WIP: native implementation of fftfit

.pre-commit-config.yaml

@@ -1,11 +1,12 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v3.2.0
     hooks:
     -   id: check-yaml
     -   id: check-merge-conflict
     -   id: check-symlinks
 -   repo: https://github.com/psf/black
-    rev: 19.3b0
+    rev: 19.10b0
     hooks:
     -   id: black
+        language_version: python3

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project, at least loosely, adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+### Added
+- Now contains an implementation of FFTFIT in `pint.profile` (PR #777)
+
 ## [0.8.1] - 2021-01-07
 ## Fixed
 - Right click to delete TOAs in pintk now works

docs/examples/Example of parameter usage.md

@@ -0,0 +1,344 @@
+---
+jupyter:
+  jupytext:
+    formats: ipynb,md
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.2'
+      jupytext_version: 1.5.2
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+---
+
+# Example of parameter usage
+
+```python jupyter={"outputs_hidden": false}
+import pint.models.model_builder as mb
+import pint.models.parameter as pp
+import astropy.units as u
+from astropy.coordinates.angles import Angle
+import pytest
+```
+
+```python jupyter={"outputs_hidden": false}
+model = mb.get_model("B1855+09_NANOGrav_dfg+12_TAI.par")
+```
+
+```python jupyter={"outputs_hidden": false}
+print(model.params)
+```
+
+## Attributions in Parameters
+
+```python jupyter={"outputs_hidden": false}
+printed = []
+for p in model.params:
+    par = getattr(model, p)
+    if type(par) in printed:
+        continue
+    print("Name           ", par.name)
+    print("Type           ", type(par))
+    print("Quantity       ", par.quantity, type(par.quantity))
+    print("Value          ", par.value)
+    print("units          ", par.units)
+    print("Uncertainty    ", par.uncertainty)
+    print("Uncertainty_value", par.uncertainty_value)
+    print("Summary        ", par)
+    print("Parfile Style  ", par.as_parfile_line())
+    print()
+    printed.append(type(par))
+# Note JUMP and DMX is different.
+```
+
+## Making a parameter
+
+```python jupyter={"outputs_hidden": false}
+t = pp.floatParameter(name="TEST", value=100, units="Hz", uncertainty=0.03)
+print(t)
+```
+
+```python jupyter={"outputs_hidden": false}
+t2 = pp.floatParameter(name="TEST", value="200", units="Hz", uncertainty=".04")
+print(t2)
+```
+
+```python jupyter={"outputs_hidden": false}
+t3 = pp.floatParameter(
+    name="TEST", value=0.3 * u.kHz, units="Hz", uncertainty=4e-5 * u.kHz
+)
+print(t3)
+print(t3.quantity)
+print(t3.value)
+print(t3.uncertainty)
+print(t3.uncertainty_value)
+```
+
+## Change Parameter quantity of value
+
+```python jupyter={"outputs_hidden": false}
+par = model.F0
+print(par)
+par.quantity = 200
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+```
+
+```python jupyter={"outputs_hidden": false}
+# Test F0
+print(par)
+par.value = 150
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for F0
+print(par)
+par.value = "100"
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for F0
+print(par)
+par.quantity = "300"
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+```
+
+```python jupyter={"outputs_hidden": false}
+# Examle  F0
+par.quantity = 0.3 * u.kHz
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+```
+
+```python jupyter={"outputs_hidden": false}
+try:
+    # Examle  F0
+    print(par)
+    par.value = 100 * u.second  # SET F0 to seconds as time.
+    print("Quantity       ", par.quantity, type(par.quantity))
+    print("Value          ", par.value)
+    print(par)
+except u.UnitConversionError as e:
+    print("Exception raised:", e)
+else:
+    raise ValueError("That was supposed to raise an exception!")
+```
+
+### For MJD parameters
+
+```python jupyter={"outputs_hidden": false}
+par = model.TZRMJD
+print(par)
+par.quantity = 54000
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for TZRMJD
+par.quantity = "54001"
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for TZRMJD
+par.value = 54002
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for TZRMJD
+par.value = "54003"
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+### For AngleParameters
+
+```python jupyter={"outputs_hidden": false}
+# Example for RAJ
+par = model.RAJ
+print(par)
+par.quantity = 50
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+import astropy
+```
+
+```python jupyter={"outputs_hidden": false}
+astropy.__version__
+```
+
+```python jupyter={"outputs_hidden": false}
+Angle(50.0 * u.hourangle)
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for RAJ
+print(par)
+par.quantity = 30.5
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for RAJ
+print(par)
+par.quantity = "20:30:00"
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for RAJ
+print(par)
+par.value = "20:05:0"
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for RAJ
+print(par)
+par.quantity = 30 * u.deg
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Quantity in deg", par.quantity.to(u.deg))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for RAJ
+print(par)
+par.value = 40 * u.rad
+print("Quantity       ", par.quantity, type(par.quantity))
+print("Quantity in rad", par.quantity.to(u.rad))
+print("Value          ", par.value)
+print(par)
+par.quantity
+```
+
+Test for wrong unit
+
+```python jupyter={"outputs_hidden": false}
+# Example for RAJ
+try:
+    print(par)
+    par.value = 40 * u.second  #  Here second is in the unit of time, not hourangle
+    print("Quantity       ", par.quantity, type(par.quantity))
+    print("Quantity in rad", par.quantity.to(u.rad))
+    print("Value          ", par.value)
+    print(par)
+    par.quantity
+except u.UnitConversionError as e:
+    print("Exception raised:", e)
+else:
+    raise ValueError("That was supposed to raise an exception!")
+```
+
+```python jupyter={"outputs_hidden": false}
+try:
+    # Example for RAJ
+    print(par)
+    par.quantity = 30 * u.hour  # Here hour is in the unit of time, not hourangle
+    print("Quantity       ", par.quantity, type(par.quantity))
+    print("Quantity in deg", par.quantity.to(u.deg))
+    print("Value          ", par.value)
+    print(par)
+    par.quantity
+except u.UnitConversionError as e:
+    print("Exception raised:", e)
+else:
+    raise ValueError("That was supposed to raise an exception!")
+```
+
+## Example for uncertainty
+
+```python jupyter={"outputs_hidden": false}
+par = model.F0
+```
+
+
+```python jupyter={"outputs_hidden": false}
+# Example for F0
+print(par.uncertainty)
+print(par.uncertainty_value)
+par.uncertainty = par.uncertainty_value / 1000.0 * u.kHz
+print(par)
+print(par.uncertainty)
+```
+
+
+```python jupyter={"outputs_hidden": false}
+# Example for F0
+par.uncertainty_value = 6e-13
+print(par)
+print(par.uncertainty)
+```
+
+```python jupyter={"outputs_hidden": false}
+# Example for F0
+par.uncertainty_value = 7e-16 * u.kHz
+print(par)
+print(par.uncertainty)
+```
+
+<!-- #region jupyter={"outputs_hidden": false} -->
+## How do "prefix parameters" and "mask parameters" work?
+<!-- #endregion -->
+
+```python
+cat = pp.prefixParameter(
+    parameter_type="float", name="CAT0", units=u.ml, long_double=True
+)
+```
+
+```python
+dir(cat)
+```
+
+```python
+cat.is_prefix
+```
+
+```python
+cat.index
+```
+
+```python
+
+```