diff --git a/.editorconfig b/.editorconfig index c664343..c80ae3c 100644 --- a/.editorconfig +++ b/.editorconfig @@ -1,4 +1,4 @@ -# Copyright (C) 2024 Andrea Raffo +# Copyright (C) 2024 Andrea Raffo # # SPDX-License-Identifier: MIT diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 6476e5b..0562988 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,4 +1,5 @@ # Copyright (C) 2024 Roberto Rossini +# # SPDX-License-Identifier: MIT version: 2 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a106f1d..ba4477c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + name: CI on: diff --git a/.gitignore b/.gitignore index 0816ecf..58006a6 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] diff --git a/README.md b/README.md index 6884ea4..af3d229 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,9 @@ + + # StripePy ## Install instructions diff --git a/pyproject.toml b/pyproject.toml index d280e36..17692a9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + [build-system] requires = [ "hatchling", diff --git a/src/__init__.py b/src/__init__.py index e69de29..55c4f7f 100644 --- a/src/__init__.py +++ b/src/__init__.py @@ -0,0 +1,3 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT diff --git a/src/stripepy/IO.py b/src/stripepy/IO.py index f75ce3c..c2931ae 100644 --- a/src/stripepy/IO.py +++ b/src/stripepy/IO.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import pathlib import shutil from typing import List diff --git a/src/stripepy/__init__.py b/src/stripepy/__init__.py index a38878b..1ad728b 100644 --- a/src/stripepy/__init__.py +++ b/src/stripepy/__init__.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + from importlib.metadata import version from .main import main diff --git a/src/stripepy/cli/call.py b/src/stripepy/cli/call.py index 5c39154..451093f 100644 --- a/src/stripepy/cli/call.py +++ b/src/stripepy/cli/call.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import multiprocessing as mp import time from typing import Any, Dict diff --git a/src/stripepy/cli/setup.py b/src/stripepy/cli/setup.py index 96b10bc..9211ec9 100644 --- a/src/stripepy/cli/setup.py +++ b/src/stripepy/cli/setup.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import argparse import math import multiprocessing as mp diff --git a/src/stripepy/configs.py b/src/stripepy/configs.py index 245224a..ae22dc1 100644 --- a/src/stripepy/configs.py +++ b/src/stripepy/configs.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import numpy as np configs = { diff --git a/src/stripepy/main.py b/src/stripepy/main.py index 4cc2716..6bb6eb7 100644 --- a/src/stripepy/main.py +++ b/src/stripepy/main.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + import logging from .cli import call, download, setup diff --git a/src/stripepy/main_over_MoDLE.py b/src/stripepy/main_over_MoDLE.py index cb843df..19cf56f 100644 --- a/src/stripepy/main_over_MoDLE.py +++ b/src/stripepy/main_over_MoDLE.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import time import h5py diff --git a/src/stripepy/others.py b/src/stripepy/others.py index a5ca8cb..090947f 100644 --- a/src/stripepy/others.py +++ b/src/stripepy/others.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import os import h5py diff --git a/src/stripepy/stripepy.py b/src/stripepy/stripepy.py index 21c28e4..4fc41e0 100644 --- a/src/stripepy/stripepy.py +++ b/src/stripepy/stripepy.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import pathlib import time from typing import Dict, List, Tuple, Union diff --git a/src/stripepy/utils/TDA.py b/src/stripepy/utils/TDA.py index a07c1f3..8b198d5 100644 --- a/src/stripepy/utils/TDA.py +++ b/src/stripepy/utils/TDA.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import numpy as np from .persistence1d import ( diff --git a/src/stripepy/utils/__init__.py b/src/stripepy/utils/__init__.py index af31bf9..5e33685 100644 --- a/src/stripepy/utils/__init__.py +++ b/src/stripepy/utils/__init__.py @@ -1 +1,5 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + from . import TDA, unionfind diff --git a/src/stripepy/utils/evaluate.py b/src/stripepy/utils/evaluate.py index e5361de..dffcdb5 100644 --- a/src/stripepy/utils/evaluate.py +++ b/src/stripepy/utils/evaluate.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import itertools import bioframe as bf diff --git a/src/stripepy/utils/finders.py b/src/stripepy/utils/finders.py index 7b4b691..c9cc5e8 100644 --- a/src/stripepy/utils/finders.py +++ b/src/stripepy/utils/finders.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + from functools import partial from multiprocessing import Pool diff --git a/src/stripepy/utils/persistence1d.py b/src/stripepy/utils/persistence1d.py index a595bf2..3e38fab 100644 --- a/src/stripepy/utils/persistence1d.py +++ b/src/stripepy/utils/persistence1d.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import numpy as np from .unionfind import UnionFind diff --git a/src/stripepy/utils/postprocessing.py b/src/stripepy/utils/postprocessing.py index 41ce85d..74899b2 100644 --- a/src/stripepy/utils/postprocessing.py +++ b/src/stripepy/utils/postprocessing.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import numpy as np from . import stripe diff --git a/src/stripepy/utils/regressions.py b/src/stripepy/utils/regressions.py index 1a917f1..5f5ce30 100644 --- a/src/stripepy/utils/regressions.py +++ b/src/stripepy/utils/regressions.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import numpy as np diff --git a/src/stripepy/utils/stripe.py b/src/stripepy/utils/stripe.py index d28cef0..ae31d73 100644 --- a/src/stripepy/utils/stripe.py +++ b/src/stripepy/utils/stripe.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + import math from typing import Tuple, Union diff --git a/src/stripepy/utils/unionfind.py b/src/stripepy/utils/unionfind.py index 1c5e901..4b91e11 100644 --- a/src/stripepy/utils/unionfind.py +++ b/src/stripepy/utils/unionfind.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + # Implementation from the library by Tino Weinkauf downloadable at: # https://www.csc.kth.se/~weinkauf/notes/persistence1d.html diff --git a/test/test_IO.py b/test/test_IO.py index 94ab764..26aea35 100644 --- a/test/test_IO.py +++ b/test/test_IO.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + import pathlib import shutil import tempfile diff --git a/test/test_others.py b/test/test_others.py index c28bcfd..64bb200 100644 --- a/test/test_others.py +++ b/test/test_others.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Roberto Rossini +# +# SPDX-License-Identifier: MIT + import functools import gc import pathlib diff --git a/test/test_stripepy.py b/test/test_stripepy.py index 361f0a1..1230381 100644 --- a/test/test_stripepy.py +++ b/test/test_stripepy.py @@ -1,3 +1,7 @@ +# Copyright (C) 2024 Andrea Raffo +# +# SPDX-License-Identifier: MIT + import numpy as np import scipy.sparse as ss