Update in online documentation

doc/source/dev_tutos.rst

@@ -0,0 +1,82 @@
+.. _devtutos:
+
+=========================
+Tutorials For Developers
+=========================
+
+Some tutorials for developers.
+
+-----------------
+
+
+-------------------
+How To Do A Release
+-------------------
+
+1. Write down the release_notes:
+
+   a) in **rST** format: ``realeas_notes_XYZ.rst``
+   b) Start with a summary **Main Changes** (TL;DR version of the whole file)
+   c) add all issues and PR related references
+   d) add list of contributors
+   e) add list of perspectives and tag contributors
+
+2. Release an alpha version:
+
+   a) Create an annotaded tag (do not use GitHub's release system) ``git tag -a X.Y.Z-alpha0 -m "annotation"``
+   b) Update the version of the repo: ``python -c "import _updateversion as up; out = up.updateversion(); print(out)"``
+   c) push on GitHub server
+   d) Verify that ONE build passes on travis:
+      the deployment on conda should pass for all travis-build, but for pypi only
+      the first build will pass
+   e) Install it locally on all available platforms and environments (by hand),
+      with all different packaging tools. And try some tests.
+   f) Easybuild: try to create a tarball for Jira machines
+   g) For IRFM servers, build the conda_recipe by hand:
+
+      .. code-block:: python
+
+	 $ if [[ "$TRAVIS_PYTHON_VERSION" == "3.7-dev" ]]; then export VADD="py37"; else export VADD="py36";  fi
+         $ export CONDA_BLD_PATH=$(pwd)/conda-bld/ # you should be in the tofu dir
+         $ export REV=$(python -c "import _updateversion as up; out=up.updateversion(); print(out)")
+         $ export VERSION=$(echo $REV | tr - .)
+         $ echo $REV
+
+#. Update the ``releases.rst`` file in the web documentation:
+
+   #. create a symbolic link from ``$TOFU_DIR/release_notes/release_notes_XYZ.rst`` to ``$TOFU_DIR/doc/source/release_notes/release_notes_XYZ.rst``
+   #. Update the ``.rst`` file
+   #. Make and publish doc (see tutorial below)
+
+#. Release the real version:
+
+   a) Follow the same steps as for alpha version, just change the tag and annotation.
+
+#. Send an email to users.
+
+
+------------------------
+How To Construct The Doc
+------------------------
+
+Adding text, updating the API:
+
+#. The easiest way is to have two different repo: ``$TOFU_DIR``, for building the doc and ``$TOFU_DIR/../test_doc/tofu/`` for seeing the resulting html (always in the ``gh-pages`` branch)
+#. If updating the API, make sure that you have installed the right version of **tofu**
+#. Change to the ``new-doc`` branch
+#. Go to ``$ cd $TOFU_DIR/doc/``
+#. Modify the corresponding file (somewhere in ``src/a-file.rst``)
+#. If you added a file
+#.  ``sphinx-apidoc -Mf -P -d 5 -o source/ ../tofu/ {../*test*,../*mag*,../*imas2tofu*,../*geom/inputs}``
+#. ``$ make clean`` (to make sure only the needed files will be stored)
+#. ``$ make html``
+#. Go to the ``gh-pages`` branch and open the ``index.html`` file (from the top)
+#. Commit and push the changes to the ``new-doc`` branch: to keep the changes in the sources
+#. Commit and push the changes to the ``gh-pages``, this will update the website.
+
+
+Adding a tutorial:
+
+#. Add your tutorial in ``$TOFU_DIR/examples/tutorials`` with the proper naming conventions
+#. The sphinx gallery is automatically updated when building the doc (as above)
+#. Change the ``index.rst`` file to include a thumbnail of your tutorial

doc/source/index.rst

@@ -79,11 +79,11 @@ Contents
    - Use existing diagnostic geometry and signals to solve the inverse problem
      and compute tomographic inversions using a choice of discretization basis
      functions and regularisation functionals.
+* Advanced tutorials for developpers: :ref:`devtutos`
 
 .. _basic: auto_examples/tutorials/tuto_plot_create_geometry.html
 .. _cameras: auto_examples/tutorials/tuto_plot_basic.html
 .. _tutorial: auto_examples/tutorials/tuto_plot_custom_emissivity.html
-.. _todos: Todos.html
 
 
 **Code documentation:**

doc/source/release_notes/release_notes_142.rst

@@ -0,0 +1,115 @@
+====================
+What's new in 1.4.2
+====================
+
+Main changes:
+=============
+
+- Python 2.7 is not supported anymore
+- Python 3.6 and 3.7 are supported
+- Several changes to try and make installation easier (on clusters, windows, mac....) and less verbose for users
+- More explicit names for default saved configurations
+- Major bug fix in one of the methods for computing synthetic signal
+- Minor bug fixes in interactive figures
+- Minor bug fixes in Plasma2D interpolation
+- New configuration (ITER) available
+- First version of a class handling 2D XRay bragg spectrometers
+- First tools for magnetic field line tracing available on WEST
+- Better documentation, more ressources
+- More informative error messages
+- extra tools for computing LOS length, closest point to magnetic axis...
+- Better PEP8 compliance
+
+
+Detailed changes:
+=================
+
+Installation / portability:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+- Bug fixes for installation on ITER and Gateway clusters #250
+- Easier installation on Mac #183 (``requirements.txt``)
+- Removed explicit compiler specification in ``setup.py`` for more flexibility
+- When sub-packages imas2tofu or mag are missing, the warning is much more concise, but the error traceback is still accessible in a hidden dictionnary for developpers #243
+- ``python setup.py clean`` now doesn't cythonize
+- Dropped python 2 support: #228
+  - merged ``_GG02`` and ``_GG03`` into the ``_GG`` file
+  - no longer being tested in travis
+  - no longer packaged in conda
+  - updated README file accordingly
+  - dropped ``funcsigs`` dependency
+  - made necessary changes in ``setup.py``
+  - ``benchmarks/calc_signal_benchmark.py``: now working with python 3
+
+Bug fixes:
+~~~~~~~~~~
+- Major bug fix in ``LOS_calc_signal()`` for computing the synthetic signal of a LOS camera using a particular algortihm : method='sum', minimize='hybrid', ani=True,  #247 #255
+- Major bug fix in ``LOS_get_sample()`` when ``minimize='hybrid'`` and ``minimize='memory'`` the limits were not set correctly
+  in some cases the formula for sampling a LOS was wrong (``los_get_sample_core_var_res``).
+- Minor bug fixes in interactive figures when ``t=None`` was used (the interactivity was lost due to wrong formatting of the time array)
+- Minor bug fixed in Plasma 2D interpolation (``interp_t`` was not being set), imporved error messages #209
+- Removed unused variable in ``_Ves_get_sampleS`` (_GG), in ``_core.py`` #190
+- Gave more explicit names to some variables in ``_core.py`` to avoid bugs/typos (eg. ``I`` to ``current``) #186
+- Removed a secondary ``init`` function for the class ``tf.geom.CoilsPF`` #187
+- ``_checkformat_inputs_dgeom`` now is a function of ``Rays`` class
+- Change default separator in ``to_dict()`` from '_' to '.', #228
+- Rays.calc_kInOut_IsoFlux() is now more flexible (accepts 3d np.arrays as well as lists of np.ndarrays), #188
+- __repr__() is now overloaded in a more robust way so it falls back to printing the class if get_summary() fails to avoid crashing in debug mode #242
+
+Documentation:
+~~~~~~~~~~~~~~
+- Updated information about support of python version
+- Added slides of talk given at PyConFR 2019 conference
+- Added a ``gallery`` in our documentation with 3 different tutorials:
+  - 5 minutes tutorial to show to create a geometry and 1D/2D cameras
+  - Guide on how to create your own Geometry from scratch (vacuum vessel, structures, etc.)
+  - How to compute the signal received by a camera using a synthetic signal.
+  For all of these tutorial, you can see directly the codes and the
+  resulting images, and you can get the source code or download it as a
+  Jupyter notebook!
+- Minor changes to the web doc: updated install instructions to be "cleaner"
+  now in rST and not HTML), small changes in navigation bar.
+- Guide on how to contribute to ToFu.
+
+New features:
+~~~~~~~~~~~~~
+- First version of ``magnetic field line tracing`` (for WEST only so far, to be improved) #213 #235
+- First version of ``2D XRay Bragg spectrometers`` for synthetic diagnostics, modelling the diagnotics geometry and providing 2d spectral fitting routines (to be improved) #267
+- When computing a signal ``LOS_calc_signal`` emissivity function can now return
+  a 1D array if ``t=None`` #217 #252
+- Three functions added to ``tf.geom.Rays``: #211
+	- ``calc_length_in_isoflux()``: compute the length inside a set of isoflux surfaces of each LOS
+	- ``calc_min_geom_radius()``: compute the minimal geometrical radius (impact parameter) of each LOS
+	- ``calc_min_rho_from_Plasma2D()``: compute the minimum normalized radius (or any field with a minimum on the axis) for each LOS
+- New ``ITER configuration`` available! #220 #227
+- More explicit names for default configurations #264
+
+Contributors:
+=============
+
+Many thanks to all developpers:
+
+- Didier Vezinet (@Didou09)
+- Laura Mendoza (@lasofivec)
+- Florian Le Bourdais (@flothesof)
+- Jorge Morales (@jmoralesFusion)
+- Koyo Munechika (@munechika-koyo)
+- Louwrens Van Dellen (@Louwrensth)
+
+
+What's next (indicative):
+=========================
+- Migrating from nosetests (ongoing for @lasofivec : issues #95 and #232 )
+- Easier binary and source installs from pip and conda for all platforms, including unit tests on alla platforms (ongoing for @lasofivec and @flothesof : issue #92 and #259 )
+- Solid angles for Volume-Of-Sight and radiative heat loads computation (ongoing for @lasofivec : Issues #71, #72, #73, #74, #75, #76, #77, #78 )
+- Tools and classes to handle 2D Bragg X-Ray crystal spectrometer (ongoing for @Didou09 : Issues #202 and #263)
+- Generic data classe to incorporate plateau-finding, data analysis and 1d Bayesian fitting routines and classes (ongoing for @Didou09 and @jmoralesFusion and @MohammadKozeiha: issues #208, #260 and #262)
+- More general magnetic field line tracing workflow
+- Better unit tests coverage
+- More complete documentation
+
+
+List of issues and PR closed:
+=============================
+- Issues: #30, #180, #183, #185, #186, #187, #188, #189, #190, #201, #209, #211, #213, #217, #220, #224, #227, #228, #230, #235, #243, #247, #248, #250, #252, #255, #264
+- PR: #173, #175, #179, #181, #182, #184, #191, #192, #193, #194, #195, #196, #197, #199, #206, #207, #210, #212, #222, #223, #225, #226, #229, #231, #233, #234, #236, #237, #238, #240, #242, #244, #245, #246, #249, #251, #253, #254, #256, #257, #258,
+  #261, #265, #267

doc/source/releases.rst

@@ -4,5 +4,6 @@ Latest release
 .. toctree::
    :maxdepth: 1
 
+   release_notes/release_notes_142.rst
    release_notes/release_notes_141.rst
    release_notes/release_notes_140.txt

doc/source/tofu.data.rst

@@ -56,3 +56,12 @@ tofu.data.\_plot module
    :members:
    :undoc-members:
    :show-inheritance:
+
+tofu.data.\_spectrafit2d module
+-------------------------------
+
+.. automodule:: tofu.data._spectrafit2d
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

doc/source/tofu.dumpro.rst

@@ -56,3 +56,4 @@ tofu.dumpro.\_plot module
    :members:
    :undoc-members:
    :show-inheritance:
+

doc/source/tofu.dust.rst

@@ -32,3 +32,4 @@ tofu.dust.\_plot module
    :members:
    :undoc-members:
    :show-inheritance:
+

doc/source/tofu.geom.rst

@@ -33,6 +33,14 @@ tofu.geom.\_comp module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_comp\_optics module
+-------------------------------
+
+.. automodule:: tofu.geom._comp_optics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_core module
 -----------------------
 
@@ -41,6 +49,14 @@ tofu.geom.\_core module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_core\_optics module
+-------------------------------
+
+.. automodule:: tofu.geom._core_optics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_def module
 ----------------------
 
@@ -65,6 +81,14 @@ tofu.geom.\_plot module
    :undoc-members:
    :show-inheritance:
 
+tofu.geom.\_plot\_optics module
+-------------------------------
+
+.. automodule:: tofu.geom._plot_optics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 tofu.geom.\_raytracing\_tools module
 ------------------------------------
 
@@ -96,3 +120,4 @@ tofu.geom.utils module
    :members:
    :undoc-members:
    :show-inheritance:
+

doc/source/tofu.rst

@@ -58,3 +58,4 @@ tofu.version module
    :members:
    :undoc-members:
    :show-inheritance:
+

release_notes/release_notes_142.rst

@@ -1,5 +1,9 @@
+====================
+What's new in 1.4.2
+====================
+
 Main changes:
-==========
+=============
 
 - Python 2.7 is not supported anymore
 - Python 3.6 and 3.7 are supported
@@ -18,10 +22,10 @@ Main changes:
 
 
 Detailed changes:
-============
+=================
 
 Installation / portability:
----------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 - Bug fixes for installation on ITER and Gateway clusters #250
 - Easier installation on Mac #183 (`requirements.txt`)
 - Removed explicit compiler specification in `setup.py` for more flexibility
@@ -37,7 +41,7 @@ Installation / portability:
   - `benchmarks/calc_signal_benchmark.py`: now working with python 3
 
 Bug fixes:
------------
+~~~~~~~~~~
 - Major bug fix in `LOS_calc_signal()` for computing the synthetic signal of a LOS camera using a particular algortihm : method='sum', minimize='hybrid', ani=True,  #247 #255
 - Major bug fix in `LOS_get_sample()` when `minimize='hybrid'` and `minimize='memory'` the limits were not set correctly
   in some cases the formula for sampling a LOS was wrong (`los_get_sample_core_var_res`).
@@ -52,7 +56,7 @@ Bug fixes:
 - __repr__() is now overloaded in a more robust way so it falls back to printing the class if get_summary() fails to avoid crashing in debug mode #242
 
 Documentation:
---------------
+~~~~~~~~~~~~~~
 - Updated information about support of python version
 - Added slides of talk given at PyConFR 2019 conference
 - Added a `gallery` in our documentation with 3 different tutorials:
@@ -67,7 +71,7 @@ Documentation:
 - Guide on how to contribute to ToFu.
 
 New features:
----------------
+~~~~~~~~~~~~~
 - First version of `magnetic field line tracing` (for WEST only so far, to be improved) #213 #235
 - First version of `2D XRay Bragg spectrometers` for synthetic diagnostics, modelling the diagnotics geometry and providing 2d spectral fitting routines (to be improved) #267
 - When computing a signal `LOS_calc_signal` emissivity function can now return

tofu/version.py

@@ -1,2 +1,2 @@
 # Do not edit, pipeline versioning governed by git tags!
-__version__ = '1.4.1-396-g806dbc9'
+__version__ = '1.4.1-303-gf837259'