Auto format copyright and add linter

.github/workflows/lint.yml

@@ -39,6 +39,23 @@ jobs:
           set -xeuo pipefail
           bash admin/run_clang_format.sh -d
 
+  copyright-check:
+    name: copyright-check
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    steps:
+      - name: Check out source tree
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Run copyright header check
+        shell: bash
+        run: |
+          set -xeuo pipefail
+          bash admin/apply_copyright.sh -d
+
   cmake-format-lint:
     name: cmake-format-lint
     runs-on: ubuntu-24.04

admin/apply_copyright.sh

@@ -14,141 +14,189 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-set -ex
+set -euo pipefail
+
 REPO_ROOT=$(git rev-parse --show-toplevel)
+CHECK_ONLY=false
+FIX_YEARS=false
+ERRORS=0
 
-# Define the Python copyright header
-PY_COPYRIGHT_HEADER='# SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+usage() {
+    echo "Usage: apply_copyright.sh [-d] [-f]"
+}
+
+while getopts ":df" opt; do
+    case "${opt}" in
+        d)
+            CHECK_ONLY=true
+            ;;
+        f)
+            FIX_YEARS=true
+            ;;
+        \?)
+            usage
+            exit 1
+            ;;
+    esac
+done
+
+if [ "${CHECK_ONLY}" = true ] && [ "${FIX_YEARS}" = true ]; then
+    usage
+    exit 1
+fi
+
+report_issue() {
+    local message="$1"
+    echo "${message}"
+    ERRORS=$((ERRORS + 1))
+}
+
+find_included_files() {
+    find "${REPO_ROOT}" -maxdepth 1 -type f "$@" -print0
+    find \
+        "${REPO_ROOT}/src" \
+        "${REPO_ROOT}/nvmolkit" \
+        "${REPO_ROOT}/tests" \
+        "${REPO_ROOT}/benchmarks" \
+        -type f "$@" -not -path "*/rdkit_extensions/*" -print0
+}
 
-'
+get_file_year() {
+    local file="$1"
+    local relative_path="${file#${REPO_ROOT}/}"
+    local commit_year
 
-# Find all Python files and add the header (excluding rdkit_extensions folder)
-find "$REPO_ROOT" -name "*.py" -not -path "*/rdkit_extensions/*" | while read -r file; do
-    # Check if the file already contains the header
-    if ! grep -q "SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES" "$file"; then
-        # Add the header to the file
-        echo "Adding copyright header to Python file: $file"
-        echo "$PY_COPYRIGHT_HEADER$(cat "$file")" > "$file"
+    commit_year=$(git log --diff-filter=A --follow --format=%ad --date=format:%Y -- "${relative_path}" | tail -n 1 || true)
+    if [ -z "${commit_year}" ]; then
+        commit_year=$(date +%Y)
+    fi
+
+    if [ "${commit_year}" -le 2025 ]; then
+        echo "2025"
     else
-        echo "Python file already has copyright header: $file"
+        echo "2026"
     fi
-done
+}
+
+get_existing_header_year() {
+    local file="$1"
+    local year_match
+
+    year_match=$(sed -nE 's/^.*SPDX-FileCopyrightText: Copyright \(c\) ([0-9]{4}).*$/\1/p' "${file}" | head -n 1)
+    if [ -n "${year_match}" ]; then
+        echo "${year_match}"
+    fi
+}
+
+make_header() {
+    local comment_prefix="$1"
+    local year="$2"
+
+    cat <<EOF
+${comment_prefix} SPDX-FileCopyrightText: Copyright (c) ${year} NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+${comment_prefix} SPDX-License-Identifier: Apache-2.0
+${comment_prefix}
+${comment_prefix} Licensed under the Apache License, Version 2.0 (the "License");
+${comment_prefix} you may not use this file except in compliance with the License.
+${comment_prefix} You may obtain a copy of the License at
+${comment_prefix}
+${comment_prefix} http://www.apache.org/licenses/LICENSE-2.0
+${comment_prefix}
+${comment_prefix} Unless required by applicable law or agreed to in writing, software
+${comment_prefix} distributed under the License is distributed on an "AS IS" BASIS,
+${comment_prefix} WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+${comment_prefix} See the License for the specific language governing permissions and
+${comment_prefix} limitations under the License.
+
+EOF
+}
+
+replace_year() {
+    local file="$1"
+    local year="$2"
 
-# Define the C++ copyright header
-CPP_COPYRIGHT_HEADER='// SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-// SPDX-License-Identifier: Apache-2.0
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-// http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-'
-
-# Find all C++ files and add the header (excluding rdkit_extensions folder)
-find "$REPO_ROOT" -type f \( -name "*.h" -o -name "*.cpp" -o -name "*.cuh" -o -name "*.cu" \) -not -path "*/rdkit_extensions/*" | while read -r file; do
-    # Check if the file already contains the header
-    if ! grep -q "SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES" "$file"; then
-        # Add the header to the file
-        echo "Adding copyright header to C++ file: $file"
-        echo "$CPP_COPYRIGHT_HEADER$(cat "$file")" > "$file"
+    sed -i -E \
+        "0,/SPDX-FileCopyrightText: Copyright \\(c\\) [0-9]{4}/s//SPDX-FileCopyrightText: Copyright (c) ${year}/" \
+        "${file}"
+}
+
+write_header() {
+    local file="$1"
+    local comment_prefix="$2"
+    local year="$3"
+    local preserve_shebang="$4"
+    local temp_file
+    local first_line
+
+    temp_file=$(mktemp)
+
+    if [ "${preserve_shebang}" = true ] && IFS= read -r first_line < "${file}" && [[ "${first_line}" == '#!'* ]]; then
+        printf '%s\n' "${first_line}" > "${temp_file}"
+        make_header "${comment_prefix}" "${year}" >> "${temp_file}"
+        tail -n +2 "${file}" >> "${temp_file}"
     else
-        echo "C++ file already has copyright header: $file"
+        make_header "${comment_prefix}" "${year}" > "${temp_file}"
+        cat "${file}" >> "${temp_file}"
     fi
-done
 
-# Define the shell script copyright header
-SH_COPYRIGHT_HEADER='# SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+    mv "${temp_file}" "${file}"
+}
+
+process_file() {
+    local file="$1"
+    local comment_prefix="$2"
+    local file_label="$3"
+    local preserve_shebang="$4"
+    local expected_year
+    local existing_year
+
+    expected_year=$(get_file_year "${file}")
+    existing_year=$(get_existing_header_year "${file}")
 
-'
-
-# Find all shell script files and add the header
-find "$REPO_ROOT" -name "*.sh" | while read -r file; do
-    # Check if the file already contains the header
-    if ! grep -q "SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES" "$file"; then
-        # Check if file starts with shebang and preserve it
-        if head -n1 "$file" | grep -q "^#!"; then
-            # File has shebang, add header after it
-            echo "Adding copyright header to shell script (after shebang): $file"
-            shebang=$(head -n1 "$file")
-            rest=$(tail -n +2 "$file")
-            echo "$shebang
-$SH_COPYRIGHT_HEADER$rest" > "$file"
+    if [ "${existing_year:-}" = "${expected_year}" ]; then
+        return
+    fi
+
+    if [ -n "${existing_year:-}" ]; then
+        if [ "${CHECK_ONLY}" = true ]; then
+            report_issue "Wrong copyright year in ${file_label} file: ${file} (expected ${expected_year})"
+            return
+        fi
+
+        if [ "${FIX_YEARS}" = true ]; then
+            echo "Fixing copyright year in ${file_label} file: ${file}"
+            replace_year "${file}" "${expected_year}"
         else
-            # No shebang, add header at the beginning
-            echo "Adding copyright header to shell script: $file"
-            echo "$SH_COPYRIGHT_HEADER$(cat "$file")" > "$file"
+            echo "${file_label} file already has copyright header with a different year: ${file}"
         fi
-    else
-        echo "Shell script already has copyright header: $file"
+        return
     fi
-done
-
-# Define the CMake copyright header
-CMAKE_COPYRIGHT_HEADER='# SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: Apache-2.0
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
 
-'
-
-# Find all CMake files and add the header
-find "$REPO_ROOT" -type f \( -name "CMakeLists.txt" -o -name "*.cmake" \) | while read -r file; do
-    # Check if the file already contains the header
-    if ! grep -q "SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES" "$file"; then
-        # Add the header to the file
-        echo "Adding copyright header to CMake file: $file"
-        echo "$CMAKE_COPYRIGHT_HEADER$(cat "$file")" > "$file"
-        # Format the CMake file after adding copyright header
-        echo "Formatting CMake file: $file"
-        cmake-format -i "$file"
-    else
-        echo "CMake file already has copyright header: $file"
-        # Still format the file to ensure consistent formatting
-        echo "Formatting CMake file: $file"
-        cmake-format -i "$file"
+    if [ "${CHECK_ONLY}" = true ]; then
+        report_issue "Missing copyright header in ${file_label} file: ${file}"
+        return
     fi
-done
+
+    echo "Adding copyright header to ${file_label} file: ${file}"
+    write_header "${file}" "${comment_prefix}" "${expected_year}" "${preserve_shebang}"
+}
+
+while IFS= read -r -d '' file; do
+    process_file "${file}" "#" "Python" false
+done < <(find_included_files -name "*.py")
+
+while IFS= read -r -d '' file; do
+    process_file "${file}" "//" "C++" false
+done < <(find_included_files \( -name "*.h" -o -name "*.cpp" -o -name "*.cuh" -o -name "*.cu" \))
+
+while IFS= read -r -d '' file; do
+    process_file "${file}" "#" "shell script" true
+done < <(find_included_files -name "*.sh")
+
+while IFS= read -r -d '' file; do
+    process_file "${file}" "#" "CMake" false
+done < <(find_included_files \( -name "CMakeLists.txt" -o -name "*.cmake" \))
+
+if [ "${CHECK_ONLY}" = true ] && [ "${ERRORS}" -ne 0 ]; then
+    exit 1
+fi

admin/distribute/merge_conda_artifacts.sh

@@ -1,4 +1,19 @@
 #!/usr/bin/env bash
+# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #
 # Merge multiple conda build_artifacts directories into one channel directory
 # so that verify_conda_version_combinations.sh can use a single local endpoint.

admin/distribute/unzip_all_conda_artifacts.sh

@@ -1,4 +1,19 @@
 #!/usr/bin/env bash
+# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #
 # Unzip all .zip files in a given folder (e.g. Azure conda artifact zips).
 # Handles nested zips: unzips top-level .zip files, then recursively unzips any

admin/distribute/verify_conda_distributable.sh

@@ -1,5 +1,18 @@
 #!/usr/bin/env bash
-
+# SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 set -exuo pipefail
 
 if [[ $# -ne 4 ]]; then