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Evolution Gymの依存パッケージをインストールする時にh5pyのインストールに失敗する

所要時間: 約 12分

「Pythonではじめるオープンエンドな進化的アルゴリズム」の出版に関わらせていただいた。この書籍の中では、 Evolution Gym というツールを使って実装例を示している。 Evolution Gym は良くできたツールなのだが、インストールに失敗するケースがいくつかあった。こちらで認識できているものについては本家にプルリクエストを送った。しかし想定していない問題があるようだった。

その問題とは h5py のインストール時に実行されるビルドに失敗するという物だった。私が使っている環境ではこの問題に気付く事ができなかった。過去のログなどを確認すると、whl形式のパッケージをダウンロードしていたようだった。whlの中にはビルド済みバイナリが含まれている。そのためビルドを実行せずインストールに成功していたようだ。

そこで今回は h5py をwhlを使わずインストールする事にした。

hdf5をインストールする

h5py は HDF というバイナリのフォーマットを取り扱うライブラリだ1。内部では HDF5 をリンクして使用している2。 事前に hdf5 を Homebrew でインストールしておく事にした。

brew install hdf5
hdf5をインストールする。

Cythonをインストールする

h5py のビルドには Cython を使うため、 Cython をインストールする。インストールの様子はhttps://blog.symdon.info/posts/1697872568/にまとめた。

h5py-3.6.0のインストールで右往左往する

Evolution Gym は h5py-3.6.0 を requirements.txt に含めている。まず、このバージョンを pip でインストールできるかを確認する事にした。 h5py-3.6.0 では以下のwhl形式が提供されている3。

  • h5py-3.6.0-cp310-cp310-macosx_10_9_x86_64.whl
  • h5py-3.6.0-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  • h5py-3.6.0-cp310-cp310-win_amd64.whl
  • h5py-3.6.0-cp37-cp37m-macosx_10_9_x86_64.whl
  • h5py-3.6.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  • h5py-3.6.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
  • h5py-3.6.0-cp37-cp37m-win_amd64.whl
  • h5py-3.6.0-cp38-cp38-macosx_10_9_x86_64.whl
  • h5py-3.6.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  • h5py-3.6.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
  • h5py-3.6.0-cp38-cp38-win_amd64.whl
  • h5py-3.6.0-cp39-cp39-macosx_10_9_x86_64.whl
  • h5py-3.6.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  • h5py-3.6.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
  • h5py-3.6.0-cp39-cp39-win_amd64.whl

インストールする環境がこの範囲に含まれていれば、whlを使ってインストールされる。

pip install 'h5py==3.6.0'
Collecting h5py==3.6.0
  Downloading h5py-3.6.0-cp38-cp38-macosx_10_9_x86_64.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 331.7 kB/s eta 0:00:00
Requirement already satisfied: numpy>=1.14.5 in /Users/foo/.venv/testing-h5py/lib/python3.8/site-packages (from h5py==3.6.0) (1.21.5)
Installing collected packages: h5py
  Attempting uninstall: h5py
    Found existing installation: h5py 3.10.0
    Uninstalling h5py-3.10.0:
      Successfully uninstalled h5py-3.10.0
Successfully installed h5py-3.6.0
whlを使用してインストールする。

whlを用いてインストールされた。以降の確認のため一度アンインストールする。

pip uninstall -y h5py
Found existing installation: h5py 3.10.0
Uninstalling h5py-3.10.0:
  Successfully uninstalled h5py-3.10.0
h5pyをアンインストールする。

先ほど一覧でしめしたwhlの対応する環境に当てはまらなければ、tarballをダウンロードしビルドされる事になる。例えばM1のmacOSを使っている場合には、ビルドが行われる。whlを使用したくない場合は pip install のオプションとして --no-binary\=h5py を指定する。

pip install 'h5py==3.6.0' --no-binary=h5py 2>&1
Collecting h5py==3.6.0
  Using cached h5py-3.6.0.tar.gz (384 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: numpy>=1.14.5 in /Users/foo/.venv/testing-h5py/lib/python3.8/site-packages (from h5py==3.6.0) (1.21.5)
Building wheels for collected packages: h5py
  Building wheel for h5py (pyproject.toml): started
  Building wheel for h5py (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error

  × Building wheel for h5py (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [528 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-13-x86_64-cpython-38
      creating build/lib.macosx-13-x86_64-cpython-38/h5py
      copying h5py/h5py_warnings.py -> build/lib.macosx-13-x86_64-cpython-38/h5py
      copying h5py/version.py -> build/lib.macosx-13-x86_64-cpython-38/h5py
      copying h5py/__init__.py -> build/lib.macosx-13-x86_64-cpython-38/h5py
      copying h5py/ipy_completer.py -> build/lib.macosx-13-x86_64-cpython-38/h5py
      creating build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/files.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/compat.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/__init__.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/selections.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/dataset.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/vds.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/selections2.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/group.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/datatype.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/attrs.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/dims.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/base.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      copying h5py/_hl/filters.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/_hl
      creating build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_attribute_create.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_file_image.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/conftest.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_h5f.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_group.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_errors.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_slicing.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_h5pl.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_attrs.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/__init__.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_attrs_data.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_h5t.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_big_endian_file.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_h5p.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_h5o.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_datatype.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/common.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_dataset.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_file.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_selections.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_dtype.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_h5.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_file2.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_completions.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_filters.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_base.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      copying h5py/tests/test_objects.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests
      creating build/lib.macosx-13-x86_64-cpython-38/h5py/tests/data_files
      copying h5py/tests/data_files/__init__.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/data_files
      creating build/lib.macosx-13-x86_64-cpython-38/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/test_vds
      copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/test_vds
      copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.macosx-13-x86_64-cpython-38/h5py/tests/data_files
      running build_ext
      warning: h5py/defs.pxd:15:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:62:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:64:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:66:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:68:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:70:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:72:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:74:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:76:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:78:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:102:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:104:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:106:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:107:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:109:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:110:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:112:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:114:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:116:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:180:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:197:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:199:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:201:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:203:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:213:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:215:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:229:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:231:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:233:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:235:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:237:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:239:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:241:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:269:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:271:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:273:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:275:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:277:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:279:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:285:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:287:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:289:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:291:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:293:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:295:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:297:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:299:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:333:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:335:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:337:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:339:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:341:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:343:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:345:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:347:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:349:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:383:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/defs.pxd:385:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:48:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:64:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:143:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:148:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:156:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:165:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:198:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:287:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_hdf5.pxd:334:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_ext.pxd:14:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_ext.pxd:25:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/api_types_ext.pxd:52:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/_conv.pyx:161:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/_conv.pyx:422:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
      warning: h5py/h5r.pxd:17:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      # License:  Standard 3-clause BSD; see "license.txt" for full license terms
      #           and contributor agreement.

      from .defs cimport *

      from ._objects cimport class ObjectID
                             ^
      ------------------------------------------------------------

      h5py/h5t.pxd:13:23: Expected an identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

      from logging import getLogger

      from .h5 import get_config
      from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
      from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
      ^
      ------------------------------------------------------------

      h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_OBJ.pxd' not found

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

      from logging import getLogger

      from .h5 import get_config
      from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
      from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
      ^
      ------------------------------------------------------------

      h5py/_conv.pyx:21:0: 'h5py/h5t/typewrap.pxd' not found

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

      from logging import getLogger

      from .h5 import get_config
      from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
      from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
      ^
      ------------------------------------------------------------

      h5py/_conv.pyx:21:0: 'h5py/h5t/py_create.pxd' not found

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

      from logging import getLogger

      from .h5 import get_config
      from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
      from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
      ^
      ------------------------------------------------------------

      h5py/_conv.pyx:21:0: 'h5py/h5t/TypeID.pxd' not found

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

      from logging import getLogger

      from .h5 import get_config
      from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
      from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
      ^
      ------------------------------------------------------------

      h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_PYTHON_OPAQUE_TAG.pxd' not found

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          void* ptr

      cdef int conv_vlen2ndarray(void* ipt,
                                 void* opt,
                                 cnp.dtype elem_dtype,
                                 TypeID intype,
                                 ^
      ------------------------------------------------------------

      h5py/_conv.pyx:687:27: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

      cdef int conv_vlen2ndarray(void* ipt,
                                 void* opt,
                                 cnp.dtype elem_dtype,
                                 TypeID intype,
                                 TypeID outtype) except -1:
                                 ^
      ------------------------------------------------------------

      h5py/_conv.pyx:688:27: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          return 0


      cdef int conv_ndarray2vlen(void* ipt,
                                 void* opt,
                                 TypeID intype,
                                 ^
      ------------------------------------------------------------

      h5py/_conv.pyx:820:27: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...


      cdef int conv_ndarray2vlen(void* ipt,
                                 void* opt,
                                 TypeID intype,
                                 TypeID outtype) except -1:
                                 ^
      ------------------------------------------------------------

      h5py/_conv.pyx:821:27: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          :return: error-code
          """
          cdef:
              int command = cdata[0].command
              size_t src_size, dst_size
              TypeID supertype
              ^
      ------------------------------------------------------------

      h5py/_conv.pyx:629:8: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          """
          cdef:
              int command = cdata[0].command
              size_t src_size, dst_size
              TypeID supertype
              TypeID outtype
              ^
      ------------------------------------------------------------

      h5py/_conv.pyx:630:8: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                               void *bkg_i,
                               hid_t dxpl) except -1 with gil:
          cdef:
              int command = cdata[0].command
              size_t src_size, dst_size
              TypeID supertype
              ^
      ------------------------------------------------------------

      h5py/_conv.pyx:752:8: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                               hid_t dxpl) except -1 with gil:
          cdef:
              int command = cdata[0].command
              size_t src_size, dst_size
              TypeID supertype
              TypeID outtype
              ^
      ------------------------------------------------------------

      h5py/_conv.pyx:753:8: 'TypeID' is not a type identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          cdef char* ctag = NULL
          try:
              if H5Tget_class(obj) == H5T_OPAQUE:
                  ctag = H5Tget_tag(obj)
                  if ctag != NULL:
                      if strcmp(ctag, H5PY_PYTHON_OPAQUE_TAG) == 0:
                                      ^
      ------------------------------------------------------------

      h5py/_conv.pyx:157:32: 'H5PY_PYTHON_OPAQUE_TAG' is not a constant, variable or function identifier
      warning: h5py/_conv.pyx:157:32: Obtaining 'const char *' from externally modifiable global Python value

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          elif command == H5T_CONV_FREE:
              pass

          elif command == H5T_CONV_CONV:
              # need to pass element dtype to converter
              supertype = typewrap(H5Tget_super(src_id))
                          ^
      ------------------------------------------------------------

      h5py/_conv.pyx:645:20: 'typewrap' is not a constant, variable or function identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

          elif command == H5T_CONV_CONV:
              # need to pass element dtype to converter
              supertype = typewrap(H5Tget_super(src_id))
              dt = supertype.dtype
              outtype = py_create(dt)
                        ^
      ------------------------------------------------------------

      h5py/_conv.pyx:647:18: 'py_create' is not a constant, variable or function identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              PyObject *pdata_elem
              char* buf = <char*>buf_i

          if command == H5T_CONV_INIT:
              cdata[0].need_bkg = H5T_BKG_NO
              if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
                                      ^
      ------------------------------------------------------------

      h5py/_conv.pyx:761:32: 'H5PY_OBJ' is not a constant, variable or function identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

          if command == H5T_CONV_INIT:
              cdata[0].need_bkg = H5T_BKG_NO
              if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
                  return -2
              supertype = typewrap(H5Tget_super(dst_id))
                          ^
      ------------------------------------------------------------

      h5py/_conv.pyx:763:20: 'typewrap' is not a constant, variable or function identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                  return -2
              supertype = typewrap(H5Tget_super(dst_id))
              for i in range(nl):
                  # smells a lot
                  memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem))
                  if supertype != py_create((<cnp.ndarray> pdata_elem).dtype, 1):
                                  ^
      ------------------------------------------------------------

      h5py/_conv.pyx:767:28: 'py_create' is not a constant, variable or function identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              if nl == 0:
                  return 0

              # need to pass element dtype to converter
              pdata_elem = pdata[0]
              supertype = py_create((<cnp.ndarray> pdata_elem).dtype)
                          ^
      ------------------------------------------------------------

      h5py/_conv.pyx:784:20: 'py_create' is not a constant, variable or function identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                  return 0

              # need to pass element dtype to converter
              pdata_elem = pdata[0]
              supertype = py_create((<cnp.ndarray> pdata_elem).dtype)
              outtype = typewrap(H5Tget_super(dst_id))
                        ^
      ------------------------------------------------------------

      h5py/_conv.pyx:785:18: 'typewrap' is not a constant, variable or function identifier

      Error compiling Cython file:
      ------------------------------------------------------------
      ...

          enum = H5Tenum_create(H5T_STD_I32LE)

          vlentype = H5Tvlen_create(H5T_STD_I32LE)

          pyobj = H5PY_OBJ
                  ^
      ------------------------------------------------------------

      h5py/_conv.pyx:894:12: 'H5PY_OBJ' is not a constant, variable or function identifier
      Loading library to get build settings and version: libhdf5.dylib
      ********************************************************************************
                             Summary of the h5py configuration

      HDF5 include dirs: []
      HDF5 library dirs: []
           HDF5 Version: (1, 14, 2)
            MPI Enabled: False
       ROS3 VFD Enabled: False
       Rebuild Required: True

      ********************************************************************************
      Executing api_gen rebuild of defs
      Executing cythonize()
      [ 1/24] Cythonizing /private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-install-8b6c2mrb/h5py_3a9bffda4ab548d5ac5aea13ae9c6ee1/h5py/_conv.pyx
      Traceback (most recent call last):
        File "/Users/foo/.venv/testing-h5py/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/foo/.venv/testing-h5py/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/Users/foo/.venv/testing-h5py/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 434, in build_wheel
          return self._build_with_temp_dir(
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir
          self.run_setup()
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 341, in run_setup
          exec(code, locals())
        File "<string>", line 104, in <module>
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/__init__.py", line 103, in setup
          return distutils.core.setup(**attrs)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/dist.py", line 989, in run_command
          super().run_command(command)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 364, in run
          self.run_command("build")
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/dist.py", line 989, in run_command
          super().run_command(command)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 131, in run
          self.run_command(cmd_name)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/dist.py", line 989, in run_command
          super().run_command(command)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-install-8b6c2mrb/h5py_3a9bffda4ab548d5ac5aea13ae9c6ee1/setup_build.py", line 170, in run
          self.extensions = cythonize(self._make_extensions(config),
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
          cythonize_one(*args)
        File "/private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-build-env-uvpwfguv/overlay/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: /private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-install-8b6c2mrb/h5py_3a9bffda4ab548d5ac5aea13ae9c6ee1/h5py/_conv.pyx
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for h5py
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects
WARNING: There was an error checking the latest version of pip.
whlを使用してインストールする。

from ~ cimport class ~ 構文が使用できなかったり、インポートする対象が存在しなかったりと、よく分からない状態になっていた。ログを見るとCythonのバージョンが正しくないといった出力もある。

構文の問題については、Cython-3.0.0のあたりで修正されたもののようだった。

The undocumented, untested and apparently useless syntax from somemodule cimport class/struct/union somename was removed. The type modifier is not needed here and a plain cimport of the name will do. (Github issue #4904)

Cython-3.0.0 Changes

issue(https://github.com/cython/cython/pull/4904)もある。tarballの中身を確認すると、確かに pyproject.toml には Cython-0.29.14 を要求する記述があった。

[build-system]
# Further build requirements - like numpy & cython - come from setup.py via
# the PEP 517 interface.
requires = [
    "setuptools",
    "wheel",
    "oldest-supported-numpy",
    "pkgconfig",
    "Cython >=0.29; python_version<'3.8'",
    "Cython >=0.29.14; python_version=='3.8'",
    "Cython >=0.29.15; python_version>='3.9'",
]
build-backend = "setuptools.build_meta"
pyproject.toml

そこで幾つかの Cython のバージョンを確認する事にした。要求されていないものについても、もしかしたらと思い確認したが、結果としては全て同じエラーになった。

  • cython-3.0.4
  • cython-0.29.14
  • cython-0.29.13
  • cython-0.29
  • cython-0.28

whl として存在している h5py はどのようにビルドされたのか、結局よく分からなかった。ただ、これ以上は深追いせず、 h5py==3.6.0 のソースコードからのビルドを諦める事にした。本当にやりたい事は「 Evolution Gym を使いたい」だけであって、 h5py==3.6.0 をソースコードからビルドしたい訳ではないからだった。

Evolution Gymはh5pyを使っているのか？

h5py==3.6.0 のソースコードからのビルドを諦めたため、一度立ち止まって別の方向を考える事にした。元々は Evolution Gym の requirements.txt にバージョン指定で記述されている事が発端だった。もし Evolution Gym で h5py で直接 import していないのであれば、そもそも requirements.txt には記述する必要はない。

そこで Evolution Gym のコードの中で h5py の記述がある場所を grep した。

$ find . -type f -exec grep --color=auto -nH --null -e h5py \{\} +
./requirements.txt:5:h5py==3.6.0
./environment.yml:12:    - h5py==3.6.0
./examples/externals/pytorch_a2c_ppo_acktr_gail/a2c_ppo_acktr/algo/gail.py:1:import h5py
./examples/externals/pytorch_a2c_ppo_acktr_gail/requirements.txt:5:h5py
./examples/externals/pytorch_a2c_ppo_acktr_gail/gail_experts/convert_to_pytorch.py:5:import h5py
./examples/externals/pytorch_a2c_ppo_acktr_gail/gail_experts/convert_to_pytorch.py:28:    with h5py.File(args.h5_file, 'r') as f:

Grep exited abnormally with code 1 at Sun Oct 22 08:21:29, duration 4.08 s

h5py は使われていたが、使われている箇所は限定的だった。しかもよく見ると git submodule として登録されている、 examples/externals/pytorch_a2c_ppo_acktr_gail で使用しているだけだった。しかも examples ディレクトリは実装例のコードがあるだけであって、 Evolution Gym 本体ではない。つまり Evolution Gym 自身は h5py を必要とせず、実装例を実行する場合に必要になるという事だった。

h5py をuninstallした状態で Evolution Gym のシミュレータを起動してみる事にした。

pyhton examples/gym_test.py
シミュレータを起動する。

https://res.cloudinary.com/symdon/image/upload/v1697685496/blog.symdon.info/1697684292/example_f99vlj.png

シミュレータは起動できた。これだけでは Evolution Gym 全体で正しく動作するとは言えないけれど、少なくとも Evolution Gym の requirements.txt には記述しなくても良さそうだった。

h5py-3.10.0をインストールする

h5py はインストールしなくても良さそうだったが、インストールできないままでは目覚めが悪い。そこで最新の h5py を入れてみる事にした。最新のバージョンは現時点で h5py-3.10.0 だった4。

pip install h5py --no-binary=h5py --no-cache
h5py-3.10.0をインストールする。
Found existing installation: h5py 3.10.0
Uninstalling h5py-3.10.0:
  Would remove:
    /Users/foo/.venv/testing-h5py/lib/python3.8/site-packages/h5py-3.10.0.dist-info/*
    /Users/foo/.venv/testing-h5py/lib/python3.8/site-packages/h5py/*
Proceed (Y/n)? Y
  Successfully uninstalled h5py-3.10.0
bash-5.2$ pip install h5py --no-binary=h5py --no-cache
Collecting h5py
  Downloading h5py-3.10.0.tar.gz (403 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 403.7/403.7 kB 1.1 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.17.3 in /Users/foo/.venv/testing-h5py/lib/python3.8/site-packages (from h5py) (1.21.5)
Building wheels for collected packages: h5py
  Building wheel for h5py (pyproject.toml) ... -
done
  Created wheel for h5py: filename=h5py-3.10.0-cp38-cp38-macosx_13_0_x86_64.whl size=1483983 sha256=12cca7e0eebba95f877a86dbfe7db5929870efa700feb274035b36e44f100012
  Stored in directory: /private/var/folders/2f/1mkpnp3n1gjd0r7l9nm_dyhr0000gn/T/pip-ephem-wheel-cache-zu_e4nqr/wheels/24/36/b8/d4f87683938866423e3ad9c8d3cfd788089776585856660d2f
Successfully built h5py
Installing collected packages: h5py
Successfully installed h5py-3.10.0

再現できなくなってしまったけれど遭遇した問題

作業をしている最中に遭遇したが、再現させようとしてできなくなってしまった問題を掲載しておく。内容が Cython と h5py のインストール時でごちゃまぜになってしまっている。一部(もしくは全部)は Cython の話をしているかもしれない。

gfortran

gfortran がないエラーに遭遇した。これは Homebrew で素直に gfortran をインストールした。

MACOSX_DEPLOYMENT_TARGET環境変数

MACOSX_DEPLOYMENT_TARGET 環境変数が設定されてないと、このバージョンの値がintとなり、strを期待している箇所との食い違いによりエラーが発生する事があった。とりあえず使っているmacOSのバージョンを調べ MACOSX_DEPLOYMENT_TARGET 環境変数に値を設定したところ、問題は解消した。

export MACOSX_DEPLOYMENT_TARGET=13.6
MACOSX_DEPLOYMENT_TARGET環境変数を設定する。
1

https://docs.h5py.org/en/stable/

2

未確認。

4

2023年 10月22日 日曜日 09時06分58秒 JST