Intial commit

mrlb05 · Sep 16, 2017 · dd17096 · dd17096
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diff --git a/.gitignore b/.gitignore
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+.DS_Store
+test.py
+tesh.sh
+nifsMerge.pyc
+nifsBaselineCalibration.pyc
+nifsDefs.pyc
+nifsReduce.pyc
+nifsSort.pyc
+hd165459
+AEGISz1284
+HD141004
+results
+
+# Compiled python modules.
+*.pyc
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2015, 2017 Marie Lemoine-Busserolle
+
+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.
diff --git a/docs/Makefile b/docs/Makefile
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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = nifty
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/Surely_Youre_Joking_Mr_Feynman.pdf b/docs/Surely_Youre_Joking_Mr_Feynman.pdf
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/faq.doctree b/docs/_build/doctrees/faq.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/nifty/api.doctree b/docs/_build/doctrees/nifty/api.doctree
diff --git a/docs/_build/doctrees/nifty/availableRecipes.doctree b/docs/_build/doctrees/nifty/availableRecipes.doctree
diff --git a/docs/_build/doctrees/nifty/changelog.doctree b/docs/_build/doctrees/nifty/changelog.doctree
diff --git a/docs/_build/doctrees/nifty/directoryModifications.doctree b/docs/_build/doctrees/nifty/directoryModifications.doctree
diff --git a/docs/_build/doctrees/nifty/future_work.doctree b/docs/_build/doctrees/nifty/future_work.doctree
diff --git a/docs/_build/doctrees/nifty/hlineRemoval.doctree b/docs/_build/doctrees/nifty/hlineRemoval.doctree
diff --git a/docs/_build/doctrees/nifty/hline_removal.doctree b/docs/_build/doctrees/nifty/hline_removal.doctree
diff --git a/docs/_build/doctrees/nifty/introduction.doctree b/docs/_build/doctrees/nifty/introduction.doctree
diff --git a/docs/_build/doctrees/nifty/known_issues.doctree b/docs/_build/doctrees/nifty/known_issues.doctree
diff --git a/docs/_build/doctrees/nifty/knownissues.doctree b/docs/_build/doctrees/nifty/knownissues.doctree
diff --git a/docs/_build/doctrees/nifty/maintenance.doctree b/docs/_build/doctrees/nifty/maintenance.doctree
diff --git a/docs/_build/doctrees/nifty/maintenance_and_package_structure.doctree b/docs/_build/doctrees/nifty/maintenance_and_package_structure.doctree
diff --git a/docs/_build/doctrees/nifty/merging.doctree b/docs/_build/doctrees/nifty/merging.doctree
diff --git a/docs/_build/doctrees/nifty/package_index.doctree b/docs/_build/doctrees/nifty/package_index.doctree
diff --git a/docs/_build/doctrees/nifty/preparingInput.doctree b/docs/_build/doctrees/nifty/preparingInput.doctree
diff --git a/docs/_build/doctrees/nifty/preparingJSONinput.doctree b/docs/_build/doctrees/nifty/preparingJSONinput.doctree
diff --git a/docs/_build/doctrees/nifty/preparing_input.doctree b/docs/_build/doctrees/nifty/preparing_input.doctree
diff --git a/docs/_build/doctrees/nifty/runningNifty.doctree b/docs/_build/doctrees/nifty/runningNifty.doctree
diff --git a/docs/_build/doctrees/nifty/running_nifty.doctree b/docs/_build/doctrees/nifty/running_nifty.doctree
diff --git a/docs/_build/doctrees/nifty/tutorials.doctree b/docs/_build/doctrees/nifty/tutorials.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 9c17e57077af89c62b541c5a9b467f75
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_downloads/Surely_Youre_Joking_Mr_Feynman.pdf b/docs/_build/html/_downloads/Surely_Youre_Joking_Mr_Feynman.pdf
diff --git a/docs/_build/html/_sources/faq.rst.txt b/docs/_build/html/_sources/faq.rst.txt
@@ -0,0 +1,12 @@
+What to do When Things Look Funny
+=================================
+
+It Crashed!
+===========
+
+Common Problems:
+----------------
+- If you downloaded from the Gemini Public Archive recently, make sure all of the
+  data is out of its proprietary period and that you have all the data you expect to have.
+
+- 
diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
@@ -0,0 +1,33 @@
+.. nifty documentation master file, created by
+   sphinx-quickstart on Sun Aug 27 21:05:51 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Nifty's documentation!
+=================================
+
+Nifty is a full-featured Gemini NIFS data reduction pipeline and data reduction package.
+
+===========
+User Manual
+===========
+
+For an in-depth explanation of the underlying Python and I/O, see
+:download:`Nifty user manual <Surely_Youre_Joking_Mr_Feynman.pdf>`.
+
+=====================
+Package Documentation
+=====================
+
+.. toctree::
+   :maxdepth: 2
+
+   nifty/introduction.rst
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/_build/html/_sources/nifty/api.rst.txt b/docs/_build/html/_sources/nifty/api.rst.txt
@@ -0,0 +1,2 @@
+API
+===
diff --git a/docs/_build/html/_sources/nifty/availableRecipes.rst.txt b/docs/_build/html/_sources/nifty/availableRecipes.rst.txt
diff --git a/docs/_build/html/_sources/nifty/changelog.rst.txt b/docs/_build/html/_sources/nifty/changelog.rst.txt
@@ -0,0 +1,35 @@
+Changelog
+---------
+
+UNRELEASED
+==========
+
+Changelog
+=========
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+Unreleased
+==========
+All in-development changes will be tracked here.
+
+- Fixing merge flip due to differences between NIFS + ALTAIR and NIFS w/o ALTAIR
+on the bottom port.
+- Adding remaining overwrite blocks.
+- Adding unit tests for each step and integration test for pipeline.
+- Fixing telluric correction and absolute flux calibration.
+
+1.0b1 - 2017-09-08
+==================
+- Preliminary Beta release. Syntax errors mean this version will not compile.
+
+1.0a1 - 2017-08-31
+==================
+
+- Preliminary Alpha release. .whl uploaded to PIP, docs uploaded to
+ReadTheDocs and preliminary DOI assigned.
+
+
+.. placeholder