{bio}[foss/2023a] pod5-file-format v0.3.10

easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb

@@ -0,0 +1,115 @@
+easyblock = 'CMakeMake'
+
+name = 'pod5-file-format'
+version = '0.3.10'
+
+homepage = 'https://github.com/nanoporetech/pod5-file-format'
+description = """POD5 is a file format for storing nanopore dna data in an easily accessible way.
+ The format is able to be written in a streaming manner which allows a sequencing
+ instrument to directly write the format."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/nanoporetech/%(name)s/archive/']
+sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = [
+    '%(name)s-%(version)s_dep_fix.patch',
+]
+checksums = [
+    {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'},
+    {'pod5-file-format-0.3.10_dep_fix.patch': 'c74ddc35f78807705940b983301ca0e1fffd2774535892c7bc85e1ec47f550ff'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('pkgconfig', '1.5.5', '-python'),
+    ('hatchling', '1.18.0'),
+    ('poetry', '1.5.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Arrow', '14.0.1'),
+    ('SciPy-bundle', '2023.07'),
+    ('zstd', '1.5.5'),
+    ('flatbuffers', '23.5.26'),
+    ('pybind11', '2.11.1'),
+    ('Boost', '1.82.0'),
+    ('build', '1.0.3'),
+    ('HDF5', '1.14.0'),
+    ('h5py', '3.9.0'),
+    ('tqdm', '4.66.1'),
+    ('polars', '0.20.2'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'installopts': '',
+}
+
+exts_list = [
+    ('attrs', '23.2.0', {
+        'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'],
+    }),
+    ('vbz_h5py_plugin', '1.0.1', {
+        'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'],
+    }),
+    ('iso8601', '2.1.0', {
+        'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'],
+    }),
+    ('pod5', version, {
+        'patches': ['pod5-file-format-%(version)s_fix_version_in_pyproject.patch'],
+        'preinstallopts': "sed -i 's/h5py~=[0-9.]*/h5py/' pyproject.toml && ",
+        'source_urls': ['https://github.com/nanoporetech/%(name)s/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'start_dir': 'python/pod5',
+        'checksums': [
+            {'pod5-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'},
+            {'pod5-file-format-0.3.10_fix_version_in_pyproject.patch':
+             '720a48a0cacca5e3f78371115070ab077ebce471ac0bbb142581f006e11db5ff'},
+        ],
+    }),
+]
+
+# Must create the _version.py file first of all
+_vtuple = ','.join(version.split('.'))
+_vertxt = [
+    "__version__=version='%(version)s'",
+    "__version_tuple__=version_tuple=(%s)" % _vtuple
+]
+_vstr = '\n'.join(_vertxt)
+
+_precopts = [
+    "cd %(start_dir)s",
+    'echo "%s" > _version.py' % _vstr,
+    "python -m pod5_make_version",
+    "cd -",
+]
+preconfigopts = " && ".join(_precopts) + " && "
+
+# The code uses BUILD_SHARED_LIB and not the standard BUILD_SHARED_LIBS, so set explicitly
+configopts = '-DBUILD_SHARED_LIB=ON -DBUILD_PYTHON_WHEEL=ON -DZSTD_ROOT=$EBROOTZSTD '
+
+installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s'
+installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl'
+
+postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl']
+
+sanity_check_paths = {
+    'files': ['bin/pod5', 'lib/libpod5_format.%s' % SHLIB_EXT],
+    'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "pod5 subset --help",
+    "python -c 'import lib_pod5'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch

@@ -0,0 +1,38 @@
+Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake'
+We want to use our pybind11 instead of the one in git submodules
+Author: Petr Král (INUITS)
+
+Updated for 0.3.10 by Åke Sandgren, 2024-04-03
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index ea58278..c3bf295 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -87,7 +87,6 @@ if (BUILD_PYTHON_WHEEL)
+         set(PYTHON_VERSION "")
+     endif()
+     find_package (Python ${PYTHON_VERSION} EXACT COMPONENTS Interpreter Development)
+-    add_subdirectory(third_party/pybind11)
+ endif()
+
+ add_subdirectory(c++)
+diff --git a/c++/CMakeLists.txt b/c++/CMakeLists.txt
+index 05c1c1b..6efb894 100644
+--- a/c++/CMakeLists.txt
++++ b/c++/CMakeLists.txt
+@@ -17,7 +17,7 @@ else()
+         COMPONENTS
+             headers
+     )
+-    find_package(Flatbuffers REQUIRED)
++    find_package(FlatBuffers REQUIRED)
+     find_package(zstd REQUIRED)
+     find_package(ZLIB REQUIRED)
+
+@@ -27,6 +27,7 @@ else()
+ endif()
+
+ find_package(Threads REQUIRED)
++find_package(pybind11 REQUIRED)
+
+ find_program(
+     FLATBUFFERS_FLATC_EXECUTABLE

easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_fix_version_in_pyproject.patch

@@ -0,0 +1,26 @@
+Set version explicitly
+There is some problem with their pyproject.toml and the version of Python
+
+Åke Sandgren, 2024-04-03
+diff --git a/python/pod5/pyproject.toml b/python/pod5/pyproject.toml
+index e00f9f9..84c7970 100644
+--- a/python/pod5/pyproject.toml
++++ b/python/pod5/pyproject.toml
+@@ -9,7 +9,7 @@ authors = [{name="Oxford Nanopore Technologies plc", email="support@nanoporetech
+ readme = "README.md"
+ requires-python = "~= 3.8"
+ description="Oxford Nanopore Technologies Pod5 File Format Python API and Tools"
+-dynamic = ["version"]
++version = '0.3.10'
+ keywords = ['nanopore']
+ classifiers=[
+     'Environment :: Console',
+@@ -62,8 +62,5 @@ Documentation = "https://pod5-file-format.readthedocs.io/en/latest/"
+ where = ["src"]
+ exclude = ["test*"]
+
+-[tool.setuptools.dynamic]
+-version = {attr = "pod5._version.__version__"}
+-
+ [tool.black]
+ target-version = ["py37"]