feature merge for recent functionality

.github/workflows/python-package.yml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v3
@@ -62,3 +62,8 @@ jobs:
     - name: Test with pytest
       run: |
         pytest
+
+    - name: run jupyter notebook tests
+      run: |
+        pip install -r examples/notebooks/requirements.txt
+        pytest --nbval-lax examples/notebooks/ -v

.gitignore

@@ -1,3 +1,9 @@
+# virtual docs
+.virtual_documents/
+
+#slurm files
+*.slurm
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

README.md

@@ -28,7 +28,13 @@ The release versions of the package are hosted at [pypi.org/project/jitr/](https
 
 Various example scripts live in [`examples/`](https://github.com/beykyle/jitr/tree/main/examples). Tutorials live in [`examples/notebooks/`](https://github.com/beykyle/jitr/tree/main/examples/notebooks).
 
-In particular, check out:
+There are some additional requirements to run the examples. Once you've cloned the repo, from the main directory, run:
+
+```
+pip install -r examples/notebooks/requirements.txt
+```
+
+Then, you can run the notebooks. In particular, check out:
 - [`examples/notebooks/reactions.ipynb`](https://github.com/beykyle/jitr/tree/main/examples/notebooks/reactions.ipynb) which demonstrates the use of the `reactions` submodule
 - [`examples/notebooks/builtin_omps_uq.ipynb`](https://github.com/beykyle/jitr/tree/main/examples/notebooks/builtin_omps_uq.ipynb) to see how to use the built-in uncertainty-quantified optical model potentials to propagate uncertainties into reaction observables
 
@@ -63,12 +69,18 @@ pip install -r ./jitr/requirements.txt
 pip install -e ./jitr
 ```
 
-then run the tests:
+then run the unit tests:
 
 ```
 pytest jitr
 ```
 
+The notebooks in `examples/notebooks/`, aside from being demos, also can be used as tests:
+```
+pip install -r examples/notebooks/requirements.txt
+pytest --nbval-lax examples/notebooks/
+```
+
 Feel free to fork and make a pull request if you have things to contribute. There are many [open issues](https://github.com/beykyle/jitr/issues), feel free to add more.
 
 

examples/coupled.py

@@ -1,14 +1,13 @@
 import numpy as np
-from matplotlib import pyplot as plt
-
 from jitr import rmatrix
-from jitr.reactions import ProjectileTargetSystem, wavefunction
+from jitr.optical_potentials.potential_forms import coulomb_charged_sphere as coul
 from jitr.optical_potentials.potential_forms import (
-    woods_saxon_potential as ws,
     surface_peaked_gaussian_potential as spg,
-    coulomb_charged_sphere as coul,
 )
-from jitr.utils import complex_det, kinematics, mass, constants
+from jitr.optical_potentials.potential_forms import woods_saxon_potential as ws
+from jitr.reactions import ProjectileTargetSystem, wavefunction
+from jitr.utils import complex_det, constants, kinematics, mass
+from matplotlib import pyplot as plt
 
 
 def interaction_3level(r, V, R0, a0, Zz, coupling_matrix):

examples/local.py

@@ -1,15 +1,13 @@
 import numpy as np
-from matplotlib import pyplot as plt
-from scipy.integrate import solve_ivp
-from numba import njit
-
 from jitr import rmatrix
-from jitr.reactions import ProjectileTargetSystem, make_channel_data, wavefunction
 from jitr.optical_potentials.potential_forms import (
-    woods_saxon_potential,
     coulomb_charged_sphere,
+    woods_saxon_potential,
 )
-from jitr.utils import delta, smatrix, schrodinger_eqn_ivp_order1, kinematics
+from jitr.reactions import ProjectileTargetSystem, make_channel_data, wavefunction
+from jitr.utils import delta, kinematics, schrodinger_eqn_ivp_order1, smatrix
+from matplotlib import pyplot as plt
+from scipy.integrate import solve_ivp
 
 # target (A,Z)
 Ca48 = (48, 20)
@@ -21,7 +19,7 @@
 
 
 def interaction(r, *params):
-    (V0, W0, R0, a0, zz, RC) = params
+    V0, W0, R0, a0, zz, RC = params
     return -woods_saxon_potential(r, V0, W0, R0, a0) + coulomb_charged_sphere(r, zz, RC)
 
 
@@ -31,7 +29,6 @@ def local_interaction_example():
     """
     Elab = 14.1
     nodes_within_radius = 3
-    n_partial_waves = 1
 
     sys = ProjectileTargetSystem(
         channel_radius=2 * np.pi * nodes_within_radius,
@@ -282,7 +279,6 @@ def rmse_RK_LM():
 
             error_matrix[l, i] = np.absolute(S_rk - S_lm[0, 0]) / np.absolute(S_rk)
 
-    lines = []
     for l in sys.l:
         plt.plot(egrid, 100 * error_matrix[l, :], label=r"$l = %d$" % l)
 

examples/nonlocal.py

@@ -1,14 +1,10 @@
 import numpy as np
-
 from jitr import rmatrix
-
-from jitr.reactions import ProjectileTargetSystem
-
 from jitr.optical_potentials.potential_forms import (
     yamaguchi_potential,
     yamaguchi_swave_delta,
 )
-
+from jitr.reactions import ProjectileTargetSystem
 from jitr.utils.constants import HBARC