GNU logs - #77394, boring messages

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This patch series updates rdkit and some of its dependencies.
The build now depends on the CMake files of the NumPy extension of
Boost.Python and rdkit depends on python-numpy anyway, so I added a package
variant of boost with it enabled.

David Elsing (5):
  gnu: inchi: Update to 1.07.3.
  gnu: yaehmop: Update to 2024.03.1.
  gnu: Add boost-with-numpy.
  gnu: Add pubchem-align3d.
  gnu: rdkit: Update to 2024.09.6.

 gnu/packages/boost.scm                        |   8 +
 gnu/packages/chemistry.scm                    | 186 +++++++++++-------
 ...rdkit-unbundle-external-dependencies.patch | 183 +++++++++++++++--
 3 files changed, 291 insertions(+), 86 deletions(-)

-- 
2.48.1

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To: David Elsing <david.elsing@HIDDEN>
Subject: bug#77394: Acknowledgement ([PATCH 0/5] Update rdkit to 2024.09.6)
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Subject: [bug#77394] [PATCH 1/5] gnu: inchi: Update to 1.07.3.
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* gnu/packages/chemistry.scm (inchi): Update to 1.07.3.
[source]: Switch to git-fetch.
[arguments]: Use gexps.  Adjust chdir-to-build-directory, build and install
phases. Enable parallel building.
[native-inputs]: Remove input label.
[license]: Change to Expat license.
---
 gnu/packages/chemistry.scm | 122 ++++++++++++++++++-------------------
 1 file changed, 59 insertions(+), 63 deletions(-)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..df5048d22e 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -146,68 +146,66 @@ (define-public inchi
   (package
     (name "inchi")
     ;; Update the inchi-doc native input when updating inchi.
-    (version "1.06")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://www.inchi-trust.org/download/"
-                                  (string-join (string-split version #\.) "")
-                                  "/INCHI-1-SRC.zip"))
-              (sha256
-               (base32
-                "1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
-              (file-name (string-append name "-" version ".zip"))))
+    (version "1.07.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/IUPAC-InChI/InChI")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0r32f6i5d8ir96ic3nvqb5lywxrznwrkk6hnz1q0a4bgsw5pmk0n"))
+       (modules '((guix build utils)))
+       (snippet '(delete-file-recursively "INCHI-1-BIN"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f ; no check target
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure) ; no configure script
-         (add-before 'build 'chdir-to-build-directory
-           (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
-         (add-after 'build 'build-library
-           (lambda _
-             (chdir "../../../INCHI_API/libinchi/gcc")
-             (invoke "make")))
-         (replace 'install
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (doc (string-append out "/share/doc/inchi"))
-                    (include-dir (string-append out "/include/inchi"))
-                    (lib (string-append out "/lib/inchi"))
-                    (inchi-doc (assoc-ref inputs "inchi-doc"))
-                    (unzip (search-input-file inputs "/bin/unzip")))
-               (chdir "../../..")
-               ;; Install binary.
-               (with-directory-excursion "INCHI_EXE/bin/Linux"
-                 (rename-file "inchi-1" "inchi")
-                 (install-file "inchi" bin))
-               ;; Install libraries.
-               (with-directory-excursion "INCHI_API/bin/Linux"
-                 (for-each (lambda (file)
-                             (install-file file lib))
-                           (find-files "." "libinchi\\.so\\.1\\.*")))
-               ;; Install header files.
-               (with-directory-excursion "INCHI_BASE/src"
-                 (for-each (lambda (file)
-                             (install-file file include-dir))
-                           (find-files "." "\\.h$")))
-               ;; Install documentation.
-               (mkdir-p doc)
-               (invoke unzip "-j" "-d" doc inchi-doc)
-               #t))))))
-    (native-inputs
-     `(("unzip" ,unzip)
-       ("inchi-doc"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append "http://www.inchi-trust.org/download/"
-                                  (string-join (string-split version #\.) "")
-                                  "/INCHI-1-DOC.zip"))
-           (sha256
-            (base32
-             "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
-           (file-name (string-append name "-" version ".zip"))))))
+     (list
+      #:tests? #f ; no check target
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure) ; no configure script
+          (add-after 'unpack 'chdir-to-build-directory
+            (lambda _ (chdir "INCHI-1-SRC/INCHI_EXE/inchi-1/gcc")))
+          (add-after 'build 'build-library
+            (lambda* (#:key parallel-build? #:allow-other-keys)
+              (chdir "../../../INCHI_API/libinchi/gcc")
+              (invoke "make" "-j" (if parallel-build?
+                                      (number->string (parallel-job-count))
+                                      "1"))))
+          (replace 'install
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let* ((bin (string-append #$output "/bin"))
+                     (doc (string-append #$output "/share/doc/inchi"))
+                     (include-dir (string-append #$output "/include/inchi"))
+                     (lib (string-append #$output "/lib/inchi")))
+                (chdir "../../..")
+                ;; Install binary.
+                (with-directory-excursion "INCHI_EXE/bin/Linux"
+                  (rename-file "inchi-1" "inchi")
+                  (install-file "inchi" bin))
+                ;; Install library.
+                (with-directory-excursion "INCHI_API/bin/Linux"
+                  (let ((libname (basename
+                                  (car
+                                   (find-files "." "libinchi\\.so\\.1\\.*")))))
+                    (install-file libname lib)
+                    (with-directory-excursion lib
+                      (symlink libname "libinchi.so.1")
+                      (symlink "libinchi.so.1" "libinchi.so"))))
+                ;; Install header files.
+                (with-directory-excursion "INCHI_BASE/src"
+                  (for-each (lambda (file)
+                              (install-file file include-dir))
+                            (find-files "." "\\.h$")))
+                ;; Install documentation.
+                (with-directory-excursion "../INCHI-1-DOC"
+                  (for-each
+                   (lambda (file)
+                     (install-file file doc))
+                   (find-files "." "\\.pdf$")))))))))
+    (native-inputs (list unzip))
     (home-page "https://www.inchi-trust.org")
     (synopsis "Utility for manipulating machine-readable chemical structures")
     (description
@@ -216,9 +214,7 @@ (define-public inchi
 unique to the compound they describe and can encode absolute stereochemistry
 making chemicals and chemistry machine-readable and discoverable.  A simple
 analogy is that InChI is the bar-code for chemistry and chemical structures.")
-    (license (license:non-copyleft
-              "file://LICENCE"
-              "See LICENCE in the distribution."))))
+    (license license:expat)))
 
 (define-public libmsym
   (package
-- 
2.48.1

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* gnu/packages/chemistry.scm (yaehmop): Update to 2024.03.1.
---
 gnu/packages/chemistry.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index df5048d22e..36227916b6 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -813,7 +813,7 @@ (define-public coordgenlibs
 (define-public yaehmop
   (package
     (name "yaehmop")
-    (version "2023.03.1")
+    (version "2024.03.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -822,7 +822,7 @@ (define-public yaehmop
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "18xnxqn8i7vswy3iffapfh9q2iimpnd23ps45hn4xxbs6dqgzprb"))
+                "1wy38cfqfs203p1k3qqsizzlpvasldjcfxmlng54y5mxzw97n55f"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
2.48.1

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* gnu/packages/boost.scm (boost-with-numpy): New variable.
---
 gnu/packages/boost.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm
index 4f54c6b578..cd625e2cbb 100644
--- a/gnu/packages/boost.scm
+++ b/gnu/packages/boost.scm
@@ -50,6 +50,7 @@ (define-module (gnu packages boost)
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages mpi))
 
@@ -359,6 +360,13 @@ (define-public boost-for-mysql
        (delete "python-minimal-wrapper")))
     (properties '((hidden? . #t)))))
 
+(define-public boost-with-numpy
+  (package
+    (inherit boost)
+    (native-inputs
+     (modify-inputs (package-native-inputs boost)
+       (append python-numpy)))))
+
 (define-public boost-sync
   (let ((commit "e690de2d30e2f1649ff500c9a6f3539814994b1c")
         (version "1.55")
-- 
2.48.1

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* gnu/packages/chemistry.scm (pubchem-align3d): New variable.
---
 gnu/packages/chemistry.scm | 46 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 36227916b6..c1e0586534 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1066,6 +1066,52 @@ (define-public ringdecomposerlib
 other ring topology descriptions.")
     (license license:bsd-3)))
 
+(define-public pubchem-align3d
+  (let ((commit "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3")
+        (revision "0"))
+    (package
+      (name "pubchem-align3d")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ncbi/pubchem-align3d")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1nj1zz5nvn5h3dyj66zi11mmvmzpq3b8y51fld9bkxnsmk17h05m"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:tests? #f ; circular dependency with rdkit
+        #:phases
+        #~(modify-phases %standard-phases
+            (delete 'configure)
+            (replace 'build
+              (lambda _
+                (invoke "g++"
+                        "-o" "libpubchem-align3d.so"
+                        "-O2" "-g" "-fPIC" "-shared"
+                        "shape_functions1.cpp" "shape_functions2.cpp"
+                        "shape_neighbor.cpp")))
+            (replace 'install
+              (lambda _
+                (for-each
+                 (lambda (file)
+                   (install-file
+                    file
+                    (string-append #$output "/include/pubchem-align3d")))
+                 (find-files "." "\\.hpp"))
+                (install-file "libpubchem-align3d.so"
+                              (string-append #$output "/lib")))))))
+      (home-page "https://github.com/ncbi/pubchem-align3d")
+      (synopsis "C++ library for aligning small molecules")
+      (description "This is a generic C++ library that can be used to rapidly
+align two small molecules in 3D space, with shape - and optionally color -
+Tanimoto scoring.")
+      (license license:public-domain))))
+
 (define-public rdkit
   (package
     (name "rdkit")
-- 
2.48.1

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* gnu/packages/chemistry.scm (rdkit): Update to 2024.09.6.
[arguments]: Disable more failing tests.
[inputs]: Add pubchem-align3d.
[native-inputs]: Replace boost with boost-with-numpy. Add python-pytest.
* gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust patch.
---
 gnu/packages/chemistry.scm                    |  14 +-
 ...rdkit-unbundle-external-dependencies.patch | 183 ++++++++++++++++--
 2 files changed, 176 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index c1e0586534..66901a22a0 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1115,7 +1115,7 @@ (define-public pubchem-align3d
 (define-public rdkit
   (package
     (name "rdkit")
-    (version "2023.09.4")
+    (version "2024.09.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1126,7 +1126,7 @@ (define-public rdkit
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8"))
+                "0nagqy5c9b86ip8qr1rnvby235am1zyc4sqm0z7wphbb70cqazxg"))
               (patches
                (search-patches "rdkit-unbundle-external-dependencies.patch"))
               (modules '((guix build utils)))
@@ -1224,10 +1224,16 @@ (define-public rdkit
                             "graphmoltestPickler" "pyPartialCharges"
                             "substructLibraryTest" "pyFeatures"
                             "pythonTestDirML" "pythonTestDirChem"
+                            "pyRealValueVect" "pyDiscreteValueVect"
+                            "pickleTestsCatch"
                             ;; Catching Python exception fails
                             "pyRanker"
                             ;; Flaky test depending on floating point rounding
                             "testConrec"
+                            ;; Expensive test which may time out
+                            "pySynthonSpaceSearch"
+                            ;; Circular import
+                            "pythonSourceTests"
                             ) "|")
                          ")")))))))))
     (inputs
@@ -1238,18 +1244,20 @@ (define-public rdkit
            freetype
            inchi
            maeparser
+           pubchem-align3d
            python
            ringdecomposerlib
            sqlite
            yaehmop))
     (native-inputs
      (list bison
-           boost
+           boost-with-numpy
            catch2-3
            eigen
            flex
            freesasa
            pkg-config
+           python-pytest
            rapidjson
            tar))
     (propagated-inputs
diff --git a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
index e22ff57ee0..3e72f40504 100644
--- a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
+++ b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
@@ -3,10 +3,10 @@ They are packaged separately as rapidjson, avalon-toolkit, freesasa,
 ringdecomposerlib and yaehmop.
 
 diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt
-index 1673386a4..c3504e6f1 100644
+index 0c1e9a0de..c3504e6f1 100644
 --- a/Code/GraphMol/MolInterchange/CMakeLists.txt
 +++ b/Code/GraphMol/MolInterchange/CMakeLists.txt
-@@ -1,18 +1,3 @@
+@@ -1,26 +1,3 @@
 -
 -if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
 -    downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
@@ -15,8 +15,16 @@ index 1673386a4..c3504e6f1 100644
 -    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
 -      ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
 -      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
+-    # comment out a line which causes a compilation error on some platforms
+-    # (based on the change which has already been applied to the RapidJSON master branch, see
+-    # https://github.com/Tencent/rapidjson/blob/ab1842a2dae061284c0a62dca1cc6d5e7e37e346/include/rapidjson/document.h#L414)
+-    file(READ ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h RAPIDJSON_DOCUMENT_H)
+-    string(REGEX REPLACE
+-           "( *)(GenericStringRef& operator=\\(const GenericStringRef& rhs\\) { s = rhs\\.s. length = rhs\\.length. })" "\\1//\\2"
+-           RAPIDJSON_DOCUMENT_H "${RAPIDJSON_DOCUMENT_H}")
+-    file(WRITE ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h "${RAPIDJSON_DOCUMENT_H}")
 -else()
--  message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
+-    message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
 -endif()
 -
 -include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include)
@@ -26,7 +34,7 @@ index 1673386a4..c3504e6f1 100644
                Parser.cpp Writer.cpp
                LINK_LIBRARIES GraphMol)
 diff --git a/External/AvalonTools/AvalonTools.cpp b/External/AvalonTools/AvalonTools.cpp
-index e6c382123..d83d80668 100644
+index f4b37ba5c..e1b25aed1 100644
 --- a/External/AvalonTools/AvalonTools.cpp
 +++ b/External/AvalonTools/AvalonTools.cpp
 @@ -24,15 +24,15 @@
@@ -55,7 +63,7 @@ index e6c382123..d83d80668 100644
  extern int RunStruchk(struct reaccs_molecule_t **mpp,
                        struct data_line_t *data_list);
 diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLists.txt
-index 3e31195fc..314ba35b5 100644
+index 30203ecdf..4e2661d7e 100644
 --- a/External/AvalonTools/CMakeLists.txt
 +++ b/External/AvalonTools/CMakeLists.txt
 @@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
@@ -151,7 +159,7 @@ index 3e31195fc..314ba35b5 100644
  rdkit_headers(AvalonTools.h DEST GraphMol)
  rdkit_test(testAvalonLib1 test1.cpp
 diff --git a/External/AvalonTools/Wrap/pyAvalonTools.cpp b/External/AvalonTools/Wrap/pyAvalonTools.cpp
-index fb24c497e..31997bc0a 100644
+index 72c7a5ee2..e7ac609ae 100644
 --- a/External/AvalonTools/Wrap/pyAvalonTools.cpp
 +++ b/External/AvalonTools/Wrap/pyAvalonTools.cpp
 @@ -12,7 +12,7 @@
@@ -164,10 +172,10 @@ index fb24c497e..31997bc0a 100644
  
  namespace python = boost::python;
 diff --git a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt
-index 43dfbdc40..81165a143 100644
+index 8baadb618..81165a143 100644
 --- a/External/FreeSASA/CMakeLists.txt
 +++ b/External/FreeSASA/CMakeLists.txt
-@@ -2,88 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT)
+@@ -2,174 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT)
    return()
  endif(NOT RDK_BUILD_FREESASA_SUPPORT)
  
@@ -223,6 +231,85 @@ index 43dfbdc40..81165a143 100644
 -  set(freesasa_additional_exports ${CMAKE_CURRENT_SOURCE_DIR}/additional_exports.def)
 -  file(WRITE ${freesasa_additional_exports}
 -    "EXPORTS\n"
+-    "freesasa_calc_structure\n"
+-    "freesasa_calc_coord\n"
+-    "freesasa_calc_tree\n"
+-    "freesasa_result_classes\n"
+-    "freesasa_result_free\n"
+-    "freesasa_classifier_from_file\n"
+-    "freesasa_classifier_free\n"
+-    "freesasa_classifier_radius\n"
+-    "freesasa_classifier_class\n"
+-    "freesasa_classifier_class2str\n"
+-    "freesasa_classifier_name\n"
+-    "freesasa_selection_new\n"
+-    "freesasa_selection_free\n"
+-    "freesasa_selection_name\n"
+-    "freesasa_selection_command\n"
+-    "freesasa_selection_area\n"
+-    "freesasa_set_verbosity\n"
+-    "freesasa_get_verbosity\n"
+-    "freesasa_set_err_out\n"
+-    "freesasa_get_err_out\n"
+-    "freesasa_structure_new\n"
+-    "freesasa_structure_free\n"
+-    "freesasa_structure_from_pdb\n"
+-    "freesasa_structure_array\n"
+-    "freesasa_structure_add_atom\n"
+-    "freesasa_structure_add_atom_wopt\n"
+-    "freesasa_structure_get_chains\n"
+-    "freesasa_structure_chain_labels\n"
+-    "freesasa_structure_n\n"
+-    "freesasa_structure_n_residues\n"
+-    "freesasa_structure_n_chains\n"
+-    "freesasa_structure_radius\n"
+-    "freesasa_structure_set_radius\n"
+-    "freesasa_structure_atom_name\n"
+-    "freesasa_structure_atom_res_name\n"
+-    "freesasa_structure_atom_res_number\n"
+-    "freesasa_structure_atom_chain\n"
+-    "freesasa_structure_atom_symbol\n"
+-    "freesasa_structure_atom_radius\n"
+-    "freesasa_structure_atom_set_radius\n"
+-    "freesasa_structure_residue_name\n"
+-    "freesasa_structure_residue_number\n"
+-    "freesasa_structure_residue_chain\n"
+-    "freesasa_structure_model\n"
+-    "freesasa_structure_coord_array\n"
+-    "freesasa_structure_residue_atoms\n"
+-    "freesasa_structure_chain_atoms\n"
+-    "freesasa_structure_chain_residues\n"
+-    "freesasa_structure_classifier_name\n"
+-    "freesasa_tree_new\n"
+-    "freesasa_tree_init\n"
+-    "freesasa_tree_add_result\n"
+-    "freesasa_tree_join\n"
+-    "freesasa_tree_export\n"
+-    "freesasa_node_free\n"
+-    "freesasa_node_area\n"
+-    "freesasa_node_children\n"
+-    "freesasa_node_next\n"
+-    "freesasa_node_parent\n"
+-    "freesasa_node_type\n"
+-    "freesasa_node_name\n"
+-    "freesasa_node_classified_by\n"
+-    "freesasa_node_atom_is_polar\n"
+-    "freesasa_node_atom_is_mainchain\n"
+-    "freesasa_node_atom_radius\n"
+-    "freesasa_node_atom_pdb_line\n"
+-    "freesasa_node_residue_number\n"
+-    "freesasa_node_residue_n_atoms\n"
+-    "freesasa_node_residue_reference\n"
+-    "freesasa_node_chain_n_residues\n"
+-    "freesasa_node_structure_n_chains\n"
+-    "freesasa_node_structure_n_atoms\n"
+-    "freesasa_node_structure_chain_labels\n"
+-    "freesasa_node_structure_model\n"
+-    "freesasa_node_structure_result\n"
+-    "freesasa_node_structure_selections\n"
+-    "freesasa_node_structure_add_selection\n"
+-    "freesasa_node_result_parameters\n"
+-    "freesasa_select_area\n"
 -    "freesasa_default_parameters DATA\n"
 -    "freesasa_protor_classifier DATA\n"
 -    "freesasa_naccess_classifier DATA\n"
@@ -236,8 +323,15 @@ index 43dfbdc40..81165a143 100644
 -
 -set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
 -file(READ ${freesasa_h} freesasa_h_data)
--string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
--string(REGEX REPLACE "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data "${freesasa_h_data}")
+-if (NOT freesasa_h_data MATCHES "RDGeneral/export")
+-  string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
+-endif()
+-if (MSVC)
+-  set (RDKIT_FREESASA_CLIB_EXPORT "RDKIT_FREESASA_CLIB_EXPORT ")
+-else()
+-  set (RDKIT_FREESASA_CLIB_EXPORT "")
+-endif()
+-string(REGEX REPLACE "(RDKIT_FREESASA_CLIB_EXPORT )?(extern const)" "${RDKIT_FREESASA_CLIB_EXPORT}\\2" freesasa_h_data "${freesasa_h_data}")
 -file(WRITE ${freesasa_h} "${freesasa_h_data}")
 -
 -add_definitions(-DUSE_THREADS=0)
@@ -258,7 +352,7 @@ index 43dfbdc40..81165a143 100644
  
  rdkit_headers(RDFreeSASA.h DEST GraphMol)
 diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeLists.txt
-index 08dd1fe04..66ecd5834 100644
+index 08dd1fe04..068435506 100644
 --- a/External/RingFamilies/CMakeLists.txt
 +++ b/External/RingFamilies/CMakeLists.txt
 @@ -1,47 +1,7 @@
@@ -314,7 +408,7 @@ diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp
 new file mode 100644
 index 000000000..e69de29bb
 diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
-index f1027b3bd..8bee2f910 100644
+index c8daef9a5..01eaddac6 100644
 --- a/External/YAeHMOP/CMakeLists.txt
 +++ b/External/YAeHMOP/CMakeLists.txt
 @@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT)
@@ -326,8 +420,8 @@ index f1027b3bd..8bee2f910 100644
 -endif()
 -
 -if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h")
--    set(RELEASE_NO "2023.03.1")
--    set(MD5 "e6450f13e02c54d024233b993c3c7ff6")
+-    set(RELEASE_NO "2024.03.1")
+-    set(MD5 "ebbddca4f79ab71544cb1fef9a7eca8a")
 -    downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz"
 -          "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5})
 -    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
@@ -372,11 +466,11 @@ index f1027b3bd..8bee2f910 100644
  rdkit_headers(EHTTools.h DEST GraphMol)
  rdkit_catch_test(testEHTLib1 test1.cpp
 diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp
-index 7a229f51f..71033dc5c 100644
+index 021c548f1..43afdca57 100644
 --- a/External/YAeHMOP/EHTTools.cpp
 +++ b/External/YAeHMOP/EHTTools.cpp
-@@ -10,7 +10,7 @@
- #include <fstream>
+@@ -13,7 +13,7 @@
+ #include <filesystem>
  
  extern "C" {
 -#include <yaehmop/tightbind/bind.h>
@@ -384,7 +478,7 @@ index 7a229f51f..71033dc5c 100644
  }
  
  namespace RDKit {
-@@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId,
+@@ -211,4 +211,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId,
  }
  
  }  // end of namespace EHTTools
@@ -404,3 +498,56 @@ index 759a9f360..114d24532 100644
                         
  add_pytest(pyEHTTools
           ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)
+diff --git a/External/pubchem_shape/CMakeLists.txt b/External/pubchem_shape/CMakeLists.txt
+index a0f16eadb..463a9e31e 100644
+--- a/External/pubchem_shape/CMakeLists.txt
++++ b/External/pubchem_shape/CMakeLists.txt
+@@ -2,47 +2,8 @@ if(NOT RDK_BUILD_PUBCHEMSHAPE_SUPPORT)
+   return()
+ endif()
+ 
+-if(NOT DEFINED PUBCHEMSHAPE_DIR)
+-  set(PUBCHEMSHAPE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/pubchem-align3d")
+-  set(fileToCheck "${PUBCHEMSHAPE_DIR}/shape_functions1.cpp")
+-  set(needDownload "TRUE")
+-  if(EXISTS "${fileToCheck}")
+-    set(needDownload "FALSE")
+-  endif()
+-else()
+-  set(needDownload "FALSE")
+-endif()
+-
+-if(needDownload)
+-  set(PUBCHEM_COMMIT_SHA daefab3)
+-  if(NOT DEFINED PUBCHEMSHAPE_URL)
+-    set(PUBCHEMSHAPE_URL "https://github.com/ncbi/pubchem-align3d/archive/${PUBCHEM_COMMIT_SHA}.tar.gz")
+-  endif()
+-  if(NOT DEFINED PUBCHEMSHAPE_MD5SUM)
+-    set(PUBCHEMSHAPE_MD5SUM "a78a6273851709083ac3803d62cb5ae6")
+-  endif()
+-  if(NOT DEFINED PUBCHEMSHAPE_BASE)
+-    string(REGEX REPLACE "^.*/" "" PUBCHEMSHAPE_BASE "${PUBCHEMSHAPE_URL}")
+-  endif()
+-  downloadAndCheckMD5(${PUBCHEMSHAPE_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${PUBCHEMSHAPE_BASE}" ${PUBCHEMSHAPE_MD5SUM})
+-  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf
+-    ${CMAKE_CURRENT_SOURCE_DIR}/${PUBCHEM_COMMIT_SHA}.tar.gz
+-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-
+-  file(GLOB tar_dirname ${CMAKE_CURRENT_SOURCE_DIR}/pubchem-align3d-${PUBCHEM_COMMIT_SHA}*)
+-  execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${tar_dirname}
+-       ${PUBCHEMSHAPE_DIR}
+-       WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-endif()
+-
+-rdkit_library(pubchem_align3d ./pubchem-align3d/shape_functions1.cpp
+-            ./pubchem-align3d/shape_functions2.cpp ./pubchem-align3d/shape_neighbor.cpp SHARED)
+-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
+-  set_target_properties(pubchem_align3d PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+-endif()
+-
+ rdkit_library(PubChemShape PubChemShape.cpp SHARED
+- LINK_LIBRARIES pubchem_align3d SmilesParse SubstructMatch)
++ LINK_LIBRARIES -lpubchem-align3d SmilesParse SubstructMatch)
+ target_compile_definitions(PubChemShape PRIVATE RDKIT_PUBCHEMSHAPE_BUILD)
+ 
+ rdkit_headers(PubChemShape.hpp DEST GraphMol)
-- 
2.48.1

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Subject: [bug#77394] [PATCH 1/5] gnu: inchi: Update to 1.07.3.
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Hello David,

thanks for the patches!

Am Sun, Mar 30, 2025 at 10:06:54PM +0000 schrieb David Elsing:
> [native-inputs]: Remove input label.
>      ;; Update the inchi-doc native input when updating inchi.
> -    (native-inputs
> -     `(("unzip" ,unzip)
> -       ("inchi-doc"
> -        ,(origin
> -           (method url-fetch)
> -           (uri (string-append "http://www.inchi-trust.org/download/"
> -                                  (string-join (string-split version #\.) "")
> -                                  "/INCHI-1-DOC.zip"))
> -           (sha256
> -            (base32
> -             "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
> -           (file-name (string-append name "-" version ".zip"))))))
> +    (native-inputs (list unzip))

You also dropped the documentation native input. Is that intended?

Andreas

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I have pushed your patches 2 and 4.

Concerning boost with numpy, I am not sure; should we add numpy
directly to boost as an input? This might actually create a circular
dependency (I have not checked). In any case, both are monster packages,
so replacing boost by a combination of the two may be a bad idea, and
your suggestion to create a separate boost-with-numpy is preferable.

I am cc-ing the science and C++ teams for their opinion.

Andreas

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Hello,

Andreas Enge <andreas@HIDDEN> writes:

> You also dropped the documentation native input. Is that intended?

Yes, it is included in the Git repo, but I forgot to mention it in the
commit message. I also forgot to update the copyright header. :)

Can you add them or should I send an updated patch?

Thank you,
David

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Hello Andreas,

Andreas Enge <andreas@HIDDEN> writes:

> I have pushed your patches 2 and 4.

Thanks!

> Concerning boost with numpy, I am not sure; should we add numpy
> directly to boost as an input? This might actually create a circular
> dependency (I have not checked). In any case, both are monster packages,
> so replacing boost by a combination of the two may be a bad idea, and
> your suggestion to create a separate boost-with-numpy is preferable.

I just checked and there does not seem to be a circular dependency.
However, boost has *much* less transitive dependencies than python-numpy
and is depended on by many packages. Its build time and compressed size
(~20 MB) is also not that large, so I think a separate package is not
that bad.

Cheers,
David

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This patch series updates rdkit and some of its dependencies.
The build now depends on the CMake files of the NumPy extension of
Boost.Python and rdkit depends on python-numpy anyway, so I added a package
variant of boost with it enabled.

David Elsing (5):
  gnu: inchi: Update to 1.07.3.
  gnu: yaehmop: Update to 2024.03.1.
  gnu: Add boost-with-numpy.
  gnu: Add pubchem-align3d.
  gnu: rdkit: Update to 2024.09.6.

 gnu/packages/boost.scm                        |   8 +
 gnu/packages/chemistry.scm                    | 186 +++++++++++-------
 ...rdkit-unbundle-external-dependencies.patch | 183 +++++++++++++++--
 3 files changed, 291 insertions(+), 86 deletions(-)

-- 
2.48.1




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Hello David,

I have just pushed with the few changes you suggested.

Concerning boost-with-numpy, it also needed a "name" field, since
otherwise there was a commandline collision between the two packages.
In the end I opted for "boost-numpy" for the name field and the variable
name, since we already have "boost-mpi" and it felt consistent.

Thanks, closing!

Andreas



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Subject: bug#77394: closed (Re: [PATCH 5/5] gnu: rdkit: Update to 2024.09.6.)
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Your bug report

#77394: [PATCH 0/5] Update rdkit to 2024.09.6

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 77394 <at> debbugs.gnu.org.

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77394: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D77394
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Date: Tue, 8 Apr 2025 13:29:40 +0200
From: Andreas Enge <andreas@HIDDEN>
To: David Elsing <david.elsing@HIDDEN>
Subject: Re: [PATCH 5/5] gnu: rdkit: Update to 2024.09.6.
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Hello David,

I have just pushed with the few changes you suggested.

Concerning boost-with-numpy, it also needed a "name" field, since
otherwise there was a commandline collision between the two packages.
In the end I opted for "boost-numpy" for the name field and the variable
name, since we already have "boost-mpi" and it felt consistent.

Thanks, closing!

Andreas



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From: David Elsing <david.elsing@HIDDEN>
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Subject: [PATCH 0/5] Update rdkit to 2024.09.6
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This patch series updates rdkit and some of its dependencies.
The build now depends on the CMake files of the NumPy extension of
Boost.Python and rdkit depends on python-numpy anyway, so I added a package
variant of boost with it enabled.

David Elsing (5):
  gnu: inchi: Update to 1.07.3.
  gnu: yaehmop: Update to 2024.03.1.
  gnu: Add boost-with-numpy.
  gnu: Add pubchem-align3d.
  gnu: rdkit: Update to 2024.09.6.

 gnu/packages/boost.scm                        |   8 +
 gnu/packages/chemistry.scm                    | 186 +++++++++++-------
 ...rdkit-unbundle-external-dependencies.patch | 183 +++++++++++++++--
 3 files changed, 291 insertions(+), 86 deletions(-)

-- 
2.48.1




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