Added setup.py and modification for live info during retrieval

.github/workflows/python-publish.yml

@@ -0,0 +1,40 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine toml
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*
+

.gitignore

@@ -3,6 +3,8 @@ scripts/results/
 
 Thumbs.db
 
+.idea
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md
+include LICENSE
+include pypret/VERSION
+

pypret/VERSION

@@ -0,0 +1 @@
+0.0.1

pypret/retrieval/nlo_retriever.py

@@ -19,7 +19,7 @@ def _scalar_objective(self, x):
         R = self._Rr(r)
         # printing and logging
         if rs.nfev % 100 == 0 and self.verbose:
-            print(rs.nfev, R)
+            self.print(rs.nfev, R)
         if self.logging:
             log.trace_error.append(R)
         rs.nfev += 1
@@ -37,7 +37,7 @@ def _vector_objective(self, x):
         R = self._Rr(np.sum(diff * diff))
         # printing and logging
         if rs.nfev % 100 == 0 and self.verbose:
-            print(rs.nfev, R)
+            self.print(rs.nfev, R)
         if self.logging:
             log.trace_error.append(R)
         rs.nfev += 1

pypret/retrieval/retriever.py

@@ -61,6 +61,21 @@ def __init__(self, pnps, logging=False, verbose=False, **kwargs):
         self.log = None
         rs = self._retrieval_state = SimpleNamespace()
         rs.running = False
+        if 'status_sig' in kwargs:
+            self.print = kwargs['status_sig'].emit
+        else:
+            self.print = print
+
+        if 'callback' in kwargs:
+            self.callback = kwargs['callback']
+        else:
+            self.callback = None
+
+        if 'step_command' in kwargs:
+            self.step_command = kwargs['step_command']
+        else:
+            self.step_command = None
+
         if (self.supported_schemes is not None and
                 pnps.scheme not in self.supported_schemes):
             raise ValueError("Retriever '%s' does not support scheme '%s'. "
@@ -139,12 +154,12 @@ def _retrieve_begin(self, measurement, initial_guess, weights):
         else:
             self.log = None
         if self.verbose:
-            print("Started retriever '%s'" % self.method)
-            print("Options:")
-            print(self.options)
-            print("Initial trace error R = {:.10e}".format(res.trace_error))
-            print("Starting retrieval...")
-            print()
+            self.print("Started retriever '%s'" % self.method)
+            self.print("Options:")
+            self.print(str(self.options))
+            self.print("Initial trace error R = {:.10e}".format(res.trace_error))
+            self.print("Starting retrieval...")
+            self.print("")
 
     def _retrieve_end(self):
         rs = self._retrieval_state

pypret/retrieval/step_retriever.py

@@ -40,8 +40,10 @@ def _retrieve(self):
             # accept the new spectrum
             spectrum[:] = new_spectrum
             if self.verbose:
+                if self.callback is not None:
+                    self.callback([rs.mu * rs.Tmn - self.Tmn_meas, self.parameter, self.pnps.process_w, new_spectrum])
                 if i == 0:
-                    print("iteration".ljust(10) + "trace error".ljust(20))
+                    self.print("iteration".ljust(10) + "trace error".ljust(20))
                 s = "{:d}".format(i + 1).ljust(10)
                 if rs.approximate_error:
                     s += "~"
@@ -50,14 +52,16 @@ def _retrieve(self):
                 s += "{:.10e}".format(R)
                 if R == res.trace_error:
                     s += "*"
-                print(s)
+                self.print(s)
             if not rs.running:
                 break
+            if self.step_command is not None:
+                self.step_command()
         if self.verbose:
-            print()
-            print("~ approximate trace error")
-            print("* accepted as best trace error")
-            print()
+            self.print("")
+            self.print("~ approximate trace error")
+            self.print("* accepted as best trace error")
+            self.print("")
 
         # return the retrieved spectrum
         # for a more detailed analysis call self.result()

setup.cfg

@@ -0,0 +1,39 @@
+[metadata]
+name = pypret_pymodaq
+version = file: pypret/VERSION
+description = fork of Python for Pulse Retrieval for PyMoDAQ 
+long_description = This project aims to provide numerical algorithms for ultrashort laser pulse measurement methods
+license = MIT
+licence_file = LICENSE
+url = https://github.com/PyMoDAQ/pypret_pymodaq
+author = S. J. Weber
+author_email = [email protected]
+classifiers =
+    Programming Language :: Python :: 3
+    Development Status :: 5 - Production/Stable
+    Environment :: Other Environment
+    Intended Audience :: Science/Research
+    Topic :: Scientific/Engineering :: Human Machine Interfaces
+    Topic :: Scientific/Engineering :: Visualization
+	License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Topic :: Software Development :: Libraries :: Python Modules
+    Topic :: Software Development :: User Interfaces
+
+[options]
+py_module = pypret
+python_requires = >=3.6, <3.9
+install_requires=
+    h5py
+	loky
+	scipy
+
+package_dir =
+    =.
+packages = find:
+include_package_data = True
+
+[options.packages.find]
+where = .
+
+

setup.py

@@ -0,0 +1,2 @@
+from setuptools import setup
+setup()