diff --git a/recipes/iced/0001-setup.py.patch b/recipes/iced/0001-setup.py.patch new file mode 100644 index 0000000000000..a388235b35345 --- /dev/null +++ b/recipes/iced/0001-setup.py.patch @@ -0,0 +1,29 @@ +diff --git a/setup.py b/setup.py +index 7e8b201..cb9a3b9 100644 +--- a/setup.py ++++ b/setup.py +@@ -1,6 +1,7 @@ + import os + import sys +-from setuptools import Extension, setup, find_packages ++from setuptools import Extension, setup, find_namespace_packages ++from Cython.Build import cythonize + import numpy as np + + +@@ -38,13 +39,13 @@ setup( + "Topic :: Utilities", + "License :: OSI Approved :: BSD License", + ], +- packages=find_packages(where="."), ++ packages=find_namespace_packages(where="."), + ext_modules=[ + Extension(name="iced._filter_", + sources=["iced/_filter_.pyx"], + include_dirs=[np.get_include()] + ), +- Extension(name="iced.normalization/_normalization_", ++ Extension(name="iced.normalization._normalization_", + sources=["iced/normalization/_normalization_.pyx"], + include_dirs=[np.get_include()] + )], diff --git a/recipes/iced/build.sh b/recipes/iced/build.sh deleted file mode 100644 index 94bc556317a9a..0000000000000 --- a/recipes/iced/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -find . -type f -name *_.c -exec rm -f {} \; -$PYTHON build_tools/cythonize.py iced -$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/iced/build_failure.linux-64.yaml b/recipes/iced/build_failure.linux-64.yaml deleted file mode 100644 index f74af48eaf70a..0000000000000 --- a/recipes/iced/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 400ed2c0710342dc29523fa08cc66e0bbb7567fabf768184c9bb8ce3c8141cf4 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. - [1;35mfull command[0m: [34m/opt/conda/conda-bld/iced_1717609030770/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/python /opt/conda/conda-bld/iced_1717609030770/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpfguomjtm[0m - [1;35mcwd[0m: /opt/conda/conda-bld/iced_1717609030770/work - Preparing metadata (pyproject.toml): finished with status 'error' - [1;31merror[0m: [1mmetadata-generation-failed[0m - - [31m[0m Encountered error while generating package metadata. - [31m>[0m See above for output. - - [1;35mnote[0m: This is an issue with the package mentioned above, not pip. - [1;36mhint[0m: See above for details. - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata - distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel - return super().prepare_metadata_for_build_wheel( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel - return self._call_hook('prepare_metadata_for_build_wheel', { - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook - self._subprocess_runner( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner - call_subprocess( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess - raise error - pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run - requirement_set = resolver.resolve( - ^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve - collected = self.factory.collect_root_requirements(root_reqs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements - reqs = list( - ^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req - cand = self._make_base_candidate_from_link( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link - self._link_candidate_cache[link] = LinkCandidate( - ^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__ - super().__init__( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ - self.dist = self._prepare() - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare - dist = self._prepare_distribution() - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution - return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement - return self._prepare_linked_requirement(req, parallel_builds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement - dist = _get_prepared_distribution( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution - abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata - self.req.prepare_metadata() - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata - self.metadata_directory = generate_metadata( - ^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata - raise MetadataGenerationFailed(package_details=details) from error - pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-holk0f44' - Removed build tracker: '/tmp/pip-build-tracker-holk0f44' - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/iced_1717609030770/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/iced/build_failure.osx-64.yaml b/recipes/iced/build_failure.osx-64.yaml deleted file mode 100644 index ed16711b8c3f8..0000000000000 --- a/recipes/iced/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 400ed2c0710342dc29523fa08cc66e0bbb7567fabf768184c9bb8ce3c8141cf4 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iced-0.5.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iced-0.5.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - iced - Processing iced/_filter_.pyx - Processing iced/normalization/_normalization_.pyx - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-zu5vyi_p - Initialized build tracking at /private/tmp/pip-build-tracker-zu5vyi_p - Created build tracker: /private/tmp/pip-build-tracker-zu5vyi_p - Entered build tracker: /private/tmp/pip-build-tracker-zu5vyi_p - Created temporary directory: /private/tmp/pip-install-usxqfwkz - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-6k98c0ng - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-zu5vyi_p' - Created temporary directory: /private/tmp/pip-modern-metadata-8ggb3l2k - Preparing metadata (pyproject.toml): started - Preparing metadata (pyproject.toml): finished with status 'error' - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata - distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel - return super().prepare_metadata_for_build_wheel( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel - return self._call_hook('prepare_metadata_for_build_wheel', { - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook - self._subprocess_runner( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner - call_subprocess( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess - raise error - pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run - requirement_set = resolver.resolve( - ^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve - collected = self.factory.collect_root_requirements(root_reqs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements - reqs = list( - ^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req - cand = self._make_base_candidate_from_link( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link - self._link_candidate_cache[link] = LinkCandidate( - ^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__ - super().__init__( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ - self.dist = self._prepare() - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare - dist = self._prepare_distribution() - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution - return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement - return self._prepare_linked_requirement(req, parallel_builds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement - dist = _get_prepared_distribution( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution - abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata - self.req.prepare_metadata() - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata - self.metadata_directory = generate_metadata( - ^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata - raise MetadataGenerationFailed(package_details=details) from error - pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-zu5vyi_p' - Removed build tracker: '/private/tmp/pip-build-tracker-zu5vyi_p' -# Last 100 lines of the build log. diff --git a/recipes/iced/meta.yaml b/recipes/iced/meta.yaml index 8468ad67754af..def2534bb8366 100644 --- a/recipes/iced/meta.yaml +++ b/recipes/iced/meta.yaml @@ -1,32 +1,38 @@ {% set name = "iced" %} -{% set version = "0.5.10" %} -{% set sha256 = "77240573bfb552d33301cf5b22f597f50c04e03c8ccea4dcc88fee884e394fd0" %} +{% set version = "0.5.13" %} +{% set sha256 = "455ecb3464cc64e0fdec776bc7b0f0cae9d729539be6865ac9d5436c5e77e6b9" %} package: name: "{{ name }}" version: "{{ version }}" source: - url: https://github.com/hiclib/{{ name }}/archive/v{{ version }}.tar.gz + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/iced-{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + - 0001-setup.py.patch build: - number: 3 + number: 0 + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + entry_points: + - ice = iced.scripts.ice:main + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - pip - python - cython - - numpy - - scipy >=0.13.3 + - numpy >=1.16.0 + - scipy >=0.19.0 run: - python - {{ pin_compatible('numpy') }} - - scipy >=0.13.3 + - scipy >=0.19.0 - pandas - scikit-learn - matplotlib-base @@ -34,10 +40,19 @@ requirements: test: imports: - iced + commands: + - ice --help about: - home: https://github.com/hiclib/iced - license: new BSD + home: "https://github.com/hiclib/iced" + license: "BSD-3-Clause" license_family: BSD license_file: LICENSE summary: "The python module iced implements the ICE normalization of hic data." + dev_url: "https://github.com/hiclib/iced" + doc_url: "https://members.cbio.mines-paristech.fr/~nvaroquaux/iced" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64