From a283e0c3ec0bc6ce7187aa7bebe541615f32daa3 Mon Sep 17 00:00:00 2001
From: Michele Nottoli <michele.nottoli@gmail.com>
Date: Tue, 24 Oct 2023 17:25:37 +0200
Subject: [PATCH] Renamed to gext.
---
.gitlab-ci.yml | 4 ++--
README.md | 14 +++++++-------
{grext => gext}/__init__.py | 2 +-
{grext => gext}/buffer.py | 0
{grext => gext}/descriptors.py | 0
{grext => gext}/fitting.py | 0
{grext => gext}/grassmann.py | 0
{grext => gext}/main.py | 0
setup.py | 2 +-
tests/test_buffer.py | 2 +-
tests/test_descriptor_fitting.py | 18 +++++++++---------
tests/test_extrapolation.py | 6 +++---
tests/test_grassmann.py | 8 ++++----
13 files changed, 28 insertions(+), 28 deletions(-)
rename {grext => gext}/__init__.py (56%)
rename {grext => gext}/buffer.py (100%)
rename {grext => gext}/descriptors.py (100%)
rename {grext => gext}/fitting.py (100%)
rename {grext => gext}/grassmann.py (100%)
rename {grext => gext}/main.py (100%)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0b1a74a..98f56a2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,7 +5,7 @@ stages:
variables:
PYLINT_CMD: >
- (pylint grext --exit-zero > pylint.out) || true
+ (pylint gext --exit-zero > pylint.out) || true
PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
default:
@@ -35,7 +35,7 @@ lint:
stage: lint
script:
- mkdir -p ./public
- - pylint grext --exit-zero | tee pylint.out
+ - pylint gext --exit-zero | tee pylint.out
- score=$(sed -n 's/^Your code has been rated at \([-0-9.]*\)\/.*/\1/p' pylint.out)
- echo "Pylint score was $score"
- anybadge --value=$score --file=public/pylint_badge.svg pylint
diff --git a/README.md b/README.md
index 77532e9..67fb2ae 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
-
-
-
+
+
+
-# grext: Grassmann Extrapolation Library
+# gext: Grassmann Extrapolation Library
This library define an `Extrapolator` class to be used for providing guesses in QM simulations. It is designed in such a way that requires minimum modifications on the QM code side.
@@ -15,10 +15,10 @@ The library can be installed using `pip`:
## Usage
The usage requires only four lines of code:
- - Add an import statement `import grext`.
+ - Add an import statement `import gext`.
- Initialize a new extrapolator by inserting the line:
- `extrapolator = grext.Extrapolator(nelectrons, nbasis, natoms)`.
+ `extrapolator = gext.Extrapolator(nelectrons, nbasis, natoms)`.
**Note:** the extrapolator can be finely controlled by passing additional keyword arguments. This is explained in the next section.
- When a new SCF calculation has been performed, load the resulting data in the extrapolator by running:
@@ -39,7 +39,7 @@ The usage requires only four lines of code:
## Further options
The behavior can be finely controlled by passing additional keyword arguments to the
-`grext.Extrapolator()` constructor. **Note: many options are not yet implemented.**
+`gext.Extrapolator()` constructor. **Note: many options are not yet implemented.**
This is an up to date list of available keyword options:
diff --git a/grext/__init__.py b/gext/__init__.py
similarity index 56%
rename from grext/__init__.py
rename to gext/__init__.py
index 06beea2..c0b8298 100644
--- a/grext/__init__.py
+++ b/gext/__init__.py
@@ -1,4 +1,4 @@
-"""The package grext provides tools for generating new guesses for the
+"""The package gext provides tools for generating new guesses for the
self consistent field in molecular dynamics simulations."""
from .main import Extrapolator
diff --git a/grext/buffer.py b/gext/buffer.py
similarity index 100%
rename from grext/buffer.py
rename to gext/buffer.py
diff --git a/grext/descriptors.py b/gext/descriptors.py
similarity index 100%
rename from grext/descriptors.py
rename to gext/descriptors.py
diff --git a/grext/fitting.py b/gext/fitting.py
similarity index 100%
rename from grext/fitting.py
rename to gext/fitting.py
diff --git a/grext/grassmann.py b/gext/grassmann.py
similarity index 100%
rename from grext/grassmann.py
rename to gext/grassmann.py
diff --git a/grext/main.py b/gext/main.py
similarity index 100%
rename from grext/main.py
rename to gext/main.py
diff --git a/setup.py b/setup.py
index 718abde..aa7212a 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
from setuptools import setup, find_packages
setup(
- name="grext",
+ name="gext",
version="0.5.0",
packages=find_packages(),
install_requires=["numpy", "scipy"],
diff --git a/tests/test_buffer.py b/tests/test_buffer.py
index 659c5bd..81f495d 100644
--- a/tests/test_buffer.py
+++ b/tests/test_buffer.py
@@ -4,7 +4,7 @@ import sys
import numpy as np
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
-from grext.buffer import CircularBuffer
+from gext.buffer import CircularBuffer
def test_buffer():
diff --git a/tests/test_descriptor_fitting.py b/tests/test_descriptor_fitting.py
index c673bce..e7d84b3 100644
--- a/tests/test_descriptor_fitting.py
+++ b/tests/test_descriptor_fitting.py
@@ -4,10 +4,10 @@ import sys
import numpy as np
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
-import grext
-import grext.descriptors
-import grext.fitting
-import grext.grassmann
+import gext
+import gext.descriptors
+import gext.fitting
+import gext.grassmann
import utils
SMALL = 1e-10
@@ -23,7 +23,7 @@ def test_descriptor_fitting(datafile):
nframes = data["trajectory"].shape[0]
# initialize an extrapolator
- extrapolator = grext.Extrapolator(nelectrons, nbasis, natoms, nframes)
+ extrapolator = gext.Extrapolator(nelectrons, nbasis, natoms, nframes)
# load data in the extrapolator
for (coords, coeff, overlap) in zip(data["trajectory"],
@@ -37,8 +37,8 @@ def test_descriptor_fitting(datafile):
for start in range(0, 9):
vectors = descriptors[start:-1]
- fit_coefficients = grext.fitting.linear(vectors, target)
- fitted_target = grext.fitting.linear_combination(vectors, fit_coefficients)
+ fit_coefficients = gext.fitting.linear(vectors, target)
+ fitted_target = gext.fitting.linear_combination(vectors, fit_coefficients)
errors.append(np.linalg.norm(target - fitted_target, ord=np.inf))
assert errors[0] < errors[-1]
@@ -47,7 +47,7 @@ def test_descriptor_fitting(datafile):
# used for the fitting
vectors = descriptors[:-1]
vectors[0] = target
- fit_coefficients = grext.fitting.linear(vectors, target)
- fitted_target = grext.fitting.linear_combination(vectors, fit_coefficients)
+ fit_coefficients = gext.fitting.linear(vectors, target)
+ fitted_target = gext.fitting.linear_combination(vectors, fit_coefficients)
assert np.linalg.norm(target - fitted_target, ord=np.inf) < SMALL
diff --git a/tests/test_extrapolation.py b/tests/test_extrapolation.py
index 5fcb992..69914ef 100644
--- a/tests/test_extrapolation.py
+++ b/tests/test_extrapolation.py
@@ -4,8 +4,8 @@ import sys
import numpy as np
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
-import grext
-import grext.grassmann
+import gext
+import gext.grassmann
import utils
SMALL = 1e-10
@@ -26,7 +26,7 @@ def test_extrapolation(datafile):
assert n < nframes
# initialize an extrapolator
- extrapolator = grext.Extrapolator(nelectrons, nbasis, natoms, n)
+ extrapolator = gext.Extrapolator(nelectrons, nbasis, natoms, n)
# load data in the extrapolator up to index n - 1
for (coords, coeff, overlap) in zip(data["trajectory"][:n],
diff --git a/tests/test_grassmann.py b/tests/test_grassmann.py
index 1602bff..04d3fb9 100644
--- a/tests/test_grassmann.py
+++ b/tests/test_grassmann.py
@@ -4,8 +4,8 @@ import sys
import numpy as np
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
-import grext
-import grext.grassmann
+import gext
+import gext.grassmann
import utils
SMALL = 1e-10
@@ -21,7 +21,7 @@ def test_grassmann(datafile):
nframes = data["trajectory"].shape[0]
# initialize an extrapolator
- extrapolator = grext.Extrapolator(nelectrons, nbasis, natoms, nframes)
+ extrapolator = gext.Extrapolator(nelectrons, nbasis, natoms, nframes)
# load data in the extrapolator
for (coords, coeff, overlap) in zip(data["trajectory"],
@@ -44,7 +44,7 @@ def test_grassmann(datafile):
assert np.trace(d) - nelectrons < SMALL
# compute the density from the inverse Grassmann map: Exp(Log(D))
- coeff_1 = grext.grassmann.exp(gamma, c0)
+ coeff_1 = gext.grassmann.exp(gamma, c0)
d_1 = coeff_1 @ coeff_1.T
# standard check on the second density
--
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