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Programming tools configuration

1 Python

1.1 PyLINT

# lint Python modules using external checkers.
#
# This is the main checker controlling the other ones and the reports
# generation. It is itself both a raw checker and an astng checker in order
# to:
# * handle message activation / deactivation at the module level
# * handle some basic but necessary stats'data (number of classes, methods...)
#
[MASTER]

# Python code to execute, usually for sys.path manipulation such as
# pygtk.require().
#init-hook=

# Profiled execution.
profile=no

# Add <file or directory> to the black list. It should be a base name, not a
# path. You may set this option multiple times.
ignore=CVS
ignore=.bzr
ignore=.svn

# Pickle collected data for later comparisons.
persistent=yes

# Set the cache size for astng objects.
cache-size=500

# List of plugins (as comma separated values of python modules names) to load,
# usually to register additional checkers.
load-plugins=


[MESSAGES CONTROL]

# Enable only checker(s) with the given id(s). This option conflict with the
# disable-checker option
#enable-checker=

# Enable all checker(s) except those with the given id(s). This option
# conflicts with the enable-checker option
#disable-checker=

# Enable all messages in the listed categories.
#enable-msg-cat=

# Disable all messages in the listed categories.
#disable-msg-cat=

# Enable the message(s) with the given id(s).
#enable-msg=

# Disable the message(s) with the given id(s).
disable-msg=I0011,R0903,C0111,W0612,W0401


[REPORTS]

# Set the output format. Available formats are text, parseable, colorized, msvs
# (visual studio) and html
output-format=text

# Include message's id in output
include-ids=yes

# Put messages in a separate file for each module / package specified on the
# command line instead of printing them on stdout. Reports (if any) will be
# written in a file name "pylint_global.[txt|html]".
files-output=no

# Tells wether to display a full report or only the messages
reports=yes

# Python expression which should return a note less than 10 (10 is the highest
# note). You have access to the variables errors warning, statement which
# respectivly contain the number of errors / warnings messages and the total
# number of statements analyzed. This is used by the global evaluation report
# (R0004).
evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)

# Add a comment according to your evaluation note. This is used by the global
# evaluation report (R0004).
comment=no

# Enable the report(s) with the given id(s).
#enable-report=

# Disable the report(s) with the given id(s).
disable-report=C0111


# checks for
# * unused variables / imports
# * undefined variables
# * redefinition of variable from builtins or from an outer scope
# * use of variable before assigment
#
[VARIABLES]

# Tells wether we should check for unused import in __init__ files.
init-import=no

# A regular expression matching names used for dummy variables (i.e. not used).
dummy-variables-rgx=_|dummy

# List of additional names supposed to be defined in builtins. Remember that
# you should avoid to define new builtins when possible.
additional-builtins=


# try to find bugs in the code using type inference
#
[TYPECHECK]

# Tells wether missing members accessed in mixin class should be ignored. A
# mixin class is detected if its name ends with "mixin" (case insensitive).
ignore-mixin-members=yes

# List of classes names for which member attributes should not be checked
# (useful for classes with attributes dynamicaly set).
ignored-classes=SQLObject

# When zope mode is activated, add a predefined set of Zope acquired attributes
# to generated-members.
zope=no

# List of members which are set dynamically and missed by pylint inference
# system, and so shouldn't trigger E0201 when accessed.
generated-members=REQUEST,acl_users,aq_parent


# checks for :
# * doc strings
# * modules / classes / functions / methods / arguments / variables name
# * number of arguments, local variables, branchs, returns and statements in
# functions, methods
# * required module attributes
# * dangerous default values as arguments
# * redefinition of function / method / class
# * uses of the global statement
#
[BASIC]

# Required attributes for module, separated by a comma
required-attributes=

# Regular expression which should only match functions or classes name which do
# not require a docstring
no-docstring-rgx=__.*__

# Regular expression which should only match correct module names
module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$

# Regular expression which should only match correct module level names
const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$

# Regular expression which should only match correct class names
class-rgx=[A-Z_][a-zA-Z0-9]+$

# Regular expression which should only match correct function names
function-rgx=[a-z_][a-z0-9_]{2,30}$

# Regular expression which should only match correct method names
method-rgx=[a-z_][a-z0-9_]{2,30}$

# Regular expression which should only match correct instance attribute names
attr-rgx=[a-z_][a-z0-9_]{2,30}$

# Regular expression which should only match correct argument names
argument-rgx=[a-z_][a-z0-9_]{2,30}$

# Regular expression which should only match correct variable names
variable-rgx=[a-z_][a-z0-9_]{1,30}$

# Regular expression which should only match correct list comprehension /
# generator expression variable names
inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$

# Good variable names which should always be accepted, separated by a comma
good-names=i,j,k,e,ex,Run,_

# Bad variable names which should always be refused, separated by a comma
bad-names=foo,bar,baz,toto,tutu,tata

# List of builtins function names that should not be used, separated by a comma
bad-functions=map,filter,apply,input


# checks for
# * external modules dependencies
# * relative / wildcard imports
# * cyclic imports
# * uses of deprecated modules
#
[IMPORTS]

# Deprecated modules which should not be used, separated by a comma
deprecated-modules=regsub,string,TERMIOS,Bastion,rexec

# Create a graph of every (i.e. internal and external) dependencies in the
# given file (report R0402 must not be disabled)
import-graph=

# Create a graph of external dependencies in the given file (report R0402 must
# not be disabled)
ext-import-graph=

# Create a graph of internal dependencies in the given file (report R0402 must
# not be disabled)
int-import-graph=


# checks for sign of poor/misdesign:
# * number of methods, attributes, local variables...
# * size, complexity of functions, methods
#
[DESIGN]

# Maximum number of arguments for function / method
max-args=5

# Maximum number of locals for function / method body
max-locals=15

# Maximum number of return / yield for function / method body
max-returns=6

# Maximum number of branch for function / method body
max-branchs=12

# Maximum number of statements in function / method body
max-statements=50

# Maximum number of parents for a class (see R0901).
max-parents=7

# Maximum number of attributes for a class (see R0902).
max-attributes=7

# Minimum number of public methods for a class (see R0903).
min-public-methods=2

# Maximum number of public methods for a class (see R0904).
max-public-methods=20


# checks for :
# * methods without self as first argument
# * overridden methods signature
# * access only to existant members via self
# * attributes not defined in the __init__ method
# * supported interfaces implementation
# * unreachable code
#
[CLASSES]

# List of interface methods to ignore, separated by a comma. This is used for
# instance to not check methods defines in Zope's Interface base class.
ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by

# List of method names used to declare (i.e. assign) instance attributes.
defining-attr-methods=__init__,__new__,setUp


# checks for :
# * unauthorized constructions
# * strict indentation
# * line length
# * use of <> instead of !=
#
[FORMAT]

# Maximum number of characters on a single line.
max-line-length=100

# Maximum number of lines in a module
max-module-lines=1000

# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
# tab).
indent-string='    '


# checks for similarities and duplicated code. This computation may be
# memory / CPU intensive, so you should disable it if you experiments some
# problems.
#
[SIMILARITIES]

# Minimum lines number of a similarity.
min-similarity-lines=4

# Ignore comments when computing similarities.
ignore-comments=yes

# Ignore docstrings when computing similarities.
ignore-docstrings=yes


# checks for:
# * warning notes in the code like FIXME, XXX
# * PEP 263: source code with non ascii character but no encoding declaration
#
[MISCELLANEOUS]

# List of note tags to take in consideration, separated by a comma.
notes=FIXME,XXX,TODO,NOTE

2 Javascript

2.1 NPM

prefix=${HOME}/environment/local/npm_packages

3 R

# Setup repository
local({
  r = getOption("repos")
  r["CRAN"] = "http://cran.univ-paris1.fr/"
  options(repos = r)
})

4 LaTeX

4.1 latexmk

#!/bin/env perl

# coming from: https://collaborating.tuhh.de/alex/latex-cookbook/-/blob/master/.latexmkrc


# This file contains instructions and configurations for the `latexmk` program.
# That program is somewhat like `make`, but tailored to LaTeX.
# LaTeX has a distinct characteristic of regularly requiring *multiple runs* of
# the same program (e.g. `lualatex`) before the build is finished.
# It's a *multi-pass* system.
# In the intermediary runs, latex generates auxiliary files responsible for resolving
# references, links, tables of content etc.

# `latexmk` knows about these dependencies (otherwise we tell it in this very config
# file, see below), detects these and runs latex (and other, outside programs)
# accordingly.

# Now, why do we need *both* `latexmk` and `make`?
# Both automate builds.

# `latexmk` is not powerful enough to cover all use cases.
# `make` is more general and more suitable to be integrated in CI.
# For our latex needs, `make` basically only delegates to `latexmk`.
# We **do not** call e.g. `lualatex` multiple times manually from `make`:
# this logic is left to `latexmk` and `.latexmkrc`.
# However, `make` can also do much more, e.g. cover `pandoc`, clean-up operations etc.
# Therefore, `make` and `latexmkrc` *together* are just super powerful and useful.


# The shebang at the top  is only to get syntax highlighting right across GitLab,
# GitHub and IDEs.
# This file is not meant to be run, but read by `latexmk`.

# ======================================================================================
# Perl `latexmk` configuration file
# ======================================================================================

# ======================================================================================
# PDF Generation/Building/Compilation
# ======================================================================================

# PDF-generating modes are:
# 1: pdflatex, as specified by $pdflatex variable (still largely in use)
# 2: postscript conversion, as specified by the $ps2pdf variable (useless)
# 3: dvi conversion, as specified by the $dvipdf variable (useless)
# 4: lualatex, as specified by the $lualatex variable (best)
# 5: xelatex, as specified by the $xelatex variable (second best)
$pdf_mode = 4;

# Treat undefined references and citations as well as multiply defined references as
# ERRORS instead of WARNINGS.
# This is only checked in the *last* run, since naturally, there are undefined references
# in initial runs.
# This setting is potentially annoying when debugging/editing, but highly desirable
# in the CI pipeline, where such a warning should result in a failed pipeline, since the
# final document is incomplete/corrupted.
#
# However, I could not eradicate all warnings, so that `latexmk` currently fails with
# this option enabled.
# Specifically, `microtype` fails together with `fontawesome`/`fontawesome5`, see:
# https://tex.stackexchange.com/a/547514/120853
# The fix in that answer did not help.
# Setting `verbose=silent` to mute `microtype` warnings did not work.
# Switching between `fontawesome` and `fontawesome5` did not help.
$warnings_as_errors = 0;

# Show used CPU time. Looks like: https://tex.stackexchange.com/a/312224/120853
$show_time = 1;

# Default is 5; we seem to need more owed to the complexity of the document.
# Actual documents probably don't need this many since they won't use all features,
# plus won't be compiling from cold each time.
$max_repeat=7;

# --shell-escape option (execution of code outside of latex) is required for the
#'svg' package.
# It converts raw SVG files to the PDF+PDF_TEX combo using InkScape.
#
# SyncTeX allows to jump between source (code) and output (PDF) in IDEs with support
# (many have it). A value of `1` is enabled (gzipped), `-1` is enabled but uncompressed,
# `0` is off.
# Testing in VSCode w/ LaTeX Workshop only worked for the compressed version.
# Adjust this as needed. Of course, only relevant for local use, no effect on a remote
# CI pipeline (except for slower compilation, probably).
#
# %O and %S will forward Options and the Source file, respectively, given to latexmk.
#
# `set_tex_cmds` applies to all *latex commands (latex, xelatex, lualatex, ...), so
# no need to specify these each. This allows to simply change `$pdf_mode` to get a
# different engine. Check if this works with `latexmk --commands`.
set_tex_cmds("--shell-escape --synctex=1 %O %S");

# option 2 is same as 1 (run biber when necessary), but also deletes the
# regeneratable bbl-file in a clenaup (`latexmk -c`). Do not use if original
# bib file is not available!
$bibtex_use = 2;  # default: 1

# Change default `biber` call, help catch errors faster/clearer. See
# https://web.archive.org/web/20200526101657/https://www.semipol.de/2018/06/12/latex-best-practices.html#database-entries
$biber = "biber --validate-datamodel %O %S";

# ======================================================================================
# Auxiliary Files
# ======================================================================================

# Let latexmk know about generated files, so they can be used to detect if a
# rerun is required, or be deleted in a cleanup.
# loe: List of Examples (KOMAScript)
# lol: List of Listings (`listings` and `minted` packages)
# run.xml: biber runs
# glg: glossaries log
# glstex: generated from glossaries-extra
push @generated_exts, 'loe', 'lol', 'lor', 'run.xml', 'glg', 'glstex';

# Also delete the *.glstex files from package glossaries-extra. Problem is,
# that that package generates files of the form "basename-digit.glstex" if
# multiple glossaries are present. Latexmk looks for "basename.glstex" and so
# does not find those. For that purpose, use wildcard.
# Also delete files generated by gnuplot/pgfplots contour plots
# (.dat, .script, .table).
$clean_ext = "%R-*.glstex %R_contourtmp*.*";

# ======================================================================================
# bib2gls as a custom dependency
# ======================================================================================

# Grabbed from latexmk CTAN distribution:
# Implementing glossary with bib2gls and glossaries-extra, with the
# log file (.glg) analyzed to get dependence on a .bib file.
# !!! ONLY WORKS WITH VERSION 4.54 or higher of latexmk

# Add custom dependency.
# latexmk checks whether a file with ending as given in the 2nd
# argument exists ('toextension'). If yes, check if file with
# ending as in first argument ('fromextension') exists. If yes,
# run subroutine as given in fourth argument.
# Third argument is whether file MUST exist. If 0, no action taken.
add_cus_dep('aux', 'glstex', 0, 'run_bib2gls');

# PERL subroutine. $_[0] is the argument (filename in this case).
# File from author from here: https://tex.stackexchange.com/a/401979/120853
sub run_bib2gls {
    if ( $silent ) {
    #    my $ret = system "bib2gls --silent --group '$_[0]'"; # Original version
        my $ret = system "bib2gls --silent --group $_[0]"; # Runs in PowerShell
    } else {
    #    my $ret = system "bib2gls --group '$_[0]'"; # Original version
        my $ret = system "bib2gls --group $_[0]"; # Runs in PowerShell
    };

    my ($base, $path) = fileparse( $_[0] );
    if ($path && -e "$base.glstex") {
        rename "$base.glstex", "$path$base.glstex";
    }

    # Analyze log file.
    local *LOG;
    $LOG = "$_[0].glg";
    if (!$ret && -e $LOG) {
        open LOG, "<$LOG";
    while (<LOG>) {
            if (/^Reading (.*\.bib)\s$/) {
        rdb_ensure_file( $rule, $1 );
        }
    }
    close LOG;
    }
    return $ret;
}