adding the software docs again...

CITATION.cff

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+If this package is useful for research leading to publication we would appreciate the following acknowledgement:
+
+"The data from the Transiting Exoplanet Survey Satellite (TESS) was acquired using the tessilator software package (Binks et al. 2023)."

LICENSE

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+MIT License
+
+Copyright (c) 2024 Alexander Binks and Hans Moritz Günther
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

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+include LICENSE
+include README.md
+include pyproject.toml

README.rst

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+.. image:: https://github.com/alexbinks/tessilator/blob/main/gif/lc_movie.gif
+  :width: 500 px
+  :align: center
+  :alt: "AB Doradus TESS periods"
+
+
+|DOI|
+
+.. |DOI| image:: https://zenodo.org/badge/588218536.svg
+        :target: https://zenodo.org/badge/latestdoi/588218536
+
+|Documentation Status|
+
+.. |Documentation Status| image:: https://readthedocs.org/projects/tessilator/badge/?version=latest
+                         :target: https://tessilator.readthedocs.io/en/latest/?badge=latest
+
+
+**WELCOME TO THE TESSILATOR**
+=============================
+
+**The one-stop shop for measuring TESS rotation periods**
+
+The tessilator is a python program designed to provide an all-in-one module to measure
+lightcurves and stellar rotation periods from the Transiting Exoplanet Survey
+Satellite (TESS). Whilst there are many useful (and powerful) software tools
+available for working with TESS data, they are mostly provided as various steps
+in the data reduction process --- to our knowledge there are no programs that
+automate the full process from downloading the data (start) to obtaining
+rotation period measurements (finish). The software provided here fills this
+gap. Using as little information as the name of the target, the tessilator is
+capable of providing a robust lightcurve analysis and produces high-quality figures
+and tables ready for publication. Sit back and let the tessilator do the hard work!
+
+The steps are:
+
+(1) download photometric time-series data from TESS.
+
+(2) scan the Gaia DR3 catalogue to quantify the level of background
+    contamination from nearby sources.
+
+(3) clean the lightcurves for poor quality data caused by systematic and
+    instrumental effects.
+
+(4) normalize and detrend lightcurves over the whole sector of observations.
+
+(5) measure stellar rotation periods using the Lomb-Scargle periodogram method
+
+(6) quantify various data quality metrics from photometric time-series data
+    which can be used by the user to assess data reliability
+
+Ways to use the tessilator
+--------------------------
+**Using TESScut to obtain "cutout" images**
+
+In this module, the data is downloaded from `TESSCut (Brasseur et al. 2019) <https://mast.stsci.edu/tesscut/>`_ -- a service which allows the user to acquire a stack of "postage-stamp" image frames ordered in time sequence and centered on the supplied sky coordinate. It uses modules from the `TesscutClass <https://astroquery.readthedocs.io/en/latest/api/astroquery.mast.TesscutClass.html>`_ to download the data, then applies steps 2-6 (above). This software is recommended for users who require a relatively fast extraction for a manageable number of targets. With the correct pre-requisite Python modules and an uninterrupted internet connection, a target with 5 sectors of TESS data takes approximately 1-2 minutes to complete (and approximately 3-4 minutes should the user want to analyse the lightcurves of a few neighbouring contaminants). The user can process a list of targets automatically by calling the ``all_sources_cutout.py`` function
+
+**Analysing full-frame calibrated images**
+
+If the user is interested in conducting a much larger survey, it is faster to run
+the tessilator using the calibrated full-frame images. These can be downloaded in
+bulk at the `MAST archive <https://archive.stsci.edu/tess/bulk_downloads/bulk_downloads_ffi-tp-lc-dv.html>`_.
+This method works much faster than TESS Cutouts because multiple lightcurves can be
+extracted simultaneously due to the vectorisation made possible with numpy/C-style
+methods. The authors have tested this method for a catalogue of ~1 million targets,
+which took less than a week to complete. The user can process a list of targets automatically by calling the ``all_sources_sector.py`` function.
+
+Notes on using the tessilator
+-----------------------------
+Should there be any problems in using this software please contact Alex Binks
+(lead author) at abinks@mit.edu
+
+If this package is useful for research leading to publication we would
+appreciate the following acknowledgement:
+
+"The data from the Transiting Exoplanet Survey Satellite (TESS) was acquired
+using the tessilator software package (Binks et al. 2024)."
+
+Licence: MIT
+
+Alexander Binks and Moritz Guenther, 2024

pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel", "setuptools_scm"]
+build-backend = 'setuptools.build_meta'

requirements.txt

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+astroquery : conda
+pyinputplus : pip

setup.cfg

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+[metadata]
+name = tessilator
+description = The one-stop shop for measuring TESS rotation periods
+long_description = file: README.rst
+author = Alex Binks & Moritz Guenther
+author_email = abinks@mit.edu
+url = https://github.com/alexbinks/tessilator
+license = MIT License
+copyright = 2024, Alex Binks & Moritz Guenther
+
+
+[options]
+zip_safe = False
+packages = find:
+install_requires =
+    numpy
+    astropy
+    astroquery
+    photutils
+    scipy
+    matplotlib
+    pyinputplus
+
+[options.entry_points]
+console_scripts =
+    run_tess_sectors = tessilator.scripts.run_tess_sectors:main
+    run_tess_cutouts = tessilator.scripts.run_tess_cutouts:main
+
+[options.extras_require]
+docs =
+    sphinx
+    sphinx-automodapi
+    sphinx-astropy
+    numpydoc
+test = 
+    pytest-astropy
+    sphinx-astropy
+
+[options.package_data]
+tessilator.tests = ABDor_tests/*, AUMic_tests/*
+
+[tool:pytest]
+addopts = -v

setup.py

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+from setuptools import setup
+setup(use_scm_version=True)

tox.ini

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+[tox]
+envlist =
+    py{39,310}-test{,-alldeps,-devdeps}{,-cov}
+    py{39,310}-test-numpy{117,118}
+    py{39,310}-test-astropy{51,lts}
+    build_docs
+    linkcheck
+    codestyle
+requires =
+    setuptools < 60.0
+    pip >= 19.3.1
+isolated_build = true
+indexserver =
+    NIGHTLY = https://pypi.anaconda.org/scipy-wheels-nightly/simple
+
+[testenv]
+# Suppress display of matplotlib plots generated during docs build
+setenv = MPLBACKEND=agg
+
+# Pass through the following environment variables which may be needed for the CI
+# passenv = HOME,WINDIR,LC_ALL,LC_CTYPE,CC,CI
+
+# Run the tests in a temporary directory to make sure that we don't import
+# this package from the source tree
+changedir = .tmp/{envname}
+
+# tox environments are constructed with so-called 'factors' (or terms)
+# separated by hyphens, e.g. test-devdeps-cov. Lines below starting with factor:
+# will only take effect if that factor is included in the environment name. To
+# see a list of example environments that can be run, along with a description,
+# run:
+#
+#     tox -l -v
+#
+description =
+    run tests
+    alldeps: with all optional dependencies
+    devdeps: with the latest developer version of key dependencies
+    oldestdeps: with the oldest supported version of key dependencies
+    cov: and test coverage
+    numpy116: with numpy 1.16.*
+    numpy117: with numpy 1.17.*
+    numpy118: with numpy 1.18.*
+    astropy30: with astropy 3.0.*
+    astropy40: with astropy 4.0.*
+    astropylts: with the latest astropy LTS
+
+# The following provides some specific pinnings for key packages
+deps =
+
+    cov: coverage
+    numpy116: numpy==1.16.*
+    numpy117: numpy==1.17.*
+    numpy118: numpy==1.18.*
+
+    astropy30: astropy==3.0.*
+    astropy40: astropy==4.0.*
+    astropylts: astropy==4.0.*
+
+    devdeps: :NIGHTLY:numpy
+    devdeps: git+https://github.com/astropy/astropy.git#egg=astropy
+
+# The following indicates which extras_require from setup.cfg will be installed
+extras =
+    test
+    alldeps: all
+
+commands =
+    pip freeze
+    !cov: pytest --pyargs tessilator {toxinidir}/docs {posargs}
+    cov: pytest --pyargs tessilator {toxinidir}/docs --cov tessilator --cov-config={toxinidir}/setup.cfg {posargs}
+    cov: coverage xml -o {toxinidir}/coverage.xml
+
+[testenv:build_docs]
+changedir = docs
+description = invoke sphinx-build to build the HTML docs
+extras = docs
+commands =
+    pip freeze
+    sphinx-build -W -b html . _build/html {posargs:-j auto}
+
+[testenv:linkcheck]
+changedir = docs
+description = check the links in the HTML docs
+extras = docs
+commands =
+    pip freeze
+    sphinx-build -W -b linkcheck . _build/html {posargs:-W}
+
+[testenv:codestyle]
+skip_install = true
+changedir = .
+description = check code style, e.g. with flake8
+deps = flake8
+commands = flake8 marxs --count --max-line-length=100