pyncbitk-runtime 29.6.0.0__tar.gz → 29.9.0.0__tar.gz

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyncbitk-runtime
-Version: 29.6.0.0
+Version: 29.9.0.0
 Summary: Runtime component of the NCBI C++ Toolkit to use in PyNCBItk.
 Keywords: bioinformatics,blast,sequence,alignment,ncbi
 Author-Email: Martin Larralde <martin.larralde@embl.de>

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/conanfile.txt

@@ -1,5 +1,5 @@
 [requires]
-ncbi-cxx-toolkit-public/29.6.0
+ncbi-cxx-toolkit-public/29.9.0
 libiconv/1.17
 [options]
 ncbi-cxx-toolkit-public/*:with_components=algo;core;objects;seqext;loaders

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/pyproject.toml

@@ -8,7 +8,7 @@ requires = [
 
 [project]
 name = "pyncbitk-runtime"
-version = "29.6.0.0"
+version = "29.9.0.0"
 description = "Runtime component of the NCBI C++ Toolkit to use in PyNCBItk."
 readme = "README.md"
 requires-python = ">=3.7"
@@ -46,7 +46,7 @@ settings = ["compiler.cppstd=20"]
 [[tool.scikit-build-core-conan.local-recipes]]
 path = "vendor/ncbi-cxx-toolkit-conan"
 name = "ncbi-cxx-toolkit-public"
-version = "29.6.0"
+version = "29.9.0"
 
 [tool.scikit-build]
 build-dir = "build/{build_type}"

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/vendor/ncbi-cxx-toolkit-conan/conandata.yml

@@ -1,4 +1,13 @@
 sources:
+  "29.9.0":
+    url: "https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release/29.9.0.tar.gz"
+    sha256: "d65585ebbf27ba4ba5397804298e5362d405cbb927ec050f74c9eeb9d2beae26"
+  "29.8.0":
+    url: "https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release/29.8.0.tar.gz"
+    sha256: "a5e5a08f6028b68fd61b0fe28ecff8d55e4398a1156913b53efeef5bce848b0a"
+  "29.7.0":
+    url: "https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release/29.7.0.tar.gz"
+    sha256: "44ea47f5f725568dadc5a149134d7e6be47a4b86f0c2a7ba5a9bc2a21bcc68a7"
   "29.6.0":
     url: "https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release/29.6.0.tar.gz"
     sha256: "c370ede357471dfb8872c13b128ea9c16040511ad90d6bce700880a463351792"
@@ -70,7 +79,7 @@ sources:
     sha256: "c8fb3f99c6fce4f170b381f3a7789c76a2ff1c23c094c9852e2e3de1fdc57277"
   "0.0.0":
     git: "https://github.com/ncbi/ncbi-cxx-toolkit-public.git"
-    branch: "master"
+    branch: "main"
 
 patches:
   "29.0.0":

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/vendor/ncbi-cxx-toolkit-conan/conanfile.py

@@ -1,7 +1,7 @@
 from conan import ConanFile
 from conan.errors import ConanInvalidConfiguration, ConanException
 from conan.tools.microsoft import check_min_vs, is_msvc_static_runtime, is_msvc
-from conan.tools.files import apply_conandata_patches, export_conandata_patches, get, copy, replace_in_file
+from conan.tools.files import apply_conandata_patches, export_conandata_patches, get, copy, replace_in_file, trim_conandata
 from conan.tools.build import check_min_cppstd, cross_building, can_run
 from conan.tools.scm import Version, Git
 from conan.tools.cmake import CMakeDeps, CMakeToolchain, CMake, cmake_layout
@@ -29,14 +29,16 @@ class NcbiCxxToolkit(ConanFile):
         "fPIC":       [True, False],
         "with_targets":  ["ANY"],
         "with_components": ["ANY"],
-        "without_req": ["ANY"]
+        "without_req": ["ANY"],
+        "with_composite": [True, False]
     }
     default_options = {
         "shared":     False,
         "fPIC":       True,
         "with_targets":   "",
         "with_components": "",
-	"without_req": ""
+        "without_req": "",
+        "with_composite": False
     }
     short_paths = True
     _dependencies = None
@@ -116,6 +118,7 @@ class NcbiCxxToolkit(ConanFile):
 
 #----------------------------------------------------------------------------
     def export(self):
+        trim_conandata(self)
         copy(self, self._dependencies_filename,
             os.path.join(self.recipe_folder, self._dependencies_folder),
             os.path.join(self.export_folder, self._dependencies_folder))
@@ -252,7 +255,7 @@ class NcbiCxxToolkit(ConanFile):
     def generate(self):
         tc = CMakeToolchain(self)
         tc.variables["NCBI_PTBCFG_PACKAGING"] = True
-        if self.options.shared:
+        if self.options.with_composite:
             tc.variables["NCBI_PTBCFG_ALLOW_COMPOSITE"] = True
         tc.variables["NCBI_PTBCFG_PROJECT_LIST"] = "-app/netcache"
         if len(self._targets) > 0:

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/vendor/ncbi-cxx-toolkit-conan/dependencies/dependencies-0.0.yml

@@ -175,7 +175,7 @@ libraries:
                 "xobjreadex","xobjimport","xunittestutil",
                 "id2cli","id2_split","snputil","uudutil","xhugeasn","xobjutil",
                 "xobjread","id2","id1cli","xobjmgr","id1","seqsplit","valerr",
-                "xobjmanip","valid","xlogging",
+                "xobjmanip","valid","xlogging"
             ]
   sqlitewrapp:  ["sqlitewrapp"]
   sraread:  ["srareadx", "sraread"]
@@ -193,8 +193,10 @@ requirements:
   blast_sra_input: ["VDB"]
   dbsnp_ptis:   ["GRPC"]
   grpc_integration: ["GRPC"]
-  psg_protobuf: ["GRPC"]
+  psg_cache:    ["LMDB"]
   psg_cassandra: ["CASSANDRA"]
+  psg_myncbi:   ["CURL"]
+  psg_protobuf: ["GRPC"]
   seqdb:        ["LMDB"]
   sqlitewrapp:  ["SQLITE3"]
   sraread:      ["VDB"]
@@ -202,7 +204,7 @@ requirements:
   vdb2blast:    ["VDB"]
   writedb:      ["LMDB"]
   xcompress:    ["Z", "BZ2", "LZO", "ZSTD"]
-  xregexp:      ["PCRE", "PCRE2"]
+  xregexp:      ["PCRE2"]
   ximage:       ["Z", "JPEG", "PNG", "GIF", "TIFF"]
   xmlwrapp:     ["XML", "XSLT"]
   xncbi:        ["BACKWARD", "UNWIND"]

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/vendor/ncbi-cxx-toolkit-conan/dependencies/dependencies-28.0.yml

@@ -166,7 +166,7 @@ libraries:
                 "id2_split","writedb","seqdb","seqmasks_io","seqsplit","snputil","uudutil",
                 "valerr","valid","variation_utils","xformat","xalnmgr","xcleanup", "xhugeasn",
                 "xobjedit","xobjreadex","xobjwrite","xobjread","xlogging","xobjimport",
-                "xobjmanip","xunittestutil","xobjutil","xobjmgr",
+                "xobjmanip","xunittestutil","xobjutil","xobjmgr"
             ]
   sqlitewrapp:  ["sqlitewrapp"]
   sraread:  ["sraread"]

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/vendor/ncbi-cxx-toolkit-conan/dependencies/dependencies-29.0.yml

@@ -175,7 +175,7 @@ libraries:
                 "xobjreadex","xobjimport","xunittestutil",
                 "id2cli","id2_split","snputil","uudutil","xhugeasn","xobjutil",
                 "xobjread","id2","id1cli","xobjmgr","id1","seqsplit","valerr",
-                "xobjmanip","valid","xlogging",
+                "xobjmanip","valid","xlogging"
             ]
   sqlitewrapp:  ["sqlitewrapp"]
   sraread:  ["srareadx", "sraread"]

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/vendor/ncbi-cxx-toolkit-conan/dependencies/requirements-0.0.yml

@@ -6,23 +6,23 @@ requirements:
     BerkeleyDB: ["libdb/5.3.28"]
     BZ2:        ["bzip2/1.0.8"]
     CASSANDRA:  ["cassandra-cpp-driver/[>=2.15.3 <=2.17.1]"]
+    CURL:       ["libcurl/[>=8.8.0 <=9]"]
     GIF:        ["giflib/[>=5.2.1 <=5.2.2]"]
-    GRPC:       ["grpc/[>=1.50.1 <=1.67.1]", "protobuf/[>=3.21.12 <=5.27.0]"]
+    GRPC:       ["grpc/[>=1.50.1 <=1.72.0]", "protobuf/[>=3.21.12 <=5.27.0]"]
     Iconv:      ["libiconv/[>=1.17]"]
-    JPEG:       ["libjpeg/9e"]
+    JPEG:       ["libjpeg/[>=9e <=9f]"]
     LMDB:       ["lmdb/[>=0.9.29 <=0.9.32]"]
     LZO:        ["lzo/2.10"]
-    NGHTTP2:    ["libnghttp2/[>=1.51.0 <=1.61.0]"]
-    PCRE:       ["pcre/8.45"]
-    PCRE2:      ["pcre2/[>=10.42 <=10.44]"]
-    PNG:        ["libpng/[>=1.6.37 <=1.6.44]"]
-    SQLITE3:    ["sqlite3/[>=3.40.0 <=3.47.1]"]
-    TIFF:       ["libtiff/[>=4.3.0 <=4.6.0]"]
+    NGHTTP2:    ["libnghttp2/[>=1.51.0 <=1.66.0]"]
+    PCRE2:      ["pcre2/10.42"]
+    PNG:        ["libpng/[>=1.6.37 <=1.6.50]"]
+    SQLITE3:    ["sqlite3/[>=3.40.0 <=3.50.4]"]
+    TIFF:       ["libtiff/[>=4.3.0 <=4.7.1]"]
     XML:        ["libxml2/[>=2.11.4 <3]"]
-    XSLT:       ["libxslt/[>1.1.34 <=1.1.42]"]
-    UV:         ["libuv/[>=1.45.0 <=1.49.2]"]
+    XSLT:       ["libxslt/[>1.1.34 <=1.1.43]"]
+    UV:         ["libuv/[>=1.45.0 <=1.46.0]"]
     Z:          ["zlib/[>=1.2.11 <2]"]
-    ZSTD:       ["zstd/[>=1.5.2 <=1.5.6]"]
+    ZSTD:       ["zstd/[>=1.5.2 <=1.5.5]"]
 
 disabled:
     BACKWARD:   ["Windows", "Macos"]

{pyncbitk_runtime-29.6.0.0 → pyncbitk_runtime-29.9.0.0}/vendor/ncbi-cxx-toolkit-conan/test_package/conanfile.py

@@ -10,6 +10,9 @@ class NcbiCxxToolkitTest(ConanFile):
     def requirements(self):
         self.requires(self.tested_reference_str)
 
+    def configure(self):
+        self.options["grpc/*"].secure = True
+
     def layout(self):
         cmake_layout(self)