Start refactoring pyIRF

.gitignore

@@ -1,4 +1,5 @@
 # Byte-compiled / optimized / DLL files
+data
 __pycache__/
 *.py[cod]
 *$py.class
@@ -41,6 +42,10 @@ pip-delete-this-directory.txt
 docs/api
 docs/_build
 
+# Results and plots
+*.fits.gz
+*.png
+
 # Unit test / coverage reports
 htmlcov/
 .tox/

.mailmap

@@ -0,0 +1,4 @@
+Michele Peresano <michele.peresano@cea.fr> Michele Peresano <michele.peresano@.cea.fr>
+
+Thomas Vuillaume <thomas.vuillaume@lapp.in2p3.fr> vuillaut <thomas.vuillaume@gmail.com>
+Thomas Vuillaume <thomas.vuillaume@lapp.in2p3.fr> Thomas Vuillaume <thomas.vuillaume@gmail.com>

.readthedocs.yml

@@ -0,0 +1,11 @@
+version: 2
+
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - tests
+  system_packages: false

.travis.yml

@@ -1,9 +1,9 @@
 language: generic
 
 env:
-    global:
-        - PYTHONIOENCODING=UTF8
-        - MPLBACKEND=Agg
+  global:
+    - PYTHONIOENCODING=UTF8
+    - MPLBACKEND=Agg
 
 matrix:
   include:
@@ -20,28 +20,35 @@ matrix:
         - CONDA=true
 
 before_install:
-
-    - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    - bash miniconda.sh -b -p $HOME/miniconda
-    - . $HOME/miniconda/etc/profile.d/conda.sh
-    - hash -r
-    - conda config --set always_yes yes --set changeps1 no
-    - conda update -q conda  # get latest conda version
-    - conda info -a # Useful for debugging any issues with conda
+  - travis_wait 15 ./download_test_data.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - . $HOME/miniconda/etc/profile.d/conda.sh
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda  # get latest conda version
+  - conda info -a # Useful for debugging any issues with conda
 
 install:
-    - conda env create -f environment.yml
-    - conda activate pyirf
-    - pip install travis-sphinx codecov pytest-cov
-    - python setup.py install
+  - sed -i -e "s/- python=.*/- python=$PYTHON_VERSION/g" environment.yml
+  - conda env create -f environment.yml
+  - conda activate pyirf-dev
+  # cython needed for building gammapy
+  - pip install travis-sphinx codecov pytest-cov Cython
+  - pip install .[all]
+  - python --version
 
 script:
-    - pytest --cov=pyirf
+  - pytest --cov=pyirf --cov-report=xml
+  - python examples/calculate_eventdisplay_irfs.py
+  - travis-sphinx -v --outdir=docbuild build --source=docs/
 
 after_script:
-    - if [[ "$CONDA" == "true" ]];then
-          conda deactivate
-      fi
+  - if [[ "$CONDA" == "true" ]];then
+        conda deactivate
+    fi
+  - python setup.py build_sphinx
 
 after_success:
-    - codecov
+  - codecov
+  - travis-sphinx -v --outdir=docbuild deploy

README.rst

@@ -1,23 +1,15 @@
-==================================================
-pyirf |travis| |codacy| |coverage| |documentation|
-==================================================
+==================================
+pyirf |travis| |codacy| |coverage|
+==================================
 
 .. |travis| image:: https://travis-ci.com/cta-observatory/pyirf.svg?branch=master
   :target: https://travis-ci.com/cta-observatory/pyirf
-.. |codacy|  image:: https://app.codacy.com/project/badge/Grade/669fef80d3d54070960e66351477e383
-  :target: https://www.codacy.com/gh/cta-observatory/pyirf?utm_source=github.com&utm_medium=referral&utm_content=cta-observatory/pyirf&utm_campaign=Badge_Grade
+.. |codacy| image:: https://app.codacy.com/project/badge/Grade/669fef80d3d54070960e66351477e383
+  :target: https://www.codacy.com/gh/cta-observatory/pyirf/dashboard?utm_source=github.com&utm_medium=referral&utm_content=cta-observatory/pyirf&utm_campaign=Badge_Grade
 .. |coverage| image:: https://codecov.io/gh/cta-observatory/pyirf/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/cta-observatory/pyirf
-.. |documentation| image:: https://readthedocs.org/projects/pyirf/badge/?version=latest
-  :target: https://pyirf.readthedocs.io/en/latest/?badge=latest
 
 
-Python IRF builder
+Python library to calculate IACT IRFs and Sensitivities.
 
-=== Under construction ====
-
-The current version works only for point sources.
-
-=== Documentation ====
-
-https://pyirf.readthedocs.io/
+**Documentation:** https://cta-observatory.github.io/pyirf/

docs/AUTHORS.rst

@@ -3,14 +3,16 @@
 Authors
 =======
 
-The following is a complete list of all contributors in alphabetical order by last name:
+To see who contributed to ``pyirf``, please visit the
+`GitHub contributors page <https://github.com/cta-observatory/pyirf/graphs/contributors>`__
+or run
 
-- Lea Jouvin
-- Julien Lefacheur (left)
-- Maximilian Nöthe <maximilian.noethe@tu-dortmund.de>
-- Michele Peresano <michele.peresano@cea.fr>
-- Thomas Vuillaume <thomas.vuillaume@lapp.in2p3.fr>
+.. code-block:: bash
 
-*pyirf* has been developed starting from part a previous project authored by Julien Lefacheur.  
+    git shortlog -sne
 
-For more details go to the `GitHub contributors page <https://github.com/cta-observatory/pyirf/graphs/contributors>`__.
+
+``pyirf`` started as part of `protopipe <https://github.com/cta-observatory/protopipe/>`__ by Julien Lefaucher,
+but was largely rewritten in September 2020, making use of code from the
+previous version, the `pyfact <http://github.com/fact-project/pyfact>`__ module and the
+`FACT irf <http://github.com/fact-project/irf>`__ package.

docs/benchmarks/index.rst

@@ -0,0 +1,11 @@
+.. _benchmarks:
+
+Benchmarks
+==========
+
+Functions to calculate benchmarks.
+
+-------------
+
+.. automodapi:: pyirf.benchmarks
+   :no-inheritance-diagram:

docs/binning.rst

@@ -0,0 +1,11 @@
+.. _binning:
+
+Binning and Histogram Utilities
+===============================
+
+
+Reference/API
+-------------
+
+.. automodapi:: pyirf.binning
+   :no-inheritance-diagram:

docs/changelog.rst

@@ -3,11 +3,7 @@
 Changelog
 =========
 
-This is the changelog for *pyirf*.
-
-We use a one-line description of every pull request, roughly in chronological order.
-We don't list every pull request.
-Maintenance and cleanup changes are not of interest to users and are not listed here.
+We use a one-line description of every pull request.
 
 .. RELEASE TEMPLATE
 ..
@@ -37,22 +33,24 @@ Maintenance and cleanup changes are not of interest to users and are not listed
 
 .. _pyirf_0p3_release:
 
-0.1.0 (Unreleased)
-------------------
+`0.1.0 <https://github.com/cta-observatory/pyirf/releases/tag/v0.1.0>`__ (2020-09-16)
+-------------------------------------------------------------------------------------
+
+This is a pre-release.
+
+- Released September 16th, 2020
 
-. . .
 
 .. _pyirf_0p1p0alpha_prerelease:
 
-`0.1.0-alpha <https://github.com/cta-observatory/pyirf/releases/tag/v0.1.0-alpha>`__ (May 27th, 2020)
------------------------------------------------------------------------------------------------------
+`0.1.0-alpha <https://github.com/cta-observatory/pyirf/releases/tag/v0.1.0-alpha>`__ (2020-05-27)
+-------------------------------------------------------------------------------------------------
 
 Summary
 +++++++
 
 This is a pre-release.
 
-- This is a pre-release
 - Released May 27th, 2020
 - 3 contributors
 

docs/conf.py

@@ -19,8 +19,8 @@
 # -- Project information -----------------------------------------------------
 
 project = "pyirf"
-copyright = "2020, Julien Lefaucheur, Michele Peresano, Thomas Vuillaume"
-author = "Julien Lefaucheur, Michele Peresano, Thomas Vuillaume"
+copyright = "2020, Maximilian Nöthe, Michele Peresano, Thomas Vuillaume"
+author = "Maximilian Nöthe, Michele Peresano, Thomas Vuillaume"
 
 # The full version, including alpha/beta/rc tags
 version = __version__
@@ -40,10 +40,9 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    "rinoh.frontend.sphinx",
-    "sphinx_automodapi.automodapi",
-    "sphinx.ext.autodoc",
     "numpydoc",
+    "nbsphinx",
+    "sphinx.ext.autodoc",
     "sphinx.ext.doctest",
     "sphinx.ext.intersphinx",
     "sphinx.ext.todo",
@@ -55,12 +54,14 @@
     "sphinx.ext.napoleon",
     "sphinx_automodapi.automodapi",
     "sphinx_automodapi.smart_resolver",
-    "nbsphinx",
-    "IPython.sphinxext.ipython_console_highlighting",
 ]
 
 # nbsphinx
-nbsphinx_execute = "never"
+# nbsphinx_execute = "never"
+nbsphinx_execute_arguments = [
+    "--InlineBackend.figure_formats={'svg', }",
+    "--InlineBackend.rc={'figure.dpi': 96}",
+]
 
 numpydoc_show_class_members = False
 autosummary_generate = True
@@ -79,17 +80,11 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "alabaster"
+html_theme = "sphinx_rtd_theme"
 
 html_theme_options = {
-    "github_user": "cta-observatory",
-    "github_repo": "pyirf",
-    "badge_branch": "master",
-    "codecov_button": "true",
-    "github_button": "true",
-    "travis_button": "true",
-    "sidebar_collapse": "false",
-    "sidebar_includehidden": "true",
+    'canonical_url': 'https://cta-observatory.github.io/pyirf',
+    'display_version': True,
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/contribute.rst

@@ -0,0 +1,68 @@
+.. _contribute:
+
+How to contribute
+=================
+
+
+Issue Tracker
+-------------
+
+We use the `GitHub issue tracker <https://github.com/cta-observatory/pyirf>`__
+for individual issues and the `GitHub Projects page <https://github.com/cta-observatory/pyirf/projects>`_ can give you a quick overview.
+
+If you found a bug or you are missing a feature, please check the existing
+issues and then open a new one or contribute to the existing issue.
+
+Development procedure
+---------------------
+
+
+We use the standard `GitHub workflow <https://guides.github.com/introduction/flow/>`__.
+
+If you are not part of the ``cta-observatory`` organization,
+you need to fork the repository to contribute.
+See the `GitHub tutorial on forks <https://docs.github.com/en/github/getting-started-with-github/fork-a-repo>`__ if you are unsure how to do this.
+
+#. When you find something that is wrong or missing
+
+    - Go to the issue tracker  and check if an issue already exists for your bug or feature
+    - In general it is always better to anticipate a PR with a new issue and link the two
+
+#. To work on a bug fix or new feature, create a new branch, add commits and open your pull request
+
+   - If you think your pull request is good to go and ready to be reviewed,
+     you can directly open it as normal pull request.
+
+   - You can also open it as a “Draft Pull Request”, if you are not yet finished
+     but want to get early feedback on your ideas.
+
+   - Especially when working on a bug, it makes sense to first add a new
+     test that fails due to the bug and in a later commit add the fix showing
+     that the test is then passing.
+     This helps understanding the bug and will prevent it from reappearing later.
+
+#. Wait for review comments and then implement or discuss requested changes.
+
+
+We use `Travis CI <https://travis-ci.com/github/cta-observatory/pyirf>`__ to
+run the unit tests and documentation building automatically for every pull request.
+Passing unit tests and coverage of the changed code are required for all pull requests.
+
+Further details
+---------------
+
+Please also have a look at the
+
+- ``ctapipe`` `development guidelines <https://cta-observatory.github.io/ctapipe/development/index.html>`__
+- The `Open Gamma-Ray Astronomy data formats <https://gamma-astro-data-formats.readthedocs.io/en/latest/>`__
+  which also describe the IRF formats and their definitions.
+- ``ctools`` `documentation page on IRFs <http://cta.irap.omp.eu/ctools/users/user_manual/irf_cta.html>`__
+- `CTA IRF working group wiki (internal) <https://forge.in2p3.fr/projects/instrument-response-functions/wiki>`__
+
+- `CTA IRF Description Document for Prod3b (internal) <https://gitlab.cta-observatory.org/cta-consortium/aswg/documentation/internal_reports/irfs-reports/prod3b-irf-description>`__
+
+
+Benchmarks
+----------
+
+- `Comparison with EventDisplay <../notebooks/comparison_with_EventDisplay.ipynb>`__ | *comparison_with_EventDisplay.ipynb*