Merge branch 'main' into base-hamiltonian-class

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+name: "CodeQL"
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [main]
+  schedule:
+    - cron: '0 16 * * 4'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        # Override automatic language detection by changing the below list
+        # Supported options are ['csharp', 'cpp', 'go', 'java', 'javascript', 'python']
+        language: ['python']
+        # Learn more...
+        # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        # We must fetch at least the immediate parents so that if this is
+        # a pull request then we can checkout the head.
+        fetch-depth: 2
+
+    # If this run was triggered by a pull request event, then checkout
+    # the head of the pull request instead of the merge commit.
+    - run: git checkout HEAD^2
+      if: ${{ github.event_name == 'pull_request' }}
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        queries: +security-and-quality
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2

.github/workflows/python-test.yml

@@ -0,0 +1,29 @@
+name: test python
+
+on:
+  pull_request:
+    types: [opened, reopened]
+  push:
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: [3.8, 3.9, '3.10', 3.11]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel setuptools
+        python -m pip install --upgrade .[dev]
+    - name: Test with pytest
+      run: |
+        pytest --color=yes

WrightSim/experiment/_scan.py

@@ -259,7 +259,7 @@ def efields(self, windowed=None):
         efields_shape = list(efp.shape)
         if windowed == self.windowed:
             efields_shape[-1] = self.iprime
-            efields = np.zeros((efields_shape), dtype=np.complex)
+            efields = np.zeros((efields_shape), dtype=np.complex128)
             with wt.kit.Timer():
                 for ind in np.ndindex(tuple(efields_shape[:-2])):
                     efi = self.pulse_class.pulse(efp[ind], self.t_args, pm=self.pm)
@@ -272,7 +272,7 @@ def efields(self, windowed=None):
             else:
                 efields_shape[-1] = self.t.size
 
-            efields = np.zeros((efields_shape), dtype=np.complex)
+            efields = np.zeros((efields_shape), dtype=np.complex128)
             with wt.kit.Timer():
                 for ind in np.ndindex(tuple(efields_shape[:-2])):
                     efi = self.pulse_class.pulse(efp[ind], self.t_args, pm=self.pm)

WrightSim/hamiltonian/default.py

@@ -71,13 +71,13 @@ def __init__(
             Order matters, and meaning is dependent on the individual Hamiltonian.
             Default is two values, both initially 1.0.
         omega : 1-D array <float64> (optional)
-            The energies of various transitions.
+            The energies of various transitions (wavenumbers).
             The default uses w_central and coupling parameters to compute the appropriate
                 values for a TRIVE Hamiltonian
-        w_central : float (optional)
-            The cetral frequency of a resonance for a TRIVE Hamiltonian.
+        w_central : float (optional) 
+            The central frequency (wavenumbers) of a resonance for a TRIVE Hamiltonian.
             Used only when ``omega`` is ``None``.
-        coupling : float (optional)
+        coupling : float (optional) (wavenumbers)
             The copuling of states for a TRIVE Hamiltonian.
             Used only when ``omega`` is ``None``.
         propagator : function (optional)

setup.py

@@ -14,8 +14,23 @@
     name="WrightSim",
     packages=find_packages(),
     package_data=extra_files,
-    install_requires=["h5py>=2.7.0", "numpy", "scipy", "WrightTools"],
-    extras_require={"docs": ["sphinx-gallery>=0.1.9"], "cuda": ["pycuda"]},
+    python_requires=">=3.7",
+    install_requires=[
+        "h5py>=2.7.0",
+        "numpy",
+        "scipy",
+        "WrightTools"
+    ],
+    extras_require={
+        "docs": ["sphinx-gallery>=0.1.9"], 
+        "cuda": ["pycuda"],
+        "dev": [
+            "black",
+            "pre-commit",
+            "pytest",
+            "pytest-cov",
+        ]
+    },
     version=version,
     description="A simulation package for multidimensional spectroscopy.",
     author="WrightSim Developers",

tests/mixed/default.py

@@ -0,0 +1,88 @@
+"""smokescreen checks of mixed domain default hamiltonian integration"""
+import WrightSim as ws
+import numpy as np
+import pytest
+
+
+dt = 20
+nt = 21
+wn_to_omega = 2 * np.pi * 3e-5  # cm / fs
+w_central = 3000  # wn
+coupling = 0  # wn
+
+ham = ws.hamiltonian.Hamiltonian(
+    w_central=w_central,
+    coupling=coupling,
+    tau=100,
+)
+ham.recorded_elements = [7, 8]
+
+
+@pytest.mark.skip("this test currently fails; bugfix needed")
+def test_windowed():
+    exp = ws.experiment.builtin('trive')
+    exp.w1.points = w_central  # wn
+    exp.w2.points = w_central  # wn
+    exp.d2.points = 50  # np.zeros((1,))  # fs
+    exp.d1.points = 0  # fs
+    exp.s1.points = exp.s2.points = dt  # fs
+
+    exp.d1.active = exp.d2.active = False
+
+    # 400 time points
+    exp.timestep = 1
+    exp.early_buffer = 100.
+    exp.late_buffer = 300.
+
+    scan = exp.run(ham, mp=False)
+    data = scan.sig
+
+    # shift delay so emission is timed differently
+    exp2 = ws.experiment.builtin('trive')
+    exp2.w1.points = w_central  # wn
+    exp2.w2.points = w_central  # wn
+    exp2.d2.points = 50 # np.zeros((1,))  # fs
+    exp2.d1.points = 0  # fs
+    exp2.s1.points = exp2.s2.points = dt  # fs
+
+    exp2.d1.active = exp2.d2.active = False
+
+    exp2.timestep = 1
+    exp2.early_buffer = 100.
+    exp2.late_buffer = 300.
+
+    scan2 = exp2.run(ham, mp=False, windowed=True)
+    data2 = scan2.sig
+
+    assert data2.time.size == data.time.size
+    assert data2.time.size == data2.channels[0].size
+    assert np.all(np.isclose(data2.channels[0][:], data.channels[0][:]))
+
+
+def test_frequency():
+
+    exp = ws.experiment.builtin('trive')
+    exp.w1.points = w_central  # wn
+    exp.w2.points = w_central  # wn
+    exp.d2.points = 0  # np.zeros((1,))  # fs
+    exp.d1.points = 0  # fs
+    exp.s1.points = exp.s2.points = dt  # fs
+
+    exp.d1.active = exp.d2.active = False
+
+    # 400 time points
+    exp.timestep = 1
+    exp.early_buffer = 100.
+    exp.late_buffer = 300.
+
+    scan = exp.run(ham, mp=False)
+    data = scan.sig
+    wn = np.fft.fftfreq(n=data.time.size, d=exp.timestep) / 3e-5
+    sig_fft = np.abs(np.fft.fft(data.channels[0][:]))
+
+    assert np.abs(wn[np.argmax(sig_fft)] + w_central) < np.abs(wn[1] - wn[0])
+
+
+if __name__ == "__main__":
+    test_windowed()  # fails atm
+    test_frequency()