILE"
+    echo "Updated $YAML_FILE"
+    git_add_with_retry "$YAML_FILE"
+  else
+    rm "$tmp"
+    echo "No changes needed for $YAML_FILE"
+  fi
+done
+
+# -------------------------------------------------------------------------
+# Update Dockerfiles (only C-PAC tags)
+# -------------------------------------------------------------------------
+log_info "Updating Dockerfiles"
+NEW_VERSION=$(<"$VERSION_FILE")
+
+if [[ "$OLD_VERSION" != "$NEW_VERSION" ]]; then
+  for DOCKERFILE in "$REPO_ROOT"/.github/Dockerfiles/*.Dockerfile; do
+    if grep -q "FROM ghcr\.io/fcp-indi/c-pac/.*-${OLD_VERSION}" "$DOCKERFILE"; then
+      echo "Updating C-PAC version in ${DOCKERFILE} from ${OLD_VERSION} to ${NEW_VERSION}"
+
       if [[ "$OSTYPE" == "darwin"* ]]; then
-          # Mac OSX
-          sed -i "" "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
+        # macOS sed
+        sed -i "" "s/-${OLD_VERSION}/-${NEW_VERSION}/g" "$DOCKERFILE"
       else
-          # Linux and others
-          sed -i "s/\-${VERSIONS[0]}/\-${VERSIONS[1]}/g" ${DOCKERFILE}
+        # Linux sed
+        sed -i -E "s/-${OLD_VERSION}/-${NEW_VERSION}/g" "$DOCKERFILE"
       fi
-    done
+
+      git_add_with_retry "$DOCKERFILE"
+    fi
   done
-  unset IFS
 fi
-wait_for_git_lock && git add CPAC/resources/configs .github/Dockerfiles
-
-# Overwrite top-level Dockerfiles with the CI Dockerfiles
-wait_for_git_lock && cp .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile Dockerfile
-wait_for_git_lock && cp .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile variant-lite.Dockerfile
-for DOCKERFILE in $(ls *Dockerfile)
-do
-  wait_for_git_lock && git add $DOCKERFILE
+
+# -------------------------------------------------------------------------
+# Overwrite top-level Dockerfiles
+# -------------------------------------------------------------------------
+log_info "Updating top-level Dockerfiles"
+TOP_DOCKERFILES=(
+  ".github/Dockerfiles/C-PAC.develop-jammy.Dockerfile:Dockerfile"
+  ".github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile:variant-lite.Dockerfile"
+)
+for SRC_DST in "${TOP_DOCKERFILES[@]}"; do
+  # Split SRC_DST by colon safely
+  SRC="${SRC_DST%%:*}"
+  DST="${SRC_DST##*:}"
+
+  FULL_SRC="$REPO_ROOT/$SRC"
+  FULL_DST="$REPO_ROOT/$DST"
+
+  if [[ ! -f "$FULL_SRC" ]]; then
+    echo "⚠️ Source Dockerfile does not exist: $FULL_SRC"
+    continue
+  fi
+  echo "Updating top-level Dockerfile: $FULL_DST from $FULL_SRC"
+  cp "$FULL_SRC" "$FULL_DST" && git_add_with_retry "$FULL_DST"
 done
+
+# Return to original directory
+cd "$START_DIR"
+
+# -------------------------------------------------------------------------
+# Summary
+# -------------------------------------------------------------------------
+echo
+echo "Version changed: (from ${OLD_VERSION} to ${NEW_VERSION})"
+echo "======================"

.pre-commit-config.yaml

@@ -69,7 +69,7 @@ repos:
         name: Update Dockerfiles and version comments
         entry: .github/scripts/autoversioning.sh
         language: script
-        files: '.*Dockerfile$|.*\.yaml$|^CPAC/info\.py$'
+        files: '(^CPAC/info\.py$|.*Dockerfile$|.*\.ya?ml$)'
       - id: update-yaml-comments
         name: Update YAML comments
         entry: CPAC/utils/configuration/yaml_template.py

CPAC/__init__.py

@@ -35,10 +35,14 @@ def _docs_prefix() -> str:
     return DOCS_URL_PREFIX
 
 
-license_notice = f"""Copyright (C) 2022-2024 C-PAC Developers.
+def license_notice() -> str:
+    """Get the license notice for this version."""
+    return f"""Copyright (C) 2022-2024 C-PAC Developers.
 
 This program comes with ABSOLUTELY NO WARRANTY. This is free software,
 and you are welcome to redistribute it under certain conditions. For
 details, see {_docs_prefix()}/license or the COPYING and
 COPYING.LESSER files included in the source code."""
+
+
 __all__ = ["license_notice", "version", "__version__"]

CPAC/info.py

@@ -52,16 +52,22 @@
 
 def get_cpac_gitversion() -> str | None:
     """CPAC version as reported by the last commit in git."""
-    from pathlib import Path
+    from importlib.resources import as_file, files
     import subprocess
 
-    gitpath = Path(__file__).parent.resolve()
-
-    gitpathgit = gitpath / ".git"
-    if not gitpathgit.exists():
+    with as_file(files("CPAC")) as _cpac:
+        gitpath = _cpac
+    gitpathgit = None
+    for _cpacpath in [gitpath, *gitpath.parents]:
+        git_dir = _cpacpath / ".git"
+        if git_dir.exists():
+            gitpathgit = git_dir
+            break
+    if not gitpathgit:
         return None
 
     ver = None
+
     try:
         o, _ = subprocess.Popen(
             "git describe --always", shell=True, cwd=gitpath, stdout=subprocess.PIPE

CPAC/pipeline/cpac_pipeline.py

@@ -414,7 +414,7 @@ def run_workflow(
             )
             if c.pipeline_setup["system_config"]["random_seed"] is not None
             else "",
-            license_notice=CPAC.license_notice.replace("\n", "\n    "),
+            license_notice=CPAC.license_notice().replace("\n", "\n    "),
         ),
     )
     subject_info = {}

CPAC/resources/configs/data_config_S3-BIDS-ABIDE.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version
+# Version 1.8.8.dev1
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_S3-BIDS-ADHD200.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version
+# Version 1.8.8.dev1
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_S3-BIDS-ADHD200_only2.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version
+# Version 1.8.8.dev1
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_S3-BIDS-NKI-RocklandSample.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version
+# Version 1.8.8.dev1
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_cpac_benchmark.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version
+# Version 1.8.8.dev1
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_settings_template.yml

@@ -1,5 +1,5 @@
 # CPAC Data Settings File
-# Version
+# Version 1.8.8.dev1
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/group_config_template.yml

@@ -1,5 +1,5 @@
 # CPAC Group-Level Analysis Configuration YAML file
-# Version
+# Version 1.8.8.dev1
 #
 # http://fcp-indi.github.io for more info.
 #