build: bump OpenBabel to 3.1.1 from upstream tag with in-tree <ctime> patch#3
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Clone OpenBabel from the upstream openbabel/openbabel openbabel-3-1-1 tag (version-derived, OPENBABEL-overridable) instead of the ComPlat fork, and inject the missing `#include <ctime>` into obutil.h before cmake. The 3.1.1 release tag predates upstream PR #2533, so without this it fails to compile on GCC 11+ (clock / CLOCKS_PER_SEC not declared). This folds the fix previously carried by the third-party ptrxyz/openbabel-gem@ptrxyz-ctime-fix into this ComPlat-owned gem. Clone/patch failures now abort the build instead of falling through to the fake Makefile. Fix GEMVERSION to a valid Gem::Version (3.1.1.1); the prior v3.0.0-ob3.1.1 was non-numeric and broke `gem build`. Move the verification Dockerfile off the deliberate ruby:3.1-bullseye (GCC 10) pin to ruby:3.3-bookworm (GCC 12), matching production's modern toolchain, and add CLAUDE.md documenting the build. Verified: docker build on GCC 12 succeeds, smoke test reports formula=C27H46O atoms=74, rake test passes. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
extconf.rb derives the OpenBabel git tag from OpenBabel::VERSION but never required openbabel/version. RubyGems/Bundler invoke the build as a bare `ruby extconf.rb` with the gem's lib/ off the load path, so the constant was undefined and the build died with `uninitialized constant OpenBabel (NameError)` before any clone or compile — surfacing as the generic "Could not create Makefile due to ... lack of necessary libraries and/or headers." This broke `bundle install` in chemotion_ELN / chemotion-builder. Require the version file from within extconf (path-resolved off the gem root) so the constant is always available regardless of how the build is invoked. The verification Dockerfile previously ran `ruby -I../../lib -ropenbabel/version extconf.rb`, pre-loading the constant and masking exactly this failure — which is why CI stayed green while real installs failed. Drop the preload so the image builds the gem the way RubyGems does and would catch a regression.
PiTrem
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Switches the gem to build OpenBabel 3.1.1 from the upstream
openbabel/openbabelopenbabel-3-1-1tag (version-derived,OPENBABEL-overridable) instead of the ComPlat fork, and injects the missing#include <ctime>intoobutil.hbefore cmake — the 3.1.1 release tag predates upstream PR #2533, so without it the build fails on GCC 11+ (clock/CLOCKS_PER_SECnot declared). This folds the fix previously carried by the third-partyptrxyz/openbabel-gem@ptrxyz-ctime-fixinto this ComPlat-owned gem.Also:
GEMVERSIONto a validGem::Version(3.1.1.1); the priorv3.0.0-ob3.1.1was non-numeric and brokegem build.NameError—extconf.rbderived the OpenBabel git tag fromOpenBabel::VERSIONbut never requiredopenbabel/version, so RubyGems/Bundler's bareruby extconf.rbdied withuninitialized constant OpenBabelbefore any clone. This brokebundle installin chemotion_ELN / chemotion-builder. Now required path-resolved off the gem root.Dockerfileonruby:3.3-bookworm(GCC 12) matching production, building the gem the way RubyGems does (no constant preload) so a regression of theNameErrorwould be caught.Verified: docker build on GCC 12 succeeds, smoke test reports
formula=C27H46O atoms=74,rake testpasses.