Fix issue #299

[lohedges]

This PR closes #299 but not using sire.legacy.Base.wrap for string values in the property_map, which were incorrectly being cast to GeneralUnit. This allows Mol2 files to be written from by BioSimSpace.IO.saveMolecules. This superseds #298.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

[lohedges]

Strange, I confirmed that all tests passed locally before submitting but there are failures on all platforms. Looks like an issue with RDKit conversion, which I don't think is related to this. Will debug tomorrow.

[lohedges]

It looks like the RDKit pin might have failed and it's pulling in a version that is incompatible with the one that Sire was built against.

[lohedges]

Okay, all of the failed CI runs pulled in RDKit version 2024.03.3. The last Sire devel build used 2024.03.2. Surely there can't be a breaking API change with a point release? In the Sire recipe we pin RDKit to the minor version number, i.e.:

  run_constrained:
    - {{ pin_compatible('rdkit', max_pin='x.x') }}

I'll try reproducing the environment locally to see if I can figure out what's wrong.

[lohedges]

It seems that the SONAMEs are minor version specific, so we'll need to update the pin to 'x.x.x'.

ls -l 2024.03.2/lib | head -n 20
total 30080
drwxr-xr-x 3 lester lester    4096 Jun 13 09:36 cmake
drwxr-xr-x 3 lester lester    4096 Jun 13 09:36 python3.11
lrwxrwxrwx 1 lester lester      36 May  2 17:10 libRDKitAbbreviations.so -> libRDKitAbbreviations.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      36 May  2 17:10 libRDKitAbbreviations.so.1 -> libRDKitAbbreviations.so.1.2024.03.2
-rwxr-xr-x 1 lester lester  176384 May  2 17:10 libRDKitAbbreviations.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      32 May  2 17:10 libRDKitAlignment.so -> libRDKitAlignment.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      32 May  2 17:10 libRDKitAlignment.so.1 -> libRDKitAlignment.so.1.2024.03.2
-rwxr-xr-x 1 lester lester   46376 May  2 17:10 libRDKitAlignment.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      34 May  2 17:10 libRDKitavalon_clib.so -> libRDKitavalon_clib.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      34 May  2 17:10 libRDKitavalon_clib.so.1 -> libRDKitavalon_clib.so.1.2024.03.2
-rwxr-xr-x 1 lester lester  517632 May  2 17:10 libRDKitavalon_clib.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      32 May  2 17:10 libRDKitAvalonLib.so -> libRDKitAvalonLib.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      32 May  2 17:10 libRDKitAvalonLib.so.1 -> libRDKitAvalonLib.so.1.2024.03.2
-rwxr-xr-x 1 lester lester   84336 May  2 17:10 libRDKitAvalonLib.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      31 May  2 17:10 libRDKitCatalogs.so -> libRDKitCatalogs.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      31 May  2 17:10 libRDKitCatalogs.so.1 -> libRDKitCatalogs.so.1.2024.03.2
-rwxr-xr-x 1 lester lester   16416 May  2 17:10 libRDKitCatalogs.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      39 May  2 17:10 libRDKitChemicalFeatures.so -> libRDKitChemicalFeatures.so.1.2024.03.2
lrwxrwxrwx 1 lester lester      39 May  2 17:10 libRDKitChemicalFeatures.so.1 -> libRDKitChemicalFeatures.so.1.2024.03.2

ls -l 2024.03.3/lib | head -n 20
total 30100
drwxr-xr-x 3 lester lester    4096 Jun 13 09:36 cmake
drwxr-xr-x 3 lester lester    4096 Jun 13 09:36 python3.11
lrwxrwxrwx 1 lester lester      36 Jun  4 10:34 libRDKitAbbreviations.so -> libRDKitAbbreviations.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      36 Jun  4 10:33 libRDKitAbbreviations.so.1 -> libRDKitAbbreviations.so.1.2024.03.3
-rwxr-xr-x 1 lester lester  176384 Jun  4 10:34 libRDKitAbbreviations.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      32 Jun  4 10:34 libRDKitAlignment.so -> libRDKitAlignment.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      32 Jun  4 10:33 libRDKitAlignment.so.1 -> libRDKitAlignment.so.1.2024.03.3
-rwxr-xr-x 1 lester lester   46376 Jun  4 10:34 libRDKitAlignment.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      34 Jun  4 10:34 libRDKitavalon_clib.so -> libRDKitavalon_clib.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      34 Jun  4 10:33 libRDKitavalon_clib.so.1 -> libRDKitavalon_clib.so.1.2024.03.3
-rwxr-xr-x 1 lester lester  517632 Jun  4 10:34 libRDKitavalon_clib.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      32 Jun  4 10:34 libRDKitAvalonLib.so -> libRDKitAvalonLib.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      32 Jun  4 10:33 libRDKitAvalonLib.so.1 -> libRDKitAvalonLib.so.1.2024.03.3
-rwxr-xr-x 1 lester lester   84336 Jun  4 10:34 libRDKitAvalonLib.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      31 Jun  4 10:34 libRDKitCatalogs.so -> libRDKitCatalogs.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      31 Jun  4 10:33 libRDKitCatalogs.so.1 -> libRDKitCatalogs.so.1.2024.03.3
-rwxr-xr-x 1 lester lester   16416 Jun  4 10:34 libRDKitCatalogs.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      39 Jun  4 10:34 libRDKitChemicalFeatures.so -> libRDKitChemicalFeatures.so.1.2024.03.3
lrwxrwxrwx 1 lester lester      39 Jun  4 10:33 libRDKitChemicalFeatures.so.1 -> libRDKitChemicalFeatures.so.1.2024.03.3

@chryswoods: I'll PR to Sire devel to fix this. Given how long we've been building I'm surprised that we not had this issue before. (I checked older versions and the SONAME structure is the same.)

[chryswoods]

👍

The merge-base changed after approval.