ci: Use --no-build-isolation to instal cgat #77
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As [suggested](cgat-developers/cgat-apps#134 (comment)) attempting to install dependencies (and in one instance `IsoSLAM` itself) with the `--no-build-isolation` flag in the hope that NumPy is correctly detected by `cgat` when it is built and installed. Further in light of [investigations](cgat-developers/cgat-apps#134 (comment)) also explicitly install the build requirements (`numpy` / `Cython` / `pysam` / `wheel`) prior to installing.
There is no wheel for pysam on the Windows release (see [files](https://pypi.org/project/pysam/#files)) so removing windows from the os matrix of tests.
[updated setup.py and pyproject.toml](cgat-developers/cgat-apps#136) moves some of the configuration options of `cgat-apps` from `setup.py` to `pyproject.toml`, testing to see if they install. Previously I've found that there were some errors building pysam for windows (see [log](https://github.com/sudlab/IsoSLAM/actions/runs/12049902667/job/33597647405?pr=77)) there are no wheels for pysam for windows so it attempts to build from source so I've removed Windows from the build matrix but then hit errors trying to compile [`v0.7.4`](https://github.com/sudlab/IsoSLAM/actions/runs/12050103589/job/33598275747?pr=77) ``` cgat/BamTools/bamtools.c: In function ‘__pyx_pw_4cgat_8BamTools_8bamtools_7bam2bam_filter_bam’: cgat/BamTools/bamtools.c:41504:8: warning: ‘__pyx_v_remove_contig_tids’ may be used uninitialized in this function [-Wmaybe-uninitialized] 41504 | int *__pyx_v_remove_contig_tids; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cgat/BamTools/bamtools.c: In function ‘__pyx_pf_4cgat_8BamTools_8bamtools_2bam2stats_count.constprop’: cgat/BamTools/bamtools.c:1204:40: warning: ‘__pyx_v_fastq_nreads’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1204 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ cgat/BamTools/bamtools.c:27028:11: note: ‘__pyx_v_fastq_nreads’ was declared here 27028 | int64_t __pyx_v_fastq_nreads; | ^~~~~~~~~~~~~~~~~~~~ cgat/BamTools/bamtools.c:33541:31: warning: ‘__pyx_v_fastq_counts’ may be used uninitialized in this function [-Wmaybe-uninitialized] 33541 | __pyx_v_fastq_count = (&(__pyx_v_fastq_counts[__pyx_v_read_index])); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,--rpath=/opt/hostedtoolcache/Python/3.12.7/x64/lib -Wl,--rpath=/opt/hostedtoolcache/Python/3.12.7/x64/lib build/temp.linux-x86_64-cpython-312/cgat/BamTools/bamtools.o -L/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/pysam -L/opt/hostedtoolcache/Python/3.12.7/x64/lib -L/opt/hostedtoolcache/Python/3.12.7/x64/lib -lhts -lctabixproxies.cpython-312-x86_64-linux-gnu -lcfaidx.cpython-312-x86_64-linux-gnu -lcsamfile.cpython-312-x86_64-linux-gnu -lcvcf.cpython-312-x86_64-linux-gnu -lcbcf.cpython-312-x86_64-linux-gnu -lctabix.cpython-312-x86_64-linux-gnu -lchtslib.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/cgat/BamTools/bamtools.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/pysam -Wl,-rpath,/opt/hostedtoolcache/Python/3.12.7/x64/lib -Wl,-rpath,/opt/hostedtoolcache/Python/3.12.7/x64/lib /usr/bin/ld: cannot find -lhts: No such file or directory collect2: error: ld returned 1 exit status error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for cgat Failed to build cgat ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (cgat) ``` This may be a system library that is required though :thinking:
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#104 removed the dependency on |
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As suggested attempting to install
dependencies (and in one instance
IsoSLAMitself) with the--no-build-isolationflag in the hope that NumPy iscorrectly detected by
cgatwhen it is built and installed.