Add MIT license

LICENSE.md

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2019-2025 Ádám Fekete, Gábor Csányi, Tamás K. Stenczel, Elena Gelzinyte,
+Elliott Kasoar, Alin Marin Elena
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,5 +1,6 @@
 # ABCD
 
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Doc](https://img.shields.io/badge/docs-master-green.svg)](https://libatoms.github.io/abcd/)
 [![Build Status](https://travis-ci.org/libAtoms/abcd.svg?branch=master)](https://travis-ci.org/libAtoms/abcd)
 

abcd/backends/atoms_http.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import json
 import logging
 from os import linesep

abcd/backends/atoms_pymongo.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel, Gábor Csányi
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from collections import Counter
 from collections.abc import Iterable
 from datetime import datetime

abcd/database.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 # ruff: noqa: B024, B027
 from abc import ABCMeta
 import logging

abcd/errors.py

@@ -1,3 +1,8 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
+
 class ABCDError(Exception):
     pass
 

abcd/frontends/commandline/commands.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel, Gábor Csányi, Elena Gelzinyte
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import logging
 import os
 

abcd/frontends/commandline/config.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import json
 import logging
 import os

abcd/frontends/commandline/decorators.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import logging
 
 from abcd import ABCD

abcd/frontends/commandline/parser.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel, Elena Gelzinyte
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from argparse import ArgumentParser
 import logging
 

abcd/model.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from collections import Counter, UserDict
 import datetime
 import getpass

abcd/parsers/extras.py

@@ -1,5 +1,8 @@
-# ruff: noqa: E731
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
 
+# ruff: noqa: E731
 from lark import Lark, Transformer, v_args
 
 grammar = r"""

abcd/parsers/queries.py

@@ -1,5 +1,8 @@
-# ruff: noqa: E731
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
 
+# ruff: noqa: E731
 import logging
 
 from lark import Lark, Transformer, v_args

abcd/parsers/queries_new.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import logging
 
 from lark import Lark, Transformer

abcd/queryset.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from abc import ABCMeta
 import logging
 

abcd/server/app/db.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from abcd import ABCD
 
 # from flask_paginate import Pagination, get_page_args

abcd/server/app/nav.py

@@ -1,3 +1,9 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
+from flask_nav import Nav
+from flask_nav.elements import Navbar, View, Separator, Subgroup, Link
 from hashlib import sha1
 
 from dominate import tags

abcd/server/app/views/api.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from flask import Blueprint, Response, jsonify, request
 
 bp = Blueprint("api", __name__)

abcd/server/app/views/database.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from flask import Blueprint, Response, render_template, request
 
 bp = Blueprint("database", __name__)

abcd/server/app/views/index.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from flask import Blueprint, render_template, url_for
 
 # from flask import Blueprint, render_template, flash, redirect, url_for, request

devtools/update_copyright.py

@@ -0,0 +1,94 @@
+# Copyright (c) 2025.
+# Authors: Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
+"""Add or update copyright notice to all python files."""
+
+from datetime import date
+import os
+import re
+import subprocess
+
+# git users -> real name mapping for current contributors
+USER_TO_REAL_NAME = {
+    "stenczelt": "Tamás K. Stenczel",
+    "Tamas K Stenczel": "Tamás K. Stenczel",
+    "Tamas Stenczel": "Tamás K. Stenczel",
+    "T. K. Stenczel": "Tamás K. Stenczel",
+    "Adam Fekete": "Ádám Fekete",
+    "ElliottKasoar": "Elliott Kasoar",
+    "gelzinyte": "Elena Gelzinyte",
+    "gabor1": "Gábor Csányi",
+    "gabor": "Gábor Csányi",
+}
+
+
+def get_contributors(file_path):
+    """Get list of contributors for a given file."""
+    command = f"git log --pretty=format:'%an' {file_path} | sort | uniq"
+    contributors = subprocess.check_output(command, shell=True, text=True)
+    contributors = contributors.strip().split("\n")
+
+    # Map usernames to real names, if possible
+    real_name_contributors = []
+    for contributor in contributors:
+        if contributor == "":
+            continue
+        real_name = USER_TO_REAL_NAME[contributor]
+        if real_name not in real_name_contributors:
+            real_name_contributors.append(real_name)
+
+    return real_name_contributors
+
+
+def insert_copyright(file_path, contributors):
+    """Insert a copyright notice at the top of a file."""
+    # Create the copyright notice string
+    author_names = ", ".join(contributors)
+    copyright_notice = (
+        f"# Copyright (c) {date.today().year}.\n"
+        f"# Authors: {author_names}\n"
+        f"# This program is distributed under the MIT License, see LICENSE.md.\n\n"
+    )
+
+    with open(file_path) as file:
+        content = file.read()
+
+    # replace existing notice if needed
+    pattern = re.compile(
+        r"^# Copyright \(c\) [\d-]+\.\n"
+        r"# Authors:\s*(.*?)\n"
+        r"# This program is distributed under the MIT License, see LICENSE\.md\.\n\n",
+        re.MULTILINE,
+    )
+
+    if m := pattern.match(content):
+        if m.group(1) == author_names:
+            print(file_path, "Matched! contributors unchanged")
+        else:
+            print(file_path, "Updating contributors: ", m.group(1), " ->", author_names)
+        content = pattern.sub(copyright_notice, content)
+    else:
+        print(file_path, "adding contributors", author_names)
+        content = copyright_notice + content
+
+    # Insert the copyright notice at the top
+    with open(file_path, "w") as file:
+        file.write(content)
+
+
+def process_files(directory):
+    """Process all Python files in the given directory."""
+    for root, _, files in os.walk(directory):
+        if root.startswith("./.venv"):
+            continue
+        for file in files:
+            if file.endswith(".py") and file != "__init__.py":
+                file_path = os.path.join(root, file)
+                contributors = get_contributors(file_path)
+                insert_copyright(file_path, contributors)
+
+
+if __name__ == "__main__":
+    # Replace with your folder path
+    process_files(".")

docs_src/conf.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Elliott Kasoar, Tamás K. Stenczel, Gábor Csányi
+# This program is distributed under the MIT License, see LICENSE.md.
+
 #
 # Configuration file for the Sphinx documentation builder.
 #

tests/hash.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import io
 
 import ase

tests/test_abstract_model.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import datetime
 import io
 from io import StringIO

tests/test_database.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from io import StringIO
 
 from ase.io import read

tests/test_mongodb_srv.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 """Tests for supporting `mongodb+srv://` URIs"""
 
 from pytest import fixture

tests/test_parsers.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import pytest
 
 from abcd.parsers.extras import parser as extras_parser

tutorials/gb_upload.py

@@ -1,3 +1,8 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
+import sys
 from pathlib import Path
 import sys
 

tutorials/scripts/Preprocess.py

@@ -1,3 +1,9 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
+from pathlib import Path
+from pprint import pprint
 import json
 from pathlib import Path
 

tutorials/scripts/Reader.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 import json
 from pathlib import Path
 

tutorials/scripts/Visualise.py

@@ -1,3 +1,8 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
+import io
 import uuid
 
 from ipywidgets import Dropdown, FloatSlider, Output, VBox

tutorials/scripts/Visualise_quip.py

@@ -1,3 +1,8 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
+import io
 import uuid
 
 from ipywidgets import Dropdown, FloatSlider, Output, VBox

tutorials/test_db.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from pathlib import Path
 
 from ase.io import read

tutorials/test_upload.py

@@ -1,3 +1,7 @@
+# Copyright (c) 2025.
+# Authors: Ádám Fekete, Elliott Kasoar, Tamás K. Stenczel
+# This program is distributed under the MIT License, see LICENSE.md.
+
 from abcd import ABCD
 
 if __name__ == "__main__":