feature: adapted all codes for pylopsv2

.github/workflows/build.yaml

@@ -1,23 +1,19 @@
 name: PyMarchenko-tests
 
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
+on: [push, pull_request]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/deploy-docs.yml

@@ -0,0 +1,35 @@
+name: Deploy Sphinx docs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+    contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements-dev.txt; fi
+          pip install .
+      - name: Build docs
+        run: |
+          sphinx-build -b html ./docs/source ./docs/build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: gh-pages1
+          personal_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/

.github/workflows/flake.yml

@@ -0,0 +1,24 @@
+# This workflow runs Flake8 on the PR
+# For more information see: https://github.com/marketplace/actions/python-flake8-lint
+name: PyMarchenko-flake8
+
+on: [push, pull_request]
+
+jobs:
+  flake8-lint:
+    runs-on: ubuntu-latest
+    name: Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v3
+      - name: Set up Python environment
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: flake8 Lint
+        uses: py-actions/flake8@v2
+        with:
+          ignore: "E203,E501,W503,E402"
+          max-line-length: "88"
+          path: "pymarchenko"
+          args: "--per-file-ignores=__init__.py:F401,F403,F405"

Makefile

@@ -49,3 +49,12 @@ docpush:
 	cd ../docs && git add . && git commit -m "Updated documentation" &&\
 	git push origin gh-pages && git checkout main
 
+servedoc:
+	$(PYTHON) -m http.server --directory docs/build/html/
+
+lint:
+	flake8 docs/ examples/ pyproximal/ pytests/ tutorials/
+
+typeannot:
+	mypy pyproximal/
+

docssrc/source/conf.py

@@ -53,9 +53,9 @@
 
 sphinx_gallery_conf = {
     # path to your examples scripts
-    'examples_dirs': ['../../examples', '../../tutorials',],
+    'examples_dirs': ['../../tutorials',],
     # path where to save gallery generated examples
-    'gallery_dirs': ['gallery', 'tutorials'],
+    'gallery_dirs': ['tutorials',],
     'filename_pattern': '\.py',
     # Remove the "Download all examples" button from the top level gallery
     'download_all_examples': False,
@@ -134,8 +134,7 @@
     # links
     'doc_path': 'docs/source',
     'galleries': sphinx_gallery_conf['gallery_dirs'],
-    'gallery_dir': dict(zip(sphinx_gallery_conf['gallery_dirs'],
-                            sphinx_gallery_conf['examples_dirs'])),
+    'gallery_dir': sphinx_gallery_conf['gallery_dirs'],
     'github_project': 'PyLops',
     'github_repo': 'pymarchenko',
     'github_version': 'main',

pymarchenko/imaging.py

@@ -5,7 +5,7 @@
 from multiprocessing import set_start_method
 from multiprocessing import get_context
 from scipy.signal import convolve, filtfilt
-from pylops.waveeqprocessing.marchenko import directwave#, Marchenko
+from pylops.waveeqprocessing.marchenko import directwave
 from pylops.waveeqprocessing.mdd import MDD
 from pymarchenko.marchenko import Marchenko
 from pymarchenko.raymarchenko import RayleighMarchenko
@@ -111,7 +111,49 @@ def MarchenkoImaging(vsx, vsz, r, s, dr, dt, nt, vel,
 
     Parameters
     ----------
-    
+    vsx : :obj:`numpy.ndarray`
+        X-coordinates of virtual sources
+    vsz : :obj:`numpy.ndarray`
+        Z-coordinates of virtual sources
+    r : :obj:`numpy.ndarray`
+        Receiver array
+    s : :obj:`numpy.ndarray`
+        Source array
+    dr : :obj:`float`
+        Sampling of receiver integration axis
+    dt : :obj:`float`
+        Sampling of time integration axis
+    nt : :obj:`int`
+        Number of samples in time (not required if ``R`` is in time)
+    vel : :obj:`numpy.ndarray`
+        Velocity model
+    toff : :obj:`float`
+        Time-offset to apply to traveltime
+    nsmooth : :obj:`int`
+        Number of samples of smoothing operator to apply to window
+    wav : :obj:`numpy.ndarray`, optional
+        Wavelet to apply to direct arrival when created using ``trav``
+    wav_c : :obj:`int`
+        Index of center of wavelet
+    nfmax : :obj:`int`
+        Index of max frequency to include in deconvolution process
+    igaths : :obj:`list`, optional
+        Indices of x-axis along which to compute angle gathers
+    nalpha : :obj:`int`
+        Indices of x-axis along which to compute angle gathers
+    jt : :obj:`int`
+        Subsampling to apply to time axis of inputs wavefields for MDD
+    data : :obj:`numpy.ndarray`
+        Reflection data
+    kind : :obj:`str`, optional
+        Marchenko algorithm to apply (``mck``, ``nmck``, or ``rmck``)
+    niter : :obj:`int`, optional
+        Number of iterations of Marchenko scheme
+    nproc : :obj:`int`, optional
+        Number of processes
+    nthread : :obj:`int`, optional
+        Number of threads per process
+
     Returns
     -------
     iss : :obj:`numpy.ndarray`
@@ -122,6 +164,7 @@ def MarchenkoImaging(vsx, vsz, r, s, dr, dt, nt, vel,
         Single-scattering angle gathers
     amck : :obj:`numpy.ndarray`, optional
         Marchenko angle gathers
+
     """
     # Set threads
     os.environ["OMP_NUM_THREADS"] = str(nthreads)

pymarchenko/marchenko.py

@@ -9,8 +9,8 @@
 from pylops import Diagonal, Identity, Block, BlockDiag, Restriction
 from pylops.waveeqprocessing.mdd import MDC
 from pylops.waveeqprocessing.marchenko import directwave
-from pylops.optimization.solver import cgls
-from pylops.optimization.sparsity import FISTA
+from pylops.optimization.basic import cgls
+from pylops.optimization.sparsity import fista
 from pylops.utils.backend import get_array_module, get_module_name, \
     to_cupy_conditional
 
@@ -230,8 +230,7 @@ def __init__(self, R, dt=0.004, nt=None, dr=1.,
         if self.isava is None:
             self.Iop = Identity(self.nr * self.nt2)
         else:
-            self.Iop = Restriction(self.nr * self.nt2, isava,
-                                   dims=(self.nt2, self.nr), dir=1)
+            self.Iop = Restriction((self.nt2, self.nr), isava, axis=1)
         if S is not None:
             self.Sop = BlockDiag([S, S])
 
@@ -268,9 +267,9 @@ def apply_onepoint(self, trav, G0=None, nfft=None, rtm=False, greens=False,
         **kwargs_solver
             Arbitrary keyword arguments for chosen solver
             (:py:func:`scipy.sparse.linalg.lsqr` and
-            :py:func:`pylops.optimization.solver.cgls` are used as default
+            :py:func:`pylops.optimization.basic.cgls` are used as default
             for numpy and cupy `data`, respectively.
-            :py:func:`pylops.optimization.sparsity.FISTA` is used when a
+            :py:func:`pylops.optimization.sparsity.fista` is used when a
             sparsifying transform ``S`` is provided).
 
         Returns
@@ -305,13 +304,13 @@ def apply_onepoint(self, trav, G0=None, nfft=None, rtm=False, greens=False,
 
         # Create operators
         Rop = MDC(self.Rtwosided_fft, self.nt2, nv=1, dt=self.dt, dr=self.dr,
-                  twosided=False, conj=False, transpose=False,
+                  twosided=False, conj=False,
                   saveGt=self.saveRt, prescaled=self.prescaled,
-                  usematmul=usematmul, dtype=self.dtype)
+                  usematmul=usematmul)
         R1op = MDC(self.Rtwosided_fft, self.nt2, nv=1, dt=self.dt, dr=self.dr,
-                   twosided=False, conj=True, transpose=False,
+                   twosided=False, conj=True,
                    saveGt=self.saveRt, prescaled=self.prescaled,
-                   usematmul=usematmul, dtype=self.dtype)
+                   usematmul=usematmul)
         Wop = Diagonal(w.T.ravel())
         if self.isava is not None:
             Wsop = Diagonal(w[self.isava].T.ravel())
@@ -367,7 +366,7 @@ def apply_onepoint(self, trav, G0=None, nfft=None, rtm=False, greens=False,
                               x0=self.ncp.zeros(2*(2*self.nt-1)*self.nr, dtype=self.dtype),
                               **kwargs_solver)[0]
         else:
-            f1_inv = FISTA(Mop * self.Sop, d.ravel(), **kwargs_solver)[0]
+            f1_inv = fista(Mop * self.Sop, d.ravel(), **kwargs_solver)[0]
             f1_inv = self.Sop * f1_inv
 
         f1_inv = f1_inv.reshape(2 * self.nt2, self.nr)
@@ -475,12 +474,12 @@ def apply_multiplepoints(self, trav, G0=None, nfft=None,
         # Create operators
         Rop = MDC(self.Rtwosided_fft, self.nt2, nv=nvs,
                   dt=self.dt, dr=self.dr, twosided=False,
-                  conj=False, transpose=False, prescaled=self.prescaled,
-                  usematmul=usematmul, dtype=self.dtype)
+                  conj=False, prescaled=self.prescaled,
+                  usematmul=usematmul)
         R1op = MDC(self.Rtwosided_fft, self.nt2, nv=nvs,
                    dt=self.dt, dr=self.dr, twosided=False,
-                   conj=True, transpose=False, prescaled=self.prescaled,
-                   usematmul=usematmul, dtype=self.dtype)
+                   conj=True, prescaled=self.prescaled,
+                   usematmul=usematmul)
         Wop = Diagonal(w.transpose(2, 0, 1).ravel())
         Iop = Identity(self.nr * nvs * self.nt2)
         Mop = Block([[Iop, -1 * Wop * Rop],

pymarchenko/mme.py

@@ -9,7 +9,7 @@
 from pylops import Diagonal, Identity, Block, BlockDiag
 from pylops.waveeqprocessing.mdd import MDC
 from pylops.waveeqprocessing.marchenko import directwave
-from pylops.optimization.solver import cgls
+from pylops.optimization.basic import cgls
 from pylops.utils.backend import get_array_module, get_module_name, \
     to_cupy_conditional
 
@@ -249,13 +249,13 @@ def apply_onesrc(self, Rsrc, usematmul=False, trcomp=False, ntmax=None,
 
         # Create operators
         Rop = MDC(self.Rtwosided_fft, self.nt2, nv=1, dt=self.dt, dr=self.dr,
-                  twosided=False, conj=False, transpose=False,
+                  twosided=False, conj=False,
                   saveGt=self.saveRt, prescaled=self.prescaled,
-                  usematmul=usematmul, dtype=self.dtype)
+                  usematmul=usematmul)
         R1op = MDC(self.Rtwosided_fft, self.nt2, nv=1, dt=self.dt, dr=self.dr,
-                   twosided=False, conj=True, transpose=False,
+                   twosided=False, conj=True,
                    saveGt=self.saveRt, prescaled=self.prescaled,
-                   usematmul=usematmul, dtype=self.dtype)
+                   usematmul=usematmul)
 
         # Run estimate over time steps
         U_sub_minus = np.zeros((self.nr, self.nt), dtype=self.dtype)
@@ -303,7 +303,7 @@ def _apply_onetime_multisrc(self, t0, Rop, R1op, Rsrcs, n_iter=10):
         return U_sub_minus
 
     def apply_multisrc(self, Rsrcs, usematmul=False, trcomp=False, ntmax=None,
-                     n_iter=10):
+                       n_iter=10):
         r"""Marchenko Multiple elimination for multiple shot gathers
 
         Solve the Marchenko Multiple elimination problem via
@@ -345,13 +345,13 @@ def apply_multisrc(self, Rsrcs, usematmul=False, trcomp=False, ntmax=None,
         # Create operators
         nsrc = Rsrcs.shape[0]
         Rop = MDC(self.Rtwosided_fft, self.nt2, nv=nsrc, dt=self.dt, dr=self.dr,
-                  twosided=False, conj=False, transpose=False,
+                  twosided=False, conj=False,
                   saveGt=self.saveRt, prescaled=self.prescaled,
-                  usematmul=usematmul, dtype=self.dtype)
+                  usematmul=usematmul)
         R1op = MDC(self.Rtwosided_fft, self.nt2, nv=nsrc, dt=self.dt, dr=self.dr,
-                   twosided=False, conj=True, transpose=False,
+                   twosided=False, conj=True,
                    saveGt=self.saveRt, prescaled=self.prescaled,
-                   usematmul=usematmul, dtype=self.dtype)
+                   usematmul=usematmul)
 
         # Run estimate over time steps
         U_sub_minus = np.zeros((nsrc, self.nr, self.nt), dtype=self.dtype)

pymarchenko/neumarchenko.py

@@ -9,7 +9,7 @@
 from pylops import Diagonal, Identity, Block, BlockDiag
 from pylops.waveeqprocessing.mdd import MDC
 from pylops.waveeqprocessing.marchenko import directwave
-from pylops.optimization.solver import cgls
+from pylops.optimization.basic import cgls
 from pylops.utils.backend import get_array_module, get_module_name, \
     to_cupy_conditional
 
@@ -233,13 +233,13 @@ def apply_onepoint(self, trav, G0=None, nfft=None, rtm=False, greens=False,
 
         # Create operators
         Rop = MDC(self.Rtwosided_fft, self.nt2, nv=1, dt=self.dt, dr=self.dr,
-                  twosided=False, conj=False, transpose=False,
+                  twosided=False, conj=False,
                   saveGt=self.saveRt, prescaled=self.prescaled,
-                  usematmul=usematmul, dtype=self.dtype)
+                  usematmul=usematmul)
         R1op = MDC(self.Rtwosided_fft, self.nt2, nv=1, dt=self.dt, dr=self.dr,
-                   twosided=False, conj=True, transpose=False,
+                   twosided=False, conj=True,
                    saveGt=self.saveRt, prescaled=self.prescaled,
-                   usematmul=usematmul, dtype=self.dtype)
+                   usematmul=usematmul)
         Wop = Diagonal(w.T.flatten())
 
         # Create input focusing function