Molsketch #15
Comments
|
Hello pin,
if you would like start packaging I suggest to dig in `The pkgsrc guide'
and request an account for pkgsrc-wip:
https://www.pkgsrc.org/wip/users
Usually, to start it's an:
% cd pkgsrc/wip
% mkdir <pkg> && cd <pkg>
% url2pkg <URL>
...and then adjusting the corresponding `Makefile'.
If you get stuck both #pkgsrc IRC channel at Freenode and tech-pkg@ ML
are good places to get more help!
Have fun!
|
|
Thx! |
|
Hi, I've tried looking for a different name for these packages, found that Qt5Svg is called qt5-qtsvg, but couldn't find Core or the others. Maybe I'm still not advanced enough to start packaging :( Edit: I'll give it another try using url2pkg and pkglint as described in chapter 12 of the pkgsrc guide... should read first. |
|
Ok guys, just sharing my experience... |
|
Hello @voidpin! In that way it will be easier to investigate/work on it collaboratevily! Thanks for working on it! |
|
No, thank you for your interest, I've now requested commit access to pkgsrc-wip. |
|
I can package it but I am disoriented as inside https://sourceforge.net/projects/molsketch/files/Molsketch/ there are several catalogues like nitrogen, hydrogen.. Please point exact tarball to fetch and package. |
|
The latest release is the one in the Nitrogen folder, 0.6.0. https://sourceforge.net/projects/molsketch/files/Molsketch/Nitrogen%200.6.0/Molsketch-0.6.0-src.tar.gz/download That would be awesome, thanks!! |
|
Please check: wip/molsketch It builds, installs and runs for me. |
|
Wow! Amazing, thx! :( How did you find this? I'm here to learn and hope to be able to build packages myself soon! Once again thank you! I'll be building the package tomorrow as I left my NetBSD machine at work this evening. Finally, one more noob question... should I use |
USE_LANGUAGES is typically try and fail.
And adding relative path to Most of packaging is grepping. bmake only if you run bootstrap yourself, on NetBSD native make is fine. Never run directly cmake as it is a tool inside a package. Does molsketch work? If so, I will import it into pkgsrc. |
|
Thank you! |
|
Trying to build the package. First I had to EDIT: Crazy thought... Could download the tarball of |
|
https://github.com/NetBSD/pkgsrc/blob/trunk/biology/openbabel/Makefile#L14 Please experiment and try to change this line to: |
|
:( Unfortunately it doesn't work... |
|
https://github.com/openbabel/openbabel/releases/tag/openbabel-3-0-0 Probably the best way forward is to upgrade openbabel to 3.0. The pkgsrc version uses compiler extension for, at that time, unreleased C++ standard. |
|
I will give it a try. |
|
Great stuff! Thank you so much!!! |
|
How about building the pkgsrc openbabel with |
|
At least it start the building of :( |
|
Please upgrade pkgsrc/biology/openbabel and try to build it. I will need to try to patch molsketch to build against it. |
|
Ok, will do! |
|
pkgsrc/biology/openbabel is upgraded now to 3.0.0 I am trying to build molsketch with it. Please try to build pkgsrc openbabel version 3.0.0. |
|
OK: pkgsrc/biology/openbabel 3.0.0nb1
I have ported it to openbabel. Please build openbabel 3.0.0nb1 and the newest version of molsketch. |
|
Thank you so much for this! |
|
@krytarowski I must be doing something wrong :( |
|
Please update pkgsrc-wip and retry. I have regenerated the checksum. |
|
Just saw you had pushed an update :) Cheers!! |
|
@krytarowski It works! Thank you very much!!!! |
ghost
closed this as
|
OK, so homework:
|
|
Ok, I've dropped a message to openbabel and molsketch people and waiting an answer. I'm not sure what you're asking me to do?? |
|
That was a comment what is done by the patches, to be forwarded to upstream. |
|
Pull-request for Molesketch, hvennekate/Molsketch#4 Edit: for openbabel, openbabel/openbabel#2093 |
|
@krytarowski #2093 merged into master for openbabel ;) |
|
@krytarowski |
|
I prefer to do it after merging local patches into Molsketch and releasing a new version of Molsketch, so pkgsrc will ship with 0 local patches. |
|
Fair enough, I agree with that. Its for sure cleaner. |
1.0.3: not documented 1.0.2 (July 21, 2015) * In the event of a NilAccept for the language, request.languages() would throw an AttributeError exception. Fixes #24. * Encode Location HTTP header in redirect responses in UTF-8. Per RFC 3987. Refers to #15. * Remove "Post Traceback" as it was a possible XSS vector with prior versions of WebError, and the PylonsHQ site is no longer in existence to support them. 1.0.1 (August 13th, 2012) * No changes since RC1. 1.0.1RC1 (December 12, 2011) * WARNING: pylons.lib.decorators has had two functions removed: ``determine_response_charset`` and ``encode_formencode_errors``. * Updated dependencies to latest versions of Paste, PasteDeploy, and compatibility for the latest WebOb 1.2 betas. * authenticate_form allows for GET. Patch by Domen Kožar. * jsonify now properly sets charset to utf-8. * Add ability for jsonify to handle objects with a __json__ attribute using custom JSONEncoder class similar to TG2. Patch by Bob Farrell. * Added ability for __before__ to reference a callable function. Patch contributed by mverdone. * Pulled in JSON-RPC support from agentultra's pylons fork. * Apply patch for proper pylons.__version__ under Windows. Contributed by Christoph Zwerschke. * Utilize MarkupSafe for faster HTML escaping. * Fix signed cookies by using standard base64 alphabet, and prevent timing attacks on signature comparison. * Added setup of app_globals and config to Pylons config.init_app to ensure as long as the Pylons application is loaded, the app_globals and config will be appropriately initialized. * Documentation updates.
Switched to use go-module.mk. CHANGES: * agent: Agent now properly returns a non-zero exit code on error, such as one due to template rendering failure. Using error_on_missing_key in the template config will cause agent to immediately exit on failure. In order to make agent properly exit due to continuous failure from template rendering errors, the old behavior of indefinitely restarting the template server is now changed to exit once the default retry attempt of 12 times (with exponential backoff) gets exhausted. [GH-9670] * token: Periodic tokens generated by auth methods will have the period value stored in its token entry. [GH-7885] * core: New telemetry metrics reporting mount table size and number of entries [GH-10201] * go: Updated Go version to 1.15.4 [GH-10366] FEATURES: * Couchbase Secrets: Vault can now manage static and dynamic credentials for Couchbase. [GH-9664] * Expanded Password Policy Support: Custom password policies are now supported for all database engines. * Integrated Storage Auto Snapshots (Enterprise): This feature enables an operator to schedule snapshots of the integrated storage backend and ensure those snapshots are persisted elsewhere. * Integrated Storage Cloud Auto Join: This feature for integrated storage enables Vault nodes running in the cloud to automatically discover and join a Vault cluster via operator-supplied metadata. * Key Management Secrets Engine (Enterprise; Tech Preview): This new secret engine allows securely distributing and managing keys to Azure cloud KMS services. * Seal Migration: With Vault 1.6, we will support migrating from an auto unseal mechanism to a different mechanism of the same type. For example, if you were using an AWS KMS key to automatically unseal, you can now migrate to a different AWS KMS key. * Tokenization (Enterprise; Tech Preview): Tokenization supports creating irreversible “tokens” from sensitive data. Tokens can be used in less secure environments, protecting the original data. * Vault Client Count: Vault now counts the number of active entities (and non-entity tokens) per month and makes this information available via the "Metrics" section of the UI. IMPROVEMENTS: * auth/approle: Role names can now be referenced in templated policies through the approle.metadata.role_name property [GH-9529] * auth/aws: Improve logic check on wildcard BoundIamPrincipalARNs and include role name on error messages on check failure [GH-10036] * auth/jwt: Add support for fetching groups and user information from G Suite during authentication. [GH-123] * auth/jwt: Adding EdDSA (ed25519) to supported algorithms [GH-129] * auth/jwt: Improve cli authorization error [GH-137] * auth/jwt: Add OIDC namespace_in_state option [GH-140] * secrets/transit: fix missing plaintext in bulk decrypt response [GH-9991] * command/server: Delay informational messages in -dev mode until logs have settled. [GH-9702] * command/server: Add environment variable support for disable_mlock. [GH-9931] * core/metrics: Add metrics for storage cache [GH_10079] * core/metrics: Add metrics for leader status [GH 10147] * physical/azure: Add the ability to use Azure Instance Metadata Service to set the credentials for Azure Blob storage on the backend. [GH-10189] * sdk/framework: Add a time type for API fields. [GH-9911] * secrets/database: Added support for password policies to all databases [GH-9641, and more] * secrets/database/cassandra: Added support for static credential rotation [GH-10051] * secrets/database/elasticsearch: Added support for static credential rotation [GH-19] * secrets/database/hanadb: Added support for root credential & static credential rotation [GH-10142] * secrets/database/hanadb: Default password generation now includes dashes. Custom statements may need to be updated to include quotes around the password field [GH-10142] * secrets/database/influxdb: Added support for static credential rotation [GH-10118] * secrets/database/mongodbatlas: Added support for root credential rotation [GH-14] * secrets/database/mongodbatlas: Support scopes field in creations statements for MongoDB Atlas database plugin [GH-15] * seal/awskms: Add logging during awskms auto-unseal [GH-9794] * storage/azure: Update SDK library to use azure-storage-blob-go since previous library has been deprecated. [GH-9577] * secrets/ad: rotate-root now supports POST requests like other secret engines [GH-70] * ui: Add ui functionality for the Transform Secret Engine [GH-9665] * ui: Pricing metrics dashboard [GH-10049] BUG FIXES: * auth/jwt: Fix bug preventing config edit UI from rendering [GH-141] * cli: Don't open or overwrite a raft snapshot file on an unsuccessful vault operator raft snapshot [GH-9894] * core: Implement constant time version of shamir GF(2^8) math [GH-9932] * core: Fix resource leak in plugin API (plugin-dependent, not all plugins impacted) [GH-9557] * core: Fix race involved in enabling certain features via a license change * identity: Check for timeouts in entity API [GH-9925] * secrets/database: Fix handling of TLS options in mongodb connection strings [GH-9519] * secrets/gcp: Ensure that the IAM policy version is appropriately set after a roleset's bindings have changed. [GH-93] * ui: Mask LDAP bindpass while typing [GH-10087] * ui: Update language in promote dr modal flow [GH-10155] * ui: Update language on replication primary dashboard for clarity [GH-10205] * core: Fix bug where updating an existing path quota could introduce a conflict. [GH-10285]
* Convert to use released tarball from GitHub.
* Fix build.
* Update DESCR.
* Take MAINTAINERship.
Changelog:
1.7.0
Allow building without manpage
Allow building against musl
Fix memory corruption error
Fix decompressing large files on 32-bit systems
Avoid unaligned memory access
Fix warnings with recent compilers
Use optimized endian swapping functions on macOS
1.0.6
fixes large file support for listing
1.0.5
add htole64 and le64toh on glibc < 2.9
1.0.4
Include man page in release tarball, fixed #50
1.0.3
complete autotools build, see README.md for build instructions, see #37
large-file support for 32-bit systems, see #26
creates output file with permissions of input file (if possible, i.e. not reading from stdin), see #15
better error messages on incorrect input path
list main differences between pixz and xz in README
fix issue with extreme (-e) command line option parsing, see #12
adds keep input (-k) command line option, see #14
0.3.0 (2024-03-09) ------------------ - Add ``asdf-astropy`` as a test dependency. [#34] - Drop official support for Python 3.8 [#42] - Update schemas for ASDF standard 1.6.0 [#55] 0.2.0 (2023-03-21) ------------------ - Add documentation to package. [#8] - Update asdf version and require python 3.8. [#14] - Switch to pyproject.toml. [#15]
Hi everyone,
I'm a chemist and would like to have a supported/active 2D molecular editor installed on my NetBSD amd64 machine.
How difficult would be to build and package Molsketch (https://sourceforge.net/projects/molsketch/) for NetBSD? Is it possible? I have no experience in this, but wouldn't mind getting my hands dirty and, at the same time get some experience. chemtool hasn't seen an update since 2013 and BKChem since 2010. These are the tools available on pkgsrc...
Guidance appreciated!
Thanks!
The text was updated successfully, but these errors were encountered: