Follow REUSE.software recommendations

.editorconfig

@@ -1,4 +1,5 @@
-# EditorConfig is awesome: https://EditorConfig.org
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 
 root = true
 

.github/requirements-old.txt

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # Ensure changes to these dependencies are reflected in pyproject.toml
 numpy==2.2.6
 scipy==1.15.3

.github/workflows/pytest.yaml

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 name: pytest
 on:
   push:

.gitignore

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 *.png
 __pycache__
 *.py[cod]

.pre-commit-config.yaml

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v6.0.0
@@ -34,3 +37,11 @@ repos:
   rev: 0.37.1
   hooks:
     - id: check-github-workflows
+- repo: https://github.com/hukkin/mdformat
+  rev: 1.0.0
+  hooks:
+  - id: mdformat
+- repo: https://github.com/fsfe/reuse-tool
+  rev: v6.2.0
+  hooks:
+  - id: reuse

.yamllint

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 extends: default
 
 rules:

AUTHORS.md

@@ -0,0 +1,11 @@
+<!--
+SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+SPDX-License-Identifier: GPL-3.0-or-later
+-->
+
+# Authors
+
+- [Toon Verstraelen](https://github.com/tovrstra):
+  Associate professor at [Ghent University](https://www.ugent.be/),
+  member of the [Center for Molecular Modeling](https://molmod.ugent.be/).
+  ORCID: [0000-0001-9288-5608](https://orcid.org/0000-0001-9288-5608)

README.md

@@ -1,3 +1,8 @@
+<!--
+SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+SPDX-License-Identifier: GPL-3.0-or-later
+-->
+
 # Tiny DFT
 
 Tiny DFT is a minimalistic atomic Density Functional Theory (DFT) code, mainly for educational purposes.
@@ -125,7 +130,7 @@ In order of increasing difficulty:
 
    In ZORA, the following operator should be added to the Hamiltonian:
 
-   ![t_{ab} = \int (\nabla \chi_a) (\nabla \chi_b) \frac{v_{KS}(\mathbf{r})}{4/\alpha^2 - 2v_{KS}(\mathbf{r})} \mathrm{d}\mathbf{r}](zora.png)
+   ![t_{ab} = nt (abla hi_a) (abla hi_b) rac{v_{KS}(athbf{r})}{4/lpha^2 - 2v_{KS}(athbf{r})} athrm{d}athbf{r}](zora.png)
 
    where the first factors are the gradients of the basis functions (similar to the kinetic energy operator).
    The Kohn-Sham potential from the previous outer iteration can be used.
@@ -183,7 +188,7 @@ of `z`, to make them more self-explaining and to comply with good practices.
 - `occups`: Occupation numbers
 - `olp`: Overlap integrals
 - `orb_u`: Orbital divided by r: U = R/r
-- `orb_r`: Orbital: R = U*r
+- `orb_r`: Orbital: R = U\*r
 - `priqn`: Primary quantum numbers
 - `rho`: Electron density on grid points
 - `vhartree`: Hartree potential, i.e. minus classical electrostatic potential

REUSE.toml

@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+version = 1
+
+[[annotations]]
+path = [
+    "zora.png",
+    "tests/test_tiny*/test_*.csv",
+]
+precedence = "override"
+SPDX-FileCopyrightText = "© 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>"
+SPDX-License-Identifier = "GPL-3.0-or-later"

pyproject.toml

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 [build-system]
 requires = ["setuptools>=65.0", "setuptools_scm[toml]>=7.1.0"]
 build-backend = "setuptools.build_meta"
@@ -41,7 +44,8 @@ dev = [
     "pytest-cov",
     "pytest-xdist",
     "pytest-regressions",
-    "pandas"
+    "pandas",
+    "reuse",
 ]
 
 [project.scripts]

src/tinydft/__init__.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2024 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Tiny DFT is a minimalistic atomic DFT implementation.
 
 It only supports closed-shell calculations with pure local (not even semi-local)

src/tinydft/atom.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2024 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Utilities for setting up atomic calculations.
 
 This is used by the demos and the unit tests.

src/tinydft/basis.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2024 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Radial orbital basis of Gaussian primitives and their integrals for TinyDFT."""
 
 from functools import wraps

src/tinydft/demo_evn.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2024 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Plot the energy as function of number of electrons for Carbon: N = 0 to 6."""
 
 import matplotlib.pyplot as plt

src/tinydft/demo_mendelejev.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2024 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Compute atomic DFT results for a series of elements."""
 
 import matplotlib.pyplot as plt

src/tinydft/dft.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2024 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """DFT main routines."""
 
 import autograd.numpy as agnp

src/tinydft/grid.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2024 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Tiny numerical integration library for Tiny DFT."""
 
 from collections.abc import Callable

tests/conftest.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2023 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Configuration of pytest."""
 
 import pytest

tests/test_tinybasis.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2023 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Unit tests for Tiny DFT."""
 
 import numpy as np

tests/test_tinydft.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2023 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Unit tests for Tiny DFT."""
 
 import numpy as np

tests/test_tinygrid.py

@@ -1,21 +1,5 @@
-# Tiny DFT is a minimalistic atomic DFT implementation.
-# Copyright (C) 2023 The Tiny DFT Development Team
-#
-# This file is part of Tiny DFT.
-#
-# Tiny DFT is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Tiny DFT is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-# --
+# SPDX-FileCopyrightText: © 2023 Tiny DFT Development Team <https://github.com/molmod/acid/blob/main/AUTHORS.md>
+# SPDX-License-Identifier: GPL-3.0-or-later
 """Unit tests for Tiny Grid."""
 
 import numpy as np