Patch lbvs_consent 2.1.1-2.2.0 to support openbabel-3

[jmid]

The previous PR #24545 patched conf-openbabel to install openbabel-2 or 3.

The lbvs_consent however still hardcodes an openbabel-2 include path which causes CI build errors, and thus adds noise:

lbvs_consent.2.1.1 (failed: The compilation of lbvs_consent.2.1.1 failed at "make obmaccs".)
lbvs_consent.2.1.2 (failed: The compilation of lbvs_consent.2.1.2 failed at "make obmaccs".)
lbvs_consent.2.1.3 (failed: The compilation of lbvs_consent.2.1.3 failed at "make obmaccs".)
lbvs_consent.2.2.0 (failed: The compilation of lbvs_consent.2.2.0 failed at "make obmaccs".)

This follow-up PR thus patches the Makefiles for lbvs_consent 2.1.1-2.2.0 to utilize #24545.

I've filed an upstream PR with the corresponding change here: UnixJunkie/consent#15

[jmid]

I somehow managed to include illegal white chars again... 🤦

I've therefore checked that all 4 four opam files lint locally.
lbvs_consent.2.1.1/opam and lbvs_consent.2.1.2/opam trigger a lint warning locally (and on the CI):

  warning 62: License doesn't adhere to the SPDX standard, see https://spdx.org/licenses/: "GPL"

This is unrelated to the changes in this PR though (which doesn't touch the license field)

[jmid]

I see FreeBSD failures on conf-python-3.9.0.0

#=== ERROR while compiling conf-python-3.9.0.0 ================================#
"python3": command not found.

which should be solved by #24652

[jmid]

9c86a07 adds a lower bound on cpm which seems to have restructured to have a Cpm module with the 4.0.0 release.

[jmid]

• 92fdc8e adds a lower bound for minivpt (only a dep for 2.1.1 and 2.1.2)
• 2cf1ce6 adds a lower bound for batteries which added BatString.split_on_string in 2.11.0

[jmid]

• 42ee938 bumps the batteries dependency to 3.0.0 as I couldn't find BatString.split_on_string here despite the documentation mentioning it

[jmid]

Overall there remains

• minivpt failures caused by transitive missing lower bounds, which should be fixed in Add minivpt lower bounds #24680
• extunix.0.1.4 failures on OCaml 5.0 since it requires Pervasives, which should be fixed in Add upper OCaml bound for extunix.0.1.4 #24679
• errors installing conf-rdkit system packages on Fedora and macOS - see new file: conf-pip-rdkit/conf-pip-rdkit.1.0.0/opam #24633
• errors on installing conf-python-3.9.0.0 which should be fixed in conf-python-3 - update freebsd python packages #24652

I suggest to wait until #24652 #24679 and #24680 have been merged, and then rerun CI before merging this one.
I would expect for only conf-rdkit CI failures to remain at that point.

[jmid]

Rebased on master to trigger a new run, since the above 3 PRs have now been merged.
I expect conf-rdkit CI failures.

[jmid]

There are still minivpt CI errors unfortunately. #24696 bumps its lower obuild bound to address it.

[jmid]

There are also still extunix CI failures, which #24698 should address.

[jmid]

Rebased on master again after #24696 and #24698 have been merged 🍿 🤞

[jmid]

CI revealed a missing bound on camlzip:

#=== ERROR while compiling lbvs_consent.2.1.1 =================================#
# context              2.2.0~alpha3~dev | linux/x86_64 | ocaml-base-compiler.4.05.0 | pinned(https://github.com/UnixJunkie/consent/archive/v2.1.1.tar.gz)
# path                 ~/.opam/4.05/.opam-switch/build/lbvs_consent.2.1.1
# command              ~/.opam/opam-init/hooks/sandbox.sh build dune build -p lbvs_consent -j 31
# exit-code            1
# env-file             ~/.opam/log/lbvs_consent-6-45bab3.env
# output-file          ~/.opam/log/lbvs_consent-6-45bab3.out
### output ###
#       ocamlc src/.lbvs_consent.objs/byte/lbvs_consent__MyUtils.{cmi,cmo,cmt} (exit 2)
# (cd _build/default && /home/opam/.opam/4.05/bin/ocamlc.opt -w -40 -g -bin-annot -I src/.lbvs_consent.objs/byte -I /home/opam/.opam/4.05/lib/batteries -I /home/opam/.opam/4.05/lib/bitv -I /home/opam/.opam/4.05/lib/bytes -I /home/opam/.opam/4.05/lib/cpm -I /home/opam/.opam/4.05/lib/dolog -I /home/opam/.opam/4.05/lib/minivpt -I /home/opam/.opam/4.05/lib/num -I /home/opam/.opam/4.05/lib/ocaml/threads -I /home/opam/.opam/4.05/lib/parmap -I /home/opam/.opam/4.05/lib/zip -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/byte/lbvs_consent__MyUtils.cmo -c -impl src/myUtils.ml)
# File "src/myUtils.ml", line 74, characters 2-23:
# Error: Unbound value Gzip.output_substring

Gzip.output_substring was added in camlzip.1.06 so be1abc2 adds that as a lower bound... 🍿

[jmid]

• 34f8b6a adds a lower bound to make BatString.chop available
• 9281158 adds a lower bound for parmap on the first non-rc package after 0.9.1 which is incompatible API-wise

[jmid]

The remaining failures are all from conf-rdkit. #24708 is an attempt at adding FreeBSD support for it.

[mseri]

In general I am against patches on released packages and ask to release a -1 patch version. In this case I would be in favour since it is a strict improvement over what we have and reduces drastically the failures. We need to discuss this at the next maintainer meeting and see if we all agree before we can merge

[mseri]

Since this was merged upstream and it is a specialized software that would become available on a larger set of platforms, I am going to accept and merge the change

[mseri]

Thanks and sorry for the delay