pooch
pooch copied to clipboard
Published
20 hours ago •
fatiando
fatiando
1.6.0: sphinx fails (doc/ content is not up to date?)
System information
- Operating system: Linux x86/64
- Python installation (Anaconda, system, ETS): system
- Version of Python: 3.8.13
- Version of this package: 1.6.0
- If using conda, paste the output of
conda listbelow:
Sphinx fails (using setuptools<>sphinx integration)
+ echo 'from setuptools import setup; setup()'
+ /usr/bin/python3 setup.py build_sphinx -b man --build-dir build/sphinx
running build_sphinx
Running Sphinx v4.5.0
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://3.python-requests.org/objects.inv...
intersphinx inventory has moved: http://pandas.pydata.org/pandas-docs/stable/objects.inv -> https://pandas.pydata.org/pandas-docs/stable/objects.inv
building [mo]: targets for 0 po files that are out of date
building [man]: all manpages
updating environment: [new config] 23 added, 0 changed, 0 removed
reading sources... [100%] versions
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:20: WARNING: autosummary: stub file not found 'pooch.create'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:20: WARNING: autosummary: stub file not found 'pooch.Pooch'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:20: WARNING: autosummary: stub file not found 'pooch.retrieve'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:30: WARNING: autosummary: stub file not found 'pooch.os_cache'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:30: WARNING: autosummary: stub file not found 'pooch.make_registry'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:30: WARNING: autosummary: stub file not found 'pooch.file_hash'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:30: WARNING: autosummary: stub file not found 'pooch.check_version'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:30: WARNING: autosummary: stub file not found 'pooch.get_logger'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:42: WARNING: autosummary: stub file not found 'pooch.HTTPDownloader'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:42: WARNING: autosummary: stub file not found 'pooch.FTPDownloader'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:42: WARNING: autosummary: stub file not found 'pooch.SFTPDownloader'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:42: WARNING: autosummary: stub file not found 'pooch.DOIDownloader'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:53: WARNING: autosummary: stub file not found 'pooch.Unzip'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:53: WARNING: autosummary: stub file not found 'pooch.Untar'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:53: WARNING: autosummary: stub file not found 'pooch.Decompress'. Check your autosummary_generate setting.
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/api/index.rst:63: WARNING: autosummary: stub file not found 'pooch.test'. Check your autosummary_generate setting.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
writing... python-pooch.3 { about install retrieve multiple-files sample-data hashes user-defined-cache registry-files multiple-urls protocols logging downloaders processors authentication progressbars unpacking decompressing api/index compatibility citing changes versions } /home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/index.rst:32: WARNING: more than one target found for 'any' cross-reference 'about': could be :doc:`Start here` or :std:ref:`Start here`
/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc/index.rst:68: WARNING: more than one target found for 'any' cross-reference 'citing': could be :doc:`Cite Pooch` or :std:ref:`Cite Pooch`
failed
Exception occurred:
File "/usr/lib/python3.8/site-packages/sphinx/registry.py", line 342, in create_translator
setattr(translator, 'visit_' + name, MethodType(visit, translator))
TypeError: first argument must be callable
The full traceback has been saved in /tmp/sphinx-err-nc_zwojb.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
Sphinx fails as well when used is doc/Makefile
[tkloczko@devel-g2v pooch-1.6.0]$ make -C doc html
make: Entering directory '/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/doc'
Building API docs.
sphinx-autogen -i -t _templates -o api/generated api/index.rst
[autosummary] generating autosummary for: api/index.rst
[autosummary] writing to api/generated
Failed to import pooch.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.DOIDownloader.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.Decompress.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.FTPDownloader.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.HTTPDownloader.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.Pooch.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.SFTPDownloader.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.Untar.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.Unzip.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.check_version.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.create.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.file_hash.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.get_logger.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.make_registry.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.os_cache.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.retrieve.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
WARNING: [autosummary] failed to import pooch.test.
Possible hints:
* ModuleNotFoundError: No module named 'pooch'
* ImportError: no module named pooch
* KeyError: 'pooch'
Building HTML files.
sphinx-build -b html -d _build/doctrees . _build/html
Running Sphinx v4.5.0
Theme error:
no theme named 'sphinx_book_theme' found (missing theme.conf?)
make: *** [Makefile:43: html] Error 2
</details>
Looks like some modules mentioned in documentation no longer exist 🤔
Hi @kloczek for opening this issue. From the second traceback you copied, it seems that pooch is not installed on your system/environment. Have you tried running the following?
python -c "import pooch; print(pooch.__version__)"
If Pooch is correctly installed, you should get the installed version number in your stdout.
The same goes for sphinx_book_theme which apparently is not installed either.
In the env/requirements-doc.txt file you can find the additional required packages to build the documentation. The versions are pinned because we know they work without problem with the current version of Pooch, but we try to update them as soon as we have some free time to test them.
Feel free to ping me if you need more help!
After installing just generated rpm package with pooch module
[tkloczko@devel-g2v SPECS]$ python3 -c "import pooch; print(pooch.__version__)"
v1.6.0t
So hardoced in that code version is correct.
So now during the pep517 build (without installed `pooch')
+ /usr/bin/python3 -sBm build -w --no-isolation
* Getting dependencies for wheel...
running egg_info
creating pooch.egg-info
writing pooch.egg-info/PKG-INFO
writing dependency_links to pooch.egg-info/dependency_links.txt
writing requirements to pooch.egg-info/requires.txt
writing top-level names to pooch.egg-info/top_level.txt
writing manifest file 'pooch.egg-info/SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'pooch.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching '.github'
no previously-included directories found matching 'data'
no previously-included directories found matching 'doc'
no previously-included directories found matching 'env'
no previously-included directories found matching 'paper'
warning: no previously-included files found matching '.*.yml'
warning: no previously-included files found matching '.*rc'
warning: no previously-included files found matching 'Makefile'
warning: no previously-included files found matching '.gitignore'
warning: no previously-included files found matching '.gitattributes'
warning: no previously-included files found matching 'environment.yml'
warning: no previously-included files found matching 'license_notice.py'
adding license file 'LICENSE.txt'
writing manifest file 'pooch.egg-info/SOURCES.txt'
* Building wheel...
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/pooch
copying pooch/__init__.py -> build/lib/pooch
copying pooch/core.py -> build/lib/pooch
copying pooch/downloaders.py -> build/lib/pooch
copying pooch/hashes.py -> build/lib/pooch
copying pooch/processors.py -> build/lib/pooch
copying pooch/utils.py -> build/lib/pooch
copying pooch/_version.py -> build/lib/pooch
creating build/lib/pooch/tests
copying pooch/tests/__init__.py -> build/lib/pooch/tests
copying pooch/tests/test_core.py -> build/lib/pooch/tests
copying pooch/tests/test_downloaders.py -> build/lib/pooch/tests
copying pooch/tests/test_hashes.py -> build/lib/pooch/tests
copying pooch/tests/test_integration.py -> build/lib/pooch/tests
copying pooch/tests/test_processors.py -> build/lib/pooch/tests
copying pooch/tests/test_utils.py -> build/lib/pooch/tests
copying pooch/tests/test_version.py -> build/lib/pooch/tests
copying pooch/tests/utils.py -> build/lib/pooch/tests
running egg_info
writing pooch.egg-info/PKG-INFO
writing dependency_links to pooch.egg-info/dependency_links.txt
writing requirements to pooch.egg-info/requires.txt
writing top-level names to pooch.egg-info/top_level.txt
listing git files failed - pretending there aren't any
reading manifest file 'pooch.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching '.github'
no previously-included directories found matching 'data'
no previously-included directories found matching 'doc'
no previously-included directories found matching 'env'
no previously-included directories found matching 'paper'
warning: no previously-included files found matching '.*.yml'
warning: no previously-included files found matching '.*rc'
warning: no previously-included files found matching 'Makefile'
warning: no previously-included files found matching '.gitignore'
warning: no previously-included files found matching '.gitattributes'
warning: no previously-included files found matching 'environment.yml'
warning: no previously-included files found matching 'license_notice.py'
adding license file 'LICENSE.txt'
writing manifest file 'pooch.egg-info/SOURCES.txt'
creating build/lib/pooch/tests/data
copying pooch/tests/data/large-data.txt -> build/lib/pooch/tests/data
copying pooch/tests/data/registry-custom-url.txt -> build/lib/pooch/tests/data
copying pooch/tests/data/registry-invalid.txt -> build/lib/pooch/tests/data
copying pooch/tests/data/registry.txt -> build/lib/pooch/tests/data
copying pooch/tests/data/registry_comments.txt -> build/lib/pooch/tests/data
copying pooch/tests/data/store.tar.gz -> build/lib/pooch/tests/data
copying pooch/tests/data/store.zip -> build/lib/pooch/tests/data
copying pooch/tests/data/tiny-data.tar.gz -> build/lib/pooch/tests/data
copying pooch/tests/data/tiny-data.txt -> build/lib/pooch/tests/data
copying pooch/tests/data/tiny-data.txt.bz2 -> build/lib/pooch/tests/data
copying pooch/tests/data/tiny-data.txt.gz -> build/lib/pooch/tests/data
copying pooch/tests/data/tiny-data.txt.xz -> build/lib/pooch/tests/data
copying pooch/tests/data/tiny-data.zip -> build/lib/pooch/tests/data
creating build/lib/pooch/tests/data/store
copying pooch/tests/data/store/tiny-data.txt -> build/lib/pooch/tests/data/store
creating build/lib/pooch/tests/data/store/subdir
copying pooch/tests/data/store/subdir/tiny-data.txt -> build/lib/pooch/tests/data/store/subdir
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/pooch
copying build/lib/pooch/__init__.py -> build/bdist.linux-x86_64/wheel/pooch
copying build/lib/pooch/core.py -> build/bdist.linux-x86_64/wheel/pooch
copying build/lib/pooch/downloaders.py -> build/bdist.linux-x86_64/wheel/pooch
copying build/lib/pooch/hashes.py -> build/bdist.linux-x86_64/wheel/pooch
copying build/lib/pooch/processors.py -> build/bdist.linux-x86_64/wheel/pooch
copying build/lib/pooch/utils.py -> build/bdist.linux-x86_64/wheel/pooch
copying build/lib/pooch/_version.py -> build/bdist.linux-x86_64/wheel/pooch
creating build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/__init__.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/test_core.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/test_downloaders.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/test_hashes.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/test_integration.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/test_processors.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/test_utils.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/test_version.py -> build/bdist.linux-x86_64/wheel/pooch/tests
copying build/lib/pooch/tests/utils.py -> build/bdist.linux-x86_64/wheel/pooch/tests
creating build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/large-data.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/registry-custom-url.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/registry-invalid.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/registry.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/registry_comments.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/store.tar.gz -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/store.zip -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/tiny-data.tar.gz -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/tiny-data.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/tiny-data.txt.bz2 -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/tiny-data.txt.gz -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/tiny-data.txt.xz -> build/bdist.linux-x86_64/wheel/pooch/tests/data
copying build/lib/pooch/tests/data/tiny-data.zip -> build/bdist.linux-x86_64/wheel/pooch/tests/data
creating build/bdist.linux-x86_64/wheel/pooch/tests/data/store
copying build/lib/pooch/tests/data/store/tiny-data.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data/store
creating build/bdist.linux-x86_64/wheel/pooch/tests/data/store/subdir
copying build/lib/pooch/tests/data/store/subdir/tiny-data.txt -> build/bdist.linux-x86_64/wheel/pooch/tests/data/store/subdir
running install_egg_info
Copying pooch.egg-info to build/bdist.linux-x86_64/wheel/pooch-1.6.0-py3.8.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/pooch-1.6.0.dist-info/WHEEL
creating '/home/tkloczko/rpmbuild/BUILD/pooch-1.6.0/dist/tmpj3gcqygi/pooch-1.6.0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'pooch/__init__.py'
adding 'pooch/_version.py'
adding 'pooch/core.py'
adding 'pooch/downloaders.py'
adding 'pooch/hashes.py'
adding 'pooch/processors.py'
adding 'pooch/utils.py'
adding 'pooch/tests/__init__.py'
adding 'pooch/tests/test_core.py'
adding 'pooch/tests/test_downloaders.py'
adding 'pooch/tests/test_hashes.py'
adding 'pooch/tests/test_integration.py'
adding 'pooch/tests/test_processors.py'
adding 'pooch/tests/test_utils.py'
adding 'pooch/tests/test_version.py'
adding 'pooch/tests/utils.py'
adding 'pooch/tests/data/large-data.txt'
adding 'pooch/tests/data/registry-custom-url.txt'
adding 'pooch/tests/data/registry-invalid.txt'
adding 'pooch/tests/data/registry.txt'
adding 'pooch/tests/data/registry_comments.txt'
adding 'pooch/tests/data/store.tar.gz'
adding 'pooch/tests/data/store.zip'
adding 'pooch/tests/data/tiny-data.tar.gz'
adding 'pooch/tests/data/tiny-data.txt'
adding 'pooch/tests/data/tiny-data.txt.bz2'
adding 'pooch/tests/data/tiny-data.txt.gz'
adding 'pooch/tests/data/tiny-data.txt.xz'
adding 'pooch/tests/data/tiny-data.zip'
adding 'pooch/tests/data/store/tiny-data.txt'
adding 'pooch/tests/data/store/subdir/tiny-data.txt'
adding 'pooch-1.6.0.dist-info/LICENSE.txt'
adding 'pooch-1.6.0.dist-info/METADATA'
adding 'pooch-1.6.0.dist-info/WHEEL'
adding 'pooch-1.6.0.dist-info/top_level.txt'
adding 'pooch-1.6.0.dist-info/zip-safe'
adding 'pooch-1.6.0.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built pooch-1.6.0-py3-none-any.whl
+ python3 -c 'import pooch; print(pooch.__version__)'
v1.6.0
+ pip show pooch
WARNING: Package(s) not found: pooch
Hi @kloczek for opening this issue. From the second traceback you copied, it seems that pooch is not installed on your system/environment. Have you tried running the following?
Yes because that log is from rpm package build process which build in just created lxc zone with installed only build dependencies. I'm building module out of autogenetrated from git tag tar ball. Build prpocess consist only from thee stages:
%build
%pyproject_wheel
echo 'from setuptools import setup; setup()' > setup.py
%py3_build_sphinx_man
I'm adding thad dummy setup.py file to be able use setuptools<>sphinx integration https://www.sphinx-doc.org/en/master/usage/advanced/setuptools.html Effectively those two rpm macros arte unrolled to POSIX SH code like below:
[tkloczko@devel-g2v SPECS]$ rpm -E %pyproject_wheel
\
CFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none";
CXXFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none";
FFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none -I/usr/lib64/gfortran/modules";
FCFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none -I/usr/lib64/gfortran/modules";
LDFLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,--gc-sections -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -flto=auto -flto-partition=none -fuse-linker-plugin -Wl,--build-id=sha1";
CC="/usr/bin/gcc"; CXX="/usr/bin/g++"; FC="/usr/bin/gfortran";
AR="/usr/bin/gcc-ar"; NM="/usr/bin/gcc-nm"; RANLIB="/usr/bin/gcc-ranlib";
export CFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS CC CXX FC AR NM RANLIB;
\
PBR_VERSION=%{version} \
SETUPTOOLS_SCM_PRETEND_VERSION=%{version} \
/usr/bin/python3 -sBm build -w --no-isolation
[tkloczko@devel-g2v SPECS]$ rpm -E %py3_build_sphinx_man
\
PBR_VERSION=%{version} \
SETUPTOOLS_SCM_PRETEND_VERSION=%{version} \
/usr/bin/python3 setup.py build_sphinx -b man --build-dir build/sphinx
The same goes for
sphinx_book_themewhich apparently is not installed either.
Hmm I'm not sure but probably this should be added to extensions in doc/copy.py 🤔
I'll need to package few other module which are needed to build that module as rpm package. Probably all that theme setting can be removed as I'm interested generate man page (will try that as well).
I think I'm a little bit lost here. cc @leouieda (maybe you can throw some light in here)
Your goal is to build a rmp package for Pooch? If that's so, are you having issues with any particular step? Correct me if I'm wrong, but doc building should not be part of the packaging, right? Since pooch is a thin package, I think it would be better not to include Sphinx docs in the package.
Regarding the pep517 build, I see it works flawlessly.
Answering you doubt:
Hmm I'm not sure but probably this should be added to extensions in doc/copy.py thinking
No, sphinx_book_theme should not go inside the extensions list in doc/conf.py because it's not a Sphinx extension, but a theme. Instead, Sphinx expect us to specify the theme through the html_theme variable. Refer to Sphinx book theme docs for more detailed explanation.
Probably all that theme setting can be removed as I'm interested generate man page (will try that as well).
I don't have experience in building man pages out of Python libraries. But I can image that the Sphinx theme is not something that any tool that builds them might need. What type of content would you like to have inside the man pages?
In summary
Could you provide more information about which specific problem are you facing and how can we help you? If there are several problems, please feel free to open different issues for each one of them.
Your goal is to build a rmp package for Pooch? If that's so, are you having issues with any particular step?
Yes .. with generating module documentation as man page 😃
@kloczek that's not something we've tried before really. I don't know how useful they would be or whether other Python libraries do this at all. Have you tried installing the theme in your build environment? See the requirements files in the env folder for specific versions.
You'll also need to use the steps in the Makefile since we builds the API sources in a separate step before calling sphinx to render the output.
@kloczek that's not something we've tried before really. I don't know how useful they would be or whether other Python libraries do this at all. Have you tried installing the theme in your build environment? See the requirements files in the
envfolder for specific versions.
Man pageges it is still most common documentation dormat on all unix platforms. If you are questioning use man pages I'm gessing that you are not using python on one of the unix platforms (even on MOX). Below shows nuymber of man pages documents from my current devel system
[tkloczko@devel-g2v SPECS]$ rpm -qal | grep /usr/share/man/man| wc -l
39980
I'm gessing that you are not using python on one of the unix platform
Writing this from Manjaro 🙂 and I know @santisoler uses it as well. But the HTML version is more convenient and looks nicer in my opinion.
But if you can manage to build the man pages, it's not something I'm opposed to. The cost-benefit of maintaining this if it requires extra effort on our part is probably too much for the small dev team, though.
Writing this from Manjaro 🙂 and I know @santisoler uses it as well. But the HTML version is more convenient and looks nicer in my opinion.
So please look one more time on details of make -C doc html and you will see that currently it not possible to generate documentation in html format.
I've included two outputs of generate documentation:
- as man page using sphinx-build command
- as html using OOTB doc/Makefile file.
In other words this ticket is not about generated documentation format.
Thanks @kloczek for the clarification.
As @leouieda said, we maintain HTML versions of the documentation for every package in the project. We decided to do so for several reasons, but the main one is the fact that it's way more accessible for a larger audience than man pages: if you take a look at our website analytics a large portion of the visitors are using a non *nix OS on desktop.
Besides that, most of the packages from the scientific stack don't provide their docs as man pages. It's quite standard to use Sphinx for building HTML docs and host it in own servers, GitHub Pages or even in Read The Docs. But that's not only for scientific packages, even requests doesn't provide man pages.
I do use man pages for the CLI apps I use on daily basis, but since Pooch is a Python library without CLI entry points, I think it's understandable to build its documentation as almost every other Python library is doing it.
That being said, feel free to generate man pages out of Pooch if that is what you need! We can help solving some of the issues you might encounter, but don't expect us to maintain such feature.
Regarding docs building, our current workflow for building the docs is actually working fine.
Here I copy the output of make -C doc html run in my local environment (on Pooch v1.6.0) plus the output of conda list with the list of installed packages and versions. So the doc/Makefile are working, I think you are facing a problem with your local environment.
$ make -C doc html
make: Entering directory '/home/santi/git/pooch/doc'
Building API docs.
sphinx-autogen -i -t _templates -o api/generated api/index.rst
[autosummary] generating autosummary for: api/index.rst
[autosummary] writing to api/generated
[autosummary] generating autosummary for: api/generated/pooch.DOIDownloader.rst, api/generated/pooch.Decompress.rst, api/generated/pooch.FTPDownloader.rst, api/generated/pooch.HTTPDownloader.rst, api/generated/pooch.Pooch.rst, api/generated/pooch.SFTPDownloader.rst, api/generated/pooch.Untar.rst, api/generated/pooch.Unzip.rst, api/generated/pooch.check_version.rst, api/generated/pooch.create.rst, api/generated/pooch.file_hash.rst, api/generated/pooch.get_logger.rst, api/generated/pooch.make_registry.rst, api/generated/pooch.os_cache.rst, api/generated/pooch.retrieve.rst, api/generated/pooch.test.rst
[autosummary] writing to api/generated
Building HTML files.
sphinx-build -b html -d _build/doctrees . _build/html
Running Sphinx v3.5.4
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://3.python-requests.org/objects.inv...
intersphinx inventory has moved: http://pandas.pydata.org/pandas-docs/stable/objects.inv -> https://pandas.pydata.org/pandas-docs/stable/objects.inv
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 39 source files that are out of date
updating environment: [new config] 39 added, 0 changed, 0 removed
reading sources... [100%] versions
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] versions
/home/santi/git/pooch/doc/index.rst:32: WARNING: more than one target found for 'any' cross-reference 'about': could be :doc:`Start here` or :std:ref:`Start here`
/home/santi/git/pooch/doc/index.rst:68: WARNING: more than one target found for 'any' cross-reference 'citing': could be :doc:`Cite Pooch` or :std:ref:`Cite Pooch`
generating indices... genindex py-modindex done
highlighting module code... [100%] pooch.utils
writing additional pages... search done
copying images... [100%] _static/readme-banner.png
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
make: Leaving directory '/home/santi/git/pooch/doc'
Conda packages:
$ conda list
# packages in environment at /home/santi/.mambaforge/envs/pooch:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
alabaster 0.7.12 py_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
astroid 2.3.3 pypi_0 pypi
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pyh44b312d_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
black 22.3.0 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py39hb9d737c_1004 conda-forge
build 0.7.0 pyhd8ed1ab_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
certifi 2021.10.8 py39hf3d152e_2 conda-forge
cffi 1.14.6 py39he32792d_0 conda-forge
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
click 8.1.2 py39hf3d152e_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
coverage 6.3.2 py39hb9d737c_2 conda-forge
cryptography 36.0.2 py39hd97740a_1 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
docutils 0.16 py39hf3d152e_3 conda-forge
flake8 4.0.1 pyhd8ed1ab_2 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagesize 1.3.0 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.3 py39hf3d152e_1 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
isort 4.3.21 pypi_0 pypi
jinja2 2.11.3 pyhd8ed1ab_1 conda-forge
lazy-object-proxy 1.4.3 pypi_0 pypi
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 11.2.0 h1d223b6_15 conda-forge
libgomp 11.2.0 h1d223b6_15 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_15 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
markupsafe 1.1.1 py39h3811e60_3 conda-forge
mccabe 0.6.1 py_1 conda-forge
mypy_extensions 0.4.3 py39hf3d152e_5 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
openssl 1.1.1n h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pathspec 0.9.0 pyhd8ed1ab_0 conda-forge
pep517 0.12.0 py39hf3d152e_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
platformdirs 2.5.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 py39hf3d152e_3 conda-forge
pooch 1.6.0 dev_0 <develop>
py 1.11.0 pyh6c4a22f_0 conda-forge
pycodestyle 2.8.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydata-sphinx-theme 0.4.3 pyhd8ed1ab_0 conda-forge
pyflakes 2.4.0 pyhd8ed1ab_0 conda-forge
pyftpdlib 1.5.6 py_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pylint 2.4.4 pypi_0 pypi
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.8 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 py39hf3d152e_5 conda-forge
pytest 7.1.1 py39hf3d152e_1 conda-forge
pytest-cov 3.0.0 pyhd8ed1ab_0 conda-forge
pytest-localftpserver 1.1.3 pyhd8ed1ab_0 conda-forge
python 3.9.0 hffdb5ce_5_cpython conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py39hb9d737c_4 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
setuptools 62.1.0 py39hf3d152e_0 conda-forge
six 1.16.0 pypi_0 pypi
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.1 pyhd8ed1ab_0 conda-forge
sphinx 3.5.4 pyh44b312d_0 conda-forge
sphinx-book-theme 0.0.41 pyhd8ed1ab_0 conda-forge
sphinx-panels 0.5.2 pyhd3deb0d_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlite 3.38.2 h4ff8645_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
typed-ast 1.5.2 py39h3811e60_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.11.2 pypi_0 pypi
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge
Thanks @kloczek for the clarification.
In your list of modules sphinx 3.5.0 is listed.
sphinx 3.5.x branch is no longer maintained.
In other words lookms like pooch documentation needs to be updated for lates sphinx 4.5.x.
Please try to reproduce reported issue with latest sphinx.
I see! you're trying to build Pooch v.1.6.0 docs with the latest Sphinx version (4.5.0).
We pin Sphinx versions in the environment.yml and env/requierements-docs.txt files to avoid having to solve Sphinx issues every time it or any of its extensions get an update. That's why I ran it using Sphinx 3.5.4. Sadly, we don't have the time to solve them as regularly as we would if we would leave them unpinned. Instead, we take the time to update the pinned versions and fix issues once in a while. @leouieda did it recently (see https://github.com/fatiando/pooch/pull/300).
Nevertheless, I managed to successfully build the docs of Pooch v1.6.0 using Sphinx 4.5.0:
$ make -C doc html
make: Entering directory '/home/santi/git/pooch/doc'
Building API docs.
sphinx-autogen -i -t _templates -o api/generated api/index.rst
[autosummary] generating autosummary for: api/index.rst
[autosummary] writing to api/generated
Building HTML files.
sphinx-build -b html -d _build/doctrees . _build/html
Running Sphinx v4.5.0
loading pickled environment... failed
failed: build environment version not current
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://3.python-requests.org/objects.inv...
intersphinx inventory has moved: http://pandas.pydata.org/pandas-docs/stable/objects.inv -> https://pandas.pydata.org/pandas-docs/stable/objects.inv
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 39 source files that are out of date
updating environment: [new config] 39 added, 0 changed, 0 removed
reading sources... [100%] versions
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] versions
/home/santi/git/pooch/doc/index.rst:32: WARNING: more than one target found for 'any' cross-reference 'about': could be :doc:`Start here` or :std:ref:`Start here`
/home/santi/git/pooch/doc/index.rst:68: WARNING: more than one target found for 'any' cross-reference 'citing': could be :doc:`Cite Pooch` or :std:ref:`Cite Pooch`
generating indices... genindex py-modindex done
highlighting module code... [100%] pooch.utils
writing additional pages... search done
copying images... [100%] _static/readme-banner.png
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
make: Leaving directory '/home/santi/git/pooch/doc'
$ conda list
# packages in environment at /home/santi/.mambaforge/envs/pooch:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
alabaster 0.7.12 py_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
astroid 2.3.3 pypi_0 pypi
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pyh44b312d_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
black 22.3.0 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py310h5764c6d_1004 conda-forge
build 0.7.0 pyhd8ed1ab_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
certifi 2021.10.8 py310hff52083_2 conda-forge
cffi 1.15.0 py310h0fdd8cc_0 conda-forge
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
click 8.1.2 py310hff52083_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
coverage 6.3.2 py310h5764c6d_2 conda-forge
cryptography 36.0.0 py310h9ce1e76_0
dataclasses 0.8 pyhc8e2a94_3 conda-forge
docutils 0.15.2 py310hff52083_3 conda-forge
flake8 4.0.1 pyhd8ed1ab_2 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagesize 1.3.0 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.3 py310hff52083_1 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
isort 4.3.21 pypi_0 pypi
jinja2 3.1.1 pyhd8ed1ab_0 conda-forge
lazy-object-proxy 1.4.3 pypi_0 pypi
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_15 conda-forge
libgomp 11.2.0 h1d223b6_15 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
markupsafe 2.1.1 py310h5764c6d_1 conda-forge
mccabe 0.6.1 py_1 conda-forge
mypy_extensions 0.4.3 py310hff52083_5 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
openssl 3.0.2 h166bdaf_1 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pathspec 0.9.0 pyhd8ed1ab_0 conda-forge
pep517 0.12.0 py310hff52083_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
platformdirs 2.5.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 py310hff52083_3 conda-forge
pooch 1.6.0 dev_0 <develop>
py 1.11.0 pyh6c4a22f_0 conda-forge
pycodestyle 2.8.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydata-sphinx-theme 0.7.2 pyhd8ed1ab_0 conda-forge
pyflakes 2.4.0 pyhd8ed1ab_0 conda-forge
pyftpdlib 1.5.6 py_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pylint 2.4.4 pypi_0 pypi
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.8 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 py310hff52083_5 conda-forge
pytest 7.1.1 py310hff52083_1 conda-forge
pytest-cov 3.0.0 pyhd8ed1ab_0 conda-forge
pytest-localftpserver 1.1.3 pyhd8ed1ab_0 conda-forge
python 3.10.0 h543edf9_3_cpython conda-forge
python_abi 3.10 2_cp310 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py310h5764c6d_4 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
setuptools 62.1.0 py310hff52083_0 conda-forge
six 1.16.0 pypi_0 pypi
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.1 pyhd8ed1ab_0 conda-forge
sphinx 4.5.0 pyh6c4a22f_0 conda-forge
sphinx-book-theme 0.2.0 pyhd8ed1ab_1 conda-forge
sphinx-panels 0.6.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlite 3.38.2 h4ff8645_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
typed-ast 1.5.2 py310h6acc77f_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.11.2 pypi_0 pypi
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge