try to create recipe for pgenlib

[aryarm]

for version v0.91.0 of pgenlib which adds support for numpy 2.0

see chrchang/plink-ng#272

what's weird is that it was able to compile in the github actions for the pgenlib repo but not in the bioconda env, for some reason

things I am trying:

• using a different compiler? perhaps it isn't using the same one that was used to build the wheels

[aryarm]

I tested this in a GitHub codespace, and noticed that the build seems to work when I remove --no-build-isolation, even though the build environment created by conda appears to have all of the same versions of dependencies as those installed by pip. Very interesting! Here's a diff of the logs (comparing before with --no-build-isolation to after without it):

Click here to expand the diff

--- log	2024-07-12 18:41:29.150250714 +0000
+++ log-build-isolation	2024-07-12 18:43:41.358245599 +0000
Processing /workspaces/pgenlib-0.91.0
+  Installing build dependencies: started
+  Running command pip subprocess to install build dependencies
+  Using pip 24.0 from /opt/conda/envs/py38/lib/python3.8/site-packages/pip (python 3.8)
+  Ignoring numpy: markers 'python_version >= "3.9"' don't match your environment
+  Collecting wheel
+    Obtaining dependency information for wheel from https://files.pythonhosted.org/packages/7d/cd/d7460c9a869b16c3dd4e1e403cce337df165368c71d6af229a74699622ce/wheel-0.43.0-py3-none-any.whl.metadata
+    Downloading wheel-0.43.0-py3-none-any.whl.metadata (2.2 kB)
+  Collecting setuptools
+    Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/ef/15/88e46eb9387e905704b69849618e699dc2f54407d8953cc4ec4b8b46528d/setuptools-70.3.0-py3-none-any.whl.metadata
+    Downloading setuptools-70.3.0-py3-none-any.whl.metadata (5.8 kB)
+  Collecting Cython>=0.29.21
+    Obtaining dependency information for Cython>=0.29.21 from https://files.pythonhosted.org/packages/3a/6f/8a79707ac83cf4dc79903077b856c7c31dc08675b9fbde77a38ca79814b4/Cython-3.0.10-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
+    Downloading Cython-3.0.10-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.2 kB)
+  Collecting oldest-supported-numpy>=2022.8.16
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+    Downloading oldest_supported_numpy-2023.12.21-py3-none-any.whl.metadata (9.8 kB)
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+    Link requires a different Python (3.8.19 not in: '>=3.9'): https://files.pythonhosted.org/packages/65/6e/09db70a523a96d25e115e71cc56a6f9031e7b8cd166c1ac8438307c14058/numpy-1.26.4.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.9)
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+    Link requires a different Python (3.8.19 not in: '>=3.9'): https://files.pythonhosted.org/packages/de/96/5be497058b1bbc2709739a502395044a3890920e3bec283f4dcc1fc2ac79/numpy-2.0.0rc2.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.9)
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+  Collecting numpy==1.17.3 (from oldest-supported-numpy>=2022.8.16)
+    Obtaining dependency information for numpy==1.17.3 from https://files.pythonhosted.org/packages/3a/8f/f9ee25c0ae608f86180c26a1e35fe7ea9d71b473ea7f54db20759ba2745e/numpy-1.17.3-cp38-cp38-manylinux1_x86_64.whl.metadata
+    Downloading numpy-1.17.3-cp38-cp38-manylinux1_x86_64.whl.metadata (2.0 kB)
+  Downloading wheel-0.43.0-py3-none-any.whl (65 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.8/65.8 kB 1.3 MB/s eta 0:00:00
+  Downloading setuptools-70.3.0-py3-none-any.whl (931 kB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 931.1/931.1 kB 15.8 MB/s eta 0:00:00
+  Downloading Cython-3.0.10-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 51.9 MB/s eta 0:00:00
+  Downloading oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB)
+  Downloading numpy-1.17.3-cp38-cp38-manylinux1_x86_64.whl (20.5 MB)
+     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.5/20.5 MB 54.4 MB/s eta 0:00:00
+  Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy
+    Creating /tmp/pip-build-env-baabbhw2/overlay/bin
+    changing mode of /tmp/pip-build-env-baabbhw2/overlay/bin/wheel to 757
+    changing mode of /tmp/pip-build-env-baabbhw2/overlay/bin/f2py to 757
+    changing mode of /tmp/pip-build-env-baabbhw2/overlay/bin/f2py3 to 757
+    changing mode of /tmp/pip-build-env-baabbhw2/overlay/bin/f2py3.8 to 757
+    changing mode of /tmp/pip-build-env-baabbhw2/overlay/bin/cygdb to 757
+    changing mode of /tmp/pip-build-env-baabbhw2/overlay/bin/cython to 757
+    changing mode of /tmp/pip-build-env-baabbhw2/overlay/bin/cythonize to 757
+  Successfully installed Cython-3.0.10 numpy-1.17.3 oldest-supported-numpy-2023.12.21 setuptools-70.3.0 wheel-0.43.0
+  Installing build dependencies: finished with status 'done'
+  Getting requirements to build wheel: started
+  Running command Getting requirements to build wheel
+  Compiling src/pgenlib/pgenlib.pyx because it depends on /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
+  [1/1] Cythonizing src/pgenlib/pgenlib.pyx
+  running egg_info
+  writing src/Pgenlib.egg-info/PKG-INFO
+  writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt
+  writing requirements to src/Pgenlib.egg-info/requires.txt
+  writing top-level names to src/Pgenlib.egg-info/top_level.txt
+  dependency /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
+  dependency /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
+  dependency /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
+  dependency /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
+  dependency /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
+  reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
+  reading manifest template 'MANIFEST.in'
+  adding license file 'LICENSE'
+  writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
+  Getting requirements to build wheel: finished with status 'done'
+  Created temporary directory: /tmp/pip-modern-metadata-v4hyqhtq
Building wheel for Pgenlib (pyproject.toml): started
Running command Building wheel for Pgenlib (pyproject.toml)
running bdist_wheel
running build
running build_clib
building 'clib' library
-  creating build
-  creating build/temp.linux-x86_64-cpython-38
-  creating build/temp.linux-x86_64-cpython-38/src
-  creating build/temp.linux-x86_64-cpython-38/src/plink2
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/arm
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/x86
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/zstd
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/adler32.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/adler32.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/arm/arm_cpu_features.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/arm/arm_cpu_features.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/crc32.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/crc32.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/deflate_compress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/deflate_compress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/deflate_decompress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/deflate_decompress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/gzip_compress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/gzip_compress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/gzip_decompress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/gzip_decompress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/utils.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/utils.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/x86/x86_cpu_features.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/x86/x86_cpu_features.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/zlib_compress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/zlib_compress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/libdeflate/lib/zlib_decompress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/zlib_decompress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/debug.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/debug.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/entropy_common.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/entropy_common.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/error_private.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/error_private.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/fse_decompress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/fse_decompress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/pool.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/pool.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/threading.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/threading.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/xxhash.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/xxhash.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/common/zstd_common.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/zstd_common.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/fse_compress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/fse_compress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/hist.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/hist.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/huf_compress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/huf_compress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_compress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_compress_literals.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress_literals.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_compress_sequences.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress_sequences.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_compress_superblock.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress_superblock.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_double_fast.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_double_fast.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_fast.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_fast.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_lazy.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_lazy.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_ldm.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_ldm.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstd_opt.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_opt.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/compress/zstdmt_compress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstdmt_compress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/decompress/huf_decompress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/huf_decompress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/decompress/zstd_ddict.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/zstd_ddict.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/decompress/zstd_decompress.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/zstd_decompress.o
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC -Isrc/plink2/libdeflate -c src/plink2/zstd/lib/decompress/zstd_decompress_block.c -o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/zstd_decompress_block.o
-  ar rcs build/temp.linux-x86_64-cpython-38/libclib.a build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/adler32.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/arm/arm_cpu_features.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/crc32.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/deflate_compress.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/deflate_decompress.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/gzip_compress.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/gzip_decompress.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/utils.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/x86/x86_cpu_features.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/zlib_compress.o build/temp.linux-x86_64-cpython-38/src/plink2/libdeflate/lib/zlib_decompress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/debug.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/entropy_common.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/error_private.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/fse_decompress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/pool.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/threading.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/xxhash.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/common/zstd_common.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/fse_compress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/hist.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/huf_compress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress_literals.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress_sequences.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_compress_superblock.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_double_fast.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_fast.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_lazy.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_ldm.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstd_opt.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/compress/zstdmt_compress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/huf_decompress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/zstd_ddict.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/zstd_decompress.o build/temp.linux-x86_64-cpython-38/src/plink2/zstd/lib/decompress/zstd_decompress_block.o
running build_ext
building 'pgenlib' extension
-  creating build/temp.linux-x86_64-cpython-38/src/pgenlib
-  creating build/temp.linux-x86_64-cpython-38/src/plink2/include
-  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -Isrc/pgenlib -I/opt/conda/envs/py38/lib/python3.8/site-packages/numpy/core/include -Isrc/plink2/libdeflate -I/opt/conda/envs/py38/include/python3.8 -c src/pgenlib/pgenlib.cpp -o build/temp.linux-x86_64-cpython-38/src/pgenlib/pgenlib.o -std=c++98 -Wno-unused-function -Wno-macro-redefined -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC
-  In file included from /opt/conda/envs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
-                   from /opt/conda/envs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
-                   from /opt/conda/envs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
+  gcc -pthread -B /opt/conda/envs/py38/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -O2 -isystem /opt/conda/envs/py38/include -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include -Isrc/plink2/libdeflate -I/opt/conda/envs/py38/include/python3.8 -c src/pgenlib/pgenlib.cpp -o build/temp.linux-x86_64-cpython-38/src/pgenlib/pgenlib.o -std=c++98 -Wno-unused-function -Wno-macro-redefined -DZSTD_DISABLE_ASM -DLIBDEFLATE_STATIC
+  In file included from /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
+                   from /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
+                   from /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                    from src/pgenlib/pgenlib.cpp:1293:
-  /opt/conda/envs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
+  /tmp/pip-build-env-baabbhw2/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
    17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
src/pgenlib/pgenlib.cpp:1532: warning: "likely" redefined
@@ -121,1377 +143,1347 @@
src/pgenlib/../plink2/include/plink2_base.h:275: note: this is the location of the previous definition
    275 | #  define unlikely(expr) __builtin_expect(!!(expr), 0)
        |
-  src/pgenlib/pgenlib.cpp: In function ‘npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr*)’:
-  src/pgenlib/pgenlib.cpp:5811:13: error: ‘PyDataType_ELSIZE’ was not declared in this scope; did you mean ‘PyDataType_ISUNSIZED’?
-   5811 |   __pyx_r = PyDataType_ELSIZE(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~
-        |             PyDataType_ISUNSIZED
-  src/pgenlib/pgenlib.cpp: In function ‘npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr*)’:
-  src/pgenlib/pgenlib.cpp:5845:13: error: ‘PyDataType_ALIGNMENT’ was not declared in this scope; did you mean ‘PyDataType_ISSIGNED’?
-   5845 |   __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~~
-        |             PyDataType_ISSIGNED
-  src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_5numpy_5dtype_6fields_fields(PyArray_Descr*)’:
-  src/pgenlib/pgenlib.cpp:5883:15: error: ‘PyDataType_FIELDS’ was not declared in this scope; did you mean ‘PyDataType_HASFIELDS’?
-   5883 |   __pyx_t_1 = PyDataType_FIELDS(__pyx_v_self);
-        |               ^~~~~~~~~~~~~~~~~
-        |               PyDataType_HASFIELDS
-  src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_5numpy_5dtype_5names_names(PyArray_Descr*)’:
-  src/pgenlib/pgenlib.cpp:5925:15: error: ‘PyDataType_NAMES’ was not declared in this scope; did you mean ‘PyDataType_ISNUMBER’?
-   5925 |   __pyx_t_1 = PyDataType_NAMES(__pyx_v_self);
-        |               ^~~~~~~~~~~~~~~~
-        |               PyDataType_ISNUMBER
-  src/pgenlib/pgenlib.cpp: In function ‘PyArray_ArrayDescr* __pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr*)’:
-  src/pgenlib/pgenlib.cpp:5963:13: error: ‘PyDataType_SUBARRAY’ was not declared in this scope; did you mean ‘PyDataType_HASSUBARRAY’?
-   5963 |   __pyx_r = PyDataType_SUBARRAY(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~
-        |             PyDataType_HASSUBARRAY
-  src/pgenlib/pgenlib.cpp: In function ‘npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr*)’:
-  src/pgenlib/pgenlib.cpp:5997:13: error: ‘PyDataType_FLAGS’ was not declared in this scope; did you mean ‘PyDataType_FLAGCHK’?
-   5997 |   __pyx_r = PyDataType_FLAGS(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~
-        |             PyDataType_FLAGCHK
-  src/pgenlib/pgenlib.cpp: In function ‘int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject*)’:
-  src/pgenlib/pgenlib.cpp:6031:13: error: ‘PyArray_MultiIter_NUMITER’ was not declared in this scope; did you mean ‘PyArray_MultiIter_NEXTi’?
-   6031 |   __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~~~~~~~
-        |             PyArray_MultiIter_NEXTi
-  src/pgenlib/pgenlib.cpp: In function ‘npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject*)’:
-  src/pgenlib/pgenlib.cpp:6065:13: error: ‘PyArray_MultiIter_SIZE’ was not declared in this scope; did you mean ‘PyArray_MultiIter_GOTO’?
-   6065 |   __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~~~~
-        |             PyArray_MultiIter_GOTO
-  src/pgenlib/pgenlib.cpp: In function ‘npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject*)’:
-  src/pgenlib/pgenlib.cpp:6099:13: error: ‘PyArray_MultiIter_INDEX’ was not declared in this scope; did you mean ‘PyArray_MultiIter_NEXT’?
-   6099 |   __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~~~~~
-        |             PyArray_MultiIter_NEXT
-  src/pgenlib/pgenlib.cpp: In function ‘int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject*)’:
-  src/pgenlib/pgenlib.cpp:6133:13: error: ‘PyArray_MultiIter_NDIM’ was not declared in this scope; did you mean ‘PyArray_MultiIter_NEXT’?
-   6133 |   __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~~~~
-        |             PyArray_MultiIter_NEXT
-  src/pgenlib/pgenlib.cpp: In function ‘npy_intp* __pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject*)’:
-  src/pgenlib/pgenlib.cpp:6167:13: error: ‘PyArray_MultiIter_DIMS’ was not declared in this scope; did you mean ‘PyArray_MultiIter_DATA’?
-   6167 |   __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~~~~
-        |             PyArray_MultiIter_DATA
-  src/pgenlib/pgenlib.cpp: In function ‘void** __pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject*)’:
-  src/pgenlib/pgenlib.cpp:6201:13: error: ‘PyArray_MultiIter_ITERS’ was not declared in this scope; did you mean ‘PyArray_MultiIter_NEXT’?
-   6201 |   __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~~~~~~~
-        |             PyArray_MultiIter_NEXT

[aryarm]

@mrkylesmith, can you explain those errors in the logs to me, by any chance? For example, what could this mean?

src/pgenlib/pgenlib.cpp:5811:13: error: ‘PyDataType_ELSIZE’ was not declared in this scope; did you mean ‘PyDataType_ISUNSIZED’?
-   5811 |   __pyx_r = PyDataType_ELSIZE(__pyx_v_self);
-        |             ^~~~~~~~~~~~~~~~~
-        |             PyDataType_ISUNSIZED

I think the issue is ultimately something to do with the dependencies (and not the c++ code) because it works without --no-build-isolation, but I'm hoping that a better understanding of the error messages might give me some more ideas for things I could try.

[aryarm]

lol I don't know why it decided to work all of a sudden, but I'm not complaining