Fixed issue with corr_terms and confidence envelopes, and more (#23)

* Fixed issue with use of corr_terms in likelihood function, fixed issue with confidence envelopes in trackplot, added posterior samples to deltaRA-deltaDEC plot, removed the jd_tt parameter and added the ref_epoch parameter to generate_plots, added fileprefix parameter to system class, simplified the extraction of samples by using samples_equal from dynesty, added Github Actions workflow, updated .gitignore, updated package __init__, added unit tests to tests folder, removed all binary files that are not required by the repo, tested compatibility with Python 3.11

* Install numpy separately before orbitize

* Testing installation of dependencies

* Git clone orbitize

* Updated with installing orbitize from Github

* Fixing pip install of orbitize

* Testing Github workflow

* Testing workflow

* Skip dependencies

* Testing installation

* Fixed issue in main.yml

* More testing...

* Even more testing...

* Added requirements without orbitize to workflow folder

* Testing

* Testing

* Added requirements file

* Added import sys

* Fixed issue with data_times

* Fixed minor issue

* Further testing

* Fixing PYTHONPATH

* Added orbitize requirements

* Minor fix

.github/workflows/main.yml

@@ -0,0 +1,49 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get install pandoc
+          pip install --upgrade pip
+          pip install --upgrade numpy cython
+          pip install flake8 pytest pytest-cov sphinx
+          # Install requirements.txt without orbitize
+          pip install -r .github/workflows/requirements.txt
+          git clone https://github.com/sblunt/orbitize.git $HOME/orbitize
+          pip install -r $HOME/orbitize/requirements.txt
+          ls $HOME
+          pwd
+          ls
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Run pytest
+        run: |
+          echo $PYTHONPATH
+          export PYTHONPATH=$HOME/orbitize
+          export PYTHONPATH=$PYTHONPATH:$HOME/work/backtrack/backtrack/
+          echo $PYTHONPATH
+          pytest

src/backtracks.egg-info/requires.txt → .github/workflows/requirements.txt

@@ -6,7 +6,6 @@ matplotlib
 numpy
 novas
 novas_de405
-orbitize
 pandas
 seaborn
 schwimmbad

.gitignore

@@ -1,5 +1,22 @@
+__pycache__
+*.pyc
+.DS_Store
+docs/_build
+docs/.ipynb_checkpoints/
+build/
+dist/
+backtracks.egg-info/
+.coverage*
+coverage.xml
+htmlcov/
+.tox/
 *.ipynb*
 bgstar_emcee.py
-__pycache__
 *beta_pic*
 *SAO*
+.pyproject.toml.sw
+.pytest_cache/
+tests/HD_131399_A_*.png
+tests/HD_131399_A_dynestyrun_results.pkl
+tests/gaia_query_6204835284262018688.fits
+tests/dynesty.save

backtracks/__init__.py

@@ -0,0 +1,8 @@
+from backtracks.backtracks import system
+
+__author__ = "William Balmer"
+__license__ = "BSD-3"
+__version__ = "0.3.1"
+__maintainer__ = "William Balmer"
+__email__ = "[email protected]"
+__status__ = "Development"