gencodegenes 1.1.5__tar.gz → 1.1.7__tar.gz

{gencodegenes-1.1.5 → gencodegenes-1.1.7}/MANIFEST.in

@@ -5,11 +5,16 @@ include src/gencodegenes/*.cpp
 include src/gencodegenes/*.py
 include src/gencodegenes/*.pyx
 include src/gencodegenes/*.pxd
+include src/gencodegenes/*.pyi
+include src/gencodegenes/py.typed
 include src/*.h
 include src/*.cpp
 include src/gzstream/gzstream.C
 include src/gzstream/gzstream.h
 
+include src/zlib/*.c
+include src/zlib/*.h
+
 # gencodegenes tests
 include tests/*.py
 include tests/data/*.fa

{gencodegenes-1.1.5/src/gencodegenes.egg-info → gencodegenes-1.1.7}/PKG-INFO

@@ -1,29 +1,17 @@
 Metadata-Version: 2.4
 Name: gencodegenes
-Version: 1.1.5
+Version: 1.1.7
 Summary: Package to load genes from GENCODE GTF files
-Home-page: https://github.com/jeremymcrae/gencodegenes
-Author: Jeremy McRae
-Author-email: jeremy.mcrae@gmail.com
-License: MIT
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Author-email: Jeremy McRae <jeremy.mcrae@gmail.com>
+Project-URL: homepage, https://github.com/jeremymcrae/gencodegenes
 Classifier: License :: OSI Approved :: MIT License
+Classifier: Development Status :: 4 - Beta
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: pyfaidx>=0.5.8
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
 Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
 
 
 ### GENCODEGenes

gencodegenes-1.1.7/pyproject.toml

@@ -0,0 +1,31 @@
+[build-system]
+requires = ["cython", "setuptools >= 40.6.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = 'gencodegenes'
+version = '1.1.7'
+description = 'Package to load genes from GENCODE GTF files'
+readme = 'README.md'
+requires-python = ">=3.8"
+authors = [
+    {name = 'Jeremy McRae', email = 'jeremy.mcrae@gmail.com'}
+]
+
+dependencies = [
+    'pyfaidx >= 0.5.8',
+]
+
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 4 - Beta",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[tool.setuptools]
+packages = [
+    "gencodegenes"
+]
+
+[project.urls]
+homepage = 'https://github.com/jeremymcrae/gencodegenes'

{gencodegenes-1.1.5 → gencodegenes-1.1.7}/setup.py

@@ -79,7 +79,7 @@ else:
 
 scrub_gzstream()
 
-genes = cythonize([
+extensions = [
     Extension("gencodegenes.transcript",
         extra_compile_args=EXTRA_COMPILE_ARGS,
         extra_link_args=EXTRA_LINK_ARGS,
@@ -102,33 +102,16 @@ genes = cythonize([
         include_dirs=["src/", "src/zlib"],
         libraries=libs,
         language="c++"),
-    ])
+    ]
 
 # include tx.h in the package, for downstream usage
 shutil.copy("src/tx.h", "src/gencodegenes/tx.h")
 shutil.copy("src/tx.cpp", "src/gencodegenes/tx.cpp")
 
-setup(name="gencodegenes",
-    description='Package to load genes from GENCODE GTF files',
-    long_description=io.open('README.md', encoding='utf-8').read(),
-    long_description_content_type='text/markdown',
-    version="1.1.5",
-    author="Jeremy McRae",
-    author_email="jeremy.mcrae@gmail.com",
-    license="MIT",
-    url='https://github.com/jeremymcrae/gencodegenes',
-    packages=["gencodegenes"],
-    install_requires=[
-        'pyfaidx >= 0.5.8',
-    ],
+setup(
     package_dir={'': 'src'},
-    package_data={'gencodegenes': ['transcript.pxd', 'tx.h', 'tx.cpp']},
+    package_data={'gencodegenes': ['transcript.pxd', 'tx.h', 'tx.cpp',
+        'py.typed', '*.pyi']},
     include_package_data=True,
-    classifiers=[
-        "Development Status :: 5 - Production/Stable",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "License :: OSI Approved :: MIT License",
-    ],
-    python_requires='>=3.8',
-    ext_modules=genes,
+    ext_modules=cythonize(extensions),
     test_suite="tests")

{gencodegenes-1.1.5 → gencodegenes-1.1.7}/src/gencode.cpp

@@ -113,7 +113,7 @@ static void load_transcripts(std::vector<NamedTx> & transcripts, GTF &gtf_file,
             // adjust CDS for start and stop codon coords
             include_end_codons(cds_range, info);
             Tx tx = Tx(info.name, info.chrom, info.start, info.end, info.strand[0], 
-                info.transcript_type);
+                info.transcript_type, info.attributes);
             tx.set_exons(info.exons);
             tx.set_cds(info.cds);
             transcripts.push_back({symbol, alt_ids, tx, info.is_canonical});
@@ -137,6 +137,7 @@ static void load_transcripts(std::vector<NamedTx> & transcripts, GTF &gtf_file,
         if (gtf.feature == "transcript") {
             info.start = gtf.start;
             info.end = gtf.end;
+            info.attributes = std::move(gtf.attributes);
         } else if (gtf.feature == "CDS") {
             info.cds.push_back(std::vector<int> {gtf.start, gtf.end});
             cds_range["max"] = std::max(std::max(cds_range["max"], gtf.start), gtf.end);
@@ -152,7 +153,7 @@ static void load_transcripts(std::vector<NamedTx> & transcripts, GTF &gtf_file,
     // also include the final transcript (if it transcript exists)
     if (info.name != "") {
         include_end_codons(cds_range, info);
-        Tx tx = Tx(info.name, info.chrom, info.start, info.end, info.strand[0], info.transcript_type);
+        Tx tx = Tx(info.name, info.chrom, info.start, info.end, info.strand[0], info.transcript_type, info.attributes);
         tx.set_exons(info.exons);
         tx.set_cds(info.cds);
         transcripts.push_back({symbol, alt_ids, tx, info.is_canonical});

{gencodegenes-1.1.5 → gencodegenes-1.1.7}/src/gencode.h

@@ -25,6 +25,7 @@ struct TxInfo {
     std::vector<std::vector<int> > cds;
     int offset = 0;
     int is_canonical = 0;
+    std::map<std::string, std::string> attributes;
 };
 
 // stores HGNC symbol with the transcript, so we can collect transcripts by gene