Merge branch 'rename' into 'main'

Renamed to gext.

See merge request !3

.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

README.md

-![CI_Badge](https://gitlab.mathematik.uni-stuttgart.de/nottolme/grext/badges/main/pipeline.svg)
-![Pylint Badge](https://gitlab.mathematik.uni-stuttgart.de/nottolme/grext/-/jobs/artifacts/main/raw/public/pylint_badge.svg?job=lint)
-![Coverage Badge](https://gitlab.mathematik.uni-stuttgart.de/nottolme/grext/-/jobs/artifacts/main/raw/public/coverage.svg?job=coverage)
+![CI_Badge](https://gitlab.mathematik.uni-stuttgart.de/nottolme/gext/badges/main/pipeline.svg)
+![Pylint Badge](https://gitlab.mathematik.uni-stuttgart.de/nottolme/gext/-/jobs/artifacts/main/raw/public/pylint_badge.svg?job=lint)
+![Coverage Badge](https://gitlab.mathematik.uni-stuttgart.de/nottolme/gext/-/jobs/artifacts/main/raw/public/coverage.svg?job=coverage)
 
-# 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:
 

grext/__init__.py → gext/__init__.py

-"""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

setup.py

 from setuptools import setup, find_packages
 
 setup(
-    name="grext",
+    name="gext",
     version="0.5.0",
     packages=find_packages(),
     install_requires=["numpy", "scipy"],

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():
 

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

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],

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