Merge f7672a4 into 21902eb

.readthedocs.yml

@@ -0,0 +1,21 @@
+# Read the Docs Configuration File
+
+# Build PDF aswell as HTML and JSON
+formats:
+    - pdf
+
+# Requirements file
+requirements_file:
+    requirements_dev.txt
+
+build:
+    image: latest
+
+python:
+    version: 3.6
+    setup_py_install: true
+    # From extras_require in setup.py
+    extra_requirements:
+        - dev
+        - tests
+        - docs

.shippable.yml

@@ -8,7 +8,8 @@ build:
 
   cache_dir_list:
       - $HOME/.cache/pip
-      - $HOME/data/test_data
+      - $HOME/tests/data
+      - $HOME/data
 
   ci:
     - pip install --upgrade pip

.travis.yml

@@ -8,7 +8,8 @@ python:
 cache:
   directories:
     - $HOME/.cache/pip
-    - $HOME/data/test_data
+    - $HOME/tests/data
+    - $HOME/data
 
 install:
   - pip install --upgrade pip
@@ -29,12 +30,14 @@ before_script:
   # Prepare atmosphere models
   - make atmos V=1
   # - python scripts/split_atmmodel.py -b K H J Y Z TEST
-  # - python scripts/bary_shift_atmmodel.py -b K H J Y Z TEST
+  # - python scripts/barycenter_broaden_atmmodel.py -b K H J Y Z TEST
 
 script:
     - pytest --cov=eniric --cov-report term-missing --durations 5
     - coverage xml -i
 
+    - rstcheck -r docs
+
 after_success:
   - coveralls
   - codeclimate-test-reporter

CHANGELOG.md

@@ -17,6 +17,7 @@ To get a list of commit messages since last version to help write change log try
 - Example Notebooks.
 - Add `Contributing.md` and `Contributors.md`.
 - Zip required testing data, Delete unneeded data.
+- Refactor `eniric.Qcalculator` module to `eniric.precision`.
 
 Other:
 - `Blacken` source code.

Makefile

@@ -42,7 +42,7 @@ clean-data:
 
 atmos:
 	split_atmmodel.py -b ALL
-	bary_shift_atmmodel.py -b ALL
+	barycenter_broaden_atmmodel.py -b ALL
 
 clean-build:
 	rm --force --recursive build/

README.md

@@ -1,5 +1,6 @@
 # [ENIRIC](https://github.com/jason-neal/eniric) - Extended Near InfraRed Information Content
 
+[![Documentation Status](https://readthedocs.org/projects/eniric/badge/?version=latest)](https://eniric.readthedocs.io/en/latest/?badge=latest)
 [![Python 3.6+](https://img.shields.io/badge/python-3.6+-blue.svg)](https://www.python.org/downloads/release/python-360/)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/24d3d525a79d4ae493de8c527540edef)](https://www.codacy.com/app/jason-neal/eniric?utm_source=github.com&utm_medium=referral&utm_content=jason-neal/eniric&utm_campaign=badger)
 [![Codacy Badge](https://api.codacy.com/project/badge/Coverage/24d3d525a79d4ae493de8c527540edef)](https://www.codacy.com/app/jason-neal/eniric?utm_source=github.com&utm_medium=referral&utm_content=jason-neal/eniric&utm_campaign=Badge_Coverage)
@@ -13,7 +14,7 @@
 `Eniric` is an overhaul and extension to the code used in [Figueria et al. 2016](http://dx.doi.org/10.1051/0004-6361/201526900) to analysis the precision of M-dwarf stars.
 Extending the performance and usability, it is able to be used on any synthetic spectra from the [PHOENIX-ACES](http://phoenix.astro.physik.uni-goettingen.de) and [BT-Settl](https://phoenix.ens-lyon.fr/Grids/BT-Settl/CIFIST2011_2015/FITS/) (CIFIST2001-2015) libraries.
 
-Checkout the [wiki here](https://github.com/jason-neal/eniric/wiki)!
+Checkout the documentation on [Read the Docs](https://eniric.readthedocs.io/en/latest/)!
 
 ## Features:
 `Eniric` contains a number of features to transform and prepare the spectra (observed and synthetic).
@@ -36,52 +37,42 @@ Checkout the [wiki here](https://github.com/jason-neal/eniric/wiki)!
 
 
 # [Installation](https://github.com/jason-neal/eniric/wiki/Installation)
-Currently to install `Eniric` you need to clone the repo:
-```
-git clone https://github.com/jason-neal/eniric
-cd eniric
-pip install -r requirements.txt
-python setup.py develop
-```
 
-A pip installable version is in the works...
+You can install ``Eniric`` by cloning the current ``master`` branch.
+
+It is recommended to use a ``conda`` or ``virtualenv`` environment.
+To use the most up-to-date packages install the pinned requirements from the ``requirements_dev.txt`` file
+
+    git clone https://github.com/jason-neal/eniric
+    cd eniric
+    pip install -r requirements_dev.txt
+    python setup.py develop
 
-You also need to manually install [Starfish](https://github.com/iancze/Starfish)
+
+Installation from the github repository should also be possible with `pip`.
 
 ```
-git clone git@github.com:iancze/Starfish.git
-cd Starfish
-python setup.py build_ext --inplace
-python setup.py develop
-cd ..
+  pip install https://github.com/jason-neal/eniric/archive/develop.zip#egg=eniric
 ```
-see [here](https://github.com/iancze/Starfish) for more information about installing Starfish.
-For **windows** installation of `Starfish` also see [starfish#87](see https://github.com/iancze/Starfish/issues/87).
+
+
+If there are issues with installing Starfish see [https://github.com/iancze/Starfish](https://github.com/iancze/Starfish)
+
+If you are not going to use `eniric` to analyze PHOENIX-ACES or BT-Settl synthetic spectral models then you may
+get away with not installing it (some tests will just xfail).
 
 ##### Requirements for `Eniric` :
 These should be automatically installed (if not present) when installing `eniric`.
 - astropy
 - joblib>=0.12.3
 - matplotlib
-- numpy
+- numpy>=0.15.4
 - pandas
 - pyyaml
 - scipy
+- Starfish
 - tqdm
 
-If want to use known working pinned versions they can be found in `requirements_dev.txt`.
-To install these run `pip install -r requirements_dev.txt`.
-
-##### Extra requirements for Starfish:
-- corner
-- cython
-- h5py
-- scikit-learn
-
-If you are not going to use `eniric` to analyze PHOENIX-ACES or BT-Settl synthetic spectral models then you may
-get away with not installing it (some tests will just xfail).
-
-
 ## Preparation
 #### Data download
 To download the data for eniric, an atmopsheric transmission spectra and some test Spectra run the
@@ -127,12 +118,12 @@ To perform telluric masking and account for the transmission of Earth's atmosphe
 `Eniric` includes the telluric spectra uses in Figueira et al. 2016, averaged over 2014.
 To automatically prepare the telluric masks, splitting into bands and applying the barycentric expansion run the following scripts:
 - `split_atmmodel.py`
-- `bary_shift_atmmodel.py`
+- `barycenter_broaden_atmmodel.py`
 
 These will split the large telluirc spectra into the bands specified in the `config.yaml` so that the
  opening and slicing of the large telluric spectrum is not performed continually.
 
-To change the telluric line cutoff depth you to 4% can pass (default = 2%) you can pass it like this
+The default depth is 2%. To change the telluric line cutoff depth to 4% you can pass it like this
 
     `split_atmmodel.py --cutoff-depth 4`
 
@@ -160,7 +151,7 @@ You will need to configure the path to the phoenix models in ´config.yaml´
 
 e.g.
 
-    phoenix_precision.py -t 3900 -l 4.5, -m 0.5 -r 100000 -v 1.0 -b J K
+    phoenix_precision.py -t 3900 -l 4.5 -m 0.5 -r 100000 -v 1.0 -b J K
 
 Will calculate the RV precision in the `J` and `K`-band of the PHOENIX-ACES spectra with parameters \[Teff=3900K, logg=4.5, \[Fe/H\]=0.5\] observed at a resolution of 100,000 and rotating with 1.0 km/s.
 For more details on the command line arguments to use see the [wiki](https://github.com/jason-neal/eniric/wiki) or type
@@ -223,4 +214,4 @@ It had a number of efficiency issues with convolution which were improved upon
 
 To reproduce the updated results for [Figueira et al. 2016](http://dx.doi.org/10.1051/0004-6361/201526900) run
 
-    phoenix_precision.py -t 3900 3500 2800 2600 -l 4.5, -m 0.5 -r 60000 80000 100000 -v 1.0 5.0 10.0 -b Z Y J H K
+    phoenix_precision.py -t 3900 3500 2800 2600 -l 4.5 -m 0.5 -r 60000 80000 100000 -v 1.0 5.0 10.0 -b Z Y J H K

appveyor.yml

@@ -3,13 +3,13 @@ environment:
     # For Python versions available on Appveyor, see
     # http://www.appveyor.com/docs/installed-software#python
     - PYTHON: "C:\\Python36"
-    - PYTHON: "C:\\Python37"
-    - PYTHON: "C:\\Python36-x64"
     - PYTHON: "C:\\Python37-x64"
 
 cache:
   - "%LOCALAPPDATA%\\pip\\Cache -> appveyor.yml" # Use cache unless appveyor.yml changes.
-  - "data\\test_data -> appveyor.yml"           # Use cache unless appveyor.yml changes.
+  - "tests\\data -> appveyor.yml"
+  - "data\\ -> appveyor.yml"
+  - "tests\\data -> appveyor.yml"
 
 install:
   - SET PATH=%PYTHON%;%PYTHON%\Scripts\;%path%
@@ -32,7 +32,7 @@ install:
 
   # Prepare atmosphere models
   - cmd: "%PYTHON%\\python.exe scripts\\split_atmmodel.py -b ALL"
-  - cmd: "%PYTHON%\\python.exe scripts\\bary_shift_atmmodel.py -b ALL"
+  - cmd: "%PYTHON%\\python.exe scripts\\barycenter_broaden_atmmodel.py -b ALL"
 
 build: off
 

conftest.py

@@ -33,7 +33,7 @@ def model_parameters(request):
     return request.param
 
 
-# Define some fixtures for Qcalculator.
+# Define some fixtures for eniric.precision.
 per_s_cm2 = (1 / u.second) / (u.centimeter ** 2)
 
 

docs/.rstcheck.cfg

@@ -0,0 +1,5 @@
+[rstcheck]
+ignore_directives=
+ignore_roles=
+ignore_messages=(Unknown directive type "autoclass".|No directive entry for "autoclass" in module "docutils.parsers.rst.languages.en".|Unknown directive type "automodule".|Unknown directive type "autofunction".|No directive entry for "autofunction" in module "docutils.parsers.rst.languages.en".|No directive entry for "automodule" in module "docutils.parsers.rst.languages.en".)
+report=warning

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+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)