Poll How do you pronounce zsh?
As people migrate to Catalina there is an option to update your default shell.
zsh is the new default shell for new users (bash is the default shell in macOS Mojave and earlier), so if you are upgrading you may want to change your default shell to zsh.
Paul Falstad wrote the first version of Zsh in 1990[6] while a student at Princeton University.[7] The name zsh derives from the name of Yale professor Zhong Shao (then a teaching assistant at Princeton University) — Paul Falstad regarded Shao's login-id, "zsh", as a good name for a shell.
You might also like to look at oh-my-zsh
A delightful community-driven (with 1,300+ contributors) framework for managing your zsh configuration. Includes 200+ optional plugins (rails, git, OSX, hub, capistrano, brew, ant, php, python, etc), over 140 themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.
So while it was pretty obvious how to pronounce "Bash" (The shell's name is an acronym for Bourne-again shell, a pun on the name of the Bourne shell that it replaced), but what about "zsh"?
Chemical Information and Computer Applications Group
My Royal Society of Chemistry annual subscription letter just arrived. This is a good time to think about Interest Group membership, if you are a member of the RSC you can join several interest groups for free, however disappointingly many people fail to take advantage of this opportunity.
Interest Groups are scientific networks run by members for their community. Each group is themed around a specific area or application of the chemical sciences. They organise an annual series of events to cater for both their members and the wider scientific community. These events vary from: multi-day conferences and workshops to training events.
The Chemical Information and Computer Applications Group (CICAG) is one such group (Group number 86), you can find out more on the CICAG website.
The storage, retrieval, analysis and preservation of chemical information and data are of critical importance for research, development and education in the chemical sciences. All chemists, and everybody else who works with chemical substances, need tools and techniques for handling chemical information.
CICAG works to:
- Support users of chemical information, data and computer applications and advance excellence in the chemical sciences
- Inform RSC members and others of the latest developments in these rapidly evolving areas;
- Promote the wider recognition of excellence in chemical information and computer applications at this level
This year CICAG has been involved in a workshop on Computational Tool for Drug Discovery, 2nd Conference on Artificial Intelligence in Chemistry, and the 20 Years of Rule of Five Meeting. In addition CICAG has supported the Sheffield Cheminformatics Meeting, Dial a Molecule, Artificial Intelligence and Augmented Intelligence for Automated Investigations for Scientific Discovery network and the In Silico Toxicology Networking Meeting. In addition to other outreach activities.
RSC CICAG publish a regular Newsletter which keeps members in touch with the Group's activities and includes articles, reviews of interest, news and events.
If you would like to join the group you can do so by adding interest group 86 to the last page of the renewal form and returning it to the RSC or you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141).
Scientific Applications under Catalina: Update 8
General Issues with Catalina
If you want an overview of Catalina I'd recommend the excellent ars-technical's review.
According to Wikipedia Santa Catalina is a rocky island off the coast of the U.S. state of California in the Gulf of Santa Catalina.
By Thomas Pekin - Thomas Pekin, CC BY-SA 2.5
Apple has officially confirmed that the following Macs are compatible with Catalina:
- MacBook (Early 2015 or newer)
- MacBook Air (Mid 2012 or newer)
- MacBook Pro 13"/15" (Mid 2012 or newer)
- Mac mini (Late 2012 or newer)
- iMac (Late 2012 or newer)
- iMac Pro (2017 or newer)
- Mac Pro (Late 2013 or newer)
There are a number of changes to the security, in particular installation into the root folder is not allowed. After upgrade you may find it moves items into a folder on your desktop called “Relocated Items,” in the Security folder.
zsh is the new default shell for new users (bash is the default shell in macOS Mojave and earlier), so if you are upgrading you may want to change your default shell to zsh. There is an Apple Support page giving details
zsh is highly compatible with the Bourne shell (sh) and mostly compatible with bash, with some differences. For more about zsh and its comprehensive command-line completion system, enter man zsh in Terminal.
You might also like to look at oh-my-zsh
A delightful community-driven (with 1,300+ contributors) framework for managing your zsh configuration. Includes 200+ optional plugins (rails, git, OSX, hub, capistrano, brew, ant, php, python, etc), over 140 themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.
This book might also be useful Moving to zsh.
Notarization
I suspect many users will now see more Notarization warnings.
Notarization gives users more confidence that the Developer ID-signed software you distribute has been checked by Apple for malicious components. Notarization is not App Review. The Apple notary service is an automated system that scans your software for malicious content, checks for code-signing issues, and returns the results to you quickly. If there are no issues, the notary service generates a ticket for you to staple to your software; the notary service also publishes that ticket online where Gatekeeper can find it.
You can notarize several different types of software deliverables, including:
- macOS apps
- Non-app bundles, such as kernel extensions
- Disk images (UDIF format)
- Flat installer packages
Beginning in macOS 10.14.5, all new or updated kernel extensions and all software from developers new to distributing with Developer ID must be notarized in order to run. Beginning in macOS 10.15, notarization is required by default for all software.
Apple have been warning for several years now that all support for 32-bit apps would end, Apple has a page describing the reasons for moving to 64-bit. In addition support for the legacy Java 6 has finished. Catalina does include Python 3 by default, where older versions of the operating system only included Python 2.7
Anyone tried running 32-bit apps using emulation (Parallels or VMWARE?).
Scientific Applications
I've contacted all developers I know and their responses to date are shown below.
4-Peaks no issues reported
alvaDesc software is completely 64 bit and it is ready for Catalina.
Anaconda Anaconda’s default install location in the root folder is not allowed, suggestion is Start fresh with a new Anaconda installation. Pay attention during installation to make sure that your install path is a subfolder of your home folder, such as /Users/me/anaconda3. You may be able to move the Anaconda folder from "Relocated Items" to a new location but be aware it may include hard coded paths. More discussion here.
APE A plasmid Editor If you are having trouble with crashing in Mojave or Catalina, re-download to get the latest update.
Avogadro no issues reported
BBEdit version 13 is compatible with macOS Catalina
BioSolveIT report SeeSAR and infiniSee have been tested successfully on Catalina
Brainsight Brainsight 2.4b6 and later have been tested against Catalina and there are no known problems.
ChemAxon Most of our software in general requires Java, so as long as the appropriate Java version is installed, there should be no problem. However maybe notarisation issues first time using. More info.
ChemDraw I've posted question on forum but no response yet. A reader reported "ChemDraw 18.2 appears to run with no new issues".
ChemDoodle ChemDoodle v9 and ChemDoodle 3D v4 are fully supported, signed for Gatekeeper, and notarized by Apple on macOS Catalina. There is only a single reported issue from some users, where either program will fail to fully startup on Catalina if they were installed prior to upgrading the OS to Catalina. In these cases, removing the “ChemDoodleSettings” folder or the “ChemDoodle3DSettings” folder in the user’s Documents folder and restarting the application will resolve the issue. We have no other known issues on Catalina at this time.
Conquest and Mercury from CCDC CSD software from the CCDC. The full CSD software suite, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner and other components, have been tested and are working on Catalina. Whilst our applications are all signed, due to the new "notarisation" feature on Catalina, users may need to authorise the software via the Security option in System Preferences at the point of installation. Our next major software release, the 2020.0 CSD Release which will be available before the end of 2019, will be formally supported on macOS 10.15 Catalina, as well as 10.14 Mojave and 10.13 High Sierra.
Cresset testing this week.
CrystalDiffract 6.8.3 is a 64-bit “Cocoa” app and works fine.
CrystalMaker X 10.4.6 - another 64-bit app “Cocoa” app - also runs seamlessly with “Catalina”
SingleCrystal 3 is a 32-bit app and so won’t run. However…
SingleCrystal 4 PUBLIC BETA works beautifully on Catalina. More information - including a sign-up form - can be found at:
SingleCrystal 4 PUBLIC BETA will run until the end of December and is free to eligible users. All applications are code-signed and officially “notarized” by Apple.”
CYLView 1.0 does not work under Catalina.
Delta Delta V5.3.1 is not supported by Apple macOS 10.15 Catalina. Delta will not install or operate under macOS 10.15 Catalina. We are working on an update for Delta to run on macOS 10.15 Catalina and will post it as soon as it is available.
DEVONagent here's a minor incompatibility that keeps the application's splash screen from being closed. You can expect a free maintenance update for DEVONagent that addresses this issue later this month.
DEVONthink version 3 is 64-bit compliant
Elemental We have a new one. Think it got stuck in “notarization”. Will appear on the support site in a few days hopefully.
EndNote EndNote X9 for macOS will be extensively updated for compatibility prior to the launch of Catalina.
EnzymeX no issues reported
EverNote No issues with Evernote but Safari extensions dropped so no Evernote Web Clipper
Findings seems to be working fine, no issues reported.
Fujitsu ScanSnap If you own one of the older Fujitsu ScanSnap scanners like the S300M, S500M, S510M or S1500(M). Fujitsu has announced that they will not update the ScanSnap Manager software that drives these scanners to make them compatible to macOS Catalina; only the newer ScanSnap Home will be available for current and future versions of the Mac operating system.
Gaussaian All 64-bit versions of Gaussian 16 for macOS will work fine with macOS Catalina.
Homebrew some issues reported, brew update / brew upgrade seems to resolve many. Probably need to have updated Xcode to version 11.x
All the ICM products are compatible with Catalina:
Other products that are compatible include:
IDL Through beta testing, we have identified an issue that requires a patch to IDL 8.7 in order to run on this new OS X release. The issue is caused by the existing 32-bit applications used in IDL (Applescripts and IDLSnapFileOpen), and they will be replaced with 64-bit versions. Other related concerns on this OS X release will also be addressed. This patch to IDL will be available very soon after the release of Catalina.
Igor Pro With Catalina, Apple dropped support for 32-bit applications, dropped the QuickTime framework that Igor uses to support most movie features, and added strict security features that prevent XOPs from running without special security certification ("notarization"). We recommend that you avoid Catalina if you need to use Igor Pro. However, we expect Igor Pro 8.04 (currently in beta) to work with the caveats explained below. We do not consider any version of Igor Pro 8 to be supported on Catalina, though we will do our best to fix Catalina specific bugs. Igor Pro 6 will not run because Catalina supports 64-bit applications only. The 64-bit Igor Pro 7 application (Igor64.app) may run, but WaveMetrics and/or third-party XOPs may not load. Igor Pro 7 is no longer maintained and will not receive any changes to improve Catalina support.
iNMR iNMR has been recently recompiled with Xcode 10.3. iNMR is a 64-bit app since 2012. No issues reported.
KaleidaGraph is currently still a 32-bit application and will not run under Mac OS 10.15. A 64-bit version is under development, although it will not be released before Catalina and we do not have a release date at this time. We will notify registered users as soon as a beta version is ready for testing.
KNIME most recent version of KNIME Analytics Platform is notarized and, hence, works with macOS Catalina.
Matlab R2019b supports Catalina
Mathematica Wolfram products based on Wolfram Language 12.0 or later are fully 64 bit on macOS, and are therefore compatible with macOS 10.15, as well as earlier versions.
Mendeley Mendeley Desktop does not support OSX Catalina. If you choose to upgrade to OSX Catalina you may be unable to install or access Mendeley Desktop. You should alternatively use https://mendeley.com/library
Microsoft Office To provide you with the best experience, Office for Mac supports Apple’s three most recent versions of macOS. With the release of macOS 10.15 Catalina, Office 365 for Mac and Office 2019 for Mac support macOS 10.15, 10.14, and 10.13.
Mnova Mnova 14.1 is compatible with Catalina OS.
MOE MOE is now fully compatible with Catalina. Remember if you change to using zsh instead of BASH you will need to copy things from your BASH profile over.
MOPAC no issues reported.
Papers We have gotten a few reports of crashes happening on the new Mac OS 10.15(codename Catalina) for Papers 3. We have developed a fix and you should be able to update your Papers 3 to the new version. If you updated to Catalina before updating Papers 3 you can download the new version here
Parallels Parallels Desktop 15 for Mac is the fastest, easiest, and most powerful application for running Windows applications on a Mac without rebooting. Parallels Desktop 15 now supports Catalina, Sidecar, and DirectX 11.
PGOPHER not yet supported by PGOPHER. (Apple no longer supports 32 bit programs, and the required uderlying 64 bit library required has only recently become available in a useable state, and some development work is required for this to work with PGOPHER.)
pro Fit the latest version of pro Fit, version 7.0.15, runs on Catalina.
PYMOL The +python37 variant of pymol runs fine under its Qt interface on Catalina
QMForge 2.4 apparently doesn't work on Catalina, hoping to get a fix in the coming weeks.
RDKit no reported issues
Schrodinger Unfortunately, MacOS Catalina is not yet supported by Schrödinger products and is being tested. We are planning to start supporting it from our 19-4 release.
- Spartan’18 Parallel Suite
- Spartan’18 (single core)
- Spartan Student Edition v.7
- Odyssey Instructor Edition v.6
- Odyssey Student Edition v.6
Are all compatible with Catalina.
SPSS We’ve spent weeks testing against the beta and now the generally available operating system. Overall, SPSS Statistics and Catalina are compatible.
Stardrop is compatible.
Swiss-PdbViewer is a 32 bits application and will * NOT * run on OSX Catalina. If you absolutely need it, refrain from updating, boot from an older OSX version, or use the PC version within a virutal machine. I currently have no plan to update it to run on OSX 10.15
VMD is a 32-bit app and will not run under Catalina.
Vortex Should just work. Isn’t notorized yet though so right click Open if it complains. You only have to right click Open once.
WINEIn downloading WINE devel portable from https://dl.winehq.org/wine-builds/macosx/ , you can run the wine64 binary through the terminal, with ‘$ wine64 wine cfg’ to configure it and ‘$wine64
Wizard has been tested to work with Catalina.
wxMacMolPlt The currently available (64 bit) binary does run on Catalina. However, while it is “signed” it is not “notarized” so you do have to jump through a couple hoops to convince the OS to launch it the first time.
Xcode need to update to version 11.x
XQuartz some users reporting issues, seems to be a mixture of enhanced security and/or folders moved to relocated items. Best solution seems to be to reinstall XQuartz.
I’ll add more updates later, feel free to contact me and thanks for the comments to date.
CSFP - A New Molecular Fingerprint
An interesting paper in JCIM, Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration DOI.
The very popular ECFP fingerprint enumerates all circular substructures, i.e. substructures with a central atom and a spherical extension around them. However, not all chemical reasonable substructures are circular. They could be shaped as paths, cycles or any other irregular form and consequently cannot be represented as single features in ECFPs. To overcome these limitations, we developed a novel algorithm named CONSENS systematically enumerating all connected substructures within given size limits. CONSENS is the central element of a novel fingerprint named CSFP - Connected Subgraph Fingerprint. CSFPs are not only richer in represented substructures, furthermore they allow finegrained control to the chemical model encoded.
ConsensLib is a header-only C++ library for efficient enumeration of connected induced subgraphs. The CONSENS (Connected Subgraph Enumeration Strategy) algorithm enumerates all node sets that form a connected subgraph of a given query graph. It is available on GitHub https://github.com/rareylab/ConsensLib.
Modin for distributed Pandas calculations
Modin is a library designed to accelerate Pandas by automatically distributing the computation across all of the system’s available CPU cores. Modin uses Ray to provide an effortless way to speed up your pandas notebooks, scripts, and libraries. Unlike other distributed DataFrame libraries, Modin provides seamless integration and compatibility with existing pandas code. Even using the DataFrame constructor is identical. Modin is a DataFrame designed for datasets from 1MB to 1TB+
It can be installed using PIP
pip install modin
If you don't have Ray or Dask installed, you will need to install Modin with one of the targets:
pip install modin[ray] # Install Modin dependencies and Ray to run on Ray
pip install modin[dask] # Install Modin dependencies and Dask to run on Dask
pip install modin[all] # Install all of the above
Currently, Modin depends on pandas version 0.23.4.
I've added Modin to the Open Source Data Science Python Libraries.