exovetter 0.0.1__tar.gz → 0.0.3__tar.gz

exovetter-0.0.3/.bandit.yaml

@@ -0,0 +1,2 @@
+exclude_dirs:
+  - tests

exovetter-0.0.3/.github/workflows/ci_workflows.yml

@@ -0,0 +1,74 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  pep_and_audit:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+    - name: Lint with pyflakes
+      run: |
+        python -m pip install --upgrade pip pyflakes
+        pyflakes
+    # Make sure that packaging will work
+    - name: pep517 build
+      run: |
+        python -m pip install --upgrade setuptools build twine
+        python -m build --sdist .
+        twine check dist/*
+    # This test turned off for the moment
+    #- name: Security audit
+    #  run: |
+    #    python -m pip install --upgrade bandit
+    #    bandit -r . -c .bandit.yaml
+
+  initial_tests:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - name: Install and build
+      run: |
+        sudo apt-get install libxml2-utils
+        python -m pip install --upgrade pip setuptools
+        python -m pip install -e .[test,all]
+    - name: Test with stable deps and coverage
+      run: pytest --remote-data
+#      run: pytest --cov=./ --cov-report=xml --remote-data
+#    - name: Coverage report
+#      uses: codecov/codecov-action@v3
+
+#  dev_deps_tests:
+#    runs-on: ubuntu-latest
+#    steps:
+#    - name: Checkout code
+#      uses: actions/checkout@v4
+#    - name: Set up Python
+#      uses: actions/setup-python@v4
+#      with:
+#        python-version: '3.x'
+#    - name: Install and build
+#      run: |
+#        sudo apt-get install libxml2-utils
+#        python -m pip install --upgrade pip setuptools
+#        python -m pip install git+https://github.com/astropy/astropy.git@main#egg=astropy
+#        python -m pip install git+https://github.com/lightkurve/lightkurve.git@main#egg=lightkurve
+#        python -m pip install -e .[test,all]
+#    - name: Test with dev deps
+#      run: pytest --remote-data

exovetter-0.0.3/.github/workflows/publish.yml

@@ -0,0 +1,38 @@
+name: Release
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    if: github.repository == 'spacetelescope/exovetter'
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install python-build and twine
+      run: python -m pip install build "twine>=3.3"
+
+    - name: Build package
+      run: python -m build --sdist --wheel .
+
+    - name: List result
+      run: ls -l dist
+
+    - name: Check dist
+      run: python -m twine check --strict dist/*
+
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}

exovetter-0.0.3/.readthedocs.yml

@@ -0,0 +1,30 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  apt_packages:
+    - graphviz
+  tools:
+    python: "3.11"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - all
+
+# Don't build any extra formats
+formats: []

exovetter-0.0.3/PKG-INFO

@@ -0,0 +1,89 @@
+Metadata-Version: 2.1
+Name: exovetter
+Version: 0.0.3
+Summary: Exoplanet vetting package
+Home-page: https://github.com/spacetelescope/exovetter
+Author: Susan Mullally et al.
+Author-email: smullally@stsci.edu
+License: BSD 3-Clause
+Requires-Python: >=3.7
+Description-Content-Type: text/x-rst
+License-File: LICENSE.rst
+Requires-Dist: numpy
+Requires-Dist: astropy>=3
+Requires-Dist: scipy
+Provides-Extra: all
+Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: scikit-learn; extra == "all"
+Requires-Dist: lightkurve>=2; extra == "all"
+Requires-Dist: lpproj; extra == "all"
+Provides-Extra: test
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-remotedata; extra == "test"
+Requires-Dist: pytest-doctestplus; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx-astropy; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+
+exovetter: Exoplanet Vetting
+============================
+
+.. image:: https://readthedocs.org/projects/exovetter/badge/?version=latest
+    :target: https://exovetter.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. image:: https://github.com/spacetelescope/exovetter/workflows/CI/badge.svg
+    :target: https://github.com/spacetelescope/exovetter/actions
+    :alt: Github Actions CI Status
+
+.. image:: https://codecov.io/gh/spacetelescope/exovetter/branch/master/graph/badge.svg?token=H3UC4Q0H6R
+    :target: https://codecov.io/gh/spacetelescope/exovetter
+    :alt: Coverage report
+
+.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
+    :target: http://www.astropy.org
+    :alt: Powered by Astropy Badge
+
+This is a Python package for exoplanet vetting.
+
+License
+-------
+
+This project is Copyright (c) Space Telescope Science Institute and licensed
+under the terms of the BSD 3-Clause license. This package is based upon
+the `Astropy package template <https://github.com/astropy/package-template>`_
+which is licensed under the BSD 3-clause license. See `LICENSE.rst` and
+the licenses folder for more information.
+
+
+Contributing
+------------
+
+We love contributions! exovetter is open source,
+built on open source, and we'd love to have you hang out in our community.
+
+**Imposter syndrome disclaimer**: We want your help. No, really.
+
+There may be a little voice inside your head that is telling you that you're not
+ready to be an open source contributor; that your skills aren't nearly good
+enough to contribute. What could you possibly offer a project like this one?
+
+We assure you - the little voice in your head is wrong. If you can write code at
+all, you can contribute code to open source. Contributing to open source
+projects is a fantastic way to advance one's coding skills. Writing perfect code
+isn't the measure of a good developer (that would disqualify all of us!); it's
+trying to create something, making mistakes, and learning from those
+mistakes. That's how we all improve, and we are happy to help others learn.
+
+Being an open source contributor doesn't just mean writing code, either. You can
+help out by writing documentation, tests, or even giving feedback about the
+project (and yes - that includes giving feedback about the contribution
+process). Some of these contributions may be the most valuable to the project as
+a whole, because you're coming to the project with fresh eyes, so you can see
+the errors and assumptions that seasoned contributors have glossed over.
+
+Note: This disclaimer was originally written by
+`Adrienne Lowe <https://github.com/adriennefriend>`_ for a
+`PyCon talk <https://www.youtube.com/watch?v=6Uj746j9Heo>`_, and was adapted by
+exovetter based on its use in the README file for the
+`MetPy project <https://github.com/Unidata/MetPy>`_.

{exovetter-0.0.1 → exovetter-0.0.3}/README.rst

@@ -1,5 +1,17 @@
 exovetter: Exoplanet Vetting
-----------------------------
+============================
+
+.. image:: https://readthedocs.org/projects/exovetter/badge/?version=latest
+    :target: https://exovetter.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. image:: https://github.com/spacetelescope/exovetter/workflows/CI/badge.svg
+    :target: https://github.com/spacetelescope/exovetter/actions
+    :alt: Github Actions CI Status
+
+.. image:: https://codecov.io/gh/spacetelescope/exovetter/branch/master/graph/badge.svg?token=H3UC4Q0H6R
+    :target: https://codecov.io/gh/spacetelescope/exovetter
+    :alt: Coverage report
 
 .. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
     :target: http://www.astropy.org

{exovetter-0.0.1 → exovetter-0.0.3}/docs/index.rst

@@ -8,4 +8,6 @@ exovetter
   :maxdepth: 2
 
   install
-  api
+  vetters
+  vetters_low_level
+  utils

exovetter-0.0.3/docs/install.rst

@@ -0,0 +1,52 @@
+.. _install_instructions:
+
+============
+Installation
+============
+
+``exovetter`` requires the following packages on install:
+
+* numpy
+* astropy
+* scipy
+
+We also recommend you have the following packages install to access all the
+functionality that ``exovetter`` provides:
+
+* matplotlib
+* scikit-learn
+* lightkurve
+* lpproj
+
+.. _install_stable:
+
+Install the Stable Version
+==========================
+
+.. warning:: Do not use the released version yet. This package is still in heavy development. See :ref:`install_dev` instead.
+
+To install the released version from PyPI::
+
+    pip install exovetter[all]
+
+.. _install_dev:
+
+Install the Development Version
+===============================
+
+First, clone this repository to your local machine::
+
+    git clone https://github.com/spacetelescope/exovetter.git
+
+Then, in the source directory, do the following to install it as an
+"editable" install, along with all the dependencies::
+
+    pip install -e .[test,docs,all]
+
+Post-Install
+============
+
+To see whether your installation is successful, you can try to import the
+package in a Python session:
+
+    >>> import exovetter

exovetter-0.0.3/docs/utils.rst

@@ -0,0 +1,23 @@
+.. _utils:
+
+===============
+Utility Modules
+===============
+
+These provide low-level functionality for ``exovetter``.
+
+.. automodapi:: exovetter.const
+    :no-inheritance-diagram:
+    :include-all-objects:
+
+.. automodapi:: exovetter.model
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.lightkurve_utils
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.trapezoid_fit
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.utils
+    :no-inheritance-diagram:

exovetter-0.0.3/docs/vetters.rst

@@ -0,0 +1,11 @@
+.. _vetters-main:
+
+=======
+Vetters
+=======
+
+``exovetter`` provides the following vetters that are built upon
+:ref:`vetters-building-blocks`.
+
+.. automodapi:: exovetter.vetters
+    :no-main-docstr:

exovetter-0.0.3/docs/vetters_low_level.rst

@@ -0,0 +1,40 @@
+.. _vetters-building-blocks:
+
+=======================
+Vetters Building Blocks
+=======================
+
+The high-level vetter classes in :ref:`vetters-main` utilize lower level
+implementations laid out in :ref:`vetters-low-level` and pass around a data
+structure for Threshold Crossing Event (TCE) as documented in
+:ref:`vetters_tce_data_structure`.
+
+
+.. _vetters-low-level:
+
+Low-Level Vetter API
+====================
+
+.. automodapi:: exovetter.lpp
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.modshift
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.odd_even
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.sweet
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.transit_coverage
+    :no-inheritance-diagram:
+
+
+.. _vetters_tce_data_structure:
+
+Data Structure: Tce Class
+=========================
+
+.. automodapi:: exovetter.tce
+    :no-inheritance-diagram:

exovetter-0.0.3/example_notebooks/Centorid_Vetting_Example.ipynb

@@ -0,0 +1,222 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "029ab771-1196-408e-a57b-520e813bb764",
+   "metadata": {},
+   "source": [
+    "# Example: Centroid Vetting.\n",
+    "### How to look for centroid offset between in and out of transit\n",
+    "In this example we show how to use the vetting module to visualize the transit and take the difference between the in transit and out of transit to determine if there is a centroid offset between the two."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "3c1ea491-efeb-4662-9f9f-84a5327229f3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy\n",
+    "import matplotlib\n",
+    "import exovetter as exo\n",
+    "from exovetter import const\n",
+    "from exovetter import utils\n",
+    "import exovetter.vetters as vet\n",
+    "import lightkurve as lk\n",
+    "import astropy.units as u"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "e6212cc7-f877-40fb-9d61-618d751f4df6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#Name of our first TOI Example\n",
+    "candidate = \"TOI 1013.01\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d69d0c9d-ed1b-4a6c-a8cb-a62cf09b1bc3",
+   "metadata": {},
+   "source": [
+    "### Use a utility function get_mast_tce to get the properties of the candidate and put into a tce."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "9be9771e-7a96-4867-8df4-2b603e453ed3",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[{'period': <Quantity 5.42555479 d>,\n",
+       "  'epoch': <Quantity 58493.86798 d>,\n",
+       "  'epoch_offset': <Quantity -2400000.5 d>,\n",
+       "  'depth': <Quantity 0.01493963>,\n",
+       "  'duration': <Quantity 0.15745833 d>,\n",
+       "  'target': 'TOI 1013.01'}]"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tce = utils.get_mast_tce(candidate)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4ba5953d-50f5-40ac-9973-4bce4927f039",
+   "metadata": {},
+   "source": [
+    "### Grab the light curve using lightkurve"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "56e7d673-878b-4ebb-9d6d-71b442547a73",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lc = lk.search_lightcurve(candidate, sector=33, exptime=120).download()\n",
+    "lc.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "254d0d3f-c1b3-4663-a2c2-38713c6dcb86",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#Visualize the transits\n",
+    "#Initiate the vetter\n",
+    "viz = vet.VizTransits()\n",
+    "\n",
+    "#Run the vetter on the tce and lightcurve of your choice.\n",
+    "viz.run(tce[0], lc, plot=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cc645b95-4488-45a1-ab74-a5105f0039ea",
+   "metadata": {},
+   "source": [
+    "## Run the Centroid Vetter\n",
+    "The Centroid Vetter is run in the same way. It returns the average offset and significance that it is on the target.\n",
+    "You get several plots showing the out of transits, in transit and difference image. The centroids of each are measured using a Gaussian.\n",
+    "For the OOT and In-Transit, the centroid is constrained to the central +/-1pixel in box row and column direction.\n",
+    "As input, the Centroid Vetter requires a Target Pixel File objects from lightkurve.\n",
+    "\n",
+    "This example shows no significant offset between the out of transit location and the difference image centroid."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "85219b48-3ca3-42d2-a0c4-a6aabf2df99b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "tpf = lk.search_targetpixelfile(candidate, sector=33, exptime=120).download()\n",
+    "cent = vet.Centroid()\n",
+    "cent.run(tce[0],tpf, plot=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d02f48c6-9c09-4d06-84cd-7f82ac711b64",
+   "metadata": {},
+   "source": [
+    "## Example 2. An example with a small put possible offset.\n",
+    "Here we will do the same thing on TOI 565.01"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26ac4dd8-600e-4eac-adf4-4536a8057dae",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "candidate = \"TOI 565.01\"\n",
+    "tce = utils.get_mast_tce(candidate)\n",
+    "tce"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bb624aac-2c6f-4671-b879-766ab8e8e924",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lc = lk.search_lightcurve(candidate)[0].download()\n",
+    "lc.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f9b699d3-22b4-4f0d-a7df-c64421a40445",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "viz = vet.VizTransits(max_transits=8)\n",
+    "viz.run(tce[0],lc, plot=True, )"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ce1e2dcc-2ec1-4e85-8278-38f40464541d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#Examine difference images and measure centroids\n",
+    "tpf = lk.search_targetpixelfile(candidate)[0].download()\n",
+    "cent = vet.Centroid()\n",
+    "cent.run(tce[0],tpf,plot=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c1451eae",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}