pyncbitk-runtime 29.9.0.0__tar.gz → 30.0.0.0__tar.gz

{pyncbitk_runtime-29.9.0.0 → pyncbitk_runtime-30.0.0.0}/PKG-INFO

@@ -1,35 +1,14 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: pyncbitk-runtime
-Version: 29.9.0.0
+Version: 30.0.0.0
 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>
-License: MIT License
-         
-         Copyright (c) 2024 Martin Larralde <martin.larralde@embl.de>
-         
-         Permission is hereby granted, free of charge, to any person obtaining a copy
-         of this software and associated documentation files (the "Software"), to deal
-         in the Software without restriction, including without limitation the rights
-         to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-         copies of the Software, and to permit persons to whom the Software is
-         furnished to do so, subject to the following conditions:
-         
-         The above copyright notice and this permission notice shall be included in all
-         copies or substantial portions of the Software.
-         
-         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-         SOFTWARE.
-         
+License-Expression: MIT AND NCBI-PD
+License-File: COPYING
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: C++
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

{pyncbitk_runtime-29.9.0.0 → pyncbitk_runtime-30.0.0.0}/conanfile.txt

@@ -1,5 +1,5 @@
 [requires]
-ncbi-cxx-toolkit-public/29.9.0
+ncbi-cxx-toolkit-public/30.0.0
 libiconv/1.17
 [options]
 ncbi-cxx-toolkit-public/*:with_components=algo;core;objects;seqext;loaders

{pyncbitk_runtime-29.9.0.0 → pyncbitk_runtime-30.0.0.0}/pyproject.toml

@@ -2,17 +2,18 @@
 build-backend = "scikit_build_core_conan.build"
 requires = [
     "scikit-build-core-conan==0.7.1 ; python_version <= '3.8'", 
-    "scikit-build-core-conan>=0.8.0 ; python_version > '3.8'", 
+    "scikit-build-core-conan~=0.8.0 ; python_version > '3.8'", 
     "cython >=3.0"
 ]
 
 [project]
 name = "pyncbitk-runtime"
-version = "29.9.0.0"
+version = "30.0.0.0"
 description = "Runtime component of the NCBI C++ Toolkit to use in PyNCBItk."
 readme = "README.md"
 requires-python = ">=3.7"
-license = { file = "COPYING" }
+license = "MIT AND NCBI-PD"
+license-files = ["COPYING"]
 authors = [
   { name = "Martin Larralde", email = "martin.larralde@embl.de" },
 ]
@@ -21,7 +22,6 @@ classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Programming Language :: C++",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
@@ -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 = "29.9.0"
+version = "30.0.0"
 
 [tool.scikit-build]
 build-dir = "build/{build_type}"

{pyncbitk_runtime-29.9.0.0 → pyncbitk_runtime-30.0.0.0}/vendor/ncbi-cxx-toolkit-conan/README.md

@@ -32,10 +32,6 @@ then the Toolkit itself. It is not always clear what exactly is required. Conan'
 
 First, you need Conan (and, to install Conan, you need Python). For instructions of how to install Conan, please refer to [Conan's documentation](https://docs.conan.io/2/installation.html).
 
-On February 22, 2023 Conan 2.0 was released. It is a major upgrade, which features new public API, new build system integration and new graph model to represent relations between packages. What is important is that it is not always backward compatible with Conan 1.X.
-
-The Toolkit recipe is fully compatible both with Conan 1.X and 2.X. We strongly recommend using Conan2.
-
 Install Conan:
 
     pip install conan
@@ -73,7 +69,7 @@ Clone this repository and export the recipe into the local Conan cache:
 
     git clone https://github.com/ncbi/ncbi-cxx-toolkit-conan.git
     cd ncbi-cxx-toolkit-conan
-    conan export . --version 29.0.0
+    conan export . --version 30.0.0
 
 Please check *conandata.yml* file in this repository for the list of existing NCBI C++ Toolkit versions.
 
@@ -100,7 +96,7 @@ Copy *blast_demo.cpp* into a local directory. Next to it, create [*conanfile.py*
 It is also possible to use [*conanfile.txt*](https://docs.conan.io/2/reference/conanfile_txt.html) - a simplified version of *conanfile.py*:
 
     [requires]
-    ncbi-cxx-toolkit-public/29.0.0
+    ncbi-cxx-toolkit-public/30.0.0
     [layout]
     cmake_layout
     [generators]
@@ -221,7 +217,8 @@ Here is the list of the Toolkit components:
 |loader-wgs| ncbi_xloader_vdbgraph ncbi_xloader_wgs|
 |loaders| data_loaders_util ncbi_xloader_patcher xflatfile|
 |objects| access biblio biotree blastdb blastxml blastxml2 cdd cn3d docsum efetch entrez2 entrez2cli entrezgene featdef gbproj gbseq gencoll_client generalasn genesbyloc genome_collection homologene insdseq local_taxon macro medlars medline mim mmdb ncbimime objcoords objprt pcassay pcassay2 pcsubstance proj pub pubmed remap remapcli scoremat searchbyrsid seq seqcode seqedit seqset seqtest submit taxon1 taxon3 tinyseq trackmgr trackmgrcli variation xnetblast xnetblastcli|
-|psg-client| psg_client psg_protobuf|
+|psg-client| psg_client|
+|psg-server| psg_cache psg_ipg psg_myncbi psg_cassandra psg_protobuf|
 |seqext| blast_services blastdb_format id1 id1cli id2 id2_split id2cli seqdb seqmasks_io seqsplit snputil uudutil valerr valid variation_utils writedb xalnmgr xcleanupxdiscrepancy xformat xhugeasn xlogging xobjedit xobjimport xobjmanip xobjmgr xobjread xobjreadex xobjutil xobjwrite xunittestutil xvalidate|
 |sqlitewrapp| sqlitewrapp|
 |sraread| sraread srareadx|
@@ -233,7 +230,7 @@ Here is the list of the Toolkit components:
 ## Supported 3rd party packages.
 
 The Toolkit uses a number of 3-rd party packages. In the Toolkit code they are known by their aliases.
-The following is the list of packages supported by *ncbi-cxx-toolkit-public* Conan recipe, as of October 2024:
+The following is the list of packages supported by *ncbi-cxx-toolkit-public* Conan recipe, as of January 2026:
 
 |Alias|Conan package|
 |--------|------------|
@@ -246,7 +243,7 @@ The following is the list of packages supported by *ncbi-cxx-toolkit-public* Con
 |LMDB|lmdb|
 |LZO|lzo|
 |NGHTTP2|libnghttp2|
-|PCRE|pcre|
+|PCRE2|pcre2|
 |PNG|libpng|
 |PROTOBUF|protobuf|
 |SQLITE3|sqlite3|
@@ -289,9 +286,9 @@ First two parameters to *NCBI_generate_cpp* receive lists of generated files - s
 First, make sure your project contains proper requirements. For example, conanfile.txt may request *protobuf* and *grpc*:
 
     [requires]
-    ncbi-cxx-toolkit-public/29.0.0
+    ncbi-cxx-toolkit-public/30.0.0
     protobuf/5.27.0
-    grpc/1.67.1
+    grpc/1.72.0
 
 Next, you can use their own mechanisms, or the same NCBI function *NCBI_generate_cpp*:
 

{pyncbitk_runtime-29.9.0.0 → pyncbitk_runtime-30.0.0.0}/vendor/ncbi-cxx-toolkit-conan/conandata.yml

@@ -1,4 +1,7 @@
 sources:
+  "30.0.0":
+    url: "https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release/30.0.0.tar.gz"
+    sha256: "cde821b44c4f9711b464c56b66b61c5ff419e13b759cc88896154114da6d41a3"
   "29.9.0":
     url: "https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release/29.9.0.tar.gz"
     sha256: "d65585ebbf27ba4ba5397804298e5362d405cbb927ec050f74c9eeb9d2beae26"

pyncbitk_runtime-30.0.0.0/vendor/ncbi-cxx-toolkit-conan/dependencies/dependencies-30.0.yml

@@ -0,0 +1,244 @@
+version: 30.0
+#----------------------------------------------------------------------------
+components:
+  - algo
+  - algo-ms
+  - algo-structure
+  - align-format
+  - bamread
+  - blast
+  - core
+  - dbapi
+  - eutils
+  - grpc
+  - image
+  - loader-asncache
+  - loader-bam
+  - loader-blastdb
+  - loader-cdd
+  - loader-genbank
+  - loader-lds2
+  - loader-snp
+  - loader-sra
+  - loader-wgs
+  - loaders
+  - objects
+  - psg-client
+  - psg-server
+  - seqext
+  - sqlitewrapp
+  - sraread
+  - xmlwrapp
+  - web
+#----------------------------------------------------------------------------
+libraries:
+  algo:     ["ncbi_algo",
+                  "prosplign","xalgoalignsplign",
+                  "cobalt","proteinkmer","xalgocontig_assembly","xalgoalignutil","xblastformat",
+                  "phytree_format","xblast","xalgoseqqa",
+                  "xprimer","xalgognomon","xalgowinmask",
+                  "xalgoblastdbindex","xalgophytree","xalgoseq",
+                  "xalgoalignnw","xalgodustmask","xalgosegmask","xid_mapper",
+                  "xalgotext","composition_adjustment","fastme",
+             "utrtprof"
+            ]
+  algo-ms:  ["ncbi_algo_ms",
+                "xomssa","omssa","pepXML"
+            ]
+  algo-structure:
+            ["ncbi_algo_structure",
+                "xcd_utils","xstruct_util","xstruct_thread","xstruct_dp"
+            ]
+  align-format:
+            ["xalntool",
+             "ncbi_align_format",
+                "align_format"
+            ]
+  bamread:  ["bamread"]
+  blast:    ["xngalign","vdb2blast",
+             "igblast",
+             "ncbi_blastinput",
+                "blastinput",
+             "blast_sra_input",
+             "xmergetree",
+             "xalgoblastdbindex_search",
+             "gumbelparams"
+            ]
+  core:     ["xconnext","xxconnect2","xalgovmerge", "ncbi_xcache_netcache",
+             "ncbi_core",
+                "xconnserv","xcompress","xthrserv","xregexp","xser",
+                "sequtil","xconnect","xdiff","xqueryparse","xutil",
+                "tables","xncbi",
+             "zcf"
+            ]
+  dbapi:    ["sdbapi",
+             "dbapi_util_blobstore",
+             "ncbi_xdbapi_ftds","ncbi_xdbapi_ftds14",
+             "ncbi_dbapi",
+                "dbapi",
+             "ncbi_dbapi_driver",
+                "dbapi_driver",
+             "ct_ftds14", "tds_ftds14"
+            ]
+  eutils:   ["eutils_client",
+             "ncbi_eutils",
+                "eutils", "egquery", "ehistory", "einfo", "elink",
+                "epost", "esearch", "espell", "esummary", 
+                "linkout", "uilist"
+            ]
+  grpc:     ["grpc_integration"]
+  image:    ["ncbi_image",
+                "ximage"
+            ]
+  loader-asncache:
+            [
+             "ncbi_xloader_asn_cache",
+             "asn_cache",
+             "ncbi_xcache_bdb",
+             "ncbi_bdb",
+                "bdb"
+            ]
+  loader-bam: ["ncbi_xloader_bam"]
+  loader-blastdb:
+            ["ncbi_xloader_blastdb_rmt",
+             "ncbi_xloader_blastdb"
+            ]
+  loader-cdd:
+            ["ncbi_xloader_cdd",
+             "cdd_access"
+            ]
+  loader-genbank:
+            [
+             "ncbi_xobjsimple",
+                "xobjsimple",
+             "ncbi_xloader_genbank",
+             "ncbi_xreader_cache",
+             "ncbi_xreader_gicache",
+             "ncbi_xreader_id1",
+             "ncbi_xreader_id2",
+             "ncbi_xreader_pubseqos",
+             "ncbi_xreader_pubseqos2",
+             "ncbi_xreader",
+             "eMyNCBI_result"
+            ]
+  loader-lds2:
+            ["ncbi_xloader_lds2",
+             "ncbi_lds2",
+                "lds2"
+            ]
+  loader-snp: ["ncbi_xloader_snp", "dbsnp_ptis"]
+  loader-sra: ["ncbi_xloader_sra", "ncbi_xloader_csra"]
+  loader-wgs: ["ncbi_xloader_vdbgraph", "ncbi_xloader_wgs"]
+  loaders:  ["xflatfile",
+             "data_loaders_util",
+             "ncbi_xloader_patcher"
+            ]
+  objects:  ["searchbyrsid",
+             "ncbi_trackmgr",
+                "gbproj","trackmgrcli","trackmgr",
+             "ncbi_mmdb",
+                "ncbimime","cdd","cn3d","mmdb",
+             "pcassay2",
+             "ncbi_misc",
+                "proj","remapcli","remap","pcassay","entrezgene",
+                "pcsubstance","entrez2cli","biotree",
+                "access","docsum","entrez2","featdef","gbseq",
+                "genesbyloc","insdseq","mim","objcoords","objprt",
+                "tinyseq",
+             "gencoll_client",
+             "local_taxon",
+             "macro",
+             "homologene",
+             "ncbi_seq",
+                "blastdb","xnetblastcli","xnetblast",
+                "scoremat","seqedit","submit",
+                "genome_collection","seqtest","taxon1","taxon3","variation","seqset",
+                "seq","blastxml","blastxml2","seqcode",
+             "efetch",
+             "ncbi_pub",
+                "pub","pubmed","medlars","medline","biblio",
+             "ncbi_general",
+                "generalasn"
+            ]
+  psg-client:   ["psg_client"
+                ]
+  psg-server:   ["psg_cache", "psg_ipg", "psg_myncbi", "psg_cassandra", "psg_protobuf"
+                ]
+  seqext:   ["ncbi_validator",
+                "xvalidate",
+             "ncbi_xdiscrepancy",
+                "xdiscrepancy",
+             "ncbi_seqext",
+                "xobjwrite","xformat",
+                "blastdb_format","writedb","seqmasks_io","xcleanup",
+                "blast_services","seqdb","variation_utils","xalnmgr","xobjedit",
+                "xobjreadex","xobjimport","xunittestutil",
+                "id2cli","id2_split","snputil","uudutil","xhugeasn","xobjutil",
+                "xobjread","id2","id1cli","xobjmgr","id1","seqsplit","valerr",
+                "xobjmanip","valid","xlogging"
+            ]
+  sqlitewrapp:  ["sqlitewrapp"]
+  sraread:  ["srareadx", "sraread"]
+  xmlwrapp: ["xmlreaders",
+             "xmlwrapp"
+            ]
+  web:      ["xsoap_server", "xsoap",
+             "ncbi_web",
+                "xcgi_redirect","xcgi","xhtml"
+            ]
+#----------------------------------------------------------------------------
+requirements:
+  bamread:      ["VDB"]
+  bdb:          ["BerkeleyDB"]
+  blast_sra_input: ["VDB"]
+  dbsnp_ptis:   ["GRPC"]
+  grpc_integration: ["GRPC"]
+  psg_cache:    ["LMDB"]
+  psg_cassandra: ["CASSANDRA"]
+  psg_myncbi:   ["CURL"]
+  psg_protobuf: ["GRPC"]
+  seqdb:        ["LMDB"]
+  sqlitewrapp:  ["SQLITE3"]
+  sraread:      ["VDB"]
+  tds_ftds14:   ["Iconv"]
+  vdb2blast:    ["VDB"]
+  writedb:      ["LMDB"]
+  xcompress:    ["Z", "BZ2", "LZO", "ZSTD"]
+  xregexp:      ["PCRE2"]
+  ximage:       ["Z", "JPEG", "PNG", "GIF", "TIFF"]
+  xmlwrapp:     ["XML", "XSLT"]
+  xncbi:        ["BACKWARD", "UNWIND"]
+  xconnext:     ["NCBICRYPT"]
+  xxconnect2:   ["UV", "NGHTTP2"]
+  xfcgi:        ["FASTCGI"]
+#----------------------------------------------------------------------------
+dependencies:
+  algo:         ["align-format","sqlitewrapp"]
+  algo-ms:      ["algo"]
+  algo-structure: ["algo","objects"]
+  align-format: ["loader-genbank", "web"]
+  bamread:      ["objects"]
+  blast:        ["loader-blastdb", "algo", "sraread"]
+  core:         []
+  dbapi:        ["core"]
+  eutils:       ["objects","xmlwrapp"]
+  grpc:         ["core"]
+  image:        ["core"]
+  loader-asncache:  ["seqext"]
+  loader-bam:       ["bamread", "seqext"]
+  loader-blastdb:   ["seqext"]
+  loader-cdd:       ["seqext"]
+  loader-genbank:   ["psg-client", "dbapi"]
+  loader-lds2:      ["seqext", "sqlitewrapp"]
+  loader-snp:       ["sraread", "grpc"]
+  loader-sra:       ["sraread"]
+  loader-wgs:       ["sraread"]
+  loaders:      ["loader-asncache", "loader-blastdb", "loader-genbank", "loader-lds2"]
+  objects:      ["sqlitewrapp","core"]
+  psg-client:   ["seqext"]
+  psg-server:   ["objects","xmlwrapp"]
+  seqext:       ["eutils", "objects"]
+  sqlitewrapp:  ["core"]
+  sraread:      ["seqext"]
+  xmlwrapp:     ["core"]
+  web:          ["core"]

pyncbitk_runtime-30.0.0.0/vendor/ncbi-cxx-toolkit-conan/dependencies/requirements-30.0.yml

@@ -0,0 +1,31 @@
+version: 30.0
+#----------------------------------------------------------------------------
+requirements:
+    BACKWARD:   ["backward-cpp/1.6"]
+    UNWIND:     ["libunwind/[>=1.6.2 <=1.8.1]"]
+    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 <=1.72.0]", "protobuf/[>=3.21.12 <=5.27.0]"]
+    Iconv:      ["libiconv/1.17"]
+    JPEG:       ["libjpeg/[>=9e <=9f]"]
+    LMDB:       ["lmdb/[>=0.9.29 <=0.9.32]"]
+    LZO:        ["lzo/2.10"]
+    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 <=1.1.43]"]
+    UV:         ["libuv/[>=1.45.0 <=1.46.0]"]
+    Z:          ["zlib/[>=1.2.11 <2]"]
+    ZSTD:       ["zstd/[>=1.5.2 <=1.5.5]"]
+
+disabled:
+    BACKWARD:   ["Windows", "Macos"]
+    UNWIND:     ["Windows", "Macos"]
+    BerkeleyDB: ["Windows"]
+    CASSANDRA:  ["Windows", "Macos"]