`jupyter nbconvert –to pdf .ipynb`

Sometimes, I like to check off an item, and then I want it to be visually dimmed, the text should be struck out, but still readable (so I can see what I have already done).

This is all possible in OmniOutliner with mouse clicks. The magic here comes in an Apple Script ([resides here on GitHub](https://github.com/hydroclaus/OO_strikethrough)). Even more, it is possible to include a buttom in the customized toolbar. When you push this button, the script is executed. To achieve this, follow these steps:

– copy the apple script to `~/Library/Application Scripts/com.omnigroup.OmniOutliner5`
– you can add a custom icon to the applescript file itself in order to do this (copy an image to the pasteboard, go to the file in the Finder, show info, click on the generic icon in the info pane to highlight it, paste) — Thanks Greg on Omnis Slack channel for this!
– control-click on the tool bar, select “Customize Toolbar…”, and drag the script, that should appear, onto the toolbar (to where the jiggling icons are)

[{.aligncenter}](/wp-content/uploads/2025/11/Screenshot-2025-11-18-at-10.16.30.png)

– select one or multiple files in finder
– perform OCR

The reason for is is the acquisition of a new scanner.

It turns out, I first found [OCRmyPDF](https://ocrmypdf.readthedocs.io/en/latest/index.html), which I installed via [Homebrew](https://brew.sh/). Then I was looking into watching folder (which I might still look into, option from [stackexchange](https://stackoverflow.com/q/6475252/1510463)).

After this, I followed basically this solution

– [Easier OCR on macOS](https://lukasschwab.me/blog/gen/ocr.html)
– and added the ability to select and process multiple files via [Creating macOS Monterey Shortcuts for Multiple files | by richard moult](https://medium.com/@richardmoult75/creating-macos-monterey-shortcuts-for-multiple-files-9ead8f371bf4)

Find below the picture of the shortcut. Two important things:

1. inside the loop you have to select the proper variable name that refers to the current file (`Repeat Item`)
2. the shell script reads like this (where `$1` and `$2` refer to the input filename and output filename, respectively, setup in a list

export PATH=/opt/homebrew/bin:$PATH && ocrmypdf –force-ocr $1 $2

## Update 2024-Oct-19

– I am using [Hazel](https://www.noodlesoft.com/whats-new-in-hazel-5/) now to watch the FTP folder into which the scanner puts the PDFs
– Hazel does basically two things:
1. check if a new PDF comes into this folder, and if so it performs OCR via this embedded Script, where `$1` refers to the filename that is passed as a *full* path into the sh script, hence the basename is extracted via `basename`, without the extension, hence two arguments in the round brackets:

# /bin/bash
base_name=$(basename $1 .pdf)
# echo ${base_name}
# echo ${base_name}.pdf
cd <>
ocrmypdf ${base_name}.pdf ${base_name}_ocr.pdf

2. perform for each kind of PDF an extra rule, which renames the pdf, assigns a color label (because why not) and adds a task to my OmniFocus system via AppleScript, in which it adds a due date, and links to this PDF as a reference (this is wonderful and makes my life much easier)

set theDate to current date
set theTask to “NameOfTask”

set theNote to “Scanned and processed on ” & (theDate as string) & return

tell application “OmniFocus”
tell front document
set theTag to first flattened tag where its name = “MyTag”
set theProject to first flattened project where its name = “MyProject”
set theDueDate to theDate + (24 * hours)
tell theProject
set theOtherTask to make new task with properties {name:theTask, note:theNote, primary tag:theTag, due date:theDueDate}
tell the note of theOtherTask
make new file attachment with properties {file name:theFile, embedded:false}
end tell
end tell
end tell
end tell

This is just wonderful!

We think, very useful for the team! 😉

Time | ID | Session | Title | Authors
:–:|:–:|–|:–:|–
08:55–09:05 | EGU24-7899 | [HS8.1.7](https://meetingorganizer.copernicus.org/EGU24/session/48382) | [Immobilization of Per- and Polyfluoroalkyl Substances (PFAS) – Experimental and Model-based Analysis of Leaching Behavior](https://meetingorganizer.copernicus.org/EGU24/EGU24-7899.html) | Claus Haslauer, Thomas Bierbaum, Simon Kleinknecht, and Tobias Junginger
15:25–15:35 | EGU24-7820 | [HS3.9](https://meetingorganizer.copernicus.org/EGU24/session/48170) | [Data-driven surrogate-based Bayesian model calibration for predicting vadose zone temperatures in drinking water supply pipes](https://meetingorganizer.copernicus.org/EGU24/EGU24-7820.html) | Ilja Kröker, Elisabeth Nißler, Sergey Oladyshkin, Wolfgang Nowak, and Claus Haslauer

Looking forward to meet you in Vienna!
[The conference](https://www.egu24.eu) is in Vienna, Austria & Online | 14–19 April 2024

– at U of Stuttgart news
– at LinkedIn of U of Stuttgart

Steve has a [long career in hydrogeology](https://thewaterdroplet.substack.com/p/35-years-in-hydrogeology-a-career), we “share” the same Phd-advisor, and he almost hired me once. I guess it’s fair to assume, I am biased in his favour.

Steadily, Steve is covering important hydrogeological issues such as [land subsidence](https://thewaterdroplet.substack.com/p/what-is-land-subsidence), [groundwater recharge](https://thewaterdroplet.substack.com/p/what-is-groundwater-recharge), [PFAS / forever chemicals](https://thewaterdroplet.substack.com/p/what-are-forever-chemicals), groundwater management issues [in California](https://thewaterdroplet.substack.com/p/groundwater-in-california) and in [the south/central US](https://thewaterdroplet.substack.com/p/the-ogallala-aquifer).

Since you are already on this site, there is a good chance that you will be interested in [The Water Droplet](https://thewaterdroplet.substack.com). So I encourage you to head over there!

[NetNewsWire 6](https://netnewswire.com) is now [on the (iOS, iPadOS) AppStore](https://nnw.ranchero.com/2021/06/22/netnewswire-for-ios.html)!

Together [with NetNewsWire 6 on macOS](https://nnw.ranchero.com/2021/04/01/netnewswire-for-mac.html) it is a wonderful open RSS solution, offers iCloud sync that works well (and makes me think about my long-time, by now beloved, but not mentioned [on _DavidSmith’s blog](https://www.david-smith.org/blog/archives/) in quite some time, [Feed Wrangler](https://feedwrangler.net) subscription).

One feature that I use more than anticipated is NNW’s novel ability to subscribe to Twitter Accounts (even searches) like a feed. It’s not surprising given twitter’s gradual and steady deterioration of the timeline.

How else, other than NNW, do you keep track of RSS feeds?

Speaking of blogging, [Macdrifter seems to back from his hiatus](http://www.macdrifter.com). What a nice polarity to twitter – few posts, a lot of content! Also, I completely stole the title of this post from him.

## Marble Quarry

Admittedly, this video is another link [from Jason Kotke](https://kottke.org/21/06/the-best-commercial-about-a-rock-quarry-youll-see-today), but it has a strong connection to fractured rock hydrogeology, and hence is relevant for this site. The combination of the visuals from the open pit mine with its bulldozers together with the audio from an opera, is more delightful than expected. Then again, I am not so sure what to expect from an ad for a quarry.

## Trinkwasser in Deutschland — Mengenproblematik

Obwohl wir (in Stuttgart) bisher eher ein durchschnittlich nasses Jahr haben, werden die Rufe nach mangelnder Wasserverfügbarkeit lauter.

[Dürreperioden: Wird in Franken das Trinkwasser knapp? – Nürnberg – nordbayern.de](https://www.nordbayern.de/region/durreperioden-wird-in-franken-das-trinkwasser-knapp-1.11080126)

[Bundesamt für Bevölkerungsschutz warnt vor Trinkwasserknappheit](https://www.zeit.de/wissen/umwelt/2021-05/bbk-trinkwasserknappheit-deutschland-grundwasserspiegel-landwirtschaft-armin-schuster)

[Ein neuer See fürs Fränkische Seenland? – Gunzenhausen, Treuchtlingen, Weißenburg, Roth, Wassertrüdingen, Wassertrüdingen | Nordbayern](https://www.nordbayern.de/region/gunzenhausen/ein-neuer-see-furs-frankische-seenland-1.11173625)

Maybe the picture below tells you a little bit about my state of mind. This is how my bedroom and office has been looking. Thermally enhanced wall vapour extraction. The person who built a wastewater pipe in the shape of a double-S (yes, literally) should be ashamed for a long time.

The thing that has been bothering me substantially before Christmas: too many meetings.
To some extent, the “too many meetings” problem has been going on before Corona. At the early times of Corona (Spring 2020), there might have been actually less meetings. Currently, the situation seems as bad as it has ever been. One Webex or Zoom, meeting after meeting. It’s difficult to find time to get anything done. This has become very clear over the Christmas holidays.

[This article](https://www.bbc.com/worklife/article/20191111-blame-your-worthless-workdays-on-meeting-recovery-syndrome) (via [Rui
Carmo](https://taoofmac.com/space/links/2020/12/08/1051)) gets many things right.
This I found particularly interesting:

> It’s even worse when a worker has several meetings that are separated by 30
> minutes. “Not enough time to transition in a non-MRS situation to get anything
> done, and in an MRS situation, not quite enough time to recover for the next
> meeting,”

One remedy sounds simple but I am not sure how to achieve this: less meetings

> Less time in meetings would ultimately lead to more employee engagement in the
> meetings they do attend, which experts agree is a proven remedy for future
> cases of MRS.

So, “just” saying “no” more often!(?) Maybe more [tools and
automation](https://www.relay.fm/automators/57)? Maybe [this high – profile
advice](https://barackobama.medium.com/how-i-approach-the-toughest-decisions-dc1b165cdf2d) will help me to decide if I should accept a meeting. Also important: [he emphasises](https://twitter.com/BarackObama/status/1336679633769680898) that everybody should be prepared, everybody should speak. Breaks sometimes are no real
breaks but are giving your brain time to digest thoughts. Even more, breaks are always necessary. And: everything is uncertain!

It is one thing to realise that everything is uncertain, but as [@dougmcneall](https://twitter.com/dougmcneall/status/1343175788145897472) points out:

> Making constant risk decisions is exhausting.

This brings us to Corona. During which the usual exhausted-ness seems to be amplified, e.g., with [sub-optimal working conditions](https://twitter.com/Hydrology_WSL/status/1347434945933942785), and with kids at home. Like [Hayley Fowler points out](https://twitter.com/HayleyJFowler/status/1346399804600029191): I’m just tired of everything. Like [Brent Simmons point outs](https://twitter.com/brentsimmons/status/1350165117913231372):

> “I’ve been haunted since hearing, in the early days of the pandemic, that if we all wore masks for six weeks this thing would be over. I was there. I’ve done that for six weeks, and another six weeks, and another. And now it’s worse than ever. It’s a challenge not to be angry. There are healthy, uninfected people right now, today, who are excited for the vaccine and who will die before they get it.

## Teaching Experiences

– webex (which we use at the University of Stuttgart), has now the ability to share the iPad’s screen! It might have been there before, but I realised it existed only on Monday. Before, I knew that zoom can do it. Anyways, this has proven to be a nice tool for teaching sequentially and more spontaneously than an animated slideshow.

– I’ve upgraded to [JupyterLab 3](https://jupyterlab.readthedocs.io/en/latest/user/debugger.html) with it’s visual debugger. Very nice, also for teaching! [This ranked list of awesome Jupyter Notebook, Hub and Lab projects](https://github.com/ml-tooling/best-of-jupyter) (extensions, kernels, tools), that is updated weekly, provides also very many useful hints!

## Ending

– [France](https://geoservices.ign.fr/documentation/diffusion/telechargement-donnees-libres.html) and [Switzerland](https://www.swisstopo.admin.ch/en/swisstopo/free-geodata.html) have a great [free data policy](https://twitter.com/seamap/status/1345607567804915712)

– The [Acropolis museum is now accessible online](https://www.theacropolismuseum.gr/en/digital-museum)

– I re-built an old Dell Latitude 6410 with Ubuntu 20.10 – and it works great (except for the screen after sleeping). But it has been serving us (and my kid) great for instructional videos and moodle!

## With Input from
– [Brian Romans ?? (@clasticdetritus) / Twitter](https://twitter.com/clasticdetritus)
– [Don Melton (@donmelton) / Twitter](https://twitter.com/donmelton)
– [Rui Carmo (@rcarmo) / Twitter](https://twitter.com/rcarmo)
– [Dr Doug McNeall (@dougmcneall) / Twitter](https://twitter.com/dougmcneall)
– [Prof Hayley J. Fowler (@HayleyJFowler) / Twitter](https://twitter.com/HayleyJFowler)
– [Barack Obama (@BarackObama) / Twitter](https://twitter.com/BarackObama)
– [Brent Simmons (@brentsimmons) / Twitter](https://twitter.com/brentsimmons)
– [Massimiliano Zappa (@Hydrology_WSL) / Twitter](https://twitter.com/Hydrology_WSL)