diff --git a/src/BerkeleyDB/BUILD b/src/BerkeleyDB/BUILD index 4cc755ea..b83ed163 100644 --- a/src/BerkeleyDB/BUILD +++ b/src/BerkeleyDB/BUILD @@ -23,11 +23,11 @@ cc_binary( ], tags = ["berkeleydb"], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "@berkeleydb", ], ) @@ -157,12 +157,13 @@ cc_binary( "@berkeleydb", ], ) + cc_binary( name = "iwbdb_merge_into_tdt", srcs = [ "iwbdb_merge_into_tdt.cc", ], - tags = ["berkeleydb"], + tags = ["berkeleydb"], deps = [ "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", diff --git a/src/Duplicates/BUILD b/src/Duplicates/BUILD index 3726817a..58926ae2 100644 --- a/src/Duplicates/BUILD +++ b/src/Duplicates/BUILD @@ -14,10 +14,10 @@ cc_binary( ], deps = [ ":topological_torsion_lib", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", - "//Foundational/iwaray:iwaray", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwaray", + "//Foundational/iwmisc", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", "//Molecule_Lib:substructure_cc_proto", @@ -33,23 +33,23 @@ cc_library( "topological_torsion.h", ], deps = [ - "//Foundational/iwstring:iwstring", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", "//Foundational/iwmisc:sparse_fp_creator", - "//Molecule_Lib:iwmolecule" + "//Foundational/iwstring", + "//Molecule_Lib:iwmolecule", ], ) cc_test( name = "topological_torsion_test", + timeout = "short", srcs = [ "topological_torsion_test.cc", ], deps = [ ":topological_torsion_lib", - "@googletest//:gtest_main", - "@googletest//:gtest", "//Molecule_Lib:moleculeio", + "@googletest//:gtest", + "@googletest//:gtest_main", ], - timeout="short", ) diff --git a/src/Foundational/iwmisc/BUILD b/src/Foundational/iwmisc/BUILD index 9d347e15..eabc1ef4 100644 --- a/src/Foundational/iwmisc/BUILD +++ b/src/Foundational/iwmisc/BUILD @@ -1,3 +1,4 @@ +load("@rules_go//proto:def.bzl", "go_proto_library") load("@rules_proto//proto:defs.bzl", "proto_library") proto_library( @@ -5,16 +6,16 @@ proto_library( srcs = [ "for_testing.proto", ], + visibility = ["//visibility:public"], ) cc_proto_library( name = "for_testing_cc_proto", deps = [ "for_testing_proto", - ] + ], ) - cc_library( name = "activity_from_file", srcs = [ @@ -117,8 +118,8 @@ cc_library( "toml_support.h", ], deps = [ + "@com_google_absl//absl/status", "@tomlplusplus//:toml++", - "@com_google_absl//absl/status:status", ], ) @@ -185,7 +186,7 @@ cc_library( visibility = ["//visibility:public"], deps = [ "//Foundational/iwstring", - "@com_google_absl//absl/strings:strings", + "@com_google_absl//absl/strings", "@re2", ], ) @@ -251,10 +252,10 @@ cc_library( hdrs = [ "sorted_list.h", ], + visibility = ["//visibility:public"], deps = [ "//Foundational/iwaray", ], - visibility = ["//visibility:public"], ) cc_binary( @@ -346,5 +347,5 @@ cc_test( ":ltoml", "@googletest//:gtest_main", "@tomlplusplus//:toml++", - ] + ], ) diff --git a/src/Foundational/iwstring/BUILD b/src/Foundational/iwstring/BUILD index 1ba5d85e..68e5b959 100644 --- a/src/Foundational/iwstring/BUILD +++ b/src/Foundational/iwstring/BUILD @@ -79,6 +79,7 @@ cc_binary( cc_test( name = "iwstring_test", + timeout = "short", srcs = [ "iwstring_test.cc", ], @@ -87,7 +88,6 @@ cc_test( "@googletest//:gtest", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( diff --git a/src/Molecule_Lib/BUILD b/src/Molecule_Lib/BUILD index 73c15ba2..f270d4ab 100644 --- a/src/Molecule_Lib/BUILD +++ b/src/Molecule_Lib/BUILD @@ -1,5 +1,5 @@ -load("@rules_proto//proto:defs.bzl", "proto_library") load("@com_google_protobuf//:protobuf.bzl", "py_proto_library") +load("@rules_proto//proto:defs.bzl", "proto_library") package(default_visibility = ["//visibility:public"]) @@ -137,7 +137,7 @@ cc_proto_library( name = "pharmacophore_cc_proto", deps = [ ":pharmacophore_proto", - ] + ], ) py_proto_library( @@ -178,16 +178,16 @@ cc_proto_library( ":substructure_proto", ], ) + py_proto_library( name = "substructure_py_proto", srcs = ["substructure.proto"], + visibility = ["//visibility:public"], deps = [ "geometric_constraints_py_proto", ], - visibility = ["//visibility:public"], ) - proto_library( name = "reaction_proto", srcs = [ @@ -211,11 +211,11 @@ py_proto_library( srcs = [ "reaction.proto", ], + visibility = ["//visibility:public"], deps = [ "substructure_py_proto", "toggle_kekule_form_py_proto", ], - visibility = ["//visibility:public"], ) proto_library( @@ -240,10 +240,10 @@ py_proto_library( srcs = [ "toggle_kekule_form.proto", ], + visibility = ["//visibility:public"], deps = [ ":substructure_py_proto", ], - visibility = ["//visibility:public"], ) cc_library( @@ -299,7 +299,6 @@ cc_library( "mdl_file_data.cc", "mdl_molecule.cc", "misc2.cc", - "moleculeio.cc", "mol2graph.cc", "mol2graph_proto.cc", "molecule.cc", @@ -308,6 +307,7 @@ cc_library( "moleculeb.cc", "moleculed.cc", "moleculeh.cc", + "moleculeio.cc", "moleculer.cc", "numass.cc", "ostream_and_type.cc", @@ -382,7 +382,6 @@ cc_library( "mdl_file_data.h", "mdl_molecule.h", "misc2.h", - "moleculeio.h", "mol2graph.h", "mol2graph_proto.h", "molecule.h", @@ -390,6 +389,7 @@ cc_library( "molecule_mdl.h", "molecule_smi.h", "molecule_to_query.h", + "moleculeio.h", "moleculej.h", "numass.h", "ostream_and_type.h", @@ -446,8 +446,7 @@ cc_library( ], ) - -cc_library ( +cc_library( name = "charge_assigner", srcs = [ "charge_assigner.cc", @@ -460,7 +459,7 @@ cc_library ( ], ) -cc_library ( +cc_library( name = "donor_acceptor", srcs = [ "donor_acceptor.cc", @@ -606,10 +605,10 @@ cc_library( "molecular_formula.h", ], deps = [ - "//Foundational/iwstring:iwstring", - "//Foundational/iwmisc", ":iwmolecule", ":moleculeio", + "//Foundational/iwmisc", + "//Foundational/iwstring", ], ) @@ -649,6 +648,7 @@ cc_test( cc_test( name = "cahn_ingold_prelog_test", + timeout = "short", srcs = [ "cahn_ingold_prelog_test.cc", ], @@ -657,11 +657,11 @@ cc_test( ":moleculeio", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( name = "dihedral_test", + timeout = "short", srcs = [ "dihedral_test.cc", ], @@ -670,11 +670,11 @@ cc_test( ":moleculeio", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( name = "donor_acceptor_test", + timeout = "short", srcs = [ "donor_acceptor_test.cc", ], @@ -686,11 +686,11 @@ cc_test( ":moleculeio", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( name = "element_hits_needed_test", + timeout = "short", srcs = [ "element_hits_needed_test.cc", ], @@ -699,7 +699,6 @@ cc_test( ":moleculeio", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( @@ -735,8 +734,8 @@ cc_test( ":geometric_constraints_cc_proto", ":iwmolecule", ":moleculeio", - "@googletest//:gtest_main", "@com_google_protobuf//:protobuf", + "@googletest//:gtest_main", ], ) @@ -786,14 +785,15 @@ cc_test( ], deps = [ ":iwmolecule", - ":moleculeio", ":kabsch", + ":moleculeio", "@googletest//:gtest_main", ], ) cc_test( name = "molecular_formula_test", + timeout = "short", srcs = [ "molecular_formula_test.cc", ], @@ -801,7 +801,6 @@ cc_test( "molecular_formula_lib", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( @@ -847,6 +846,7 @@ cc_test( cc_test( name = "ring_test", + timeout = "short", srcs = [ "ring_test.cc", ], @@ -855,7 +855,6 @@ cc_test( ":moleculeio", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( @@ -899,19 +898,20 @@ cc_test( cc_test( name = "substructure_a_test", + timeout = "short", srcs = ["substructure_a_test.cc"], - timeout="short", deps = [ ":iwmolecule", ":moleculeio", ":substructure_cc_proto", - "@googletest//:gtest_main", "@com_google_protobuf//:protobuf", + "@googletest//:gtest_main", ], ) cc_test( name = "ss_bonds_test", + timeout = "short", srcs = [ "ss_bonds_test.cc", ], @@ -922,7 +922,6 @@ cc_test( "@com_google_protobuf//:protobuf", "@googletest//:gtest_main", ], - timeout="short", ) cc_test( diff --git a/src/Molecule_Tools/BUILD b/src/Molecule_Tools/BUILD index c7797ddc..0d7e57f7 100644 --- a/src/Molecule_Tools/BUILD +++ b/src/Molecule_Tools/BUILD @@ -1,6 +1,6 @@ +load("@com_google_protobuf//:protobuf.bzl", "py_proto_library") load("@rules_cc//cc:defs.bzl", "cc_binary") load("@rules_proto//proto:defs.bzl", "proto_library") -load("@com_google_protobuf//:protobuf.bzl", "py_proto_library") load("//build_deps:install.bzl", "local_install") local_install( @@ -17,9 +17,9 @@ local_install( ":dbf", ":dicer", ":dicer_to_topological_types", + ":ec_fingerprint", ":echoqry", ":echorxn", - ":ec_fingerprint", ":enumeration", ":extended_atom_pairs", ":ez_descriptor", @@ -58,8 +58,8 @@ local_install( ":medchemwizard", ":minor_changes", ":mkfrag", - ":mol2qry", ":mol2SAFE", + ":mol2qry", ":molecular_abstraction", ":molecular_grid", ":molecular_merge", @@ -494,6 +494,7 @@ py_proto_library( "xlogp.proto", ], ) + cc_binary( name = "abraham", srcs = [ @@ -628,9 +629,9 @@ cc_binary( deps = [ "//Foundational/cmdline:iwcmdline", "//Foundational/iwmisc:sparse_fp_creator", - "//Molecule_Tools:extended_connectivity_fp", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", + "//Molecule_Tools:extended_connectivity_fp", ], ) @@ -642,9 +643,9 @@ cc_binary( deps = [ "//Foundational/cmdline:iwcmdline", "//Foundational/iwmisc:sparse_fp_creator", - "//Molecule_Tools:extended_connectivity_fp", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", + "//Molecule_Tools:extended_connectivity_fp", ], ) @@ -702,8 +703,8 @@ cc_binary( "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", "//Molecule_Lib:substructure_cc_proto", - "@highwayhash//:highwayhash", "@com_google_protobuf//:protobuf", + "@highwayhash", ], ) @@ -821,7 +822,6 @@ cc_binary( ], ) - cc_binary( name = "enumeration", srcs = [ @@ -1324,8 +1324,8 @@ cc_binary( "mol2SAFE.cc", ], deps = [ - ":highest_ring_number", ":fragment_molecule_lib", + ":highest_ring_number", "//Foundational/cmdline:iwcmdline", "//Foundational/iwstring:absl_hash", "//Molecule_Lib:iwmolecule", @@ -1406,15 +1406,15 @@ cc_binary( "molecule_filter.cc", ], deps = [ + ":alogp_lib", ":molecule_filter_cc_proto", ":molecule_filter_lib", - ":alogp_lib", ":xlogp_lib", "//Foundational/cmdline:iwcmdline", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", "//Molecule_Tools:nvrtspsa", - ] + ], ) cc_binary( @@ -1424,11 +1424,11 @@ cc_binary( ], deps = [ "//Foundational/cmdline:iwcmdline", - "//Foundational/jama:jama", - "//Foundational/tnt:tnt", + "//Foundational/jama", + "//Foundational/tnt", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - ] + ], ) cc_binary( @@ -1529,9 +1529,9 @@ cc_binary( ], deps = [ ":dicer_fragments_cc_proto", - "//Foundational/cmdline_v2:cmdline_v2", + "//Foundational/cmdline_v2", "//Foundational/data_source:iwtfdata_record", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", ], @@ -1601,7 +1601,7 @@ cc_binary( "//Foundational/cmdline:iwcmdline", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - ] + ], ) cc_binary( @@ -1793,18 +1793,18 @@ cc_binary( cc_binary( name = "ring_extraction", srcs = [ - "ring_extraction.cc" + "ring_extraction.cc", ], deps = [ ":replacement_ring_cc_proto", - "//Molecule_Tools:reaction_duplicate", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", - "//Foundational/iwaray:iwaray", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwaray", + "//Foundational/iwmisc", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", "//Molecule_Lib:substructure_cc_proto", + "//Molecule_Tools:reaction_duplicate", "@com_google_protobuf//:protobuf", ], ) @@ -2021,13 +2021,13 @@ cc_library( hdrs = [ "alogp.h", ], + visibility = [ + "//visibility:public", + ], deps = [ "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", ], - visibility = [ - "//visibility:public", - ], ) #cc_library( @@ -2065,28 +2065,28 @@ cc_library( cc_library( name = "dicer_api", - hdrs = [ - "dicer_api.h", - ], srcs = [ "dicer_api.cc", ], - deps = [ - ":dicer_lib", + hdrs = [ + "dicer_api.h", ], visibility = [ "//visibility:public", ], + deps = [ + ":dicer_lib", + ], ) cc_library( name = "dicer_lib", - hdrs = [ - "dicer_lib.h", - ], srcs = [ "dicer_lib.cc", ], + hdrs = [ + "dicer_lib.h", + ], deps = [ "//Molecule_Lib:iwmolecule", ], @@ -2100,24 +2100,24 @@ cc_library( hdrs = [ "ec_fingerprint.h", ], + visibility = [ + "//visibility:public", + ], deps = [ ":fingerprint_writer", - "//Molecule_Lib:iwmolecule", "//Foundational/iwmisc:sparse_fp_creator", - ], - visibility = [ - "//visibility:public", + "//Molecule_Lib:iwmolecule", ], ) cc_library( name = "safe_generate_lib", - hdrs = [ - "safe_generate_lib.h", - ], srcs = [ "safe_generate_lib.cc", ], + hdrs = [ + "safe_generate_lib.h", + ], deps = [ ":dicer_fragments_cc_proto", "//Molecule_Lib:iwmolecule", @@ -2133,8 +2133,8 @@ cc_library( "molecule_filter_lib.h", ], deps = [ - ":molecule_filter_cc_proto", ":alogp_lib", + ":molecule_filter_cc_proto", ":xlogp_lib", "//Foundational/cmdline:iwcmdline", "//Molecule_Lib:iwmolecule", @@ -2182,16 +2182,16 @@ cc_binary( deps = [ ":dicer_fragments_cc_proto", ":molecule_filter_lib", - ":safe_generate_lib", ":safe_generate_cc_proto", + ":safe_generate_lib", "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/iwstring:absl_hash", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - "@com_google_protobuf//:protobuf", "@com_google_absl//absl/container:flat_hash_map", "@com_google_absl//absl/container:flat_hash_set", + "@com_google_protobuf//:protobuf", ], ) @@ -2270,6 +2270,7 @@ cc_binary( "//Molecule_Lib:moleculeio", ], ) + cc_binary( name = "substituent_model", srcs = [ @@ -3084,12 +3085,12 @@ cc_library( hdrs = [ "mpr.h", ], - deps = [ - "//Molecule_Lib:iwmolecule", - ], visibility = [ "//visibility:public", ], + deps = [ + "//Molecule_Lib:iwmolecule", + ], ) cc_library( @@ -3129,12 +3130,12 @@ cc_library( hdrs = [ "reaction_duplicate.h", ], - deps = [ - "//Molecule_Lib:iwmolecule", - ], visibility = [ "//visibility:public", ], + deps = [ + "//Molecule_Lib:iwmolecule", + ], ) cc_library( @@ -3175,12 +3176,12 @@ cc_library( hdrs = [ "ring_ext_rep.h", ], - deps = [ - "//Molecule_Lib:iwmolecule", - ], visibility = [ "//visibility:public", ], + deps = [ + "//Molecule_Lib:iwmolecule", + ], ) cc_library( @@ -3194,8 +3195,8 @@ cc_library( deps = [ ":scaffolds_cc_proto", "//Foundational/cmdline:iwcmdline", - "//Foundational/iwstring:iwstring", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", + "//Foundational/iwstring", "//Molecule_Lib:iwmolecule", "@com_google_protobuf//:protobuf", ], @@ -3274,13 +3275,13 @@ cc_library( hdrs = [ "unique_molecules_api.h", ], + visibility = [ + "//visibility:public", + ], deps = [ "//Molecule_Lib:iwmolecule", "@com_google_absl//absl/container:btree", ], - visibility = [ - "//visibility:public", - ], ) cc_library( @@ -3289,7 +3290,10 @@ cc_library( "xlogp.cc", ], hdrs = [ - "xlogp.h" + "xlogp.h", + ], + visibility = [ + "//visibility:public", ], deps = [ ":xlogp_cc_proto", @@ -3297,9 +3301,6 @@ cc_library( "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", ], - visibility = [ - "//visibility:public", - ], ) cc_test( @@ -3328,8 +3329,8 @@ cc_test( ":dicer_api", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - "@googletest//:gtest_main", "@com_google_protobuf//:protobuf", + "@googletest//:gtest_main", ], ) @@ -3339,9 +3340,9 @@ cc_test( srcs = ["ec_fingerprint_test.cc"], deps = [ ":ec_fingerprint_lib", + "//Foundational/iwmisc:sparse_fp_creator", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - "//Foundational/iwmisc:sparse_fp_creator", "@googletest//:gtest_main", ], ) @@ -3460,9 +3461,9 @@ cc_test( deps = [ ":ring_ext_rep", "//Molecule_Lib:moleculeio", + "@com_google_protobuf//:protobuf", "@googletest//:gtest", "@googletest//:gtest_main", - "@com_google_protobuf//:protobuf", ], ) @@ -3472,28 +3473,28 @@ cc_test( "safe_generate_lib_test.cc", ], deps = [ - ":safe_generate_lib", ":safe_generate_cc_proto", + ":safe_generate_lib", "//Molecule_Lib:moleculeio", + "@com_google_protobuf//:protobuf", "@googletest//:gtest", "@googletest//:gtest_main", - "@com_google_protobuf//:protobuf", - ] + ], ) cc_test( name = "scaffolds_test", + timeout = "short", srcs = [ "scaffolds_test.cc", ], deps = [ ":scaffolds_lib", "//Molecule_Lib:moleculeio", - "@googletest//:gtest_main", - "@googletest//:gtest", "@com_google_protobuf//:protobuf", + "@googletest//:gtest", + "@googletest//:gtest_main", ], - timeout="short", ) cc_test( @@ -3519,7 +3520,7 @@ cc_test( ":xlogp_lib", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:iwreaction", - "@googletest//:gtest_main", "@googletest//:gtest", - ] + "@googletest//:gtest_main", + ], ) diff --git a/src/Molecule_Tools_Bdb/BUILD b/src/Molecule_Tools_Bdb/BUILD index c3408f9f..bb16680b 100644 --- a/src/Molecule_Tools_Bdb/BUILD +++ b/src/Molecule_Tools_Bdb/BUILD @@ -1,5 +1,5 @@ -load("@rules_proto//proto:defs.bzl", "proto_library") load("@com_google_protobuf//:protobuf.bzl", "py_proto_library") +load("@rules_proto//proto:defs.bzl", "proto_library") load("//build_deps:install.bzl", "local_install") package(default_visibility = ["//visibility:public"]) @@ -17,7 +17,6 @@ local_install( ], ) - proto_library( name = "smi2rings_proto", srcs = [ @@ -35,7 +34,7 @@ cc_proto_library( proto_library( name = "substituent_identification_proto", srcs = [ - "substituent_identification.proto", + "substituent_identification.proto", ], ) @@ -99,7 +98,7 @@ cc_binary( cc_binary( name = "dicer2bdb", srcs = [ - "dicer2bdb.cc", + "dicer2bdb.cc", ], tags = ["berkeleydb"], deps = [ @@ -128,8 +127,9 @@ cc_binary( "@berkeleydb", ], ) -cc_binary( - name = "in_lilly_database_bdb", + +cc_binary( + name = "in_lilly_database_bdb", srcs = [ "in_lilly_database_bdb.cc", ], @@ -191,6 +191,7 @@ cc_binary( "@berkeleydb", ], ) + cc_binary( name = "structure_database_load", srcs = [ diff --git a/src/Obsolete/BUILD b/src/Obsolete/BUILD index 5493ade3..be810dd4 100644 --- a/src/Obsolete/BUILD +++ b/src/Obsolete/BUILD @@ -18,12 +18,12 @@ cc_binary( "concat_files_large_memory.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], -) +) cc_binary( name = "complex_chirality", @@ -34,8 +34,8 @@ cc_binary( "//Foundational/cmdline:iwcmdline", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - ] -) + ], +) cc_binary( name = "confusion_matrix", @@ -43,11 +43,11 @@ cc_binary( "confusion_matrix.cc", ], deps = [ - "//Foundational/accumulator:accumulator", - "//Foundational/cmdline_v2:cmdline_v2", + "//Foundational/accumulator", + "//Foundational/cmdline_v2", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwmisc", + "//Foundational/iwqsort", "//Utilities/GFP_Tools:metric", ], ) @@ -79,10 +79,10 @@ cc_binary( "descriptor_file_to_molecular_properties.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -92,10 +92,10 @@ cc_binary( "descriptor_file_profile_activity.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -105,26 +105,25 @@ cc_binary( "descriptor_file_same_row_order.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) cc_binary( - name = "descriptor_file_to_mahalanobis_gfp", srcs = [ "descriptor_file_to_mahalanobis_gfp.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", "//Foundational/histogram:iwhistogram", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", ], ) @@ -134,13 +133,12 @@ cc_binary( "diff_line_by_line.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], -) - +) cc_binary( name = "fingerprint_weights_to_atom_colours", @@ -152,7 +150,7 @@ cc_binary( "//Molecule_Lib:iwmfingerprint", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - ] + ], ) cc_binary( @@ -161,11 +159,11 @@ cc_binary( "folded.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -176,11 +174,11 @@ cc_binary( "gfp_bit_filter.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -191,12 +189,12 @@ cc_binary( "gfp_difference_fingerprint.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Foundational/iwmisc:sparse_fp_creator", - "//Foundational/iw_tdt:iw_tdt", "//Utilities/GFP_Tools:gfp", ], ) @@ -204,16 +202,16 @@ cc_binary( cc_binary( name = "gfp_evaluate_clustering", srcs = [ - "gfp_evaluate_clustering.cc", "cluster_eval.cc", "cluster_eval.h", + "gfp_evaluate_clustering.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -224,11 +222,11 @@ cc_binary( "gfp_group_spread.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", "//Utilities/GFP_Tools:smiles_id_dist", ], @@ -240,11 +238,11 @@ cc_binary( "gfp_leader_opt_v2.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -255,11 +253,11 @@ cc_binary( "gfp_leader_standard_threaded.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp_standard", "//Utilities/GFP_Tools:smiles_id_dist", "@onetbb//:tbb", @@ -274,11 +272,11 @@ cc_binary( "leader_parallel.h", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", "@onetbb//:tbb", ], @@ -290,11 +288,11 @@ cc_binary( "gfp_naive_bayesian_multiclass.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -305,11 +303,11 @@ cc_binary( "gfp_nearneighbours_threaded.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -320,11 +318,11 @@ cc_binary( "gfp_proximity_descriptors.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -370,11 +368,11 @@ cc_binary( "gfp_spread_threaded.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", "//Utilities/GFP_Tools:spread", ], @@ -386,12 +384,12 @@ cc_binary( "gfp_test_train_split.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", "//Foundational/histogram:iwhistogram", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", ], ) @@ -401,12 +399,12 @@ cc_binary( "gfp_vector_differences.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Foundational/iwmisc:sparse_fp_creator", - "//Foundational/iw_tdt:iw_tdt", "//Utilities/GFP_Tools:gfp", ], ) @@ -417,11 +415,11 @@ cc_binary( "nn_identify_active_outliers.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", ], ) @@ -432,16 +430,16 @@ cc_binary( "sgefa.c", "sgesl.c", ], + linkopts = [ + "-lblas", + ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", "@local_f2c//:f2c", ], - linkopts = [ - "-lblas", - ], ) cc_binary( @@ -467,7 +465,7 @@ cc_binary( "//Foundational/cmdline:iwcmdline", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - ] + ], ) cc_binary( @@ -476,10 +474,10 @@ cc_binary( "rocs_rpt2nn.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", "//Utilities/GFP_Tools:smiles_id_dist", ], @@ -488,7 +486,10 @@ cc_binary( cc_binary( name = "selimsteg_build", srcs = [ - "selimsteg_build.cc", + "selimsteg_build.cc", + ], + tags = [ + "berkeleydb", ], deps = [ "//Foundational/cmdline:iwcmdline", @@ -496,9 +497,6 @@ cc_binary( "//Molecule_Lib:moleculeio", "@berkeleydb", ], - tags = [ - "berkeleydb", - ], ) cc_binary( @@ -520,9 +518,9 @@ cc_binary( "zero_pad.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) diff --git a/src/Obsolete/Descriptor_Similarity/BUILD b/src/Obsolete/Descriptor_Similarity/BUILD index 5534a276..15ebd688 100644 --- a/src/Obsolete/Descriptor_Similarity/BUILD +++ b/src/Obsolete/Descriptor_Similarity/BUILD @@ -4,60 +4,60 @@ local_install( name = "install", srcs = [ ":descriptor_file_to_distance_matrix", - ] + ], ) cc_binary( name = "descriptor_similarity", srcs = [ + "_iwdescriptors_float.cc", "descriptor_similarity.cc", "determine_distance_type.cc", "iwdescriptor.cc", "iwdescriptor.h", "set_of_descriptors.h", - "_iwdescriptors_float.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) cc_binary( name = "descriptor_similarity_erg", srcs = [ + "_iwdescriptors_float.cc", "descriptor_similarity_erg.cc", "determine_distance_type.cc", "iwdescriptor.cc", "iwdescriptor.h", "set_of_descriptors.h", - "_iwdescriptors_float.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) cc_binary( name = "descriptor_file_to_distance_matrix", srcs = [ + "_iwdescriptors_float.cc", "descriptor_file_to_distance_matrix.cc", "determine_distance_type.cc", "iwdescriptor.cc", "iwdescriptor.h", "set_of_descriptors.h", - "_iwdescriptors_float.cc", ], deps = [ - "//Utilities/Distance_Matrix:distance_matrix_base", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", + "//Utilities/Distance_Matrix:distance_matrix_base", ], ) diff --git a/src/Utilities/Distance_Matrix/BUILD b/src/Utilities/Distance_Matrix/BUILD index f851ba3d..347b8ed3 100644 --- a/src/Utilities/Distance_Matrix/BUILD +++ b/src/Utilities/Distance_Matrix/BUILD @@ -21,10 +21,10 @@ cc_binary( ], deps = [ ":distance_matrix_base", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -97,6 +97,7 @@ cc_binary( "//Foundational/iwmisc", ], ) + cc_binary( name = "distance_matrix_simple_cluster", srcs = [ @@ -106,10 +107,10 @@ cc_binary( ], deps = [ ":distance_matrix_base", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -120,10 +121,10 @@ cc_binary( ], deps = [ ":distance_matrix_base", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) diff --git a/src/Utilities/GFP_Knn/BUILD b/src/Utilities/GFP_Knn/BUILD index 27892486..5c136706 100644 --- a/src/Utilities/GFP_Knn/BUILD +++ b/src/Utilities/GFP_Knn/BUILD @@ -1,4 +1,3 @@ -load("@rules_proto//proto:defs.bzl", "proto_library") load("//build_deps:install.bzl", "local_install") local_install( @@ -18,11 +17,11 @@ cc_binary( deps = [ ":nn_specification", ":nn_support", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp", ], ) @@ -36,11 +35,11 @@ cc_binary( ":extract_from_tdt_form", ":iwpvalue", ":nn_support", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/Distance_Matrix:distance_matrix_base", "//Utilities/GFP_Tools:bsquared", "//Utilities/GFP_Tools:gfp", @@ -54,10 +53,10 @@ cc_binary( ], deps = [ ":iwpvalue", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -70,16 +69,16 @@ cc_library( "extract_from_tdt_form.h", ], deps = [ - "//Foundational/iwstring:iwstring", + "//Foundational/iwstring", ], ) cc_library( name = "iwpvalue", srcs = [ - "iwpvalue.cc", "dq1da.c", "idamax.c", + "iwpvalue.cc", "machcon.c", "uni.c", "xerror.c", @@ -102,32 +101,32 @@ cc_library( ], deps = [ ":nn_support", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", ], ) cc_library( name = "nn_support", srcs = [ - "nn_stuff.cc", "nn_specification.cc", + "nn_stuff.cc", "prediction_weight_function.cc", ], hdrs = [ - "nn_results_.h", "nn_results.h", + "nn_results_.h", "nn_specification.h", "nn_stuff.h", "prediction_weight_function.h", ], deps = [ ":extract_from_tdt_form", - "//Foundational/iwbits:iwbits", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwbits", + "//Foundational/iwmisc", "//Utilities/Distance_Matrix:distance_matrix_base", "//Utilities/GFP_Tools:gfp", ], diff --git a/src/Utilities/GFP_Tools/BUILD b/src/Utilities/GFP_Tools/BUILD index 7de7bc45..f93418c0 100644 --- a/src/Utilities/GFP_Tools/BUILD +++ b/src/Utilities/GFP_Tools/BUILD @@ -1,9 +1,8 @@ -load("@rules_proto//proto:defs.bzl", "proto_library") -load("//build_deps:install.bzl", "local_install") load("@com_google_protobuf//:protobuf.bzl", "py_proto_library") # load("@rules_proto_grpc_cpp//:defs.bzl", "cpp_grpc_compile") - +load("@rules_proto//proto:defs.bzl", "proto_library") +load("//build_deps:install.bzl", "local_install") local_install( name = "install", @@ -19,7 +18,6 @@ local_install( ":gfp_iterative_expansion", ":gfp_leader", ":gfp_leader_standard", - ":gfp_standalone", ":gfp_leader_tbb", ":gfp_lnearneighbours", ":gfp_lnearneighbours_standard", @@ -36,6 +34,7 @@ local_install( ":gfp_spread_buckets", ":gfp_spread_omp", ":gfp_spread_standard", + ":gfp_standalone", ":gfp_svmfp_score", ":gfp_svmfp_score_tbb", ":gfp_to_descriptors", @@ -43,10 +42,10 @@ local_install( ":gfp_to_svm_lite.v2", ":iwstats", ":marvin2gfp", + ":nn2csv", ":nn_leader_and_jp", ":nn_merge", ":nn_merge_from_smiles", - ":nn2csv", ":nplotnn", ":parallel_nn_search_to_gfp_spread", ":random_fingerprint", @@ -144,7 +143,7 @@ cc_proto_library( name = "nn_request_cc_proto", deps = [ ":nn_request_proto", - ] + ], ) py_proto_library( @@ -258,11 +257,11 @@ cc_binary( "gfp_distance_filter_standard.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Utilities/GFP_Tools:gfp_standard", ], ) @@ -274,7 +273,7 @@ cc_binary( ], deps = [ ":gfp", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", "//Foundational/iw_tdt", @@ -441,29 +440,29 @@ cc_binary( ) cc_binary( - name = "gfp_server", - srcs = [ - "gfp_server.cc", - ], - deps = [ - "nn_request_cc_proto", - "//Foundational/cmdline:iwcmdline", - "//Foundational/data_source:iwstring_data_source", - "//Molecule_Lib:iwmfingerprint", - "//Molecule_Lib:iwmolecule", - "//Molecule_Lib:moleculeio", - "//Molecule_Tools:mpr", - "//Molecule_Tools:maccskeys_fn5_lib", - "//Utilities/GFP_Tools:gfp_standard", - "//Utilities/GFP_Tools:nearneighbours_cc_proto", - "@cppzmq//:cppzmq", - "@libzmq//:libzmq", - "@com_google_protobuf//:protobuf", - ], - tags = [ - "gfp_server", - "zeromq", - ], + name = "gfp_server", + srcs = [ + "gfp_server.cc", + ], + tags = [ + "gfp_server", + "zeromq", + ], + deps = [ + "nn_request_cc_proto", + "//Foundational/cmdline:iwcmdline", + "//Foundational/data_source:iwstring_data_source", + "//Molecule_Lib:iwmfingerprint", + "//Molecule_Lib:iwmolecule", + "//Molecule_Lib:moleculeio", + "//Molecule_Tools:maccskeys_fn5_lib", + "//Molecule_Tools:mpr", + "//Utilities/GFP_Tools:gfp_standard", + "//Utilities/GFP_Tools:nearneighbours_cc_proto", + "@com_google_protobuf//:protobuf", + "@cppzmq", + "@libzmq", + ], ) # cc_binary( @@ -746,12 +745,12 @@ cc_binary( ], deps = [ ":gfp_bit_subset", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Foundational/iwmisc:normalisation", - "//Foundational/iw_tdt:iw_tdt", "//Utilities/GFP_Tools:gfp", ], ) @@ -769,12 +768,12 @@ cc_binary( ], deps = [ "gfp_bit_subset", - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", "//Foundational/iwmisc:normalisation", - "//Foundational/iw_tdt:iw_tdt", "//Utilities/GFP_Tools:gfp", "@onetbb//:tbb", ], @@ -865,12 +864,12 @@ cc_binary( "nn_merge_from_smiles.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", - "//Foundational/iw_tdt:iw_tdt", + "//Foundational/iw_tdt", + "//Foundational/iwmisc", + "//Foundational/iwqsort", "//Utilities/GFP_Tools:smiles_id_dist", ], ) @@ -938,10 +937,10 @@ cc_binary( "marvin2gfp.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", "//Foundational/iwmisc:sparse_fp_creator", ], ) @@ -990,11 +989,11 @@ cc_binary( "random_fingerprint.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwbits:iwbits", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwbits", + "//Foundational/iwmisc", ], ) diff --git a/src/Utilities/General/BUILD b/src/Utilities/General/BUILD index dc5b7bbb..5e7a29d9 100644 --- a/src/Utilities/General/BUILD +++ b/src/Utilities/General/BUILD @@ -1,10 +1,11 @@ -load("@rules_proto//proto:defs.bzl", "proto_library") load("@com_google_protobuf//:protobuf.bzl", "py_proto_library") +load("@rules_proto//proto:defs.bzl", "proto_library") load("//build_deps:install.bzl", "local_install") local_install( name = "install", srcs = [ + ":_inventory", ":average", ":bucketise", ":byte_offset_index", @@ -30,7 +31,6 @@ local_install( ":fetch_smiles_quick", ":grep_by_column", ":grid_overlap", - ":_inventory", ":isolation_forest", ":iwcut", ":iwsplit", @@ -40,10 +40,10 @@ local_install( ":mispredicted", ":model_average", ":nextdir", + ":nn_single_linkage", ":normalise", ":notenoughvariance", ":numeric_differences", - ":nn_single_linkage", ":ppv", ":random_column_order", ":random_records", @@ -181,10 +181,10 @@ cc_binary( ], deps = [ "//Foundational/accumulator", - "//Foundational/cmdline_v2:cmdline_v2", + "//Foundational/cmdline_v2", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwmisc", + "//Foundational/iwqsort", ], ) @@ -347,8 +347,8 @@ cc_binary( "//Foundational/data_source:iwtfdata_record", "//Foundational/iwstring", "//Molecule_Tools:dicer_fragments_cc_proto", - "@com_google_absl//absl/log:initialize", "@com_google_absl//absl/container:flat_hash_map", + "@com_google_absl//absl/log:initialize", ], ) @@ -464,10 +464,10 @@ cc_binary( "grep_by_column.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -492,10 +492,10 @@ cc_binary( "inventory.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -505,11 +505,11 @@ cc_binary( "exon_correlated.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwmisc", + "//Foundational/iwqsort", ], ) @@ -525,11 +525,11 @@ cc_binary( "-lgomp", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwbits:iwbits", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwbits", + "//Foundational/iwmisc", ], ) @@ -579,10 +579,10 @@ cc_binary( "just_columns_with_same_sign.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -632,11 +632,11 @@ cc_binary( "nextdir.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwmisc", + "//Foundational/iwqsort", ], ) @@ -646,10 +646,10 @@ cc_binary( "nn_single_linkage.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -687,10 +687,10 @@ cc_binary( "numeric_differences.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) @@ -700,12 +700,12 @@ cc_binary( "ppv.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", + "//Foundational/iwmisc", "//Foundational/iwmisc:activity_from_file", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwqsort", ], ) @@ -742,11 +742,11 @@ cc_binary( "rmsigma.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwmisc", + "//Foundational/iwqsort", ], ) @@ -782,11 +782,11 @@ cc_binary( "spearman_rank.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwmisc", + "//Foundational/iwqsort", ], ) @@ -824,11 +824,11 @@ cc_binary( "svmfp_error_vs_distance.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", + "//Foundational/iwmisc", "//Foundational/iwmisc:activity_from_file", - "//Foundational/iwmisc:iwmisc", ], ) @@ -882,12 +882,12 @@ cc_binary( "test_train_split_random.cc", ], deps = [ - "//Foundational/accumulator:accumulator", - "//Foundational/iwbits:iwbits", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", - "//Foundational/iwqsort:iwqsort", + "//Foundational/iwbits", + "//Foundational/iwmisc", + "//Foundational/iwqsort", ], ) @@ -897,10 +897,10 @@ cc_binary( "unbalanced_quotes.cc", ], deps = [ - "//Foundational/accumulator:accumulator", + "//Foundational/accumulator", "//Foundational/cmdline:iwcmdline", "//Foundational/data_source:iwstring_data_source", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", ], ) diff --git a/src/Vendor/BUILD b/src/Vendor/BUILD index 913f5662..93386ad6 100644 --- a/src/Vendor/BUILD +++ b/src/Vendor/BUILD @@ -1,4 +1,3 @@ -load("@rules_proto//proto:defs.bzl", "proto_library") load("//build_deps:install.bzl", "local_install") local_install( @@ -26,23 +25,22 @@ cc_binary( ], ) - cc_binary( name = "iwclogp", srcs = [ - "iwclogp.cc", "biobyte_stuff.c", + "iwclogp.cc", ], tags = [ "vendor", ], deps = [ - "@biobyte//:biobyte", "//Foundational/cmdline:iwcmdline", - "//Foundational/iwmisc:iwmisc", + "//Foundational/iwmisc", "//Foundational/iwmisc:sparse_fp_creator", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", + "@biobyte", ], ) @@ -58,20 +56,19 @@ cc_binary( ], ) -cc_binary( +cc_binary( name = "rcorina", srcs = [ "rcorina.cc", ], + tags = [ + "vendor", + ], deps = [ "//Foundational/cmdline:iwcmdline", - "//Foundational/string_data_source:string_data_source", + "//Foundational/string_data_source", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - "@corina//:corina", - ], - tags = [ - "vendor", + "@corina", ], ) - diff --git a/src/hello_world/BUILD b/src/hello_world/BUILD deleted file mode 100644 index 5a26b838..00000000 --- a/src/hello_world/BUILD +++ /dev/null @@ -1,8 +0,0 @@ -cc_binary( - name = "hello_world", - srcs = [ - "hello_world.cc", - ], - deps = [ - ], -) diff --git a/src/hello_world/hello_world.cc b/src/hello_world/hello_world.cc deleted file mode 100644 index 63f2a911..00000000 --- a/src/hello_world/hello_world.cc +++ /dev/null @@ -1,6 +0,0 @@ -#include - -int -main() { - std::cout << "Hello world\n"; -} diff --git a/src/julia/BUILD b/src/julia/BUILD index 8059b5dc..c34b9d87 100644 --- a/src/julia/BUILD +++ b/src/julia/BUILD @@ -1,106 +1,104 @@ -cc_library ( +cc_library( name = "lillymol_julia", srcs = [ "lillymol.cc", ], + tags = [ + "julia", + ], deps = [ ":resizable_array_holder", "//Molecule_Lib:iwmolecule", - "//Molecule_Lib:ring_data", - "//Molecule_Lib:moleculeio", "//Molecule_Lib:iwreaction", - "//Molecule_Tools:xlogp_lib", + "//Molecule_Lib:moleculeio", + "//Molecule_Lib:ring_data", "//Molecule_Tools:alogp_lib", + "//Molecule_Tools:xlogp_lib", "@com_gitlab_libeigen_eigen//:eigen", - "@libcxxwrap//:libcxxwrap", - "@julia//:julia", - ], - tags = [ - "julia", + "@julia", + "@libcxxwrap", ], ) -cc_library ( +cc_library( name = "lillymol_substructure", srcs = [ "lillymol_substructure.cc", ], + tags = [ + "julia", + ], deps = [ ":resizable_array_holder", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - "@libcxxwrap//:libcxxwrap", - "@julia//:julia", - ], - tags = [ - "julia", + "@julia", + "@libcxxwrap", ], ) - cc_library( name = "bag_julia", srcs = [ "bag.cc", ], - deps = [ - "@libcxxwrap//:libcxxwrap", - "@julia//:julia", - ], tags = [ "julia", ], + deps = [ + "@julia", + "@libcxxwrap", + ], ) cc_shared_library( name = "lillymol_shared", - deps = [ - ":lillymol_julia", - ], dynamic_deps = [ ], shared_lib_name = "lillymol_julia.so", tags = [ "julia", ], + deps = [ + ":lillymol_julia", + ], ) cc_shared_library( name = "lillymol_substructure_shared", - deps = [ - ":lillymol_julia", - ], dynamic_deps = [ ], shared_lib_name = "lillymol_substructure_julia.so", tags = [ "julia", ], + deps = [ + ":lillymol_julia", + ], ) - cc_shared_library( name = "box_shared", - deps = [ - ":bag_julia", - ], dynamic_deps = [ ], shared_lib_name = "bag_julia.so", tags = [ "julia", ], + deps = [ + ":bag_julia", + ], ) -cc_library ( +cc_library( name = "resizable_array_holder", hdrs = [ - "resizable_array_holder.h" - ], - deps = [ - "//Foundational/iwaray", + "resizable_array_holder.h", ], tags = [ "julia", ], + deps = [ + "//Foundational/iwaray", + ], ) diff --git a/src/pybind/BUILD b/src/pybind/BUILD index 620791bc..ed64cdd5 100644 --- a/src/pybind/BUILD +++ b/src/pybind/BUILD @@ -1,37 +1,36 @@ - -package(default_visibility = ["//visibility:public"]) - # load("@rules_python_pytest//python_pytest:defs.bzl", "py_pytest_test") load("@rules_python//python:py_test.bzl", "py_test") +package(default_visibility = ["//visibility:public"]) + cc_library( name = "lillymol_pybind", srcs = [ "lillymol_pybind.cc", ], + copts = [ + "-save-temps", + ], deps = [ ":molecule", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", "//Molecule_Tools:alogp_lib", "//Molecule_Tools:xlogp_lib", -# "@com_google_pybind11_protobuf", + # "@com_google_pybind11_protobuf", "@pybind11", "@python", ], - copts = [ - "-save-temps", - ], ) cc_shared_library( name = "lillymol", + shared_lib_name = "lillymol.so", deps = [ ":lillymol_pybind", "//Molecule_Lib:iwmolecule", "//Molecule_Lib:moleculeio", - ], - shared_lib_name = "lillymol.so", + ], ) cc_library( @@ -41,10 +40,10 @@ cc_library( ], deps = [ ":molecule", - "//Molecule_Lib:iwmfingerprint", "//Molecule_Lib:atom_pair_fingerprint", - "//Molecule_Lib:linear_fingerprint", + "//Molecule_Lib:iwmfingerprint", "//Molecule_Lib:iwmolecule", + "//Molecule_Lib:linear_fingerprint", "//Molecule_Lib:moleculeio", "//Molecule_Tools:ec_fingerprint_lib", "@pybind11", @@ -54,10 +53,10 @@ cc_library( cc_shared_library( name = "lillymol_fingerprint", + shared_lib_name = "lillymol_fingerprint.so", deps = [ ":lillymol_pybind_fingerprints", ], - shared_lib_name = "lillymol_fingerprint.so" ) cc_library( @@ -76,10 +75,10 @@ cc_library( cc_shared_library( name = "lillymol_query", + shared_lib_name = "lillymol_query.so", deps = [ ":lillymol_pybind_substructure_query", ], - shared_lib_name = "lillymol_query.so", ) cc_library( @@ -96,11 +95,11 @@ cc_library( ) cc_shared_library( - name = "lillymol_standardise", - deps = [ - ":lillymol_pybind_chemical_standardisation", - ], - shared_lib_name = "lillymol_standardise.so", + name = "lillymol_standardise", + shared_lib_name = "lillymol_standardise.so", + deps = [ + ":lillymol_pybind_chemical_standardisation", + ], ) cc_library( @@ -117,11 +116,11 @@ cc_library( ) cc_shared_library( - name = "lillymol_set_of_atoms", - deps = [ - ":lillymol_pybind_set_of_atoms", - ], - shared_lib_name = "lillymol_set_of_atoms.so", + name = "lillymol_set_of_atoms", + shared_lib_name = "lillymol_set_of_atoms.so", + deps = [ + ":lillymol_pybind_set_of_atoms", + ], ) cc_library( @@ -138,11 +137,11 @@ cc_library( ) cc_shared_library( - name = "lillymol_ring", - deps = [ - ":lillymol_pybind_ring", - ], - shared_lib_name = "lillymol_ring.so", + name = "lillymol_ring", + shared_lib_name = "lillymol_ring.so", + deps = [ + ":lillymol_pybind_ring", + ], ) cc_library( @@ -159,11 +158,11 @@ cc_library( ) cc_shared_library( - name = "lillymol_atom", - deps = [ - ":lillymol_pybind_atom", - ], - shared_lib_name = "lillymol_atom.so", + name = "lillymol_atom", + shared_lib_name = "lillymol_atom.so", + deps = [ + ":lillymol_pybind_atom", + ], ) cc_library( @@ -180,11 +179,11 @@ cc_library( ) cc_shared_library( - name = "lillymol_bond", - deps = [ - ":lillymol_pybind_bond", - ], - shared_lib_name = "lillymol_bond.so", + name = "lillymol_bond", + shared_lib_name = "lillymol_bond.so", + deps = [ + ":lillymol_pybind_bond", + ], ) #cc_library( @@ -222,11 +221,11 @@ cc_library( ) cc_shared_library( - name = "lillymol_io", - deps = [ - ":lillymol_pybind_io", - ], - shared_lib_name = "lillymol_io.so", + name = "lillymol_io", + shared_lib_name = "lillymol_io.so", + deps = [ + ":lillymol_pybind_io", + ], ) cc_library( @@ -244,11 +243,11 @@ cc_library( ) cc_shared_library( - name = "molecule_shared", - deps = [ - ":molecule", - ], - shared_lib_name = "lillymol_molecule_misc.so", + name = "molecule_shared", + shared_lib_name = "lillymol_molecule_misc.so", + deps = [ + ":molecule", + ], ) cc_library( @@ -266,18 +265,18 @@ cc_library( ) cc_shared_library( - name = "lillymol_reaction", - deps = [ - ":lillymol_pybind_reaction", - ], - shared_lib_name = "lillymol_reaction.so", + name = "lillymol_reaction", + shared_lib_name = "lillymol_reaction.so", + deps = [ + ":lillymol_pybind_reaction", + ], ) cc_library( name = "tsubstructure", srcs = [ + "lillymol_pybind_tsubstructure.cc", "tsubstructure.cc", - "lillymol_pybind_tsubstructure.cc", ], hdrs = [ "tsubstructure.h", @@ -286,16 +285,17 @@ cc_library( "//Molecule_Lib:iwmolecule", "//Molecule_Lib:iwreaction", "//Molecule_Lib:moleculeio", - "@pybind11", + "@pybind11", "@python", - ], + ], ) -cc_shared_library( - name = "tsubstructure_shared", - deps = [ - ":tsubstructure", - ], - shared_lib_name = "lillymol_tsubstructure.so", + +cc_shared_library( + name = "tsubstructure_shared", + shared_lib_name = "lillymol_tsubstructure.so", + deps = [ + ":tsubstructure", + ], ) cc_library( @@ -316,17 +316,17 @@ cc_library( "//Molecule_Tools_Bdb:selimsteg", "//Molecule_Tools_Bdb:structure_database_shared", "@berkeleydbshared//:berkeleydb", - "@pybind11", + "@pybind11", "@python", ], ) cc_shared_library( name = "lillymol_tools_shared", + shared_lib_name = "lillymol_tools.so", deps = [ ":lillymol_tools", ], - shared_lib_name = "lillymol_tools.so", ) # Cannot figure out how to make this work. TODO:ianwatson @@ -338,4 +338,3 @@ cc_shared_library( # ":lillymol_pybind", # ], #) - diff --git a/src/xgboost/BUILD b/src/xgboost/BUILD index 724898ca..9673084d 100644 --- a/src/xgboost/BUILD +++ b/src/xgboost/BUILD @@ -1,12 +1,13 @@ -load("@rules_proto//proto:defs.bzl", "proto_library") load("@com_google_protobuf//:protobuf.bzl", "py_proto_library") +load("@rules_proto//proto:defs.bzl", "proto_library") +load("@rules_proto_grpc_go//:defs.bzl", "go_proto_compile", "go_proto_library") load("//build_deps:install.bzl", "local_install") local_install( name = "install", srcs = [ ":xgboost_model_evaluate", - ] + ], ) proto_library( @@ -21,15 +22,15 @@ proto_library( cc_proto_library( name = "xgboost_model_cc_proto", - deps = [ - ":xgboost_model_proto", - ], tags = [ "xgboost", ], visibility = [ "//visibility:public", ], + deps = [ + ":xgboost_model_proto", + ], ) py_proto_library( @@ -42,6 +43,22 @@ py_proto_library( ], ) +#go_proto_compile( +# name = "xgboost_model_go_proto", +# protos = [ +# ":xgboost_model_proto", +# ], +#) + +go_proto_library( + name = "xgboost_model_go_proto", + importpath = "xgboost", + protos = [ + ":xgboost_model_proto", + ], + visibility = ["//visibility:public"], +) + proto_library( name = "random_forest_model_proto", srcs = [ @@ -53,7 +70,7 @@ cc_proto_library( name = "random_forest_model_cc_proto", deps = [ "random_forest_model_proto", - ] + ], ) py_proto_library( @@ -68,15 +85,15 @@ cc_binary( srcs = [ "xgboost_model_evaluate.cc", ], + tags = [ + "xgboost", + ], deps = [ ":xgboost_model_cc_proto", - "//Foundational/cmdline_v2:cmdline_v2", + "//Foundational/cmdline_v2", "//Foundational/data_source:iwstring_data_source", "//Foundational/iwmisc", - "@xgboost//:xgboost", - "@dlmc//:dlmc", - ], - tags = [ - "xgboost", + "@dlmc", + "@xgboost", ], )