[Blends-commit] [Git][blends-team/debug][master] 2 commits: Debug covid-19 task
Andreas Tille
gitlab at salsa.debian.org
Tue Mar 24 10:11:33 GMT 2020
Andreas Tille pushed to branch master at Debian Blends Team / debug
Commits:
65aabb81 by Andreas Tille at 2020-03-24T11:10:20+01:00
Debug covid-19 task
- - - - -
511ee055 by Andreas Tille at 2020-03-24T11:11:23+01:00
Fix comments
- - - - -
11 changed files:
- + tasks/covid-19
- tasks/debug
- − tasks/definitions
- − tasks/enumerations
- − tasks/experimental
- − tasks/italic
- − tasks/oldddtp
- − tasks/overlong
- − tasks/screenshots
- − tasks/verbose_without_reason
- − tasks/works
Changes:
=====================================
tasks/covid-19
=====================================
@@ -0,0 +1,86 @@
+Task: Covid-19
+Metapackage: false
+Description: This task exists only for tagging COVID-19 relevant cases
+ The Debian Med team intends to take part at the
+ COVID-19 Biohackathon (April 5-11, 2020)
+ This task was created only for the purpose to list relevant packages.
+
+X-Mark: <bio>
+
+Recommends: cwltool, snakemake
+
+Recommends: augur, auspice
+
+Recommends: chime
+
+Recommends: chip-seq
+
+Recommends: fastqc
+
+Recommends: nextstrain-ncov
+Remark: needs auspice
+
+Recommends: r-bioc-rcpi
+
+Recommends: r-cran-mediana
+
+Recommends: r-bioc-tcgabiolinks
+Remark: Non-distributable due to locfit dependency
+
+Recommends: r-cran-spp
+
+X-Mark: TODO: Check out
+X-Mark: https://www.bioinformatics.babraham.ac.uk/projects/index.html
+X-Mark: for further tools
+
+X-Mark: </bio>
+
+X-Mark: <imaging>
+
+Recommends: aeskulap
+
+Recommends: conquest-common
+
+Suggests: conquest-dbase, conquest-mysql, conquest-postgres, conquest-sqlite
+
+Recommends: dcmtk
+
+Recommends: ginkgocadx
+
+Recommends: imagej
+
+Recommends: libgdcm-tools
+
+Recommends: slicer
+Remark: slicer was removed from Debian (see #644352)
+ Its re-introduction into Debian is prepared by the Debian Med team here
+ https://salsa.debian.org/med-team/slicer
+
+Recommends: orthanc
+
+Suggests: orthanc-webviewer, orthanc-dicomweb, orthanc-imagej, orthanc-postgresql, orthanc-mysql
+
+Recommends: orthanc-wsi
+
+X-Mark: </imaging>
+
+X-Mark: <tools>
+
+X-Mark: https://opensourceventilator.ie/
+X-Mark: -> https://gitlab.com/open-source-ventilator/OpenLung
+
+X-Mark: https://www.mikrocontroller.net/topic/491565
+X-Mark: -> https://github.com/jcl5m1/ventilator
+
+X-Mark: https://sormasorg.helmholtz-hzi.de/Open_source.html
+X-Mark: -> https://github.com/hzi-braunschweig/SORMAS-Project
+
+X-Mark: </tools>
+
+X-Mark: <preconditions>
+
+Recommends: streamlit
+Remark: Needs help from Debian Science team
+ This is a machine learning framework which is required by chime.
+
+X-Mark: </preconditions>
=====================================
tasks/debug
=====================================
@@ -13,232 +13,3 @@ Remark: Something from new ...
Depends: seaview, xplanet, libc6
Remark: Some packages with interesting release, version, architecture sets
-
-Depends: kolab-cyrus-common,
-Remark: General problem: Homepage set verbatim in Description.
- While in principle the Homepage information should be not kept in the
- long description any more a lot of (IMHO not carefully maintained) packages
- just provide this in the end of the long description and many of these
- use even indentation to force verbose rendering. This conflicts with
- the URL detection algorithm in the Preprocessor.
- .
- A possible temporary solution might be to remove leading spaces from
- strings matching '^\s*Homepage:\s+http:'.
- .
- It would be even better to finally do a mass bug filing to get rid of
- this way to specify Homepages.
-
-Depends: libapache-dbi-perl
-Remark: Different levels of lists are simply mixed up
- These modules are supposed to be used with the Apache server together with
- an embedded perl interpreter like mod_perl. They provide support for basic
- authentication and authorization as well as support for persistent database
- connections via Perl's Database Independent Interface (DBI).
- .
- o AuthDBI.pm provides authentication and authorization:
- - optional shared cache for passwords to minimize database load
- - configurable cleanup-handler deletes outdated entries from the cache
- .
- o DBI.pm provides persistent database connections:
- - connections can be established during server-startup
- - configurable rollback to ensure data integrity
- - configurable verification of the connections to avoid time-outs.
-
-Depends: cli-common
-Remark: Different levels of lists are simply mixed up / Intention of author unclear (*/+ usage)
- This package must be installed if a CLI (Common Language Infrastructure)
- runtime environment is desired.
- .
- It covers useful integration and information for CLI implementations in
- Debian GNU/Linux, including:
- * The CLI policy describes how CLI packages should behave and integrate.
- * A FAQ for package maintainers of CLI/.NET applications.
- * Integration for CLRs (Common Language Runtime):
- + Installing libraries into existing GACs (Global Assembly Cache)
-
-Depends: finch
-Remark: Different levels of lists are simply mixed up / Intention of author unclear (*/+ usage)
- Finch is a text/console-based, modular instant messaging client capable of
- using AIM/ICQ, Yahoo!, MSN, IRC, Jabber, Napster, Zephyr, Gadu-Gadu, Bonjour,
- Groupwise, Sametime, SILC, and SIMPLE all at once.
- .
- Some extra packages are recommended to use the core functionality present
- in most finch installations:
- * gstreamer0.10-plugins-base, gstreamer0.10-plugins-good
- - Sound support.
- .
- More extra packages are suggested to use increased functionality:
- * libx11-6
- - To use the Clipboard and/or Toaster plugins.
-
-Depends: fantasdic
-Remark: Markdown is confused by '-' following a non space character
-
-Depends: libbitcollider-dev, libbitcollider1
-Remark: Suspected trouble to dectect list if bullets are in second (instead of third column)
- This is the development headers for the bitcollider libs.
- .
- Think of it as a really big file hash database on the internet with
- constant contributions from others of metadata on files.
- .
- Bitcollider is a small program to reliably identify and describe files
- on your machine. When run with a specific file as input, this program
- does two major things:
- .
- * It examines the file, calculating a distinctive digital fingerprint,
- or bitprint, and taking note of some other identifying information that
- can be extracted from the file, like file length and the local filename.
- * It launches your web browser to do a lookup at our website, submitting
- this identifying information as the search terms.
- .
- At bitzi.com you'll see what - if anything - others have said about your
- file, and have a chance to contribute descriptions or comments yourself.
- If your automatic submission included information useful to our database,
- that new information will be contributed to the database under your screen
- name.
- .
- The funny thing is that the same situation is true for **ion3-doc** except that
- there is an additional blank line inserted.
- .
- Should we even indent expressions matching '^ [-*+o] ' in the preprocessing
- to avoid such wrongly formatted descriptions?
-
-Depends: gdesklets-data
-Remark: List is not intended (rather a table)
-
-Depends: gimageview
-Remark: Unable to detect second order list
- GImageView is image viewer. It has some useful features such as:
- .
- * simple GUI
- * tabbed thumbnail viewer for directories
- * low memory use
- * image file management tool
- * slide show
- * read/write many image cache formats of thumbnail
- * read : Konqueror, GQview, Electric Eyes (Picview)
- * write : Nautilus, .xvpics
- .
- Supported image formats are:
- * JPEG, PNG, PNM, GIF, TIFF, XBM, XPM, XWD, BMP and PCX.
- .
- You can drop image and drop it into Gimp window from GImageView one.
-
-Depends: irssi-plugin-otr
-Remark: Unable to detect second order list; But regarding content this is not really a second order list but rather a definition list
- Off-the-Record (OTR) Messaging Plugin for the Irssi Chat Client
- .
- This plugin adds Off-the-Record messaging support for the irssi IRC client.
- Although primarily designed for use with the bitlbee IRC2IM gateway, it works
- within any query window, provided that the conversation partner's IRC client
- supports OTR.
- .
- OTR allows you to have private conversations over IM by providing:
- - Encryption
- - No one else can read your instant messages.
- - Authentication
- - You are assured the correspondent is who you think it is.
- - Deniability
- - The messages you send do _not_ have digital signatures that are
- checkable by a third party. Anyone can forge messages after a
- conversation to make them look like they came from you. However,
- _during_ a conversation, your correspondent is assured the messages
- he sees are authentic and unmodified.
- - Perfect forward secrecy
- - If you lose control of your private keys, no previous conversation
- is compromised.
-
-Depends: js2-mode
-Remark: Unable to detect second order list
- This JavaScript editing mode supports:
- .
- - the full JavaScript language through version 1.7
- - support for most Rhino and SpiderMonkey extensions from 1.5 to 1.7
- - accurate syntax highlighting using a recursive-descent parser
- - syntax-error and strict-mode warning reporting
- - "bouncing" line indentation to choose among alternate indentation points
- - smart line-wrapping within comments and strings
- - code folding:
- - show some or all function bodies as {...}
- - show some or all block comments as /*...*/
- - context-sensitive menu bar and popup menus
- - code browsing using the imenu' package
- - typing helpers (e.g. inserting matching braces/parens)
- - many customization options
-
-Depends: amsynth
-Remark: No idea why this does not work even after substitution from 'o' to '*'
- amSynth features:
- * two analogue-style audio oscillators, featuring:
- o sine wave
- o saw/triangle wave with adjustable shape
- o square/pulse wave with adjustable pulsewidth
- o noise generation
- o "random" wave (noise with sample & hold)
- o oscillator sync
- o of course, detune and range control
- * mixer section with ring modulation
- * analogue-style low-pass filter
- o 24dB/octave curve
- o dedicated ADSR envelope
- o cutoff and resonance control
- o keyboard pitch tracking
- * amplifier with dedicated ADSR envelope
- * modulation LFO
- o up to 58Hz modulation
- o routable to all sections (pitch, filter, amplifier)
- * Effects
- o High quality stereo reverb (freeverb)
- o Distortion/crunch
- * Easy navigation and manipulation of presets
- * Stand-alone OSS or ALSA Midi/Audio client
- .
-
-Depends: apg
-Remark: Turning an second order enumeration might make sense in principle but it should not be forced by proken markdown formatting
- APG (Automated Password Generator) is the tool set for random
- password generation. It generates some random words of required type
- and prints them to standard output. This binary package contains only
- the standalone version of apg.
- Advantages:
- * Built-in ANSI X9.17 RNG (Random Number Generator)(CAST/SHA1)
- * Built-in password quality checking system (now it has support for Bloom
- filter for faster access)
- * Two Password Generation Algorithms:
- 1. Pronounceable Password Generation Algorithm (according to NIST
- FIPS 181)
- 2. Random Character Password Generation Algorithm with 35
- configurable modes of operation
- * Configurable password length parameters
- * Configurable amount of generated passwords
- * Ability to initialize RNG with user string
- * Support for /dev/random
- * Ability to crypt() generated passwords and print them as additional output.
- * Special parameters to use APG in script
- * Ability to log password generation requests for network version
- * Ability to control APG service access using tcpd
- * Ability to use password generation service from any type of box (Mac,
- WinXX, etc.) that connected to network
- * Ability to enforce remote users to use only allowed type of password
- generation
- The client/server version of apg has been deliberately omitted.
- .
- Upstream URL: http://www.adel.nursat.kz/apg/download.shtml
-
-Depends: libocamlbricks-ocaml-dev
-
-Depends: m-tx, alsa-firmware-loaders, garlic-doc
-
-Depends: non-existing-package
-Homepage: http://nowhere.com
-
-Depends: another-non-existing-package
-Pkg-Description: Non existing package for testing
- This package doese not exist and will never be. It does not even
- have a homepage.
-
-Depends: further-non-existing-package
-Homepage: http://somewhere.com
-Pkg-Description: Further non existing package for testing
- This package doese not exist and will never be. But at least it
- has a homepage.
=====================================
tasks/definitions deleted
=====================================
@@ -1,18 +0,0 @@
-Task: Definitions
-Description: Examples for definition lists in descriptions
- Here some new techniques are tested - currently the
- markdown formatting is tested. This task contains some
- examples of definition lists.
-
-Depends: glam2
-
-Depends: casu
-
-Depends: cvsutils, flim, fontforge, gatos, gitpkg, gnus-bonus-el, isdnutils, jigit
-
-Depends: josm-plugins, joystick, kdebluetooth, kicad, kipi-plugins, hugin-tools
-
-Depends: gigtools, lbdb, lcdf-typetools, libbttracker-utils, ike-scan, jifty
-
-Depends: dvb-apps
-Remark: Works as list because of substituting '.' to '*'; however, a definition list is intended
=====================================
tasks/enumerations deleted
=====================================
@@ -1,7 +0,0 @@
-Task: Enumerations
-Description: Examples for enumerations in descriptions
- Here some new techniques are tested - currently the
- markdown formatting is tested. This task provides examples
- for Enumerations in descriptions.
-
-Depends: developers-reference, flamethrower
=====================================
tasks/experimental deleted
=====================================
@@ -1,6 +0,0 @@
-Task: Experimental
-Description: Packages with uploads to experimental
- Here some packages are tested which have at least one version
- in experimental.
-
-Depends: paml, python-pynast, fldigi, meld, swig
=====================================
tasks/italic deleted
=====================================
@@ -1,96 +0,0 @@
-Task: Italics formating
-Description: Examples for definition markdown italics formatting
- Here some new techniques are tested - currently the
- markdown formatting is tested. This task contains some
- examples of italics formatting.
- .
- Packages listed as "Depends" seem to have a problem, packages
- listed as "Suggests" are rather an enhancement than a problem.
- .
- Some translations (for instance German bhl do better than the
- original text)
-
-Depends: alltray
-Remark: Fluxbox is rendered italic
- With AllTray you can dock any application with no native tray icon
- (like Evolution, Thunderbird, Terminals) into the system tray.
- A high-light feature is that a click on the "close" button
- will minimize back to system tray. It works well with Gnome,
- KDE, XFCE 4*, Fluxbox* and WindowMaker*.
- (*) No drag 'n drop support. Enable with "-nm" option.
- .
- Homepage: http://alltray.sourceforge.net/
-
-Depends: bhl
-Remark: Unwanted italics?
- The german translation just leaves out the '*' which might be wanted
- or not. It just explains the shortcut - but isn't it usual to mark it
- this way: _B_rut to _H_tml and _L_aTeX. Italics looks hardly visible here.
- BHL is an Emacs mode that enables you to convert brut text files into
- HTML, LaTeX and SGML files. "BHL" is an acronym for: "from *B*rut to
- *H*tml and *L*aTeX" (SGML was implemented later).
- .
- In order to convert TXT files into other formats, you need to use some
- syntactical elements. The purpose of this mode is to use the most
- invisible and convenient syntax. Invisible syntax means that the
- source file must be as readable as possible (like any TXT file must be).
- Convenient syntax means that the syntax must fit user's habits.
-
-Depends: dis51
-Remark: Unwanted italics by trying to specify a regexp
- Dis51 is a simple 8051 disassembler. It takes an object file in
- Intel Hex (*.ihx or *.hex) format as input, and outputs an assembly
- language file.
-
-Depends: flip
-Remark: The '**' in **NIX just vanishes
- This program converts line endings of text files between MS-DOS and
- **IX formats. It detects binary files in a nearly foolproof way and
- leaves them alone unless you override this. It will also leave files
- alone that are already in the right format and preserves file
- timestamps. User interrupts are handled gracefully and no garbage or
- corrupted files left behind. 'flip' does not convert files to a
- different character set, and it can not handle Apple Macintosh
- line endings (CR only). For that (and more), you can use the 'recode'
- program (package 'recode').
-
-Depends: ghemical
-Remark: The last line is featuring two asterisks which are removed by markdown
- ...
- basis sets ranging from STO-3G to 6-31G**.
-
-Depends: js2-mode
-Remark: The string /*...*/ is broken by markdown; and second level list is not detected
- This JavaScript editing mode supports:
- .
- - the full JavaScript language through version 1.7
- - support for most Rhino and SpiderMonkey extensions from 1.5 to 1.7
- - accurate syntax highlighting using a recursive-descent parser
- - syntax-error and strict-mode warning reporting
- - "bouncing" line indentation to choose among alternate indentation points
- - smart line-wrapping within comments and strings
- - code folding:
- - show some or all function bodies as {...}
- - show some or all block comments as /*...*/
- - context-sensitive menu bar and popup menus
- - code browsing using the imenu' package
- - typing helpers (e.g. inserting matching braces/parens)
- - many customization options
-
-X-Comment: These are actually fine and Markdown just ignores the '*'
-X-Comment: clig, cvsnt, fbpanel, gap-small-groups-extra, gdesklets-data,
- gnome-schedule, jed-extra, kmplayer, kvm
-
-X-Comment: kmplayer-plugin
- Only in testing so currently hidden from Blends-Webtools
-
-Depends: latrine
-Remark: Reference to dict-freedict-*-* packages is broken
- ...
- http://sourceforge.net/projects/freedict/, provides dictionaries for about 50
- language combinations, which should be compatible with LaTrine. These
- dictionaries are also available via the Debian dict-freedict-*-* packages.
-
-Suggests: bochs-svga, crashme
-
-Suggests: apache2-prefork-dev, aolserver4-core-4.5.1, apache2.2-common, bbdb, calibre, cl-trivial-gray-streams, cli-uno-bridge, dbench, dctc, foomatic-filters-ppds, gfs-tools, gfs2-tools, killer, libclass-prototyped-perl
=====================================
tasks/oldddtp deleted
=====================================
@@ -1,8 +0,0 @@
-Task: Old DDTP
-Description: Pachages with outdated translations
- Here some packages are tested which have DDTP translations but for older
- versions which are hidden by new sentinel code.
-
-Depends: bluez-cups, njplot, dosfstools, hal, pymol
-
-
=====================================
tasks/overlong deleted
=====================================
@@ -1,6 +0,0 @@
-Task: Overlong
-Description: Examples for way to long descriptions
- This page contains some bad examples for descriptions
- which were much longer than acceptable
-
-Depends: emacs-goodies-el
=====================================
tasks/screenshots deleted
=====================================
@@ -1,8 +0,0 @@
-Task: Screenshots
-Description: Packages featuring several screenshots
- Here some packages are tested which are featuring more than
- five screenshots.
-
-Depends: smc, gnome-utils, dia, ttf-indic-fonts-core, msttcorefonts, couchdb,
- banshee, midori, cheese, cacti, ttf-droid, software-center,
- gedit, glpi, gcompris, sgt-puzzles, ttf-umefont
=====================================
tasks/verbose_without_reason deleted
=====================================
@@ -1,9 +0,0 @@
-Task: Verbose without reason
-Description: Some long descriptions which are verbose without reason
- Here some new techniques are tested - currently the
- markdown formatting is tested. This task contains those
- packages which just feature broken indentation because of using
- at least two spaces in the beginning of each line without any
- reason - or for a wrong reason when a list was intended.
-
-Depends: balazar, funcoeszz, gnugk, libbobcat2
=====================================
tasks/works deleted
=====================================
@@ -1,79 +0,0 @@
-Task: Works with markdown
-Description: Descriptions which are working with markdown
- Here some new techniques are tested - currently the
- markdown formatting is tested. These packages are
- random positive examples.
- .
- The preformatting in Python seems to work for airport-utils
- even if the perl code as suggested at
- http://lists.debian.org/debian-devel/2009/04/msg00712.html
- leads to a second level list in the last item.
- .
- The description of geordi requires masking the a '#' in
- the first column. It is rendered on this page as well to
- make sure everything works as expected.
- .
- Check whether non-ASCI characters in descriptions are working
- (ggz-python-games)
-
-Depends: airport-utils
-Remark: This package is OK despite the strange formatting of the last paragraph
- .
- For all:
- - airport-modem: modem control utility, displays modem state, starts/stops
- modem connections, displays the approximate connection time (Extreme only)
- - airport-hostmon: wireless hosts monitor, lists wireless hosts connected
- to the base station (see airport2-portinspector for the Snow)
- .
- Please note that it fails in the Perl implementation mentioned at
- http://lists.debian.org/debian-devel/2009/04/msg00712.html because the
- last item is rendered as a second order list there (but I have no idea
- why.
-
-Depends: geordi
-Remark: Works because of substituting '#' in first column is escaped
-
-Depends: ggz-python-games
-Remark: Just testing non-ASCII characters in long description
-
-Depends: crash, alsa-utils, ccmalloc, ftp-proxy, global, lam-runtime, libapache2-modxslt
-Remark: Works because of substituting 'o' to '*'
-
-Depends: acidlab
-Remark: Works because of substituting 'o' to '*', otherwise there would be no list at all
- The Analysis Console for Intrusion Databases (ACID) is a PHP-based analysis
- engine to search and process a database of security events generated by
- various IDSes, firewalls, and network monitoring tools. The features currently
- include:
- .
- \o Query-builder and search interface for finding alerts matching
- on alert meta information (e.g. signature, detection time) as well as
- the underlying network evidence (e.g. source/destination address, ports,
- payload, or flags).
- .
- \o Packet viewer (decoder) will graphically display the layer-3 and
- layer-4 packet information of logged alerts
- .
- \o Alert management by providing constructs to logically group alerts
- to create incidents (alert groups), deleting the handled alerts or
- false positives, exporting to email for collaboration, or archiving of
- alerts to transfer them between alert databases.
- .
- \o Chart and statistic generation based on time, sensor, signature, protocol,
- IP address, TCP/UDP ports, or classification
- .
- ACID has the ability to analyze a wide variety of events which are
- post-processed into its database. Tools exist for the following formats:
- .
- \o using Snort (www.snort.org)
- - Snort alerts
- - tcpdump binary logs
- .
- \o using logsnorter (www.snort.org/downloads/logsnorter-0.2.tar.gz)
- - Cisco PIX
- - ipchains
- - iptables
- - ipfw
- .
- Homepage: http://acidlab.sourceforge.net/
-
View it on GitLab: https://salsa.debian.org/blends-team/debug/-/compare/68149169c2a37d4be4330a5d27dfbebd60f2bf74...511ee05577937f4bbd32df5d2673c46ff28b4601
--
View it on GitLab: https://salsa.debian.org/blends-team/debug/-/compare/68149169c2a37d4be4330a5d27dfbebd60f2bf74...511ee05577937f4bbd32df5d2673c46ff28b4601
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