Merge remote-tracking branch 'upstream/release-v0.10.x' into stable

# Conflicts:
#	README.rst
#	doc/conf.py
#	megaradrp/__init__.py
#	megaradrp/recipes/auxiliary/acquisitionlcb.py
#	megaradrp/recipes/calibration/lcbstdstar.py
#	megaradrp/recipes/calibration/mosstdstar.py
#	setup.py

.readthedocs.yml

@@ -0,0 +1,25 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: doc/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: 
+  - htmlzip
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+  - requirements: doc/requirements.txt
+

.travis.yml

@@ -4,11 +4,15 @@ sudo: false
 matrix:
   include:
     - python: "2.7"
-      env: DEPS="numpy scipy astropy==2.0 enum34"
+      env: DEPS="numpy scipy astropy==2.0.16 enum34"
     - python: "3.5"
-      env: DEPS="numpy scipy astropy==3.0" COVERAGE=true
+      env: DEPS="numpy scipy astropy==3.2.3"
     - python: "3.6"
-      env: DEPS="numpy scipy astropy==3.0"
+      env: DEPS="numpy scipy astropy==4.0.1"
+    - python: "3.7"
+      env: DEPS="numpy scipy astropy==4.0.1" COVERAGE=true
+    - python: "3.8"
+      env: DEPS="numpy scipy astropy==4.0.1"
 
 cache:
   pip: true
@@ -19,15 +23,14 @@ install:
   - pip install Cython
   - pip install "numpy>=1.16"
   - pip install git+git://github.com/guaix-ucm/numina.git#egg=numina
-  - pip install $DEPS scikit-image pip pytest setuptools Cython six>=1.7
-  - pip install pytest-benchmark pytest-cov
+  - pip install $DEPS scikit-image pytest setuptools six>=1.7 jsonschema
   - pip install pytest-remotedata
   - if [[ $COVERAGE == true ]]; then pip install coveralls; fi
   - if [[ $COVERAGE == true ]]; then pip install codeclimate-test-reporter; fi
 
 script:
-  - py.test -s -v megaradrp
-  - if [[ $COVERAGE == true ]]; then py.test megaradrp --cov=megaradrp; fi
+  - pytest megaradrp
+  - if [[ $COVERAGE == true ]]; then coverage run --source megaradrp -m pytest; fi
 
 after_success:
   - if [[ $COVERAGE == true ]]; then coveralls; fi

README.rst

@@ -3,37 +3,51 @@
 MEGARA DRP
 ==========
 
-|zenodo|
+|zenodo| |docs| |pypi| |travis| |coveralls|
 
-.. image:: https://readthedocs.org/projects/megara-drp/badge/?version=latest
-   :target: https://readthedocs.org/projects/megara-drp/?badge=latest
-   :alt: Documentation Status
 
-.. image:: https://travis-ci.org/guaix-ucm/megaradrp.svg?branch=master
-    :target: https://travis-ci.org/guaix-ucm/megaradrp
+This is Megara DRP, the data reduction pipeline for MEGARA, 
+the optical Integral-Field Unit and Multi-Object Spectrograph
+designed for the Gran telescopio Canarias (GTC).
+
 
-.. image:: https://coveralls.io/repos/guaix-ucm/megaradrp/badge.svg?branch=master&service=github 
-    :target: https://coveralls.io/github/guaix-ucm/megaradrp?branch=master 
+You can install `megaradrp` using
+the `released code in PyPI <https://pypi.org/project/megaradrp/>`_ or
+the `development version in Github <https://github.com/guaix-ucm/megaradrp>`_.
 
+The installation instructions are available in the
+`online documentation <https://megaradrp.readthedocs.io/en/latest/installation.html>`_
+or `doc/installation.rst <doc/installation.rst>`_ in the source distribution.
 
-This is Megara DRP, the data reduction pipeline for MEGARA
+
+Licensing
+---------
 
 Megara DRP is distributed under GNU GPL, either version 3 of the License,
 or (at your option) any later version. See the file LICENSE.txt for details.
 
-Python 2.7 or 3.4 (or greater) is required. Megara DRP requires the following packages
-installed in order to be able to be installed and work properly:
-
- - setuptools (http://peak.telecommunity.com/DevCenter/setuptools)
- - numpy >= 1.7 (http://www.numpy.org/)
- - scipy (http://www.scipy.org)
- - astropy >= 2.0 (http://www.astropy.org/)
- - numina >= 0.21 (http://guaix.fis.ucm.es/projects/numina/)
- - scikit-image (http://scikit-image.org/)
+Authors
+-------
 
 Webpage: https://guaix.fis.ucm.es/megara
 
 Maintainers: Sergio Pacual sergiopr@fis.ucm.es, Nicolás Cardiel cardiel@ucm.es
 
 .. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.593647.svg
    :target: https://zenodo.org/record/593647
+
+.. |docs| image:: https://readthedocs.org/projects/megaradrp/badge/?version=latest
+   :target: https://readthedocs.org/projects/megaradrp/?badge=latest
+   :alt: Documentation Status
+
+.. |pypi| image:: https://badge.fury.io/py/megaradrp.svg
+    :target: https://badge.fury.io/py/megaradrp
+
+.. |travis| image:: https://img.shields.io/travis/guaix-ucm/megaradrp/master?logo=travis%20ci&logoColor=white&label=Travis%20CI
+    :target: https://travis-ci.org/guaix-ucm/megaradrp
+    :alt: megaradrp's Travis CI Status
+
+.. |coveralls| image:: https://coveralls.io/repos/guaix-ucm/megaradrp/badge.svg?branch=master&service=github
+    :target: https://coveralls.io/github/guaix-ucm/megaradrp?branch=master
+     :alt: megaradrp's Coverall Status
+

doc/calibration/index.rst

@@ -78,6 +78,5 @@ MEGARA team.
    fiberflat
    twilight
    bpm
-   linearity
    lcbstd
    mosstd

doc/conf.py

@@ -27,8 +27,8 @@
 
 project = u'MEGARA Data Reduction Pipeline'
 copyright = u'2013-2020, Universidad Complutense de Madrid'
-version = '0.9'
-release = '0.9.3'
+version = '0.10'
+release = '0.10.1'
 show_authors = True
 
 numpydoc_show_class_members = False

doc/installation.rst

@@ -9,13 +9,14 @@ Requirements
 The MEGARA Pipeline package requires the following packages installed in order to
 be able to be installed and work properly:
 
- - `python <https://www.python.org>`_ either 2.7 or >= 3.4
+ - `python <https://www.python.org>`_ either 2.7 or >= 3.5
  - `setuptools <http://peak.telecommunity.com/DevCenter/setuptools>`_
- - `numpy <http://www.numpy.org/>`_ >= 1.7
- - `scipy <http://www.scipy.org/>`_
- - `astropy <http://www.astropy.org/>`_ >= 2.0
+ - `numpy <https://www.numpy.org/>`_ >= 1.7
+ - `scipy <https://www.scipy.org/>`_
+ - `astropy <https://www.astropy.org/>`_ >= 2.0
  - `numina <https://pypi.python.org/pypi/numina/>`_ >= 0.17
- - `scikit-image <http://scikit-image.org/>`_
+ - `scikit-image <https://scikit-image.org/>`_
+ - `jsonschema <https://python-jsonschema.readthedocs.io/en/stable/>`_
 
 Additional packages are optionally required:
 
@@ -27,16 +28,6 @@ Additional packages are optionally required:
 Installing MEGARA DRP
 *********************
 
-Using Conda
-===========
-
-`megaradrp` can be installed with conda using a custom channel.
-
-From the shell, execute:::
-
- conda install -c conda-forge megaradrp
-
-
 Using pip
 =========
 To install with pip, simply run:::
@@ -50,6 +41,14 @@ To install with pip, simply run:::
     your Numpy installation, which may not always be desired.
 
 
+Using Conda
+===========
+
+`megaradrp` can be installed with conda using a custom channel.
+
+From the shell, execute:::
+
+ conda install -c conda-forge megaradrp
 
 
 Building from source
@@ -119,148 +118,38 @@ It's a great way to quickly test new libraries without cluttering your
 global site-packages or run multiple projects on the same machine which 
 depend on a particular library but not the same version of the library.
 
-Install virtualenv
-------------------
-I install it with the package system of my OS, so that it ends in my
-global site-packages.
-
-With Fedora/EL is just::
-
-  $ sudo yum install python-virtualenv
-
+Since Python version 3.3, there is also a module in the standard library 
+called `venv` with roughly the same functionality.
 
 Create virtual environment
 --------------------------
-Create the virtual environment enabling the packages already installed
-in the global site-packages via the OS package system. Some requirements
-(in particullar numpy and scipy) are difficult to build: they require
-compiling and external C and FORTRAN libraries to be installed.
-
-So the command is::
-
-  $ virtualenv --system-site-packages myenv
+In order to create a virtual environment called e.g. megara using `venv`:
 
-If you need to create the virtualenv without global packages, drop the
-system-site-packages flag.
+  $ python3 -m venv megara
 
 Activate the environment
 ------------------------
 Once the environment is created, you need to activate it. Just change
-directory into it and load with your command line interpreter the 
-script bin/activate.
+directory into it and source the script `bin/activate`.
 
 With bash::
 
-  $ cd myenv
+  $ cd megara
   $ . bin/activate
-  (myenv) $
+  (megara) $
 
 With csh/tcsh::
 
-  $ cd myenv
+  $ cd megara
   $ source bin/activate
-  (myenv) $
+  (megara) $
 
 Notice that the prompt changes once you are activate the environment. To 
 deactivate it just type deactivate::
 
-  (myenv) $ deactivate
+  (megara) $ deactivate
   $ 
 
-*********************
-Installing MEGARA DFP
-*********************
-
-This section described how to install the MEGARA Pipeline inside
-the GTC Control system.
-
-In the following we assume that we are installing with user `gcsop`.
-
-Login in the `gcsop` account and activate the GTC environment::
-
-    $ /opt/gcs/tools/nrp -p linux -s bash
-
-Change working directory to ``/work/gcsop/src_python/gtc``::
-
-    $ cd /work/gcsop/src_python/gtc
-    $ ls
-    AL  DSL  SSL
-
-We have to install `numina` under `DSL` and `megaradrp` under `AL`.
-
-
-Please refer to :ref:`Numina manual <numina:solaris10>` to install Numina
-and its dependences under Solaris 10.
-
-Install numina
-==============
-
-First, install all the dependencies:
-
- - setuptools
- - six
- - numpy >= 1.7
- - scipy
- - astropy >= 1.0
- - PyYaml
- - singledispatch
-
-If you are installing a development version, Cython is also required.
-
-Most are available as precompiled packages in Linux.
-Please refer to :ref:`Numina manual <numina:solaris10>` to install Numina
-and its dependences under Solaris 10.
-
-Then, download the source code, either from PyPI or github::
-
-    $ pwd
-    /work/gcsop/src_python/gtc/DSL/
-    $ git clone https://github.com/guaix-ucm/numina.git
-    $ cd numina
-
-Create a file `numina.mod` with the following content::
-
-    NAME=numina
-    TYPE=device
-
-    l:numina:python:y
-
-And then build and install using `nmk`::
-
-    $ nmk -t module.rebuild
-    $ nmk -t module.install
-
-Install megaradrp
-=================
-
-Change directory to `/work/gcsop/src_python/gtc/AL/` and download the source code
-of `megaradrp`, either from `PyPI <https://pypi.python.org/pypi/megaradrp>`_
-or from `github <https://github.com/guaix-ucm/megaradrp>`_::
-
-    $ pwd
-    /work/gcsop/src_python/gtc/AL/
-    $ git clone https://github.com/guaix-ucm/megaradrp.git
-    $ cd megaradrp
-
-Create a file `megaradrp.mod` with the following content::
-
-    NAME=megaradrp
-    TYPE=device
-
-    l:megaradrp:python:y
-
-And then build and install using `nmk`::
-
-    $ nmk -t module.rebuild
-    $ nmk -t module.install
-
-You can check that everything works by running the `numina` command line tool::
-
-    $ numina show-instruments
-    Instrument: MEGARA
-     has configuration 'default'
-     has pipeline 'default', version 1
-
 .. _virtualenv: http://pypi.python.org/pypi/virtualenv
 .. _sphinx: http://sphinx.pocoo.org
 

doc/reference/datatype.rst

@@ -0,0 +1,9 @@
+==================================================================
+:mod:`megaradrp.datatype` --- MEGARA types of data
+==================================================================
+
+
+.. automodule:: megaradrp.datatype
+    :members:
+    :undoc-members:
+

doc/reference/index.rst

@@ -26,8 +26,9 @@ Reference
    processing
    products
    recipes
-   types
+   ntypes
    datamodel
+   datatype
    utils
    validators
    visualization

doc/reference/instrument.rst

@@ -7,5 +7,11 @@
    :synopsis:  Static configuration
 
 
-.. autoclass:: megaradrp.instrument.loader.Loader
+.. automodule:: megaradrp.instrument.components
+   :members:
 
+.. automodule:: megaradrp.instrument.configs
+   :members:
+
+.. automodule:: megaradrp.instrument.focalplane
+   :members: