From fc7f56eb1f9961938f805ea87e61cfcf7f4c1a95 Mon Sep 17 00:00:00 2001
From: liu-687 <liu687@163.com>
Date: Mon, 29 Jun 2026 15:37:15 +0800
Subject: [PATCH 1/2] feat: add pip installation support with optional
 torch-scatter dependency

- Move torch-scatter from core dependencies to optional extra 'scatter'
- Add lazy import in grid_int.py with helpful error message for LDOS users
- Add conditional pytest skip markers for scatter-dependent tests
- Create requirements.txt / requirements-dev.txt / requirements-full.txt
- Update CI workflow to install scatter extra
- Update README and docs with pip installation instructions

BREAKING CHANGE: torch-scatter is no longer installed by default.
Users needing LDOS calculations should install with pip install dftio[scatter]
---
 .github/workflows/test.yml |   2 +-
 README.md                  |  19 ++-
 dftio/op/grid_int.py       |  12 +-
 docs/installation.md       |  26 +++-
 install.sh                 |   4 +-
 pyproject.toml             |  12 +-
 requirements-dev.txt       |   6 +
 requirements-full.txt      |   3 +
 requirements.txt           |  14 ++
 test/test_grid_int.py      |   9 ++
 test/test_ldos.py          |   9 ++
 uv.lock                    | 277 ++++++++++++++++++++-----------------
 12 files changed, 251 insertions(+), 142 deletions(-)
 create mode 100644 requirements-dev.txt
 create mode 100644 requirements-full.txt
 create mode 100644 requirements.txt

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3c3f514..0306949 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -25,7 +25,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        uv sync --group dev
+        uv sync --group dev --extra scatter
 
     - name: Run tests
       run: |
diff --git a/README.md b/README.md
index ead0025..b69983d 100644
--- a/README.md
+++ b/README.md
@@ -39,13 +39,28 @@ uv sync
 uv sync --find-links https://data.pyg.org/whl/torch-2.5.0+cu121.html
 ```
 
-### Using pip (from PyPI - coming soon)
+### Using pip
 
 ```bash
+# Basic install (all core features except grid integration / LDOS)
 pip install dftio
+
+# Install with grid integration support (LDOS calculations)
+pip install "dftio[scatter]" -f https://data.pyg.org/whl/torch-2.5.0+cpu.html
+
+# Install with all optional dependencies (includes scatter + dev tools)
+pip install "dftio[full]" -f https://data.pyg.org/whl/torch-2.5.0+cpu.html
+
+# For GPU users, replace 'cpu' with your CUDA version (e.g., cu121)
+pip install "dftio[scatter]" -f https://data.pyg.org/whl/torch-2.5.0+cu121.html
+
+# Or install from requirements files
+pip install -r requirements.txt          # core only
+pip install -r requirements-full.txt     # core + scatter
+pip install -r requirements-dev.txt      # core + dev tools
 ```
 
-**Note**: dftio depends on `torch-scatter` which requires special handling. The install script automatically manages this for you.
+**Note**: The `scatter` extra installs `torch-scatter`, which is only needed for LDOS (Local Density of States) calculations via `dftio.calc.ldos`. All other dftio functionality (parsing, data structures, CLI) works without it.
 
 ## Supports
 
diff --git a/dftio/op/grid_int.py b/dftio/op/grid_int.py
index 0e6b4cc..2ff497b 100644
--- a/dftio/op/grid_int.py
+++ b/dftio/op/grid_int.py
@@ -1,7 +1,6 @@
 from ..datastruct import PrimitiveFieldsNeighborList
 import torch
 import ase.data as data
-from torch_scatter import scatter_sum
 import numpy as np
 
 atomic_numbers_r = dict(zip(data.atomic_numbers.values(), data.atomic_numbers.keys()))
@@ -32,7 +31,16 @@ def __init__(self, atomic_numbers, pbc, cell, coordinates, grids, atomic_basis,
         self.cell_shift = torch.from_numpy(np.concatenate(self.cell_shift, axis=0, dtype=np.int32))
 
     def integrate(self, weights=None):
-        
+        try:
+            from torch_scatter import scatter_sum
+        except ImportError:
+            raise ImportError(
+                "torch-scatter is required for grid integration (LDOS calculations). "
+                "Install it with: pip install torch-scatter -f https://data.pyg.org/whl/torch-2.5.0+cpu.html\n"
+                "Or: pip install dftio[scatter] -f https://data.pyg.org/whl/torch-2.5.0+cpu.html\n"
+                "Or: pip install dftio[full] -f https://data.pyg.org/whl/torch-2.5.0+cpu.html"
+            )
+
         ngrid = len(self.grids)
         dtype = weights.dtype if weights is not None else self.dtype
         results = torch.zeros(ngrid, dtype=dtype)
diff --git a/docs/installation.md b/docs/installation.md
index 55dc088..7263122 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -38,11 +38,27 @@ If you prefer to manage the installation yourself, you can use `uv`.
     ```
     Including the `--group dev` flag will also install the packages required for testing and building documentation.
 
-## Using pip (from PyPI)
+## Using pip
 
-*Coming soon. Once `dftio` is published to the Python Package Index (PyPI), you will be able to install it directly with `pip`.*
+You can install `dftio` directly with pip:
 
 ```bash
-# This will be enabled in a future release
-# pip install dftio
-```
\ No newline at end of file
+# Basic install (all core features except grid integration / LDOS)
+pip install dftio
+
+# Install with grid integration support for LDOS calculations
+pip install "dftio[scatter]" -f https://data.pyg.org/whl/torch-2.5.0+cpu.html
+
+# Install with all optional dependencies (scatter + dev tools)
+pip install "dftio[full]" -f https://data.pyg.org/whl/torch-2.5.0+cpu.html
+
+# For GPU users, replace 'cpu' with your CUDA version (e.g., cu121, cu124)
+pip install "dftio[scatter]" -f https://data.pyg.org/whl/torch-2.5.0+cu121.html
+
+# Or install from requirements files
+pip install -r requirements.txt          # core only
+pip install -r requirements-full.txt     # core + scatter
+pip install -r requirements-dev.txt      # core + dev tools
+```
+
+> **Note:** The `scatter` extra installs `torch-scatter`, which is only needed for LDOS (Local Density of States) calculations via `dftio.calc.ldos`. All other dftio functionality works without it.
\ No newline at end of file
diff --git a/install.sh b/install.sh
index aee3fc9..aa826e3 100755
--- a/install.sh
+++ b/install.sh
@@ -45,9 +45,9 @@ if ! command -v uv &> /dev/null; then
 fi
 
 # Sync dependencies with the specified find-links
-echo "Installing dftio with torch_scatter ($VARIANT version)..."
+echo "Installing dftio with torch_scatter ($VARIANT version) [scatter extra]..."
 echo "Using Python: $(which python)"
-uv sync --python $(which python) --find-links "$FIND_LINKS_URL"
+uv sync --python $(which python) --extra scatter --find-links "$FIND_LINKS_URL"
 
 echo ""
 echo "✅ Installation complete!"
diff --git a/pyproject.toml b/pyproject.toml
index fc0ab25..1df0754 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,6 @@ dependencies = [
     "lmdb==1.4.1",
     "sisl>=0.14.3",
     "dpdata>=0.2.20",
-    "torch-scatter==2.1.2",
     "tqdm",
 ]
 
@@ -35,6 +34,17 @@ dev = [
     "sphinx-autodoc-typehints",
 ]
 
+[project.optional-dependencies]
+scatter = ["torch-scatter==2.1.2"]
+full = ["dftio[scatter]"]
+dev = [
+    "pytest>=7.2.0",
+    "pytest-order==1.2.0",
+    "pytest-cov",
+    "jupyter-book>=0.15,<1.0",
+    "sphinx-autodoc-typehints",
+]
+
 [project.scripts]
 dftio = "dftio.__main__:main"
 
diff --git a/requirements-dev.txt b/requirements-dev.txt
new file mode 100644
index 0000000..bd08d74
--- /dev/null
+++ b/requirements-dev.txt
@@ -0,0 +1,6 @@
+-r requirements.txt
+pytest>=7.2.0
+pytest-order==1.2.0
+pytest-cov
+jupyter-book>=0.15,<1.0
+sphinx-autodoc-typehints
diff --git a/requirements-full.txt b/requirements-full.txt
new file mode 100644
index 0000000..ac1c596
--- /dev/null
+++ b/requirements-full.txt
@@ -0,0 +1,3 @@
+--find-links https://data.pyg.org/whl/torch-2.5.0+cpu.html
+-r requirements.txt
+torch-scatter==2.1.2
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..d94c09d
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,14 @@
+numpy
+scipy>=1.11,<1.12
+matplotlib
+torch>=2.0.0,<2.5.1
+ase
+pyyaml
+future
+dargs==0.4.4
+e3nn>=0.5.1
+h5py>=3.7.0,<3.11.0,!=3.10.0
+lmdb==1.4.1
+sisl>=0.14.3
+dpdata>=0.2.20
+tqdm
diff --git a/test/test_grid_int.py b/test/test_grid_int.py
index c17f7a9..ccd2d30 100644
--- a/test/test_grid_int.py
+++ b/test/test_grid_int.py
@@ -5,6 +5,14 @@
 from dftio.datastruct import AtomicBasis
 import ase.data as data
 
+try:
+    import torch_scatter  # noqa: F401
+    _SCATTER_AVAILABLE = True
+except ImportError:
+    _SCATTER_AVAILABLE = False
+
+needs_scatter = pytest.mark.skipif(not _SCATTER_AVAILABLE, reason="torch-scatter not installed")
+
 class MockAtomicBasis:
     def __init__(self, atomic_numbers):
         self.atomic_numbers = atomic_numbers
@@ -44,6 +52,7 @@ def test_single_grid_integrator_init(mock_atomic_basis):
     assert sgi.coordinates.shape == (1, 3)
     assert sgi.grids.shape == (1, 3)
 
+@needs_scatter
 def test_integrate(mock_atomic_basis):
     """Test integrate method."""
     atomic_numbers = [1]
diff --git a/test/test_ldos.py b/test/test_ldos.py
index b04fd4a..c83348a 100644
--- a/test/test_ldos.py
+++ b/test/test_ldos.py
@@ -4,6 +4,14 @@
 from dftio.calc.ldos import LDOS
 from dftio.datastruct import AtomicBasis
 
+try:
+    import torch_scatter  # noqa: F401
+    _SCATTER_AVAILABLE = True
+except ImportError:
+    _SCATTER_AVAILABLE = False
+
+needs_scatter = pytest.mark.skipif(not _SCATTER_AVAILABLE, reason="torch-scatter not installed")
+
 class MockAtomicBasis:
     def __init__(self, atomic_numbers):
         self.atomic_numbers = atomic_numbers
@@ -40,6 +48,7 @@ def test_ldos_init(mock_atomic_basis):
     assert ldos.natoms == 1
     assert ldos.nspin == 2
 
+@needs_scatter
 def test_ldos_get(mock_atomic_basis):
     """Test LDOS get method."""
     atomic_numbers = [1]
diff --git a/uv.lock b/uv.lock
index 5063123..3500fdb 100644
--- a/uv.lock
+++ b/uv.lock
@@ -120,7 +120,7 @@ name = "cffi"
 version = "2.0.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "pycparser", marker = "implementation_name != 'PyPy'" },
+    { name = "pycparser" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/eb/56/b1ba7935a17738ae8453301356628e8147c79dbb825bcbc73dc7401f9846/cffi-2.0.0.tar.gz", hash = "sha256:44d1b5909021139fe36001ae048dbdde8214afa20200eda0f64c068cac5d5529", size = 523588, upload-time = "2025-09-08T23:24:04.541Z" }
 wheels = [
@@ -257,7 +257,7 @@ resolution-markers = [
     "(python_full_version < '3.10' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version < '3.10' and platform_machine != 'AMD64' and sys_platform == 'win32') or (python_full_version < '3.10' and platform_python_implementation != 'CPython' and sys_platform == 'linux') or (python_full_version < '3.10' and platform_python_implementation != 'CPython' and sys_platform == 'win32') or (python_full_version < '3.10' and sys_platform != 'linux' and sys_platform != 'win32')",
 ]
 dependencies = [
-    { name = "colorama", marker = "python_full_version < '3.10' and sys_platform == 'win32'" },
+    { name = "colorama", marker = "sys_platform == 'win32'" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/b9/2e/0090cbf739cee7d23781ad4b89a9894a41538e4fcf4c31dcdd705b78eb8b/click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a", size = 226593, upload-time = "2024-12-21T18:38:44.339Z" }
 wheels = [
@@ -277,7 +277,7 @@ resolution-markers = [
     "(python_full_version == '3.10.*' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version == '3.10.*' and platform_machine != 'AMD64' and sys_platform == 'win32') or (python_full_version == '3.10.*' and platform_python_implementation != 'CPython' and sys_platform == 'linux') or (python_full_version == '3.10.*' and platform_python_implementation != 'CPython' and sys_platform == 'win32') or (python_full_version == '3.10.*' and sys_platform != 'linux' and sys_platform != 'win32')",
 ]
 dependencies = [
-    { name = "colorama", marker = "python_full_version >= '3.10' and sys_platform == 'win32'" },
+    { name = "colorama", marker = "sys_platform == 'win32'" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/3d/fa/656b739db8587d7b5dfa22e22ed02566950fbfbcdc20311993483657a5c0/click-8.3.1.tar.gz", hash = "sha256:12ff4785d337a1bb490bb7e9c2b1ee5da3112e94a8622f26a6c77f5d2fc6842a", size = 295065, upload-time = "2025-11-15T20:45:42.706Z" }
 wheels = [
@@ -311,7 +311,7 @@ resolution-markers = [
     "(python_full_version < '3.10' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version < '3.10' and platform_machine != 'AMD64' and sys_platform == 'win32') or (python_full_version < '3.10' and platform_python_implementation != 'CPython' and sys_platform == 'linux') or (python_full_version < '3.10' and platform_python_implementation != 'CPython' and sys_platform == 'win32') or (python_full_version < '3.10' and sys_platform != 'linux' and sys_platform != 'win32')",
 ]
 dependencies = [
-    { name = "numpy", marker = "python_full_version < '3.10'" },
+    { name = "numpy" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/f5/f6/31a8f28b4a2a4fa0e01085e542f3081ab0588eff8e589d39d775172c9792/contourpy-1.3.0.tar.gz", hash = "sha256:7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4", size = 13464370, upload-time = "2024-08-27T21:00:03.328Z" }
 wheels = [
@@ -372,7 +372,7 @@ resolution-markers = [
     "(python_full_version == '3.10.*' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version == '3.10.*' and platform_machine != 'AMD64' and sys_platform == 'win32') or (python_full_version == '3.10.*' and platform_python_implementation != 'CPython' and sys_platform == 'linux') or (python_full_version == '3.10.*' and platform_python_implementation != 'CPython' and sys_platform == 'win32') or (python_full_version == '3.10.*' and sys_platform != 'linux' and sys_platform != 'win32')",
 ]
 dependencies = [
-    { name = "numpy", marker = "python_full_version == '3.10.*'" },
+    { name = "numpy" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/66/54/eb9bfc647b19f2009dd5c7f5ec51c4e6ca831725f1aea7a993034f483147/contourpy-1.3.2.tar.gz", hash = "sha256:b6945942715a034c671b7fc54f9588126b0b8bf23db2696e3ca8328f3ff0ab54", size = 13466130, upload-time = "2025-04-15T17:47:53.79Z" }
 wheels = [
@@ -425,7 +425,7 @@ resolution-markers = [
     "(python_full_version == '3.11.*' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version == '3.11.*' and platform_machine != 'AMD64' and sys_platform == 'win32') or (python_full_version == '3.11.*' and platform_python_implementation != 'CPython' and sys_platform == 'linux') or (python_full_version == '3.11.*' and platform_python_implementation != 'CPython' and sys_platform == 'win32') or (python_full_version == '3.11.*' and sys_platform != 'linux' and sys_platform != 'win32')",
 ]
 dependencies = [
-    { name = "numpy", marker = "python_full_version >= '3.11'" },
+    { name = "numpy" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/58/01/1253e6698a07380cd31a736d248a3f2a50a7c88779a1813da27503cadc2a/contourpy-1.3.3.tar.gz", hash = "sha256:083e12155b210502d0bca491432bb04d56dc3432f95a979b429f2848c3dbe880", size = 13466174, upload-time = "2025-07-26T12:03:12.549Z" }
 wheels = [
@@ -523,7 +523,7 @@ wheels = [
 
 [package.optional-dependencies]
 toml = [
-    { name = "tomli", marker = "python_full_version < '3.10'" },
+    { name = "tomli" },
 ]
 
 [[package]]
@@ -583,7 +583,7 @@ wheels = [
 
 [package.optional-dependencies]
 toml = [
-    { name = "tomli", marker = "python_full_version >= '3.10' and python_full_version <= '3.11'" },
+    { name = "tomli", marker = "python_full_version <= '3.11'" },
 ]
 
 [[package]]
@@ -659,9 +659,25 @@ dependencies = [
     { name = "scipy" },
     { name = "sisl" },
     { name = "torch" },
+    { name = "tqdm" },
+]
+
+[package.optional-dependencies]
+dev = [
+    { name = "jupyter-book" },
+    { name = "pytest", version = "8.4.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
+    { name = "pytest", version = "9.0.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },
+    { name = "pytest-cov" },
+    { name = "pytest-order" },
+    { name = "sphinx-autodoc-typehints" },
+]
+full = [
+    { name = "torch-scatter", version = "2.1.2", source = { registry = "https://data.pyg.org/whl/torch-2.5.0+cpu.html" }, marker = "(platform_machine != 'x86_64' and sys_platform == 'linux') or (platform_machine != 'AMD64' and sys_platform == 'win32') or (platform_python_implementation != 'CPython' and sys_platform == 'linux') or (platform_python_implementation != 'CPython' and sys_platform == 'win32') or (sys_platform != 'linux' and sys_platform != 'win32')" },
+    { name = "torch-scatter", version = "2.1.2+pt25cpu", source = { registry = "https://data.pyg.org/whl/torch-2.5.0+cpu.html" }, marker = "(platform_machine == 'x86_64' and platform_python_implementation == 'CPython' and sys_platform == 'linux') or (platform_machine == 'AMD64' and platform_python_implementation == 'CPython' and sys_platform == 'win32')" },
+]
+scatter = [
     { name = "torch-scatter", version = "2.1.2", source = { registry = "https://data.pyg.org/whl/torch-2.5.0+cpu.html" }, marker = "(platform_machine != 'x86_64' and sys_platform == 'linux') or (platform_machine != 'AMD64' and sys_platform == 'win32') or (platform_python_implementation != 'CPython' and sys_platform == 'linux') or (platform_python_implementation != 'CPython' and sys_platform == 'win32') or (sys_platform != 'linux' and sys_platform != 'win32')" },
     { name = "torch-scatter", version = "2.1.2+pt25cpu", source = { registry = "https://data.pyg.org/whl/torch-2.5.0+cpu.html" }, marker = "(platform_machine == 'x86_64' and platform_python_implementation == 'CPython' and sys_platform == 'linux') or (platform_machine == 'AMD64' and platform_python_implementation == 'CPython' and sys_platform == 'win32')" },
-    { name = "tqdm" },
 ]
 
 [package.dev-dependencies]
@@ -678,20 +694,27 @@ dev = [
 requires-dist = [
     { name = "ase" },
     { name = "dargs", specifier = "==0.4.4" },
+    { name = "dftio", extras = ["scatter"], marker = "extra == 'full'" },
     { name = "dpdata", specifier = ">=0.2.20" },
     { name = "e3nn", specifier = ">=0.5.1" },
     { name = "future" },
     { name = "h5py", specifier = ">=3.7.0,!=3.10.0,<3.11.0" },
+    { name = "jupyter-book", marker = "extra == 'dev'", specifier = ">=0.15,<1.0" },
     { name = "lmdb", specifier = "==1.4.1" },
     { name = "matplotlib" },
     { name = "numpy" },
+    { name = "pytest", marker = "extra == 'dev'", specifier = ">=7.2.0" },
+    { name = "pytest-cov", marker = "extra == 'dev'" },
+    { name = "pytest-order", marker = "extra == 'dev'", specifier = "==1.2.0" },
     { name = "pyyaml" },
     { name = "scipy", specifier = ">=1.11,<1.12" },
     { name = "sisl", specifier = ">=0.14.3" },
+    { name = "sphinx-autodoc-typehints", marker = "extra == 'dev'" },
     { name = "torch", specifier = ">=2.0.0,<2.5.1" },
-    { name = "torch-scatter", specifier = "==2.1.2" },
+    { name = "torch-scatter", marker = "extra == 'scatter'", specifier = "==2.1.2" },
     { name = "tqdm" },
 ]
+provides-extras = ["scatter", "full", "dev"]
 
 [package.metadata.requires-dev]
 dev = [
@@ -747,7 +770,7 @@ name = "exceptiongroup"
 version = "1.3.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "typing-extensions", marker = "python_full_version < '3.11'" },
+    { name = "typing-extensions" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/0b/9f/a65090624ecf468cdca03533906e7c69ed7588582240cfe7cc9e770b50eb/exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88", size = 29749, upload-time = "2025-05-10T17:42:51.123Z" }
 wheels = [
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+    { name = "pandas" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/19/ec/e50d833518f10b0c24feb184b209bb6856f25b919ba8c1f89678b930b1cd/xarray-2025.6.1.tar.gz", hash = "sha256:a84f3f07544634a130d7dc615ae44175419f4c77957a7255161ed99c69c7c8b0", size = 3003185, upload-time = "2025-06-12T03:04:09.099Z" }
 wheels = [
@@ -3623,9 +3642,9 @@ resolution-markers = [
     "(python_full_version == '3.11.*' and platform_machine != 'x86_64' and sys_platform == 'linux') or (python_full_version == '3.11.*' and platform_machine != 'AMD64' and sys_platform == 'win32') or (python_full_version == '3.11.*' and platform_python_implementation != 'CPython' and sys_platform == 'linux') or (python_full_version == '3.11.*' and platform_python_implementation != 'CPython' and sys_platform == 'win32') or (python_full_version == '3.11.*' and sys_platform != 'linux' and sys_platform != 'win32')",
 ]
 dependencies = [
-    { name = "numpy", marker = "python_full_version >= '3.11'" },
-    { name = "packaging", marker = "python_full_version >= '3.11'" },
-    { name = "pandas", marker = "python_full_version >= '3.11'" },
+    { name = "numpy" },
+    { name = "packaging" },
+    { name = "pandas" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/39/ad/b072c970cfb2e2724509bf1e8d7fb4084cc186a90d486c9ac4a48ff83186/xarray-2025.11.0.tar.gz", hash = "sha256:d7a4aa4500edbfd60676b1613db97da309ab144cac0bcff0cbf483c61c662af1", size = 3072276, upload-time = "2025-11-17T16:12:09.167Z" }
 wheels = [

From f706c722df2b7646d94c656134311efa3db34097 Mon Sep 17 00:00:00 2001
From: liu-687 <liu687@163.com>
Date: Mon, 29 Jun 2026 16:01:30 +0800
Subject: [PATCH 2/2] fix: address CodeRabbit review - exception chaining, full
 extra consistency, and test coverage

- Use raise ImportError(...) from err to preserve original exception context
- Rework error message to avoid hardcoding CPU wheel URL; prioritize dftio[scatter] extra
- Fix full extra to include both scatter and dev, matching documentation
- Update requirements-full.txt to include dev dependencies
- Quote /Users/liu687/anaconda3/bin/python in install.sh to handle paths with spaces
- Add test_integrate_without_scatter_raises_error to cover no-scatter path
---
 README.md             |  2 +-
 dftio/op/grid_int.py  | 12 +++++++-----
 docs/installation.md  |  2 +-
 install.sh            |  2 +-
 pyproject.toml        |  2 +-
 requirements-full.txt |  1 +
 test/test_grid_int.py | 38 ++++++++++++++++++++++++++++++++++++++
 uv.lock               |  7 +++++++
 8 files changed, 57 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index b69983d..535e4bf 100644
--- a/README.md
+++ b/README.md
@@ -56,7 +56,7 @@ pip install "dftio[scatter]" -f https://data.pyg.org/whl/torch-2.5.0+cu121.html
 
 # Or install from requirements files
 pip install -r requirements.txt          # core only
-pip install -r requirements-full.txt     # core + scatter
+pip install -r requirements-full.txt     # core + scatter + dev
 pip install -r requirements-dev.txt      # core + dev tools
 ```
 
diff --git a/dftio/op/grid_int.py b/dftio/op/grid_int.py
index 2ff497b..97691b0 100644
--- a/dftio/op/grid_int.py
+++ b/dftio/op/grid_int.py
@@ -33,13 +33,15 @@ def __init__(self, atomic_numbers, pbc, cell, coordinates, grids, atomic_basis,
     def integrate(self, weights=None):
         try:
             from torch_scatter import scatter_sum
-        except ImportError:
+        except ImportError as err:
             raise ImportError(
                 "torch-scatter is required for grid integration (LDOS calculations). "
-                "Install it with: pip install torch-scatter -f https://data.pyg.org/whl/torch-2.5.0+cpu.html\n"
-                "Or: pip install dftio[scatter] -f https://data.pyg.org/whl/torch-2.5.0+cpu.html\n"
-                "Or: pip install dftio[full] -f https://data.pyg.org/whl/torch-2.5.0+cpu.html"
-            )
+                "Install dftio with the scatter extra:\n"
+                "  pip install \"dftio[scatter]\" -f https://data.pyg.org/whl/torch-<version>+<variant>.html\n"
+                "Or install all optional dependencies:\n"
+                "  pip install \"dftio[full]\" -f https://data.pyg.org/whl/torch-<version>+<variant>.html\n"
+                "For detailed instructions, see: https://deepmodeling.github.io/dftio/installation.html"
+            ) from err
 
         ngrid = len(self.grids)
         dtype = weights.dtype if weights is not None else self.dtype
diff --git a/docs/installation.md b/docs/installation.md
index 7263122..6c77f41 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -57,7 +57,7 @@ pip install "dftio[scatter]" -f https://data.pyg.org/whl/torch-2.5.0+cu121.html
 
 # Or install from requirements files
 pip install -r requirements.txt          # core only
-pip install -r requirements-full.txt     # core + scatter
+pip install -r requirements-full.txt     # core + scatter + dev
 pip install -r requirements-dev.txt      # core + dev tools
 ```
 
diff --git a/install.sh b/install.sh
index aa826e3..eb138d0 100755
--- a/install.sh
+++ b/install.sh
@@ -47,7 +47,7 @@ fi
 # Sync dependencies with the specified find-links
 echo "Installing dftio with torch_scatter ($VARIANT version) [scatter extra]..."
 echo "Using Python: $(which python)"
-uv sync --python $(which python) --extra scatter --find-links "$FIND_LINKS_URL"
+uv sync --python "$(which python)" --extra scatter --find-links "$FIND_LINKS_URL"
 
 echo ""
 echo "✅ Installation complete!"
diff --git a/pyproject.toml b/pyproject.toml
index 1df0754..c09e7f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ dev = [
 
 [project.optional-dependencies]
 scatter = ["torch-scatter==2.1.2"]
-full = ["dftio[scatter]"]
+full = ["dftio[scatter]", "dftio[dev]"]
 dev = [
     "pytest>=7.2.0",
     "pytest-order==1.2.0",
diff --git a/requirements-full.txt b/requirements-full.txt
index ac1c596..72d4ecb 100644
--- a/requirements-full.txt
+++ b/requirements-full.txt
@@ -1,3 +1,4 @@
 --find-links https://data.pyg.org/whl/torch-2.5.0+cpu.html
 -r requirements.txt
+-r requirements-dev.txt
 torch-scatter==2.1.2
diff --git a/test/test_grid_int.py b/test/test_grid_int.py
index ccd2d30..b69671a 100644
--- a/test/test_grid_int.py
+++ b/test/test_grid_int.py
@@ -78,3 +78,41 @@ def test_integrate(mock_atomic_basis):
     weights = torch.tensor([1.0])
     result_w = sgi.integrate(weights=weights)
     assert result_w.shape == (1,)
+
+
+def test_integrate_without_scatter_raises_error(mock_atomic_basis, monkeypatch):
+    """Test that integrate() raises helpful ImportError when torch-scatter is not installed."""
+    import builtins
+    import sys
+
+    # Remove torch_scatter from sys.modules so cached import is bypassed
+    sys.modules.pop("torch_scatter", None)
+    sys.modules.pop("torch_scatter.scatter_sum", None)
+
+    # Store the original import function
+    _original_import = builtins.__import__
+
+    def _mock_import(name, globals=None, locals=None, fromlist=(), level=0):
+        if name == "torch_scatter":
+            raise ModuleNotFoundError("No module named 'torch_scatter'")
+        return _original_import(name, globals, locals, fromlist, level)
+
+    monkeypatch.setattr(builtins, "__import__", _mock_import)
+
+    atomic_numbers = [1]
+    pbc = [True, True, True]
+    cell = np.eye(3)
+    coordinates = np.array([[0.0, 0.0, 0.0]])
+    grids = np.array([[0.1, 0.1, 0.1]])
+
+    sgi = SingleGridIntegrator(
+        atomic_numbers=atomic_numbers,
+        pbc=pbc,
+        cell=cell,
+        coordinates=coordinates,
+        grids=grids,
+        atomic_basis={"H": mock_atomic_basis},
+    )
+
+    with pytest.raises(ImportError, match="torch-scatter is required"):
+        sgi.integrate()
diff --git a/uv.lock b/uv.lock
index 3500fdb..4334c06 100644
--- a/uv.lock
+++ b/uv.lock
@@ -672,6 +672,12 @@ dev = [
     { name = "sphinx-autodoc-typehints" },
 ]
 full = [
+    { name = "jupyter-book" },
+    { name = "pytest", version = "8.4.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
+    { name = "pytest", version = "9.0.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },
+    { name = "pytest-cov" },
+    { name = "pytest-order" },
+    { name = "sphinx-autodoc-typehints" },
     { name = "torch-scatter", version = "2.1.2", source = { registry = "https://data.pyg.org/whl/torch-2.5.0+cpu.html" }, marker = "(platform_machine != 'x86_64' and sys_platform == 'linux') or (platform_machine != 'AMD64' and sys_platform == 'win32') or (platform_python_implementation != 'CPython' and sys_platform == 'linux') or (platform_python_implementation != 'CPython' and sys_platform == 'win32') or (sys_platform != 'linux' and sys_platform != 'win32')" },
     { name = "torch-scatter", version = "2.1.2+pt25cpu", source = { registry = "https://data.pyg.org/whl/torch-2.5.0+cpu.html" }, marker = "(platform_machine == 'x86_64' and platform_python_implementation == 'CPython' and sys_platform == 'linux') or (platform_machine == 'AMD64' and platform_python_implementation == 'CPython' and sys_platform == 'win32')" },
 ]
@@ -694,6 +700,7 @@ dev = [
 requires-dist = [
     { name = "ase" },
     { name = "dargs", specifier = "==0.4.4" },
+    { name = "dftio", extras = ["dev"], marker = "extra == 'full'" },
     { name = "dftio", extras = ["scatter"], marker = "extra == 'full'" },
     { name = "dpdata", specifier = ">=0.2.20" },
     { name = "e3nn", specifier = ">=0.5.1" },