Small updates before the first day

Makefile

@@ -46,6 +46,7 @@ ipynb/index.html: ipynb/index.rst
 	jupyter-nbconvert $< --reveal-prefix='./reveal.js' --to slides --template $(TPL_FILE)
 
 presentations: $(IPYNBPRES) ipynb/index.html
+	echo $(IPYNBPRES)
 
 serve: $(IPYNBPRES) ipynb/index.html
 	cd $(IPYNBDIR) && python3 -m http.server

README.md

@@ -10,7 +10,7 @@ Before considering performances, we will address the problem of evaluating
 performance, a.k.a. profiling Python code.
 
 
-Formated output of the notebooks is available here: https://python-uga.gricad-pages.univ-grenoble-alpes.fr/training-hpc 
+Formated output of the notebooks is available here: https://python-uga.gricad-pages.univ-grenoble-alpes.fr/training-hpc
 
 ## Format et dates
 
@@ -36,30 +36,30 @@ sur 2 semaines
 ## Planning
 
 - Introduction, rappels langage Python et gestion de src [1j : 12/06] (Pierre,
-Raphaël et Loïc)
+Franck)
 
-- Numpy / Scipy [0.5j : 13/06] (Loïc et Raphaël)
+- Numpy / Scipy [0.5j : 13/06] (Pierre, Franck)
 
   - fancy indexing, masking
   - presentation of the example "dtw_cort_dist"
   - broadcast
   - vectorizing
 
-- Visualization - Matplotlib and other tools [0.25j : 13/06] (Loïc et Raphaël)
+- Visualization - Matplotlib and other tools [0.25j : 13/06] (Matthieu, Pierre)
 
-  - matplotlib object oriented (axes, features...) (Loïc)
-  - figures et animations (Loïc)
-  - voir graph plotting python jackc (Raphaël)
-  - point bokeh, plotly, seaborn (Raphaël)
+  - matplotlib object oriented (axes, features...) (Pierre)
+  - figures et animations (Matthieu)
+  - voir graph plotting python jackc (Matthieu)
+  - point bokeh, plotly, seaborn (Matthieu)
 
-- Pandas [0.25j : 13/06] (Eric - Raphaël)
+- Pandas [0.25j : 13/06] (Pierre)
   - load, query, display, export
 
-- Packaging, documentation and testing [0.5j : 17/06] (Raphaël et Pierre)
+- Packaging, documentation and testing [0.5j : 17/06] (Pierre)
 
 - General introduction HPC with Python [0.25j] (Pierre)
 
-- Profiling [0.25j] (Pierre et Franck)
+- Profiling [0.25j] (Franck, Pierre)
 
   See the book "High performance Python".
 
@@ -70,13 +70,13 @@ Raphaël et Loïc)
   - kcachegrind
   - Memory (memory_profiler, ...)
 
-- Wrapping low level code and/or compiled code [0.5j] (Franck et Loic)
+- Wrapping low level code and/or compiled code [0.5j] (Franck)
 
   Mainly for legacy code...
 
   ctypes, cffi, cython, cppyy, pybind11, f2py, pyo3, swig
 
-- Different ways to speed up native Python code [0.5j] (Pierre - Franck)
+- Different ways to speed up native Python code [0.5j] (Pierre, Franck)
 
   - using on the fly compiler (like e.g. numba)
   - using static compilers (like e.g. pythran)
@@ -85,26 +85,23 @@ Raphaël et Loïc)
 
 - Tools for parallelisation [0.25j]
 
-  threading / multiprocessing / concurrent.futures / OpenMP / mpi4py / GPU /joblib / dask (Pierre - Franck)
+  threading / multiprocessing / concurrent.futures / OpenMP / mpi4py / GPU /joblib / dask (Franck)
 
-- Déploiement sur cluster et mésocentre (lien singularity, charlie cloud) [0.25j] (Franck - Raphaël)
+- Déploiement sur cluster et mésocentre (lien singularity, charlie cloud) [0.25j] (Franck)
 
 - Travaux sur projets personnels [0.5j au moins]
 
-
 ### Présence formateurs
 
 - m: matin
 - a: après-midi
 
-|         | m 12 | a 12 | m 13 | a 13 | m 17 | a 17 | m 18 | a 18 | m 19 | a 19 |
+|         | m 23 | a 23 | m 24 | a 24 | m 27 | a 27 | m 28 | a 28 | m 30 | a 30 |
 |---------|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
 | Eric    | (x)  | (x)  | (x)  | (x)  | (x)  |      | (x)  | (x)  | (x)  | (x)  |
-| Franck  |      |      |      |      |      |  x   |  x   |  x   |  x   |  x   |
-| Loïc    |      |      |  x   |  x   |      |  x   |      |      |      |      |
-| Raphaël |      |      |  x   |  x   |  x   |      |      |      |      |  x   |
-| Pierre  |  x   |   x  |      |      |  x   |  x   | (x)  |  x   |  x   | (x)  |
-| Cyrille |      |      |      |      |      |      |      |      |      |      |
+| Franck  |  x   |   x  |  x   |  x   |  x   |  x   |  x   |      |  x   |  x   |
+| Pierre  |  x   |   x  |  x   |  x   |  x   |  x   |  x   |  x   |      |      |
+| Matthieu|      |      |  x   |  x   |      |      |  x   |  x   |  x   |  x   |
 
 ## To be done before the first day of the training session
 

check_env.py

@@ -3,17 +3,6 @@ import sys
 if sys.version_info[:2] < (3, 6):
     raise RuntimeError("Python version >= 3.6 required.")
 
-try:
-    import conda
-except ImportError:
-    print(
-        "Problem: the conda package not importable.\n"
-        "Please run this script in the base conda environment"
-    )
-    sys.exit(1)
-else:
-    print("Good! conda package importable!")
-
 try:
     import numpy, scipy, matplotlib, pandas
 except ImportError:

install.md

+# Setup your environment
+
+We will have to use Python 3 (with Miniconda3), a good Python IDE (like
+Spyder) and a version-control tool (Mercurial, or Git if you know it and really
+like it).
+
+In the following, we give indications about how to install these tools and how
+to get the repository of this course locally on your computer. Please, if you
+encounter problems, fill an issue
+[here](https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/issues)
+to explain what you did and what are the errors (please copy / paste the error
+log).
+
+Be careful to execute all the commands in the given order, read the outputs of
+the commands and answer to the questions asked by the programs!
+
+Note that you can copy/paste the commands! On Linux, you can use the middle
+button of the mouse to paste the text that has been previously selected. It's
+very convenient! Try to use that!
+
+**Note for Windows users**
+
+You can now install Ubuntu inside Windows. It is called the [Windows Subsystem
+for Linux (WSL)](https://ubuntu.com/wsl). There are some specific instructions
+for WSL in the file
+[notes_wsl.md](https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/blob/master/notes_wsl.md).
+
+#### Install Miniconda and Python
+
+The first step is to install miniconda3 (see
+[here](https://docs.conda.io/en/latest/miniconda.html)). On Linux, one just
+need to execute these commands in a terminal:
+
+```bash
+# wget is used to download a file
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+# this file (Miniconda3-latest-Linux-x86_64.sh) contains bash code and has to
+# be executed with the command `bash`
+bash Miniconda3-latest-Linux-x86_64.sh
+```
+
+You have to answer to different questions. In particular, answer "yes" to the
+last question about the initialization of conda. When it's done, close the
+terminal (with `ctrl-d`) and reopen a new terminal (with `ctrl-alt-t`). The
+string "(base)" should be in the line in the terminal.
+
+If the string "(base)" is not in the line in a new terminal, you might try to
+run `$HOME/miniconda3/bin/conda init` and then reopen a new terminal (with
+`ctrl-alt-t`).
+
+You have to activate the `conda-forge` conda channel with:
+
+```bash
+conda config --add channels conda-forge
+```
+
+#### Install few packages in your base conda environment
+
+```bash
+# download a requirement file
+wget https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/raw/master/requirements.txt
+conda install mamba
+# install with conda
+mamba install --file requirements.txt -y
+```
+
+#### Install and setup Mercurial
+
+To install and setup Mercurial, you can do:
+
+```bash
+pip install conda-app -U
+```
+
+Note: if you get an error, you may need to rerun the command with the option `--no-cache-dir`.
+
+When `conda-app` has been installed, use it to install Mercurial!
+
+```bash
+conda-app install mercurial
+```
+
+This last command can take some time. **Be patient!** When it's done, close the
+terminal (`ctrl-d`) and reopen a new terminal (`ctrl-alt-t`)! Then, you should
+be able to run the following commands without errors:
+
+```bash
+hg version
+which hg
+```
+
+The last command should reply a path containing `miniconda`. You now needs to
+create a configuration file for Mercurial. You can open it with the text editor
+`gedit` with the command:
+
+```bash
+gedit ~/.hgrc &
+```
+
+Fill the file with the following text. Copy/paste it, adapt it to your case and
+don't forget to save the file!
+
+```
+[ui]
+username=myusername <email@adress.org>
+editor=nano
+tweakdefaults = True
+
+[extensions]
+hgext.extdiff =
+# To use Mercurial with GitHub and Gitlab
+hggit =
+
+[extdiff]
+cmd.meld =
+```
+
+Warning: Mercurial **has to be correctly setup**! Since we will use [the Gitlab
+instance of UGA](https://gricad-gitlab.univ-grenoble-alpes.fr), the Mercurial
+extension hg-git has to be activated so the line `hggit =` in the configuration
+file is mandatory.
+
+You can check that Mercurial is correctly configured by executing `hg version
+-v`.
+
+To learn more on Mercurial, see [here](
+https://fluiddyn.readthedocs.io/en/latest/mercurial_heptapod.html).
+
+#### Clone this repository
+
+Once everything is installed and setup, you should be able to clone the
+repository of the training with:
+
+```bash
+hg clone https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc.git
+```
+
+Please tell me by [creating an issue in the main repository of this
+course](https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/issues)
+if it does not work.
+
+Once the repository is cloned you should have a new directory `training-hpc`
+(use the command `ls` to see it) and you should be able to enter into it with
+`cd training-hpc`.

requirements.txt

 # to be used with:
 # conda install --file requirements.txt
 # utilities
-python==3.7.3
+python==3.8
 ipython
+# ide
 spyder
-jupyter
-nbconvert>=5.5
-invoke
+# jupyter
+jupyterlab
+jupyterlab-spellchecker
+jupyterlab_code_formatter
+ipympl
+bash_kernel
+nbconvert>=6
 # base numerics
 numpy
 scipy
 matplotlib
 pandas
 h5py
-#vizu
+# utilities
+invoke
+# visualization
 # pyviz  # (not available in conda-forge)
 # wrapper
 cffi
@@ -26,4 +33,4 @@ transonic
 # parallel
 mpi4py
 dask
-joblib
\ No newline at end of file
+joblib