Fix merge errors

.github/workflows/ci_test.yml

@@ -2,9 +2,9 @@ name: enterprise CI targets
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, dev ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, dev ]
   release: 
     types:
       - published
@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
     - name: Checkout repository
@@ -38,6 +38,9 @@ jobs:
         sudo apt-get install libsuitesparse-dev
         curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
+      env:
+        SUITESPARSE_INCLUDE_DIR: "/usr/local/opt/suite-sparse/include/suitesparse/"
+        SUITESPARSE_LIBRARY_DIR: "/usr/local/opt/suite-sparse/lib"
       run: |
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install -r requirements_dev.txt
@@ -69,7 +72,7 @@ jobs:
     - name: Set up Python 
       uses: actions/setup-python@v4
       with:
-        python-version: "3.7"
+        python-version: "3.8"
     - name: Install non-python dependencies on linux
       run: |
         sudo apt-get install libsuitesparse-dev
@@ -115,7 +118,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.7'
+        python-version: '3.8'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -130,4 +133,4 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        twine upload dist/*
+        twine upload dist/*

CONTRIBUTING.rst

@@ -57,12 +57,38 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `enterprise` for local development.
+Ready to contribute? Here's how to set up ``enterprise`` for local development.
 
-1. Fork the `enterprise` repo on GitHub.
+Install the dependencies
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+``enterprise`` relies on a lot of other software to function.
+If you use the Anaconda distribution of Python, you can get all of this software using ``conda``.
+First, you install the latest stable version of ``enterprise``, which will come with all of the dependencies.
+Then you remove ``enterprise`` leaving everything else intact.
+This way you can use your development version of ``enterprise`` instead of the stable version.
+We will also need some additional software that is required to run the tests.
+
+Start with a virtual environment with the extra dependencies required for running tests. In this case it is called ``ent_dev``::
+
+    $ conda create -n ent_dev -y -c conda-forge python=3.9 black=22.3.0 flake8 sphinx_rtd_theme pytest-cov
+    $ conda activate ent_dev
+
+Now install everything else by running the commands::
+
+    $ conda install -c conda-forge enterprise-pulsar
+    $ conda remove enterprise-pulsar --force
+    $ pip install coverage-conditional-plugin
+
+
+Get the enterprise source code and get to work!
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+1. Fork the ``enterprise`` repo on GitHub.
 2. Clone your fork locally::
 
     $ git clone git@github.com:your_name_here/enterprise.git
+    $ cd enterprise/
     
 3. Set `enterprise/master` as upstream remote::
     
@@ -73,17 +99,25 @@ Ready to contribute? Here's how to set up `enterprise` for local development.
     $ git pull upstream master
 
 4. This is how you set up your fork for local development:
-
+    
     .. note:: 
-        You will need to have ``tempo`` and ``suitesparse`` installed before  
-        running the commands below. 
+        You will need to have ``tempo2`` and ``suitesparse`` installed before  
+        running these commands.
 
- ::
+        If you installed the dependencies via conda, you are good to go!
 
-    $ cd enterprise/
+    If you set up a ``conda`` virtual environment with the dependencies already,
+    you can add your local fork of ``enterprise`` to it by running::
+
+    $ pip install -e .
+
+    If you manually installed the dependencies, this will make and activate a 
+    Python3 virtual env with your local fork of ``enterprise``::
+    
     $ make init
     $ source .enterprise/bin/activate  
 
+
 5. Create a branch for local development::
 
     $ git checkout -b name-of-your-bugfix-or-feature
@@ -93,7 +127,6 @@ Ready to contribute? Here's how to set up `enterprise` for local development.
 6. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox (tox not implemented yet). Also check that any new docs are formatted correctly::
 
     $ make test
-    $ make lint
     $ make docs
 
    To get flake8 and tox, just pip install them into your virtualenv.
@@ -114,9 +147,8 @@ Before you submit a pull request, check that it meets these guidelines:
 1. The pull request should include tests.
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring.
-3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
-   https://travis-ci.org/nanograv/enterprise/pull_requests
-   and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for all supported versions of Python: 3.8, 3.9, 3.10, and 3.11. You
+   can see the progress of the tests in the `Checks` tab of your GitHub pull request.
 
 Tips
 ----
@@ -130,3 +162,4 @@ To track and checkout another user's branch::
     $ git remote add other-user-username https://github.com/other-user-username/enterprise.git
     $ git fetch other-user-username
     $ git checkout --track -b branch-name other-user-username/branch-name
+

README.md

@@ -5,7 +5,7 @@
 [![Build Status](https://github.com/nanograv/enterprise/workflows/CI-Tests/badge.svg)](https://github.com/nanograv/enterprise/actions)
 [![Documentation Status](https://readthedocs.org/projects/enterprise/badge/?version=latest)](https://enterprise.readthedocs.io/en/latest/?badge=latest)
 [![Test Coverage](https://codecov.io/gh/nanograv/enterprise/branch/master/graph/badge.svg?token=YXSX3293VF)](https://codecov.io/gh/nanograv/enterprise)
-![Python Versions](https://img.shields.io/badge/python-3.7%2C%203.8%2C%203.9%2C%203.10-blue.svg)
+![Python Versions](https://img.shields.io/badge/python-3.8%2C%203.9%2C%203.10%2C%203.11-blue.svg)
 
 [![Zenodo DOI 4059815](https://zenodo.org/badge/DOI/10.5281/zenodo.4059815.svg)](https://doi.org/10.5281/zenodo.4059815)
 
@@ -14,7 +14,7 @@ Inference SuitE) is a pulsar timing analysis code, aimed at noise
 analysis, gravitational-wave searches, and timing model analysis.
 
 -   Note: `enterprise>=3.0` does not support Python2.7. You must use
-    Python \>= 3.7.
+    Python \>= 3.8.
 -   Free software: MIT license
 -   Documentation: <https://enterprise.readthedocs.io>.
 

docs/index.rst

@@ -15,7 +15,7 @@ Welcome to enterprise's documentation!
 .. image:: https://codecov.io/gh/nanograv/enterprise/branch/master/graph/badge.svg?token=YXSX3293VF
         :target: https://codecov.io/gh/nanograv/enterprise
         :alt: Test Coverage
-.. image:: https://img.shields.io/badge/python-3.6%2C%203.7%2C%203.8-blue.svg
+.. image:: https://img.shields.io/badge/python-3.8%2C%203.9%2C%203.10%2C%203.11-blue.svg
         :alt: Python Versions
 
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4059815.svg

docs/installation.rst

@@ -23,6 +23,17 @@ Installation
 .. .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
 
 
+Using conda
+-----------
+
+``enterprise`` is available via conda-forge as `enterprise-pulsar <https://anaconda.org/conda-forge/enterprise-pulsar>`_.
+If you use the Anaconda distribution of Python, we strongly recommend installing via the ``conda`` command:
+
+.. code-block:: console
+
+    $ conda install -c conda-forge enterprise-pulsar
+
+
 From sources
 ------------
 
@@ -57,3 +68,11 @@ If you want to run tests or do any other development then also run:
 
 .. _Github repo: https://github.com/nanograv/enterprise
 .. _tarball: https://github.com/nanograv/enterprise/tarball/master
+
+
+Tips
+----
+
+If you have a computer with an Apple Silicon chip, see `these instructions`_ on how to install Apple Intel packages using Rosetta.
+
+.. _these instructions: https://conda-forge.org/docs/user/tipsandtricks.html#installing-apple-intel-packages-on-apple-silicon

enterprise/pulsar.py

@@ -9,10 +9,9 @@
 import pickle
 from io import StringIO
 
-import astropy.constants as const
-import astropy.units as u
 import numpy as np
 from ephem import Ecliptic, Equatorial
+from astropy.time import Time
 
 import enterprise
 from enterprise.signals import utils
@@ -36,6 +35,13 @@
     logger.warning("PINT not installed. Will use libstempo instead.")  # pragma: no cover
     pint = None
 
+try:
+    import astropy.constants as const
+    import astropy.units as u
+except ImportError:  # pragma: no cover
+    const = None
+    u = None
+
 if pint is None and t2 is None:
     err_msg = "Must have either PINT or libstempo timing package installed"
     raise ImportError(err_msg)
@@ -110,7 +116,11 @@ def _get_radec_from_ecliptic(self, elong, elat):
 
     def _get_pos(self):
         return np.array(
-            [np.cos(self._raj) * np.cos(self._decj), np.sin(self._raj) * np.cos(self._decj), np.sin(self._decj)]
+            [
+                np.cos(self._raj) * np.cos(self._decj),
+                np.sin(self._raj) * np.cos(self._decj),
+                np.sin(self._decj),
+            ]
         )
 
     def sort_data(self):
@@ -368,7 +378,11 @@ def __init__(self, toas, model, sort=True, drop_pintpsr=True, planets=True):
             "AstrometryEquatorial" if "AstrometryEquatorial" in model.components else "AstrometryEcliptic"
         )
 
-        self._pos_t = model.components[which_astrometry].ssb_to_psb_xyz_ICRS(model.get_barycentric_toas(toas)).value
+        self._pos_t = (
+            model.components[which_astrometry]
+            .ssb_to_psb_xyz_ICRS(Time(model.get_barycentric_toas(toas), format="mjd"))
+            .value
+        )
 
         self.sort_data()