cgat-0.7.4 pip install : FileNotFoundError: [Errno 2] No such file or directory: 'requires.txt' #134
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oh I see what the potential problem is... im not sure why our testing didnt pick this up. In the latest release connected_components.h isnt in the setup.py. In the meantime can you use the 0.7.2 version? |
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I will fix this in next few days and make a new release |
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Iv pulled the release for the moment |
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you able to test this pull, it should fix the issues? |
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Sorry for the delay, only work on the project that uses this part time and have been on annual leave. In a clean environment this now installs... (tmp-3c6c4b33689cb6a) ❱ git clone https://github.com/cgat-developers/cgat-apps.git
Cloning into 'cgat-apps'...
remote: Enumerating objects: 39732, done.
remote: Counting objects: 100% (1615/1615), done.
remote: Compressing objects: 100% (775/775), done.
pReceiving objects: 13% (5474/39732), 25.81 MiB | 5.33 MiB/s/s/s
remote: Total 39732 (delta 784), reused 1355 (delta 725), pack-reused 38117 (from 1)
Receiving objects: 100% (39732/39732), 390.89 MiB | 4.12 MiB/s, done.
Resolving deltas: 100% (24717/24717), done.
(tmp-3c6c4b33689cb6a) ❱ cd cgat-apps
(tmp-3c6c4b33689cb6a) ❱ git switch AC-fixsetup
branch 'AC-fixsetup' set up to track 'origin/AC-fixsetup'.
Switched to a new branch 'AC-fixsetup'
(tmp-3c6c4b33689cb6a) ❱ pip install .
Processing /home/neil/tmp/cgat/cgat-apps
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: cgat
Building wheel for cgat (pyproject.toml) ... \
done
Created wheel for cgat: filename=cgat-0.7.4-cp312-cp312-linux_x86_64.whl size=10638983 sha256=a0474c183080bdfadba0946cd20ce9c4539f6b88eb15f40f7586668822453751
Stored in directory: /home/neil/.cache/pip/wheels/e2/2f/5d/1497f4f335bec91ea7fb6335d7da2df5e56a38796409b114e2
Successfully built cgat
Installing collected packages: cgat
Successfully installed cgat-0.7.4 |
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I'm getting bitten by this in CI now as Log file can be found here but since they disappear after a while the output from I've highlighted where |
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Looking at your github actions file, have you tried adding |
ns-rse
added a commit
to sudlab/IsoSLAM
that referenced
this issue
Nov 27, 2024
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.
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Thanks for the suggestion @Acribbs we have progress! I added the
I first looked in It would probably be possible to port much of
I could migrate some of this if it would be helpful, but the v0.7.4 release which was pulled has these build requirements in place already (although much of the metadata and setup is still via I checked installation the other day of |
ns-rse
added a commit
to sudlab/IsoSLAM
that referenced
this issue
Nov 27, 2024
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`) prior to installing.
ns-rse
added a commit
to sudlab/IsoSLAM
that referenced
this issue
Nov 27, 2024
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` / `bdist_wheel``) prior to installing.
ns-rse
added a commit
to sudlab/IsoSLAM
that referenced
this issue
Nov 27, 2024
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.
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made an update to code in #136 , can you take a look, then can release v0.7.4.1 |
ns-rse
added a commit
to sudlab/IsoSLAM
that referenced
this issue
Nov 28, 2024
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.
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Further to cgat-core #177 I'm still having trouble installing
cgaton my system.NB I've read the install instructions and have seen the preferred approach is to use Conda environments but would prefer to use plain virtual environments because of the recent furore and potential licensing issues associated with Conda.
In #177 I attempted to abstract out the problem from the
pyproject.tomlI mentioned and manually install packages and dependencies. I continue with that approach here.Downloading the source, extracting and attempting to install...
requires.txtLooking for
requires.txtin the package files.Searching for
requires.txtThe file doesn't exist.
Checking
cgat-0.7.2The file is present in the previous release, but its an empty file...
ls -l requires.txt .rw-r--r-- neil neil 0 B Fri Apr 5 11:17:00 2024 requires.txt 11:43:26 am GMT percentage: neil ~/work/git/hub/cgat-developers/cgat-0.7.2 cat requires.txtWorkaround
Add an empty file to
cgat-0.7.4and its possible topip install ., but it fails further alongThere are some warnings about the
cgat.VCFTools/cgat.BamTools/cgat.Components/cgat.FastqToolsnot being correctly configured forsetuptoolsbut the install proceeds.Compilation of the C++ code fails because there is a missing header file
connected_components.h.Trying to install
cgat-0.7.2Dropping back a version I encounter again the Numpy issue described in #177 as the very first thing
setup.pydoes is check thatnumpycan be imported. It should be importable because I have explicitly installed it...However this is not detected correctly...
I decided to try using the Setuptools method of Declaring required dependency using
setup.cfg(although the current ecosystem is standardising on thepyproject.tomlformat as per PEP621).setup.cfg[project] install_requires = "Cython", "numpy", "pysam" [egg_info] tag_build = tag_date = 0setup.pyDisable the checks for these packages at the start1
Try installing but it now doesn't install because an attempt is made to import from
Cython, which I have explicitly manually installed along withpysam, fails.Possible solutions?
connected_components.hseems like it would be needed to build and install the package (after adding back in an emptyrequires.txt.pyproject.tomlwould perhaps help with some of these problems assetup.pytries to import and use some of the packages it depends on before they have been pulled in and installed as dependencies.Footnotes
I note the comments in
setup.pyaboutIs there a way to do this more elegantly?. The traditional method of specifying dependencies insetup.pyis within the call tosetup()seesetup.pytab here but as mentioned the preferred configuration is now viapyproject.tomland I think the reason this inelegant solution exists is because the packages are imported and used before they have been installed as dependencies. ↩The text was updated successfully, but these errors were encountered: