other:newppl:starting
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other:newppl:starting [2022/11/18 17:10] jypeter [Text editors] Improved |
other:newppl:starting [2023/02/03 12:14] jypeter [NetCDF and related Conventions] Added link to Gridspec |
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| <note important>A //jupyter notebook// is **not** a text editor! | <note important>A //jupyter notebook// is **not** a text editor! | ||
| - | You need a correct text editor to efficiently work with scripts and programs</note> | + | **You need a correct text editor to efficiently work with scripts and programs** |
| - | There are **lots** of text editors used on Linux computers/servers (vi, vim, gvim, emacs, nano, ...), that you can use: | + | {{ :other:newppl:real_programmers.png?direct&600 |}} [[https://www.explainxkcd.com/wiki/index.php/378:_Real_Programmers|xkcd & Real Programmers]]</note> |
| - | * in basic text terminals (if you know the basic commands and shortcuts) | + | |
| - | * or in graphics mode (you may need to have an [[other:x_conf|X server configured]]) | + | |
| - | === emacs === | + | There are **lots of text editors available** on Linux computers/servers (''emacs'', ''nano'', ''vi'', ''vim'', ''gvim'', ''gedit'', ...). You can use them: |
| + | * In basic **text terminals** | ||
| + | * useful if you are in a hurry, and/or working on a remote server with a bad network connection or have no local [[other:x_conf|X server]] running | ||
| + | * you should know the basic commands and shortcuts! Some text editors (e.g ''nano'') fortunately display some help at the bottom of the screen | ||
| - | {{ :other:newppl:real_programmers.png?direct&600 |}} | + | * With a **full Graphical User Interface** (aka //GUI//) allowing you to use the mouse+menus/buttons/etc... |
| + | * you will need to have a //local// [[other:x_conf|X server]] running, if you want to use the text editor GUI on a //remote// server | ||
| - | * Starting emacs: | + | === emacs === |
| - | * ''emacs some_text_file &'' | + | |
| - | * or just ''emacs &'' | + | |
| - | * All the basic functions of emacs are available from the pull-down menus at the top, but the **real power** comes from knowing (a few of) the keyboard shortcuts! | + | |
| - | * **Bonus!** Many emacs shortcuts can be used in the shell or in Python, and will also make it possible to use emacs in text mode (if you get lost on a remote server without graphics...) | + | |
| - | * Understanding keyboard shortcuts: ''C-s'' (means ''CTRL-s'') and will //Search forward// and ''M-f'' (means ''Alt-f'' on a regular keyboard) and will //Move forward a word// | + | |
| - | * The usual Linux copy/paste behavior works: | + | |
| - | * Select and Copy text (at the same time) with the left button | + | |
| - | * Paste text with the middle button | + | |
| - | * **Built-in emacs tutorial, highly recommended!** Spend one hour in the tutorial, and save hundreds of hours in the rest of your life! | + | |
| - | * ''Help''=>''Emacs Tutorial'' | + | |
| - | * or ''Help''=>''Emacs Tutorial (choose language)...'' | + | |
| - | * Annotated reference card: {{:other:newppl:emacs_jyp.pdf}} | + | |
| - | * Recommended {{:other:newppl:emacs_linux_22-11-18.tar|.emacs configuration file}} | + | |
| - | * Location: ''~/.emacs'': ''.emacs'' (//dot-emacs//) file in your home directory | + | |
| - | * **Editing remote text files** with emacs and the ''tramp'' mode: | + | |
| - | * If you use the following syntax, emacs will use the ''tramp'' mode and ''scp'' to transfer remote files to your computer when you open them, and then ''scp'' to send the modified files back when you save them: | + | |
| - | * ''/ssh:user@server:/path/file'' | + | |
| - | * e.g. ''/ssh:your_login@ssh1.lsce.ipsl.fr:/home/users/your_login/my_script.py'' | + | |
| - | * Hint: if you use the {{:other:newppl:emacs_linux_22-11-18.tar|recommended configuration file}} or have activated the '' '(recentf-mode t)'' mode, you can access recent files in ''File''=>''Open Recent'' | + | |
| - | * More: [[https://www.emacswiki.org/emacs/TrampMode|tramp mode on EmacsWiki]] and [[https://www.gnu.org/software/tramp/|tramp user manual]] | + | |
| - | * Use the built-in psyhotherapist to solve your scientific problems (with ''M-x doctor''). See also [[https://www.masteringemacs.org/article/fun-games-in-emacs|Fun and Games in Emacs]]\\ <code>I am the psychotherapist. Please, describe your problems. Each time | + | |
| - | you are finished talking, type RET twice. | + | |
| - | My climate model does not work | + | <note important>Read the **dedicated [[other:emacs_doc|Using emacs]] page**, and become a power user!</note> |
| - | Why do you say your climate model does not work? | ||
| - | I get wrong results | ||
| - | |||
| - | Is it because of your plans that you say you get wrong results?</code> | ||
| - | * Emacs on windows: | ||
| - | * Install [[other:win10wsl|WSL]] and emacs | ||
| - | * Not tested recently: use {{:other:emacs_win_7_64_140408.zip|a config file for Windows}}, after installing [[other:win7apps#gnu_emacs_gnuwin_diffutils|an emacs compiled for running directly in Windows]] | ||
| - | * [[https://www.gnu.org/software/emacs/manual/|GNU Emacs Manuals Online]] | ||
| === vi (vim, gvim) === | === vi (vim, gvim) === | ||
| Line 498: | Line 470: | ||
| === Notepad++ === | === Notepad++ === | ||
| - | [[other:win10apps#notepad|Notepad++]] seems like a nice and powerful text editor for **Windows**, if you don't have the time and resource to install WSL+emacs | + | [[other:win10apps#notepad|Notepad++]] is a nice and powerful text editor for **Windows**, but it is also very easy to [[other:emacs_doc#windows_installation|install emacs on Windows]] |
| - | ==== NetCDF and file formats ==== | + | ==== NetCDF and related Conventions ==== |
| + | |||
| + | === Super-short introduction to NetCDF === | ||
| * What are binary ({{:other:newppl:binaire_jyp.pdf}}) and NetCDF ({{:other:newppl:netcdf_jyp.pdf}}) files? | * What are binary ({{:other:newppl:binaire_jyp.pdf}}) and NetCDF ({{:other:newppl:netcdf_jyp.pdf}}) files? | ||
| Line 506: | Line 480: | ||
| * The NetCDF file format is **self-documented**, and the metadata of climate data files often follows the [[http://cfconventions.org/|CF (Climate and Forecast) Metadata Conventions]] | * The NetCDF file format is **self-documented**, and the metadata of climate data files often follows the [[http://cfconventions.org/|CF (Climate and Forecast) Metadata Conventions]] | ||
| * The files in the [[https://esgf-node.ipsl.upmc.fr/projects/esgf-ipsl/|CMIPn (n ≥ 5) database]] are written with the [[https://cmor.llnl.gov/|CMOR 3 library]] in order to make sure that they follow exactly the requested standards | * The files in the [[https://esgf-node.ipsl.upmc.fr/projects/esgf-ipsl/|CMIPn (n ≥ 5) database]] are written with the [[https://cmor.llnl.gov/|CMOR 3 library]] in order to make sure that they follow exactly the requested standards | ||
| - | * You can use [[other:win7apps#panoply|Panoply]] and [[http://meteora.ucsd.edu/~pierce/ncview_home_page.html|ncview]] for visualizing quickly the NetCDF files | + | |
| - | * [[https://code.zmaw.de/projects/cdo/wiki/Cdo#Documentation|Climate Data Operators]] for manipulating NetCDF files (and some other formats) | + | |
| - | * [[http://nco.sourceforge.net/#RTFM|netCDF Operator (NCO)]] for manipulating NetCDF files | + | === Some ways of working with NetCDF without programming === |
| - | * [[http://cfconventions.org/|NetCDF CF (Climate and Forecast) Metadata Conventions]]: this will help you understand the information you get when you do a ''ncdump -h some_climate_data_file.nc'' | + | |
| - | * Using Python to work with NetCDF data: | + | * Displaying the content of a NetCDF file in a text format\\ Check the ''ncdump'' [[https://docs.unidata.ucar.edu/nug/current/netcdf_utilities_guide.html#ncdump_guide|options]]. People usually want to quickly check the metadata, and use other programs to work with the actual data |
| - | * Using the [[http://uv-cdat.llnl.gov/documentation/cdms/cdms.html|cdms2]] module if you work with the [[other:python:starting#uv-cdat|UV-CDAT distribution]] | + | * ''ncdump some_climate_data_file.nc'': dump the full content to text |
| - | * Using the [[http://unidata.github.io/netcdf4-python/|netCDF4]] module | + | * ''ncdump -h some_climate_data_file.nc'': only display the metadata |
| + | * You can use [[other:win7apps#panoply|Panoply]] and [[http://meteora.ucsd.edu/~pierce/ncview_home_page.html|ncview]] for quickly visualizing NetCDF files | ||
| + | * Manipulating NetCDF files: | ||
| + | * [[https://code.zmaw.de/projects/cdo/wiki/Cdo#Documentation|Climate Data Operators]] (''cdo'') | ||
| + | * [[http://nco.sourceforge.net/#RTFM|netCDF Operator]] (//NCO// operators) | ||
| + | |||
| + | |||
| + | === NetCDF related Conventions === | ||
| + | |||
| + | * [[https://arxiv.org/abs/1911.08638|Gridspec: A standard for the description of grids used in Earth System models]] | ||
| + | * A nice document for discovering the different type of (ir)regular grids used in climate models! | ||
| + | |||
| + | * [[http://cfconventions.org/|NetCDF CF (Climate and Forecast) Metadata Conventions]] | ||
| + | * [[https://ugrid-conventions.github.io/ugrid-conventions/|UGRID Conventions]] for storing unstructured (or flexible mesh) model data | ||
| + | * [[http://sgrid.github.io/sgrid/|SGRID Conventions]] for storing staggered data on structured grids that are consistent with the UGRID conventions | ||
| + | |||
| + | === Using NetCDF with Python === | ||
| + | |||
| + | |||
| + | Check the [[other:python:jyp_steps#using_netcdf_files_with_python|dedicated section]] of the //Python// page | ||
| ==== Programming languages ==== | ==== Programming languages ==== | ||
other/newppl/starting.txt · Last modified: 2024/07/02 10:22 by jypeter
