Merge pull request #157 from Spin-Chemistry-Labs/131-move-anisotropy-…

…and-mary-to-a-new-experimentspy-module

131 move anisotropy and mary to a new experimentspy module

.github/workflows/coverage.yaml

@@ -0,0 +1,42 @@
+name: Coverage
+
+on: push
+jobs:
+  run-radicalpy-coverage:
+    name: Run coverage on RadicalPy
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python "3.11" 🐍
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+        cache: 'pip'
+    - name: Install packages 📦
+      run: >-
+        python -m
+        pip install -r requirements.txt
+    - name: Install coverage
+      run: >-
+        python -m
+        pip install coverage
+    - name: Reset coverage
+      run: >-
+        coverage erase
+    - name: Run coverage
+      run: >-
+        coverage run -a -m
+        unittest
+        discover -v
+    - name: Run examples
+      run: >-
+        for file in $(ls examples/aniso*.py); do
+          PYTHONPATH=. coverage run -a $file --fast
+        done
+    - name: Create report
+      run: >-
+        coverage report && coverage xml && ls -lrt
+    - name: Code Coverage Report
+      uses: irongut/[email protected]
+      with:
+        filename: coverage.xml

.github/workflows/lint.yaml

@@ -1,6 +1,6 @@
 name: Lint
 
-on: [push, pull_request]
+on: [push]
 
 jobs:
   lint:

.github/workflows/run-tests.yml → .github/workflows/run-tests.yaml

@@ -12,7 +12,7 @@ jobs:
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python }} 🐍
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
         cache: 'pip'
@@ -25,3 +25,12 @@ jobs:
         python -m
         unittest
         discover -v
+    - name: Run examples
+      if: runner.os == 'Linux'
+      # This is bash.
+      # Need a separate branch to iterate over files on Windows.
+      run: >-
+        for file in $(ls examples/*.py); do
+          echo "Running example: $file"
+          PYTHONPATH=. python $file --fast
+        done

examples/T1_T2_relaxation_rate.py

@@ -10,6 +10,7 @@
     aqueous_glycerol_viscosity,
     rotational_correlation_time_for_protein,
 )
+from radicalpy.utils import is_fast_run
 
 
 def main():
@@ -26,9 +27,9 @@ def main():
     plt.axis("on")
     plt.rc("axes", edgecolor="k")
     for t in temperatures:
-        plt.plot(ratio, eta[t] * f, label=f"{t}$^\circ$C")
+        plt.plot(ratio, eta[t] * f, label=f"{t}$^\\circ$C")
     plt.xlabel("Glycerol fraction", size=14)
-    plt.ylabel("Viscosity ($mN \, s \, m^{-2}$)", size=14)
+    plt.ylabel(r"Viscosity ($mN \, s \, m^{-2}$)", size=14)
     plt.legend()
     plt.tick_params(labelsize=14)
     path = __file__[:-3] + f"_{0}.png"
@@ -47,7 +48,7 @@ def main():
     plt.axis("on")
     plt.rc("axes", edgecolor="k")
     for t in temperatures:
-        plt.plot(ratio, tau_c[t] * f2, label=f"{t}$^\circ$C")
+        plt.plot(ratio, tau_c[t] * f2, label=f"{t}$^\\circ$C")
     plt.xlabel("Glycerol fraction", size=14)
     plt.ylabel(r"$\tau _C$ ($\mu s$)", size=14)
     plt.legend()
@@ -73,7 +74,7 @@ def main():
     plt.axis("on")
     plt.rc("axes", edgecolor="k")
     for t in temperatures:
-        plt.plot(ratio, 1 / t1[t], label=f"{t}$^\circ$C")
+        plt.plot(ratio, 1 / t1[t], label=f"{t}$^\\circ$C")
     plt.xlabel("Glycerol fraction", size=14)
     plt.ylabel(r"1 / T1 ($s$)", size=14)
     plt.legend()
@@ -86,7 +87,7 @@ def main():
     plt.axis("on")
     plt.rc("axes", edgecolor="k")
     for t in temperatures:
-        plt.plot(ratio, 1 / t2[t], label=f"{t}$^\circ$C")
+        plt.plot(ratio, 1 / t2[t], label=f"{t}$^\\circ$C")
     plt.xlabel("Glycerol fraction", size=14)
     plt.ylabel(r"1 / T2 ($s$)", size=14)
     plt.legend()
@@ -96,4 +97,7 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    if is_fast_run():
+        main()  # quick enough
+    else:
+        main()

examples/anisotropy_3d_polar.py

@@ -4,22 +4,26 @@
 import numpy as np
 
 import radicalpy as rp
+from radicalpy.experiments import anisotropy
 from radicalpy.simulation import State
+from radicalpy.utils import is_fast_run
 
 
-def main():
-    theta = np.linspace(0, np.pi, 17)
-    phi = np.linspace(0, 2 * np.pi, 32)
+# def main(theta_steps=35, phi_steps=58, tmax=15e-6, dt=5e-9):
+def main(theta_steps=17, phi_steps=32, tmax=5e-6, dt=5e-9):
+    theta = np.linspace(0, np.pi, theta_steps)
+    phi = np.linspace(0, 2 * np.pi, phi_steps)
 
     flavin = rp.simulation.Molecule.fromdb("flavin_anion", ["N5", "N10"])
     Z = rp.simulation.Molecule("zorro", [])
     sim = rp.simulation.HilbertSimulation([flavin, Z])
 
-    time = np.arange(0, 5e-6, 5e-9)
+    time = np.arange(0, tmax, dt)
     B0 = 0.05
     k = 1e6
 
-    results = sim.anisotropy(
+    results = anisotropy(
+        sim,
         init_state=State.SINGLET,
         obs_state=State.SINGLET,
         time=time,
@@ -41,10 +45,15 @@ def main():
     print(f"{Y_av=}")
     print(f"{delta_phi_s=}")
     print(f"{gamma_s=}")
-    plt.show()
+    # plt.show()
+    path = __file__[:-3] + f"_{3}.png"
+    plt.savefig(path)
 
     return 0
 
 
 if __name__ == "__main__":
-    main()
+    if is_fast_run():
+        main(theta_steps=7, phi_steps=6, tmax=10e-6, dt=1e-6)
+    else:
+        main()

examples/anisotropy_3d_polar_paper.py

@@ -7,10 +7,10 @@
 from radicalpy import kinetics, relaxation
 from radicalpy.experiments import anisotropy
 from radicalpy.simulation import State
+from radicalpy.utils import is_fast_run
 
 
-def main():
-
+def main(theta_steps=35, phi_steps=58, tmax=15e-6, dt=5e-9):
     fad_n5_hfc = np.array(
         [
             [0.280, -0.138, 0.678],
@@ -21,14 +21,14 @@ def main():
 
     dipolar = rp.estimations.dipolar_interaction_anisotropic(r=22e-10)
 
-    theta = np.linspace(0, np.pi, 35)
-    phi = np.linspace(0, 2 * np.pi, 58)
+    theta = np.linspace(0, np.pi, theta_steps)
+    phi = np.linspace(0, 2 * np.pi, phi_steps)
 
     flavin = rp.simulation.Molecule.fromisotopes(isotopes=["14N"], hfcs=[fad_n5_hfc])
     Z = rp.simulation.Molecule("zorro", [])
     sim = rp.simulation.HilbertSimulation([flavin, Z])
 
-    time = np.arange(0, 15e-6, 5e-9)
+    time = np.arange(0, tmax, dt)
     B0 = 0.05
     k = 1e6
 
@@ -58,10 +58,15 @@ def main():
     print(f"{Y_av=}")
     print(f"{delta_phi_s=}")
     print(f"{gamma_s=}")
-    plt.show()
+    # plt.show()
+    path = __file__[:-3] + f"_{3}.png"
+    plt.savefig(path)
 
     return 0
 
 
 if __name__ == "__main__":
-    main()
+    if is_fast_run():
+        main(theta_steps=7, phi_steps=6, tmax=10e-6, dt=1e-6)
+    else:
+        main()

examples/anisotropy_3d_polar_paper_2.py

@@ -7,10 +7,10 @@
 from radicalpy import kinetics, relaxation
 from radicalpy.experiments import anisotropy
 from radicalpy.simulation import State
+from radicalpy.utils import is_fast_run
 
 
-def main():
-
+def main(theta_steps=35, phi_steps=58, tmax=15e-6, dt=5e-9):
     fad_n5_hfc = np.array(
         [
             [0.280, -0.138, 0.678],
@@ -38,14 +38,14 @@ def main():
         * rp.data.Isotope("E").gamma_mT
     )
 
-    theta = np.linspace(0, np.pi, 35)
-    phi = np.linspace(0, 2 * np.pi, 58)
+    theta = np.linspace(0, np.pi, theta_steps)
+    phi = np.linspace(0, 2 * np.pi, phi_steps)
 
     flavin = rp.simulation.Molecule.fromisotopes(isotopes=["14N"], hfcs=[fad_n5_hfc])
     trp = rp.simulation.Molecule.fromisotopes(isotopes=["1H"], hfcs=[trp_hbeta_hfc])
     sim = rp.simulation.HilbertSimulation([flavin, trp])
 
-    time = np.arange(0, 15e-6, 5e-9)
+    time = np.arange(0, tmax, dt)
     B0 = 0.05
     k = 1e6
 
@@ -75,10 +75,15 @@ def main():
     print(f"{Y_av=}")
     print(f"{delta_phi_s=}")
     print(f"{gamma_s=}")
-    plt.show()
+    # plt.show()
+    path = __file__[:-3] + f"_{3}.png"
+    plt.savefig(path)
 
     return 0
 
 
 if __name__ == "__main__":
-    main()
+    if is_fast_run():
+        main(theta_steps=7, phi_steps=6, tmax=10e-6, dt=1e-6)
+    else:
+        main()