solver and gaussian process improvements release (2.4.0 release) (#602)

* add support for differential evolution optimizer solver
* add support for differential corrections optimizer solver
* optimizers: ability to continue runs from previous solutions (for most optimizers)
* improvements to geometry and ebai estimators to use ligeor as a new built-in dependency
* gaussian processes now use celerite2 or scikit-learn instead of celerite
* emcee sampler: additional plotting styles to check for convergence, checks to ensure starting sample is physical, and added ability to continue a previous run from any arbitrary iteration in a previous run
* new support for running jobs on external servers via crimpl
* clarified distinction between chi2 and mle

Author: kecnry

.github/workflows/ci-nosetests.yml

@@ -94,7 +94,7 @@ jobs:
         python -m pip install "numpy${{ matrix.numpy-version }}" --no-cache-dir --ignore-installed
         python -m pip install "scipy${{ matrix.scipy-version }}"
         python -m pip install "astropy${{ matrix.astropy-version }}"
-        python -m pip install nose rebound requests pytest asdf matplotlib sympy requests
+        python -m pip install nose rebound requests pytest asdf matplotlib sympy requests tqdm corner
 
     - name: Test numpy, scipy, astropy install/versions
       run: |

.gitignore

@@ -4,6 +4,9 @@
 /phoebe/atmospheres/tables/ck2004
 /phoebe/atmospheres/tables/ck2004i
 /phoebe/atmospheres/tables/phoenix
+/phoebe/atmospheres/tables/tmap
+/phoebe/atmospheres/tables/tlusty
+/phoebe/atmospheres/tables/phoenix.orig
 MANIFEST
 *_tmp*
 *after.phoebe

README.md

@@ -1,4 +1,4 @@
-PHOEBE 2.3
+PHOEBE 2.4
 ------------------------
 
 <p align="center"><a href="http://phoebe-project.org"><img src="./images/logo_blue.svg" alt="PHOEBE logo" width="160px" align="center"/></a></p>
@@ -18,6 +18,7 @@ PHOEBE 2.3
   <a href="https://ui.adsabs.harvard.edu/abs/2018ApJS..237...26H"><img src="https://img.shields.io/badge/ApJS-Horvat+2018-lightgrey.svg"/></a>
   <a href="https://ui.adsabs.harvard.edu/abs/2020ApJS..247...63J"><img src="https://img.shields.io/badge/ApJS-Jones+2020-lightgrey.svg"/></a>
   <a href="https://ui.adsabs.harvard.edu/abs/2020ApJS..250...34C/"><img src="https://img.shields.io/badge/ApJS-Conroy+2020-lightgrey.svg"/></a>
+  <img src="https://img.shields.io/badge/Kochoska+2022-lightgrey.svg"/>
 </p>
 
 <p align="center">
@@ -32,7 +33,7 @@ PHOEBE stands for PHysics Of Eclipsing BinariEs. PHOEBE is pronounced [fee-bee](
 
 PHOEBE 2 is a rewrite of the original PHOEBE code. For most up-to-date information please refer to the PHOEBE project webpage: [http://phoebe-project.org](http://phoebe-project.org)
 
-PHOEBE 2.0 is described by the release paper published in the Astrophysical Journal Supplement, [Prša et al. (2016, ApJS 227, 29)](https://ui.adsabs.harvard.edu/#abs/2016ApJS..227...29P).  The addition of support for misaligned stars in version 2.1 is described in [Horvat et al. (2018, ApJS 237, 26)](https://ui.adsabs.harvard.edu/#abs/2018ApJS..237...26H).  Interstellar extinction and support for Python 3 was added in version 2.2 and described in [Jones et al. (2020, ApJS 247, 63)](https://ui.adsabs.harvard.edu/abs/2020ApJS..247...63J).  Inclusion of a general framework for solving the inverse problem as well as support for the [web and desktop clients](http://phoebe-project.org/clients) was introduced in version 2.3 as described in [Conroy et al. (2020, ApJS 250, 34)](https://ui.adsabs.harvard.edu/abs/2020ApJS..250...34C), which also removes support for Python 2.
+PHOEBE 2.0 is described by the release paper published in the Astrophysical Journal Supplement, [Prša et al. (2016, ApJS 227, 29)](https://ui.adsabs.harvard.edu/#abs/2016ApJS..227...29P).  The addition of support for misaligned stars in version 2.1 is described in [Horvat et al. (2018, ApJS 237, 26)](https://ui.adsabs.harvard.edu/#abs/2018ApJS..237...26H).  Interstellar extinction and support for Python 3 was added in version 2.2 and described in [Jones et al. (2020, ApJS 247, 63)](https://ui.adsabs.harvard.edu/abs/2020ApJS..247...63J).  Inclusion of a general framework for solving the inverse problem as well as support for the [web and desktop clients](http://phoebe-project.org/clients) was introduced in version 2.3 as described in [Conroy et al. (2020, ApJS 250, 34)](https://ui.adsabs.harvard.edu/abs/2020ApJS..250...34C), which also removes support for Python 2.  PHOEBE 2.4 improves on the geometry and ebai estimators, updates gaussian processes to use either scikit-learn or celerite2, and adds support for submitting compute or solver runs on external servers.  These updates and fitting "best practices" will be discussed in Kochoska et al., in prep.
 
 PHOEBE 2 is released under the [GNU General Public License v3](https://www.gnu.org/licenses/gpl-3.0.en.html).
 
@@ -64,7 +65,7 @@ To install PHOEBE 2 from the source site-wide, go to the `phoebe2/` directory an
     python3 setup.py build
     sudo python3 setup.py install
 
-Note that as of the 2.3 release, PHOEBE requires Python 3.6 or later.  For further details on pre-requisites consult the [PHOEBE project webpage](http://phoebe-project.org/install/2.3).
+Note that as of the 2.3 release, PHOEBE requires Python 3.6 or later.  For further details on pre-requisites consult the [PHOEBE project webpage](http://phoebe-project.org/install/2.4).
 
 
 GETTING STARTED
@@ -78,12 +79,23 @@ PHOEBE 2 has a fairly steep learning curve. To start PHOEBE from python, issue:
 
 As of the 2.3 release, PHOEBE also includes a desktop and web client user-interface which is installed independently of the python package here.  See the [phoebe2-ui repository](https://github.com/phoebe-project/phoebe2-ui) and [phoebe-project.org/clients](http://phoebe-project.org/clients) for more details.
 
-To understand how to use PHOEBE, please consult the [tutorials, scripts and manuals](http://phoebe-project.org/docs/2.3/) hosted on the PHOEBE webpage.
+To understand how to use PHOEBE, please consult the [tutorials, scripts and manuals](http://phoebe-project.org/docs/2.4/) hosted on the PHOEBE webpage.
 
 
 CHANGELOG
 ----------
 
+### 2.4.0 - solver and gaussian process improvements release
+
+* add support for differential evolution optimizer solver
+* add support for differential corrections optimizer solver
+* optimizers: ability to continue runs from previous solutions (for most optimizers)
+* improvements to geometry and ebai estimators to use ligeor as a new built-in dependency
+* gaussian processes now use celerite2 or scikit-learn instead of celerite
+* emcee sampler: additional plotting styles to check for convergence, checks to ensure starting sample is physical, and added ability to continue a previous run from any arbitrary iteration in a previous run
+* new support for running jobs on external servers via crimpl
+* clarified distinction between chi2 and mle
+
 ### 2.3.63 - constraint feature bugfix
 
 * fix bug where creating a custom constraint for parameters within features was not correctly identifying the constrained parameter and was raising an error when attempting to set the value of the constraining parameter.

client-server/phoebe-server

@@ -101,7 +101,6 @@ from distutils.version import StrictVersion
 
 from phoebe.parameters.unit_choices import unit_choices as _unit_choices
 
-phoebe.devel_on() # currently needed for client mode, remove for actual release
 phoebe.interactive_off()
 phoebe.parameters._is_server = True
 
@@ -254,7 +253,8 @@ _available_kinds = {'component': phoebe.list_available_components(),
                     'dataset': phoebe.list_available_datasets(),
                     'figure': phoebe.list_available_figures(),
                     'compute': phoebe.list_available_computes(),
-                    'solver': phoebe.list_available_solvers()}
+                    'solver': phoebe.list_available_solvers(),
+                    'server': phoebe.list_available_servers()}
 
 # logger = phoebe.logger('INFO')
 _dir_tmpimages = os.path.join(tempfile.gettempdir(), 'phoebe-server-tmpimages')
@@ -540,6 +540,8 @@ def info():
     if client_version is not None:
         if StrictVersion(client_version) < StrictVersion('1.0.0'):
             client_warning = 'client still in development'
+        elif StrictVersion(client_version) < StrictVersion('1.1.0'):
+            client_warning = 'client does not support adding or editing servers'
 
 
     info = app._includeinfo