Preparing tofu 1.4.2-a4

.gitignore

@@ -70,3 +70,6 @@ doc/source/auto_examples/
 
 # do not commit nose tests files
 *.noseids
+
+# no pip wheel metadata
+pip-wheel-metadata/

.travis.yml

@@ -59,8 +59,9 @@ deploy:
     skip_cleanup: true
   - provider: pypi
     user: "Didou09"
-    distributions: "sdist bdist_wheel"
+    distributions: "sdist"
     skip_cleanup: true
+    skip_existing: true
     on:
       tags: true
       all_branches: true

Notes_Upgrades/meetings/nov_2019.md

@@ -0,0 +1,60 @@
+Meeting November 2019
+=====================
+
+
+Agenda
+------
+
+- How to package Tofu
+  - pip wheel
+  - where to set the requirements ?
+- Which testing package to use ?
+  - nose2
+  - pytest
+- Travis
+  - platforms / matrix
+- tutorials as tests ?
+- matplotlib blog
+
+Present
+--------
+
+- Didier Vezinet (@Didou09)
+- Florian Lebourdais (@flothesof)
+- Laura Mendoza (@lasofivec)
+
+Summary of meeting 27/11/2019
+------------------------------
+
+- Summary of the recent problems with setuptools, travis, distribution (pypi)
+  **Assignee**: Laura
+
+- Documentation problems:
+
+    - More and more users asking for doc (mostly on IMAS).
+    - docstring: 
+      Didier will update docstring of main user functions
+      **Assignee**: Didier
+  - website:
+    - add tutorials/cases with different configurations (ITER, WEST, JET, ...) [FLORIAN]
+    - add tutorial for only plot_touch: different types of shading, saving/exports and plotting selected pixels for plot_touch
+    - add tutorial for reflexions (number and types)
+    - 2d radiations with ITER data (best case) or fake data -> update the tutorial called Computing a camera image with custom emissivity
+    - sinogram: to be added to an existing tutorial
+    - how to build cameras: add more comments on how to create a camera (in the 5 minutes to Tofu) what are the different parameters. Maybe separate camera 1D and camera 2D and go into details on how it works. 
+
+    **Assignee**:  Laura + Didier + Florian ?
+    Deadline: December ?
+
+- Which tool for tests:
+  - pytest : it looks like transition nose to pytest will be easy (pytest support nose tests and nose functions not used). Will have to clean imports from nose.
+  http://doc.pytest.org/en/latest/nose.html
+  Assignee: Florian
+  Deadline: next release.
+
+- Adding Tofu to conda-forge:
+  Florian proposes to add tofu to the conda-forge. For the next release ?
+  **Assignee**: -
+  Deadline: next release ?
+
+- matplotlib blog : we will re discuss this, once the tutorial are updated and that we have more examples/images

examples/tutorials/tuto_plot_basic.py

@@ -2,8 +2,7 @@
 Getting started: 5 minutes tutorial for `tofu`
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-This is a tutorial that aims to get a new user a little familiar with tofu's
- structure.
+This is a tutorial that aims to get a new user a little familiar with tofu's structure.
 """
 
 # The following imports matplotlib, preferably using a

examples/tutorials/tuto_plot_gallery_fusion_machines.py

@@ -0,0 +1,38 @@
+"""
+A gallery of Fusion Machines
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This tutorial functions as a gallery of fusion machines that can easily be loaded with `tofu`.
+"""
+
+###############################################################################
+# We start by importing `tofu`.
+
+import tofu as tf
+
+###############################################################################
+# `tofu` provides a geometry helper function that allows creating a configuration with a single call.
+#
+# Calling with empty arguments results in a default configuration. At the time of writing, this is ITER.
+# By printing the `config` object, a text representation of its components is printed. This allows inspecting
+# component names, number of sections, color or visibility.
+
+config = tf.geom.utils.create_config()
+print(config)
+
+###############################################################################
+# To get a list of all available built-in configs, one has to know some details about `tofu`.
+# Configurations can either be accessed by names (ITER, WEST, JET).
+
+print(tf.geom.utils._DCONFIG_TABLE.keys())
+
+###############################################################################
+# With that being said, let's create a gallery of the "top 3" fusion machines provided by `tofu` to accelerate
+# diagnostic development.
+
+import matplotlib.pyplot as plt
+
+fig, ax = plt.subplots()
+for fusion_machine in ['ITER', 'WEST', 'JET']:
+    config = tf.geom.utils.create_config(fusion_machine)
+    config.plot()

tofu/imas2tofu/__init__.py

@@ -6,13 +6,13 @@
 """
 import warnings
 import traceback
+import itertools as itt
 
 try:
     try:
         from tofu.imas2tofu._core import *
     except Exception:
         from ._core import *
-    del warnings, traceback
 except Exception as err:
     if str(err) == 'imas not available':
         msg = ""
@@ -26,5 +26,72 @@
         msg += "\n\n    => the optional sub-package tofu.imas2tofu is not usable\n"
     raise Exception(msg)
 
+
+# -----------------------------------------------
+#   Check IMAS version vs latest available in linux modules
+# -----------------------------------------------
+
+_KEYSTR = 'IMAS/'
+
+
+# extract all IMAS versions from a str returned by modules
+def extractIMAS(ss, keystr=_KEYSTR):
+    if keystr not in ss:
+        raise Exception
+    ls = ss[ss.index(keystr):].split('\n')
+    ls = itt.chain.from_iterable([s.split(' ') for s in ls])
+    ls = [s for s in ls if keystr in s]
+    ls = [s[len(keystr):s.index('(')] if '(' in s else s[len(keystr):]
+          for s in ls]
+    return sorted(ls)
+
+
+# Compare current and latest available IMAS versions
+def check_IMAS_version(verb=True, keystr=_KEYSTR):
+    import subprocess
+
+    # Get currently loaded IMAS
+    cmd = "module list"
+    proc = subprocess.run(cmd, check=True, shell=True,
+                          stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    lcur = extractIMAS(proc.stdout.decode(), keystr=keystr)
+    if len(lcur) != 1:
+        msg = ("You seem to have no / several IMAS version loaded:\n"
+               + "\t- module list: {}".format(lcur))
+        raise Exception(msg)
+
+    # Get all available IMAS
+    cmd = "module av IMAS"
+    proc = subprocess.run(cmd, check=True, shell=True,
+                          stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    lav = extractIMAS(proc.stdout.decode(), keystr=keystr)
+    if len(lav) == 0:
+        msg = "There is not available IMAS version"
+        raise Exception(msg)
+
+    # Compare and warn
+    if lcur[0] not in lav:
+        msg = "The current IMAS version is not available!"
+        raise Exception(msg)
+
+    msg = None
+    if lav.index(lcur[0]) != len(lav)-1:
+        msg = ("\nYou do not seem to be using the latest IMAS version:\n"
+               + "'module list' vs 'module av IMAS' suggests:\n"
+               + "\t- Current version: {}\n".format(lcur[0])
+               + "\t- Latest version : {}".format(lav[-1]))
+        warnings.warn(msg)
+    return lcur[0], lav
+
+
+# Try comparing and warning
+try:
+    _, _ = check_IMAS_version(verb=True)
+except Exception as err:
+    # This warning is an optional luxury, should not block anything
+    pass
+
+
 __all__ = ['MultiIDSLoader', 'load_Config', 'load_Plasma2D',
            'load_Cam', 'load_Data']
+del warnings, traceback, itt, _KEYSTR

tofu/version.py

@@ -1,2 +1,2 @@
 # Do not edit, pipeline versioning governed by git tags!
-__version__ = '1.4.2a3'
+__version__ = '1.4.2a3-2-gfaeb7af'