diff --git a/debian/changelog b/debian/changelog index ea95655e9..d3a27215b 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,11 @@ +rdkit (202603.4-2.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Avoid catch2 thread safety issues + * Build the extensions for every supported python version. + + -- Maximiliano Curia Thu, 17 Sep 2026 09:08:16 +0200 + rdkit (202603.4-2) unstable; urgency=medium * Backport modified upstream commit to fix FTBFS with eigen3 >= 5.0.0 @@ -22,8 +30,8 @@ rdkit (202603.2-1) unstable; urgency=medium * New upstream version 202603.2. * debian/patches/NoDownloads.patch: Removed GraphMol/MolInterchange hunk, - functionality removed upstream. - * debian/patches/sphinx_compile_fixes.patch: Refreshed. + functionality removed upstream. + * debian/patches/sphinx_compile_fixes.patch: Refreshed. * debian/patches/fix_inchi_linking.patch: Likewise. * debian/patches/better_enums.patch: Likewise. * debian/control, debian/control.in (python3-rdkit/Depends): Added @@ -100,7 +108,7 @@ rdkit (202503.1-1) unstable; urgency=medium * New upstream release. * debian/patches/disable_riscv64_timeout_tests.patch: Refreshed. - * debian/patches/better_enums.patch: Vendorize better_enums header. + * debian/patches/better_enums.patch: Vendorize better_enums header. -- Michael Banck Sun, 06 Apr 2025 00:16:38 +0200 @@ -114,9 +122,9 @@ rdkit (202409.6-2) unstable; urgency=medium rdkit (202409.6-1) unstable; urgency=medium * New upstream point release. - * debian/patches/disable_pgsql_test.patch: Refreshed. + * debian/patches/disable_pgsql_test.patch: Refreshed. * debian/control.in, debian/control (Build-Depends): Add architecture-is- - little-endian (Closes: #1093086). + little-endian (Closes: #1093086). -- Michael Banck Tue, 04 Mar 2025 01:24:41 +0100 @@ -296,7 +304,7 @@ rdkit (202209.3-1) unstable; urgency=medium * New upstream point release. * debian/patches/postgres_Makefile_fixes.patch: Updated, removed one hunnk - that got applied upstream. + that got applied upstream. -- Michael Banck Sat, 14 Jan 2023 13:24:33 +0100 @@ -311,7 +319,7 @@ rdkit (202209.1-1) unstable; urgency=medium * debian/patches/postgres_Makefile_fixes.patch: Compile clang bytecode with -std=c++17. * debian/patches/postgres_Makefile_fixes.patch: Update RDKit version number. - * debian/gbp.conf: Set import-orig filter for upstream .gitattributes. + * debian/gbp.conf: Set import-orig filter for upstream .gitattributes. -- Michael Banck Sat, 05 Nov 2022 10:43:38 +0100 @@ -360,7 +368,7 @@ rdkit (202109.2-1) unstable; urgency=medium * New upstream release. + Includes updated PostgreSQL regression outputs (Closes: #1000579). - * debian/patches/postgres_compile_fixes.patch: Refreshed. + * debian/patches/postgres_compile_fixes.patch: Refreshed. * debian/patches/postgres_Makefile_fixes.patch: Add RDK_TOOLKIT_VERSION definition, hardcoded to current release for now. * debian/rules (DH_AUTO_CONFIGURE_OPTS): Added -DRDK_INSTALL_COMIC_FONTS=OFF @@ -373,7 +381,7 @@ rdkit (202109.2-1) unstable; urgency=medium rdkit (202103.5-1) unstable; urgency=medium * New upstream release. - * debian/patches/sphinx_compile_fixes.patch: Refreshed. + * debian/patches/sphinx_compile_fixes.patch: Refreshed. * debian/control (postgresql-PGVERSION-rdkit): Bump PostgreSQL version to 14 (Closes: #997745). @@ -392,7 +400,7 @@ rdkit (202009.5-1) unstable; urgency=medium * debian/watch: Updated. * debian/patches/sphinx_compile_fixes.patch: Drop hunk that got applied upstream. - * debian/patches/postgres_compile_fixes.patch: Refreshed. + * debian/patches/postgres_compile_fixes.patch: Refreshed. -- Michael Banck Fri, 14 May 2021 23:46:40 +0200 @@ -517,7 +525,7 @@ rdkit (201903.1-2) unstable; urgency=medium rdkit (201903.1-1) unstable; urgency=medium * New upstream release. - * debian/copyright: Removed Files-Excluded, no longer needed. + * debian/copyright: Removed Files-Excluded, no longer needed. * debian/patches/NoDownloads.patch: Remove CoordGen-specific hunks and add another CoordGen-specific hunk that drops the template.mae template support. @@ -556,7 +564,7 @@ rdkit (201809.1+dfsg-7) unstable; urgency=medium rdkit (201809.1+dfsg-6) unstable; urgency=medium * debian/patches/fix_coordgen_include_path.patch: New patch, fixes the - include path for system-installed coordgen headers. + include path for system-installed coordgen headers. -- Michael Banck Thu, 31 Jan 2019 14:20:27 +0100 diff --git a/debian/control b/debian/control index 76033e518..752dbe785 100644 --- a/debian/control +++ b/debian/control @@ -33,7 +33,7 @@ Build-Depends: architecture-is-64-bit, libsqlite3-dev, pandoc, postgresql-server-dev-all, - python3-dev, + python3-all-dev, python3-myst-parser, python3-numpy-dev, python3-pandas, diff --git a/debian/control.in b/debian/control.in index f7b49b998..baa24dde6 100644 --- a/debian/control.in +++ b/debian/control.in @@ -33,7 +33,7 @@ Build-Depends: architecture-is-64-bit, libsqlite3-dev, pandoc, postgresql-server-dev-all, - python3-dev, + python3-all-dev, python3-myst-parser, python3-numpy-dev, python3-pandas, diff --git a/debian/patches/fix_distgeom_threadsafety.patch b/debian/patches/fix_distgeom_threadsafety.patch new file mode 100644 index 000000000..e5cd3f56a --- /dev/null +++ b/debian/patches/fix_distgeom_threadsafety.patch @@ -0,0 +1,29 @@ +Description: Avoid Catch2 assertions in multithreaded test helper + Catch2 assertion macros are not thread-safe (prior catch2 3.12) and cause + assertion failures in OutputRedirect when invoked concurrently across worker + threads. +Author: Maximiliano Curia +Forwarded: no +--- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp ++++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +@@ -943,17 +943,17 @@ void runblock(const std::vector cids = + DGeomHelpers::EmbedMultipleConfs(*mol, 10, params); +- REQUIRE(cids.size() == 10); ++ TEST_ASSERT(cids.size() == 10); + std::unique_ptr field( + UFF::constructForceField(*mol, 100, cids[0])); +- REQUIRE(field); ++ TEST_ASSERT(field); + field->initialize(); + double eng = field->calcEnergy(); + if (!feq(eng, energies[i])) { + std::cerr << i << " iter " << j << " " << energies[i] << " != " << eng + << std::endl; + } +- CHECK(feq(eng, energies[i])); ++ TEST_ASSERT(feq(eng, energies[i])); + } + } + } diff --git a/debian/patches/fix_substruct_threadsafety.patch b/debian/patches/fix_substruct_threadsafety.patch new file mode 100644 index 000000000..8fe8c2cad --- /dev/null +++ b/debian/patches/fix_substruct_threadsafety.patch @@ -0,0 +1,16 @@ +Description: Avoid Catch2 assertions in substruct multithreaded test helper + Catch2 assertion macros are not thread-safe and cause assertion failures in + OutputRedirect when invoked concurrently across worker threads. +Author: Maximiliano Curia +Forwarded: no +--- a/Code/GraphMol/Substruct/testSubstructMatch.cpp ++++ b/Code/GraphMol/Substruct/testSubstructMatch.cpp +@@ -541,7 +541,7 @@ void runblock(const std::vector + +--- a/Code/cmake/Modules/RDKitUtils.cmake ++++ b/Code/cmake/Modules/RDKitUtils.cmake +@@ -190,7 +190,7 @@ macro(rdkit_python_extension) + CAR(RDKPY_NAME ${RDKPY_DEFAULT_ARGS}) + CDR(RDKPY_SOURCES ${RDKPY_DEFAULT_ARGS}) + if(RDK_BUILD_PYTHON_WRAPPERS) +- Python3_add_library(${RDKPY_NAME} MODULE ${RDKPY_SOURCES}) ++ Python3_add_library(${RDKPY_NAME} MODULE WITH_SOABI ${RDKPY_SOURCES}) + set_target_properties(${RDKPY_NAME} PROPERTIES PREFIX "") + + if(WIN32) diff --git a/debian/patches/series b/debian/patches/series index f307b3ba9..7209e96a5 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -14,3 +14,6 @@ fix-shebangs.patch remove-badges.patch d8ce92b61ce356bc2764e13f0d4b9a5df48094c5.patch fab08afd7000ac6000358a7c79e95cc1940e1c39.patch +fix_distgeom_threadsafety.patch +fix_substruct_threadsafety.patch +python_with_soabi.patch diff --git a/debian/rules b/debian/rules index 773ec51b9..7b4848f00 100755 --- a/debian/rules +++ b/debian/rules @@ -20,8 +20,8 @@ export DOCDIR := $(CURDIR)/debian/rdkit-doc/usr/share/doc/rdkit/ export RDBASE := $(CURDIR) -PY3VERS = $(shell py3versions -v -d) -PY3 = $(shell which python$(PY3VERS)) +PY3VERS = $(shell py3versions -s) +PY3DEF = $(shell py3versions -d) export DEBTMP := $(CURDIR)/debian/tmp DH_AUTO_CONFIGURE_OPTS := -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON \ @@ -91,18 +91,23 @@ override_dh_auto_clean: rdkit/ML/Data/test_data/testquant.qdat.pkl $(RM) Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean + $(RM) -rf $(CURDIR)/build-* $(RM) -rf $(CURDIR)/Code/PgSQL/rdkit/build-* override_dh_auto_configure: - dh_auto_configure -- $(DH_AUTO_CONFIGURE_OPTS) -DPYTHON_EXECUTABLE=$(PY3) ../ + for py in $(PY3VERS); do \ + dh_auto_configure --builddirectory=build-$$py -- $(DH_AUTO_CONFIGURE_OPTS) -DPython3_EXECUTABLE=/usr/bin/$$py -DPYTHON_EXECUTABLE=/usr/bin/$$py; \ + done for v in $$(pg_buildext supported-versions); do \ (mkdir -p Code/PgSQL/rdkit/build-$$v && cd Code/PgSQL/rdkit/build-$$v && cmake -DPostgreSQL_CONFIG=/usr/lib/postgresql/$$v/bin/pg_config -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/$$v/server" -DCMAKE_VERBOSE_MAKEFILE=1 -DRDKit_CodeDir=../../../Code ../); \ done override_dh_auto_build: - dh_auto_build + for py in $(PY3VERS); do \ + dh_auto_build --builddirectory=build-$$py; \ + done for v in $$(pg_buildext supported-versions); do \ - (cd Code/PgSQL/rdkit/build-$$v && make || $$(cat ../../../../obj-*/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/link.txt | sed -e 's#\.\./\.\./#../../../../obj-*/Code/#g')); \ + (cd Code/PgSQL/rdkit/build-$$v && make || $$(cat ../../../../build-$(PY3DEF)/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/link.txt | sed -e 's#\.\./\.\./#../../../../build-$(PY3DEF)/Code/#g')); \ done (cd $(CURDIR)/Code; doxygen doxygen/doxygen.config) (cd $(CURDIR)/Docs/Book; RDBASE=$(CURDIR) $(MAKE) html) @@ -110,18 +115,25 @@ override_dh_auto_build: # (cd $(CURDIR)/Docs/Book; RDBASE=$(CURDIR) $(MAKE) latexpdf) override_dh_auto_install: - dh_auto_install + for py in $(filter-out $(PY3DEF),$(PY3VERS)) $(PY3DEF); do \ + dh_auto_install --builddirectory=build-$$py; \ + done override_dh_install: - mkdir -p $(DEBTMP)/usr/lib/python3 - mv $(DEBTMP)/usr/lib/python$(PY3VERS)/site-packages $(DEBTMP)/usr/lib/python3/dist-packages - $(RM) -rf $(DEBTMP)/usr/lib/python$(PY3VERS) + mkdir -p $(DEBTMP)/usr/lib/python3/dist-packages + for py in $(PY3VERS); do \ + for dir in site-packages dist-packages; do \ + if [ -d $(DEBTMP)/usr/lib/$$py/$$dir ]; then \ + cp -a $(DEBTMP)/usr/lib/$$py/$$dir/* $(DEBTMP)/usr/lib/python3/dist-packages/; \ + fi; \ + done; \ + $(RM) -rf $(DEBTMP)/usr/lib/$$py; \ + done ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf $(DEBTMP)/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf dh_install -ppython3-rdkit /usr/lib/python3 $(RM) -rf $(DEBTMP)/usr/lib/python3/dist-packages/rdkit/docs/ $(RM) -rf $(DEBTMP)/usr/share/RDKit/Projects/__pycache__ $(RM) -rf $(DEBTMP)/usr/share/RDKit/Projects/DbCLI/__pycache__ - dh_numpy3 dh_install for v in $$(pg_buildext supported-versions); do \ mkdir -p debian/postgresql-$$v-rdkit/usr/lib/postgresql/$$v/lib/ debian/postgresql-$$v-rdkit/usr/share/postgresql/$$v/extension/; \ @@ -149,7 +161,9 @@ override_dh_python3: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) override_dh_auto_test: - cp -r rdkit obj-*/ - find $(CURDIR) -name rdchem.so - PYTHONPATH=$(wildcard $(CURDIR)/obj-*/):$(wildcard $(CURDIR)/obj-*/)/rdkit/Chem/ LD_LIBRARY_PATH="$(wildcard $(CURDIR)/obj-*/)/lib:$(LD_LIBRARY_PATH)" dh_auto_test + for py in $(PY3VERS); do \ + cp -r rdkit build-$$py/; \ + PYTHONPATH=$(CURDIR)/build-$$py:$(CURDIR)/build-$$py/rdkit/Chem LD_LIBRARY_PATH="$(CURDIR)/build-$$py/lib:$(LD_LIBRARY_PATH)" dh_auto_test --builddirectory=build-$$py; \ + done endif + diff --git a/debian/tests/control b/debian/tests/control index a1b36e426..1927706f2 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -10,6 +10,7 @@ Restrictions: Depends: @, + python3-all, Tests: importcheck, Restrictions: diff --git a/debian/tests/importcheck b/debian/tests/importcheck index 83b4d26e0..8faf05750 100644 --- a/debian/tests/importcheck +++ b/debian/tests/importcheck @@ -1,4 +1,10 @@ -#!/usr/bin/env python3 +#!/bin/sh +set -e + +cd "${AUTOPKGTEST_TMP:-/tmp}" + +for py in $(py3versions -s); do + echo "=== Testing $py ===" + $py -c "import rdkit; from rdkit import Chem" +done -import rdkit -from rdkit import Chem