605 private links
When considering automation apps for Android, Tasker immediately comes to mind. And although it has name recognition, it's source code is proprietary and the app requires the Google Play store on the device (beyond a 7-day trial version).
So, what FOSS automation apps are there out there?
- Easer by Rui Zhao. Source on Github (449 stars, 1295 commits), F-Droid. Note that there is also a beta version of this app.
- Automation by Jens Schröder. Source on developer's Gitea instance (88 commits), F-Droid.
Other non-free automation apps for Android (not recommended)
- Tasker
- Automate by LlamaLab
- AutomateIt
- MacroDroid
- RuleBot by KF Software House (Hong Kong)
Shelter is a Free and Open-Source (FOSS) app that leverages the "Work Profile" feature of Android to provide an isolated space that you can install or clone apps into.
Directories of alternatives
- https://switching.software - a list of easy-to-use alternatives to well-known software.
Ethical, easy-to-use and privacy-conscious alternatives to well-known software.
The source code for its website is published on Codeberg (meaning you can suggest changes, etc.). - https://www.privacyguides.org - lots of categories. The website itself is built from a public Github repo. Via https://mastodon.neat.computer/users/privacyguides/statuses/113002199475214098
- https://guide.yuuire.com/recommendations/software/foss-alternatives - list of open source and privacy-friendly apps. Website's source code on github
- https://divestos.org/pages/recommended_apps - F-Droid recommended apps by divestos.org.
- https://european-alternatives.eu - European alternatives for digital products.
- https://selfh.st/apps - A directory of self-hosted software.
Other lists of directories
Adopted by the Journal of Cheminformatics (Aug 2020)
- First adoption by a scientific journal announced in editorial by Egon Willighagen
- Blog post by Willighagen on the same subject
- CiTO updates (another blog post by WIllighagen)
- Citation Typing: progress but we need more uptake
- CiTO updates #4: annotations in datasets
- FAIR blog-to-blog citations
- CiTO for blog citations
BioMedCentral on the CiTO Pilot (seems to only include Journal of Cheminformatics, for now).
Usage of CiTO is spreading. This page keeps track of CiTO annotation in Wikidata.
What about adoption by tools?
Willighagen offers rudimental instructions for BibTeX (but probably only suitable for Journal of Cheminformatics at the moment) as well as for Google Docs + Zotero (not really working) in this github repo.
Markdown template with CiTO for the Journal of Cheminformatics.
The best tool with support for CiTO: pandoc scholar
Pandoc Scholar appears to be our best bet at the moment if we want to use CiTO in our manuscripts.
Krewinkel A, Winkler R. 2017. Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. PeerJ Computer Science 3:e112 https://doi.org/10.7717/peerj-cs.112
Other notes
It looks like support for CiTO should happen at the document processing tool stage, and not in our reference managers (Zotero, etc.).
I wonder if something like Biber/BibLaTeX should add support for CiTO, or if that's the wrong abstraction level.
Martin Fenner has a blog post from 2011 (Google Cache) where he shows how to use CiTO with a Wordpress plugin, unfortunately both the post and the plugin appear to have gone offline.
Recently, ORCID promoted Scite_ on their blog. But Scite describes itself as a Brooklyn-based startup (I assume that's code for venture capital-backed), although it also acknowledges funding from public institutions such as NSF and NIH. Scite uses "a deep learning model" to identify "citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence" (so they really only classify the citation as supporting or contrasting). In contrast to Scite, CiTO is an open standard that anyone can build on. Although Scite is currently much glitzier and fancier than anything CiTO can provide, we should encourage everyone to use CiTO (if they care about citation classification).
Guides and how-tos
- Introduction to Ansible playbooks
- Playbooks vs roles, and explain the difference between task, role, play and playbook
- How to install and configure Ansible on Ubuntu 18.04 - DigitalOcean
- Linux hardening using idempotency with Ansible
Ansible playbooks and roles
- I haven't published all roles that I've written, but all the roles that I do publish are collected at codeberg.org/ansible
- Ansible module (Python code) to install R packages, by yutannihilation
- Ansible role to install TeXLive
- https://ansible.jeffgeerling.com/
- https://robertdebock.nl/ansible.html
Related
Independent app stores (with their own repository of apps)
- F-Droid. The gold standard of FOSS app stores.
- UpToDown, mostly Google Play's apps it seems, but also accepts submissions from developers. Run by Spanish company, not FOSS, but can be used without user registration.
Alternative front-end clients to F-Droid
Simply front-ends to the Google Play store
Free and open source PDF readers. A list by the FSFE.
Fantastic little tool. I used it on Baahubali 2, whose subtitles were drifting more and more with time, and it corrected it without any user intervention. Very nice!
It is even integrated into Bazarr (automatic subtitle synchronisation can be enabled in Bazarr's settings).
General Julia resources
https://en.wikipedia.org/wiki/Julia_%28programming_language%29
https://old.reddit.com/r/Julia/
https://github.com/JuliaLang/
Scattering, which seems it could replace diffractometry in R
Plus, they have extensively documented its development in a series of blog posts:
http://www.yxliu.group/2020/03/scattering-1
http://www.yxliu.group/2020/03/scattering-2
http://www.yxliu.group/2020/04/scattering-3
http://www.yxliu.group/2020/04/scattering-4
http://www.yxliu.group/2020/04/rotation-test
http://www.yxliu.group/2020/04/scattering-5
http://www.yxliu.group/2020/04/scattering-6
Differential equation solver
Fraidycat is a desktop app or browser extension for Firefox or Chrome. You can use it to follow people (hundreds) on whatever platform they choose - Twitter, a blog, YouTube, Instagram or even on a public TiddlyWiki.
So it's like a feed reader, and if you use your browser sync functionality, it will sync between your devices. Really worth trying out this concept, especially if you don't want to setup your own web-based feed reader. The built-in (and increasing) support for many non-RSS sources is also nice.
Some guides on the why's and what's of password managers
- The best password manager in 2021, The New Oil
- A technical introduction to password managers, Tavis Ormandy. Via Alan Ralph.
- Wikipedia has an informative article on password managers.
- Internetstiftelsen har publicerat en utmärkt guide för hjälpa dig att komma igång med lösenordshanterare.
- Bra råd hos Myndigheten för samhällsskydd och beredskap (MSB) om hur du säkrar din lösenord.
- https://reddit.com/r/sweden/comments/1abpovo/%C3%A4r_det_inte_riskabelt_att_ha_l%C3%B6senordshanterare
- https://lemmy.ml/post/19156372
BitWarden
Open source password management solution, can be self-hosted (how-to)
Integrates with Ansible.
1Password
A cloud-hosted password manager. No longer recommended, as it has regressed into an Electron application mandating remote storage of your password vault.
KeePass
Free, open source, light-weight, and easy-to-use password manager.
These slides discuss the why? how? what? where? of KeePass (presented by F. Morsbach at the first CryptoParty in Uppsala, 2019)
KeePass is written in C# and therefore requires Microsoft's .NET platform.
- Plugins: A list of third-party plugins for KeePass
- Android: Keepass2Android
- iPhone: MiniKeePass
- Chrome / Firefox: Tusk
- Web App: KeeWeb
KeePassXC
Open source, cross-platform.
KeePassXC is developed in C++ and runs natively on all platforms.
- Easy to achieve cloud sync by simply storing your KeePassXC database inside your shared cloud folder (using Nextcloud, for example).
AuthPass
AuthPass supports the KeePass database (KDBX format).
Setup instructions.
Pass
Simple GPG/Git password manager. Adheres to the Unix philosophy, which makes it easy to integrate with anything, e.g., Ansible.
This is my password manager of choice :-)
- Excellent in combination with rofi or dmenu on the Linux desktop, and
- on Android, useable with a combination of Password Store and OpenKeychain.
- Rich ecosystem of plugins, tools: pass-rotate.
- Clever uses of pass, by Vikaly Parnas.
Dashlane
"An intuitive password manager with over with over 8 million users worldwide."
Not open source, as far as I know.
Passbolt
Free, open source, self-hosted, extensible, OpenPGP based.
LessPass
Stateless, open source password manager.
Psono
Open source and self-hosted password manager for teams.
Buttercup
Another open source password manager with desktop, mobile, and browser clients.
LastPass
One of the most widely-used password managers, but that does not mean it's the best. Parent company is LogMeIn. Completely cloud-based, and not open source, obviously. On that basis alone, I do not recommend it. LastPass has suffered a major breach, it is now effectively dead.
Password manager apps that integrate with Nextcloud?
More lists of password managers
- https://codeberg.org/alicia/awesome-privacy#password-managers
- https://nextcloud.com/blog/password-managers-for-nextcloud/
- https://github.com/Igglybuff/awesome-piracy#password-vaults
- https://protonmail.com/blog/open-source-password-managers/
- https://www.tomshardware.com/best-picks/best-password-managers
- https://european-alternatives.eu/category/password-managers
https://github.com/NLnetLabs/unbound/releases/tag/release-1.9.5
- DNS RPZ – Using DNS as a layer of defence
- Response Policy Zones in Unbound (RPZ was introduced in unbound v1.10)
- DNS-over-HTTPS in Unbound, Ralph Dolmans, APNIC
Setup your Pi-hole:
- Connect the Raspberry Pi to your router
- Open the Ubiquiti router's dashboard in your browser, and open the Services tab
- Click on the Actions button, select View Leases
- Identify your Raspberry Pi in the list (look for the hostname of your Raspberry or its MAC address)
- Click the Map Static IP button, and give your Raspberry Pi a static IP address
- Click on the Details tab inside the open dialog, and enter the IP address you just chose into the "DNS 1" field. Feel free to add another DNS provider in the "DNS 2" field (this is used in case your Pi-Hole stops working).
- Restart the Raspberry Pi
You should now be able to login to your Pi-Hole web dashboard from your browser by going to http://<ip-address>/admin (click on login and enter your password to see everything).
I have Zotero installed on three workstations and one laptop. This informs many of the choices I've made when configuring Zotero.
Manual first-time configuration of Zotero
- Install the LibreOffice plugin
- install the Firefox connector
- install the ZotFile plugin and configure its settings (see below for details)
- go into
Preferences -> Advanced -> Config editorand togglezotfile.pdfOutline.getTocfromTRUEtoFALSE(important to not break sync) - go ahead and sync.
The Zotero Connector for Firefox handles proxying nicely (just remember to enable it, for Uppsala university use %h.ezproxy.its.uu.se/%p) and makes the Firefox add-on EZProxy Redirect Foxified redundant.
Storage of PDFs when using Zotero from two or more computers (ZotFile plugin)
Zotero's storage folder for PDFs (Zotero calls them "attachments") is set in
Zotero -> Preferences -> Advanced -> Files and Folders -> Data Directory Location (on Linux, the default location is ~/Zotero).
This is a very inefficient approach when using Zotero from two or more computers, since the stored PDFs and other attachments can easily occupy tens of gigabytes which will thus occupy that space on each and every computer.
A much better solution would be to move the Zotero attachments directory to a remote filesystem that is accessible from all your computers. Zotero itself does not support this use-case, though. This is exactly the premise of the popular ZotFile plugin.
I rely on it on every day - once configured, it has worked flawlessly for me for years.
- http://zotfile.com/
- https://github.com/jlegewie/zotfile
- http://islamicate-dh.github.io/2016-05-27-set-up-zotero-between-multiple-computers/
- http://geekandgirliestuff.blogspot.com/2014/10/new-computer-fresh-zotero-install.html
Download the latest version of the ZotFile XPI, and install it in Zotero: Tools -> Add-ons Manager -> Install Add-on from File. Restart Zotero.
Make sure to uncheck the following choices under File Syncing (since ZotFile takes care of it now):
- Zotero
Preferences -> Sync -> Settings -> File Syncing -> Sync attachment files in My Library - Zotero
Preferences -> Sync -> Settings -> File Syncing -> Sync attachment files in group libraries using Zotero storage
Configure your Zotero "attachments" directory with ZotFile
- In Zotero,
Tools -> ZotFile Preferences -> General Settings -> Location of Files -> Custom Locationand set it to the root of your PDF directory (in my case,/media/bay/taha/chepec/literature/zotero). - Set your naming scheme for subfolders in
Use subfolder defined by. - I suggest you enable
Tools -> ZotFile Preferences -> Advanced Settings -> [X] Remove special chars from filename. - Set ZotFile to always rename new PDFs:
Tools -> ZotFile Preferences -> Advanced Settings -> Automatically rename new attachmentsby setting it toAlways rename.
In Zotero's own preferences, go to Advanced and set your Base directory to the same directory used for your ZotFile custom location.
If you already have items in your Zotero library, highlight all of them in Zotero's library, and select Manage Attachments -> Rename attachments. ZotFile should do its magic and rename and relocate your entire library to the directory you have configured.
Once you have done this on one computer, you then need to repeat it over again for you other computers. But a faster way is to simply copy the entire Zotero profile directory from your already-configured computer and overwrite the same folder on your other computer - and presto, all your settings are immediately in place. But beware that any Zotero configuration you had in place will be wiped out by such an operation. You might want to make a backup copy of your original Zotero profile directory first.
Known issues
Zotero Firefox Connector fails to import anything into Zotero
Seems something broke with v5.0.101. Downgrading to v5.0.100 has resolved the problem for now.
- https://forums.zotero.org/discussion/comment/421625
- https://www.zotero.org/support/troubleshooting_translator_issues
- https://www.zotero.org/support/kb/connector_zotero_unavailable
- https://www.zotero.org/support/translators
Sync breaks with large notes (>250 kB)
If you have large documents with long and complex table of contents, you might observe Zotero sync errors: The note "Contents" is too long to sync. Shorten the note and sync again.
This is because ZotFile tries to extract the TOC into a Zotero note during sync, and runs into Zotero's limit of 250 kB per note. The fix is to disable TOC extraction: Preferences -> Advanced -> Config editor and toggle zotfile.pdfOutline.getToc from TRUE to FALSE.
- https://github.com/jlegewie/zotfile/issues/394
- https://forums.zotero.org/discussion/70958/the-note-is-too-long-to-sync-shorten-the-note-and-sync-again
- https://forums.zotero.org/discussion/comment/295634#Comment_295634
Not all PDFs sync properly between your Zotero instances
It seems the issue lies in the Renaming. A number of PDFs are in fact still residing in the Zotero (not ZotFile) data directory, and those are thus not available on our second instance.
The issue is resolved by manually issuing the Rename command on that file/document.