Update CHANGELOG for v1.0

CHANGELOG-unreleased.md

@@ -9,52 +9,6 @@ the released changes.
 
 ## Unreleased
 ### Changed
-- Moved `get_derived_params` to `timing_model`
-- `check_ephemeris_connection` CI test no longer requires access to static NANOGrav site
-- `TimingModel.compare()` now calls `change_binary_epoch()`.
-- When clock files contain out-of-order entries, the exception now records the first MJDs that are out of order
-- `np.compat.long` -> `int` (former is deprecated)
-- Turned ErfaWarning into an exception during testing; cleaned up test suite.
-- macos-latest runner changed to macos-12 runner for CI tests to avoid M1 architecture issues
 ### Added
-- Added numdifftools to setup.cfg to match requirements.txt
-- Documentation: Added `convert_parfile` to list of command-line tools in RTD
-- DDH binary model
-- function `pint.utils.xxxselections` to do DMX-style selections for any parameter name
-- Plot model DM in pintk
-- More tests for pintk
-- Maximum likelihood fitting for ECORR
-    - `is_time_correlated` class attribute in correlated `NoiseComponent`s
-    - `has_time_correlated_errors` property in `TimingModel`
-    - `Residuals._calc_ecorr_chi2()` method for fast chi2 computation using Sherman-Morrison identity
-    - `pint.utils.sherman_morrison_dot` and `pint.utils.woodbury_dot`
-    - Refactored repeated code out of `Residuals.calc_phase_mean` and `Residuals.calc_time_mean`
-    - Simplified `Residuals._calc_gls_chi2()` so that it uses Woodbury identity directly
-    - Refactored WLS chi2 code out of `Residuals.calc_chi2()` into a new function `Residuals._calc_wls_chi2()`
-    - `Residuals.d_lnlikelihood_d_whitenoise_param` will throw a `NotImplementedError` when correlated noise is present.
-    - `DownhillFitter._fit_noise()` doesn't use derivatives when correlated noise is present.
-    - Documentation: Noise fitting example notebook.
-- `freeze_params` option in `wavex_setup` and `dmwavex_setup`
-- `plrednoise_from_wavex`, `pldmnoise_from_dmwavex`, and `find_optimal_nharms` functions
-- fake TOAs can be created with `subtract_mean=False`, to maintain phase coherence between different data sets
-- Binary models can be guessed by the `ModelBuilder`. Options and script are added to allow reading/conversion of the T2 binary model
-- Better explanation of ELL1H behavior when H3/H4/STIGMA supplied and when NHARMS is used
-- FDJumpDM component for System-dependent DM offsets
-- Documentation: Explanation for FDJUMP and FDJUMPDM
 ### Fixed
-- `MCMC_walkthrough` notebook now runs
-- Fixed runtime data README 
-- Fixed `derived_params` when OMDOT has 0 uncertainty
-- `model.find_empty_masks` will now also look at DMX and SWX parameters
-- Fixed `make_fake_toas_fromtim`
-- Use `Hessian` instead of `Hessdiag` in `DownhillFitter._fit_noise`; compute noise parameter uncertainties only once in `DownhillFitter.fit_toas`.
-- Consistent naming in `TimingModel.get_params_mapping()`
-- Better exceptions for unsupported/unimplemented binary models (BTX, MSS, etc.)
-- Emit warnings when `WaveX`/`DMWaveX` is used together with other representations of red/DM noise
-- `get_observatory()` no longer overwrites `include_gps` and `include_bipm` of `Observatory` objects unless explicitly stated (BIPM and GPS clock corrections no longer incorrectly applied to BAT TOAs).
-- Added back `spacecraft` as an alias for `stl_geo`
-- Fix bug 1729 (missing f-string)
-- Fixed common failure of test_observatory
-- pintk now shows scaled error bars
-- Docstring of `DispersionJump`
 ### Removed

CHANGELOG.md

@@ -7,6 +7,58 @@ and this project, at least loosely, adheres to [Semantic Versioning](https://sem
 This file contains the released changes to the codebase. See CHANGELOG-unreleased.md for
 the unreleased changes. This file should only be changed while tagging a new version.
 
+## [1.0] 2024-04-26
+### Changed
+- Moved `get_derived_params` to `timing_model`
+- `check_ephemeris_connection` CI test no longer requires access to static NANOGrav site
+- `TimingModel.compare()` now calls `change_binary_epoch()`.
+- When clock files contain out-of-order entries, the exception now records the first MJDs that are out of order
+- `np.compat.long` -> `int` (former is deprecated)
+- Turned ErfaWarning into an exception during testing; cleaned up test suite.
+- macos-latest runner changed to macos-12 runner for CI tests to avoid M1 architecture issues
+### Added
+- Added numdifftools to setup.cfg to match requirements.txt
+- Documentation: Added `convert_parfile` to list of command-line tools in RTD
+- DDH binary model
+- function `pint.utils.xxxselections` to do DMX-style selections for any parameter name
+- Plot model DM in pintk
+- More tests for pintk
+- Maximum likelihood fitting for ECORR
+    - `is_time_correlated` class attribute in correlated `NoiseComponent`s
+    - `has_time_correlated_errors` property in `TimingModel`
+    - `Residuals._calc_ecorr_chi2()` method for fast chi2 computation using Sherman-Morrison identity
+    - `pint.utils.sherman_morrison_dot` and `pint.utils.woodbury_dot`
+    - Refactored repeated code out of `Residuals.calc_phase_mean` and `Residuals.calc_time_mean`
+    - Simplified `Residuals._calc_gls_chi2()` so that it uses Woodbury identity directly
+    - Refactored WLS chi2 code out of `Residuals.calc_chi2()` into a new function `Residuals._calc_wls_chi2()`
+    - `Residuals.d_lnlikelihood_d_whitenoise_param` will throw a `NotImplementedError` when correlated noise is present.
+    - `DownhillFitter._fit_noise()` doesn't use derivatives when correlated noise is present.
+    - Documentation: Noise fitting example notebook.
+- `freeze_params` option in `wavex_setup` and `dmwavex_setup`
+- `plrednoise_from_wavex`, `pldmnoise_from_dmwavex`, and `find_optimal_nharms` functions
+- fake TOAs can be created with `subtract_mean=False`, to maintain phase coherence between different data sets
+- Binary models can be guessed by the `ModelBuilder`. Options and script are added to allow reading/conversion of the T2 binary model
+- Better explanation of ELL1H behavior when H3/H4/STIGMA supplied and when NHARMS is used
+- FDJumpDM component for System-dependent DM offsets
+- Documentation: Explanation for FDJUMP and FDJUMPDM
+### Fixed
+- `MCMC_walkthrough` notebook now runs
+- Fixed runtime data README 
+- Fixed `derived_params` when OMDOT has 0 uncertainty
+- `model.find_empty_masks` will now also look at DMX and SWX parameters
+- Fixed `make_fake_toas_fromtim`
+- Use `Hessian` instead of `Hessdiag` in `DownhillFitter._fit_noise`; compute noise parameter uncertainties only once in `DownhillFitter.fit_toas`.
+- Consistent naming in `TimingModel.get_params_mapping()`
+- Better exceptions for unsupported/unimplemented binary models (BTX, MSS, etc.)
+- Emit warnings when `WaveX`/`DMWaveX` is used together with other representations of red/DM noise
+- `get_observatory()` no longer overwrites `include_gps` and `include_bipm` of `Observatory` objects unless explicitly stated (BIPM and GPS clock corrections no longer incorrectly applied to BAT TOAs).
+- Added back `spacecraft` as an alias for `stl_geo`
+- Fix bug 1729 (missing f-string)
+- Fixed common failure of test_observatory
+- pintk now shows scaled error bars
+- Docstring of `DispersionJump`
+
+
 ## [0.9.8] 2023-12-04
 ### Changed
 - `WAVE` parameters can be added to a `Wave` model with `add_wave_component()` in `wave.py` 

CODE_OF_CONDUCT.md

@@ -37,7 +37,7 @@ This Code of Conduct applies within all community spaces, and also applies when
 
 ## Actions
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the any of the project maintainers:  Scott Ransom <[email protected]>, Jing Luo <[email protected]>, Paul Demorest <[email protected]>, Anne Archibald <[email protected]>, or Paul Ray <paul.ray@nrl.navy.mil>.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the any of the project maintainers:  Scott Ransom <[email protected]>, Paul Demorest <[email protected]>, Anne Archibald <[email protected]>, or Paul Ray <paul.s.ray3.civ@us.navy.mil>.
 
 The project maintainers are obligated to respect the privacy and security of the reporter of any incident.
 

README.rst

@@ -58,8 +58,8 @@ IMPORTANT Notes!
 PINT has a naming conflict with the `pint <https://pypi.org/project/Pint/>`_ units package available from PyPI (i.e. using pip) and conda.  
 Do **NOT** ``pip install pint`` or ``conda install pint``!  See below!
 
-PINT requires ``longdouble`` (80- or 128-bit floating point) arithmetic within ``numpy``, which is currently not supported natively on M1/M2 Macs. 
-However, you can use an x86 version of ``conda`` even on an M1/M2 Mac (which will run under Rosetta emulation): 
+PINT requires ``longdouble`` (80- or 128-bit floating point) arithmetic within ``numpy``, which is currently not supported natively on M1/M2/M3 Macs. 
+However, you can use an x86 version of ``conda`` even on an M1/M2/M3 Mac (which will run under Rosetta emulation): 
 see `instructions for using Apple Intel packages on Apple 
 silicon <https://conda-forge.org/docs/user/tipsandtricks.html#installing-apple-intel-packages-on-apple-silicon>`_. 
 It's possible to have `parallel versions of conda for x86 and 
@@ -121,7 +121,7 @@ If you have tasks that aren't covered in the material above, you can
 email [email protected] or one of the people below:
 
 * Scott Ransom ([email protected])
-* Paul Ray (Paul.Ray@nrl.navy.mil)
+* Paul Ray (paul.s.ray3.civ@us.navy.mil)
 * David Kaplan ([email protected])  
 
 Want to do something new? Submit a github `issue <https://github.com/nanograv/PINT/issues>`_.

src/pint/polycos.py

@@ -32,6 +32,7 @@
 ----------
 http://tempo.sourceforge.net/ref_man_sections/tz-polyco.txt
 """
+
 import astropy.table as table
 import astropy.units as u
 import numpy as np
@@ -84,7 +85,7 @@ class PolycoEntry:
     """One Polyco entry.
 
     Referenced from polyco.py authored by
-        - Paul S. Ray <paul.ray@nrl.navy.mil>
+        - Paul S. Ray <paul.s.ray3.civ@us.navy.mil>
         - Matthew Kerr <[email protected]>
 
     Parameters