Re: Understanding pybuild
Hi Dmitry, Dmitry Shachnev writes: > On Thu, Dec 19, 2019 at 01:09:40PM +0100, Ole Streicher wrote: >> 2. dh_auto_test then tries runs the tests in .pybuild. If the test need >> data files installed, they must be copied manually (right?). > > You can use debian/pybuild.testfiles to copy the test files. See pybuild(1) > for details. That would formalize it a bit, but still does not solve the underlying problem: it requires that I maintain the list of these files manually, while upstream already does this (by adding them to the list of data files). And also, the built time tests are with pybuild not done with the files (anc compilations) that are finally installed, but the installed files (especially Python extensions) are created again from scratch, doubling the compile time and introducing another difficile source of error. Best regards Ole
Re: Understanding pybuild
Hi Ole! On Thu, Dec 19, 2019 at 01:09:40PM +0100, Ole Streicher wrote: > Hi, > > I am currently updating scikit-image (skimage) to its newest version, > and I have some difficulties to understand how pybuild works (for > setup.py packages): > > 1. first, dh_auto_build calls "python3.X setup.py build" to create the > packages (Python files and compiled extensions) in > ..pybuild/cpython3_3.X/. This however does not include the copying of any > data files. > > 2. dh_auto_test then tries runs the tests in .pybuild. If the test need > data files installed, they must be copied manually (right?). You can use debian/pybuild.testfiles to copy the test files. See pybuild(1) for details. -- Dmitry Shachnev signature.asc Description: PGP signature
Re: kmer: Python2 removal in sid/bullseye
Hi Scott, thanks a lot for your hint. On Thu, Dec 19, 2019 at 01:34:08PM -0500, Scott Talbert wrote: > > The 'file' class doesn't exist anymore in Python 3. You'll have to rewrite > myfile to not use it. OK, I simply went with ... @@ -608,6 +608,11 @@ Last-Update: Thu, 19 Dec 2019 10:43:09 +0100 # from __future__ import generators # Necessary before Python 2.3 +-class myfile(file): ++class myfile(): + "A temporary anonymous file" + def __init__(self): + filename = tempfile.mktemp() @@ -27,8 +27,8 @@ class ListLikeFileIter: self._fileIter = iter(self._fileptr.readline,"") def __del__(self): ... This brings me to the next error where a Module written in C is not found: python3 /usr/bin/../lib/atac/bin/AtacDriver.py /tmp/atac-test.XqdEPl/results/work/LeprvsTuber.matches.extended Traceback (most recent call last): File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 26, in import localAlignerInterface ModuleNotFoundError: No module named 'localAlignerInterface' PYTHONPATH=/usr/bin/../lib/atac/lib Chainer failed. The file /usr/lib/atac/lib/localAlignerInterfacemodule.so exists but it seems the Python3 script can't load it. Kind regards Andreas. -- http://fam-tille.de
Re: kmer: Python2 removal in sid/bullseye
On Thu, 19 Dec 2019, Andreas Tille wrote: Traceback (most recent call last): File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 18, in import MyFile File "/usr/lib/atac/lib/MyFile.py", line 6, in class myfile(file): NameError: name 'file' is not defined PYTHONPATH=/usr/bin/../lib/atac/lib Chainer failed. The 'file' class doesn't exist anymore in Python 3. You'll have to rewrite myfile to not use it. Scott
Re: kmer: Python2 removal in sid/bullseye
Control: tags -1 help Hi, I tried to convert kmer to Python3 in Git[1]. Unfortunately I'm stumbling upon an issue in the test suite: ... python3 /usr/bin/../lib/atac/bin/AtacDriver.py /tmp/atac-test.doxZJ4/results/work/LeprvsTuber.matches.extended Traceback (most recent call last): File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 18, in import MyFile File "/usr/lib/atac/lib/MyFile.py", line 6, in class myfile(file): NameError: name 'file' is not defined PYTHONPATH=/usr/bin/../lib/atac/lib Chainer failed. Any idea what's wrong here? Kind regards Andreas. [1] https://salsa.debian.org/med-team/kmer -- http://fam-tille.de
Understanding pybuild
Hi, I am currently updating scikit-image (skimage) to its newest version, and I have some difficulties to understand how pybuild works (for setup.py packages): 1. first, dh_auto_build calls "python3.X setup.py build" to create the packages (Python files and compiled extensions) in ..pybuild/cpython3_3.X/. This however does not include the copying of any data files. 2. dh_auto_test then tries runs the tests in .pybuild. If the test need data files installed, they must be copied manually (right?). 3. dh_auto_install finally calls "python3.X setup.py install ..." to install the complete packages (Python files, extensions, and data files) from their original place to debian/tmp/. This includes a re-compilation of the extensions. What I do not understand now is: what is the purpose of step 1? Except for the tests, these files seem to be unused. And for the tests, they are not complete, since the data files are missing. And what is the canonical way to get the data files copied to ..pybuild/...? They are already marked as such in setup.py. Doing this manually by the Debian maintainer seems a constant source of error. Best Ole
