jmp1985
commented
1 year ago Hi Joel
Sorry for the late reply. Hmmm it seems that the tag falls foul of the python version standards. You can see here: https://peps.python.org/pep-0440/ that the version needs to match this.
[N!]N(.N)*[{a|b|rc}N][.postN][.devN]
Epoch segment: N!
Release segment: N(.N)*
Pre-release segment: {a|b|rc}N
Post-release segment: .postN
Development release segment: .devNWhich we can test with things like:
from packaging.version import Version, parse
parse("v1.0") parse("v1.0.0dev1") parse("v1.0.0a1") parse("v1.0.0b") parse("v1.0.0rc1") parse("v1.0.0post1")
So it seems that python won't play nicely with other names. Perhaps we can use a variant of this for our tag. May if we tag doppio releases with v1.0.0dev1 or something instead?
I think the tag needs to fit into this scheme but I am happy to use whatever version tag you prefer for doppio wihtin this scheme.
Best wishes James
From: JatGreer @.> Sent: 15 May 2023 10:08 To: rosalindfranklininstitute/parakeet @.> Cc: Subscribed @.***> Subject: [rosalindfranklininstitute/parakeet] doppio beta tag causing unknown pip installation error (Issue #52)
This error is apparent on my latest git clone of the doppio repo - my first since the doppio beta tag was introduced. The full error trace and list of potentially useful commands is below. The commit of parakeet that I am trying to install is git checkout 17a0c864f6cfd84b5fd56b60fa446f7b021d338c and has been checkout out. I have also pre-installed python-multem and guanaco according to the version numbers which can be found below.
Please could you let me know if you can replicate this error? If necessary to quickly fix things, it's fine with me to remove the doppio beta tag. Looks like maybe pypi cannot not happily recognise 'v0.4.3-doppio-beta' as a version identifier and needs a boring X.X.X identifier instead?
(roodmus) @.***:~/Software/roodmus_setup/parakeet$ pip install -e . Obtaining file:///home/jg/Software/roodmus_setup/parakeet Installing build dependencies ... done Checking if build backend supports build_editable ... done Getting requirements to build editable ... done Installing backend dependencies ... done Preparing editable metadata (pyproject.toml) ... error error: subprocess-exited-with-error
× Preparing editable metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [50 lines of output]
Traceback (most recent call last):
File "/home/jg/miniconda3/envs/roodmus/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details. (roodmus) @.***:~/Software/roodmus_setup/parakeet$ git branch
-
(HEAD detached at 17a0c86) master (roodmus) @.:~/Software/roodmus_setup/parakeet$ git log commit 17a0c864f6cfd84b5fd56b60fa446f7b021d338c (HEAD, tag: v0.4.3-doppio-beta) Author: James Parkhurst @.> Date: Fri Mar 3 12:04:22 2023 +0000
Propagate directory and relion option in metadata output
Fixes #48
commit 2ebd0598b874728e15cd9f6b284ca4ced0dd3ced Author: James Parkhurst @.***> Date: Fri Mar 3 09:50:49 2023 +0000
Update readmecommit b488327ccb1be0f0817536af33f54348027d05d0 Author: James Parkhurst @.***> Date: Fri Mar 3 09:46:46 2023 +0000
Add news fragmentcommit 8bd8a5f468aeea85f1c92a6df0bfd178e35fc808 Author: Dimitrios Bellos @.***> Date: Fri Mar 3 09:44:07 2023 +0000
Documentation Update - Docker, Singularity, Baskerville (#44)
* I have updated the Docker, Singularity and Baskerville installation instructions in installation.rst(roodmus) @.***:~/Software/roodmus_setup/parakeet$ pip list Package Version
alabaster 0.7.12 appdirs 1.4.4 astunparse 1.6.3 Babel 2.11.0 beautifulsoup4 4.12.2 bs4 0.0.1 ccpem-utils 0.0.1.dev9 certifi 2023.5.7 cfgv 3.3.1 charset-normalizer 3.1.0 click 8.1.3 cloudpickle 2.2.1 contourpy 1.0.7 cssselect 1.2.0 cycler 0.11.0 dask 2023.5.0 dask-jobqueue 0.8.1 distlib 0.3.6 distributed 2023.5.0 docutils 0.17.1 fake-useragent 1.1.3 filelock 3.12.0 fonttools 4.39.4 fsspec 2023.5.0 gemmi 0.6.1 glob2 0.7 guanaco 0.3.0 h5py 3.8.0 HeapDict 1.0.1 identify 2.5.24 idna 3.4 imageio 2.28.1 imagesize 1.4.1 importlib-metadata 6.6.0 Jinja2 3.1.2 joblib 1.2.0 kiwisolver 1.4.4 lazy_loader 0.2 locket 1.0.0 lxml 4.9.2 maptools 0.3.5 MarkupSafe 2.1.2 matplotlib 3.7.1 mdtraj 1.9.7 mrcfile 1.4.3 msgpack 1.0.5 networkx 3.1 nodeenv 1.8.0 numpy 1.24.3 packaging 23.1 pandas 2.0.1 pandas-stubs 2.0.1.230501 parse 1.19.0 partd 1.4.0 Pillow 9.5.0 pip 23.1.2 pipenv 2022.11.5 platformdirs 3.5.1 pre-commit 3.3.1 profet 0.0.1 psutil 5.9.5 pydantic 1.10.7 pyee 8.2.2 Pygments 2.13.0 pyparsing 3.0.9 pypdb 2.2 pyppeteer 1.0.2 pyquery 2.0.0 python-dateutil 2.8.2 python-multem 0.3.3 pytz 2023.3 PyWavelets 1.4.1 PyYAML 6.0 requests 2.30.0 requests-html 0.10.0 roodmus 0.0.18 scikit-image 0.20.0 scikit-learn 1.2.2 scipy 1.9.3 seaborn 0.12.2 setuptools 66.0.0 six 1.16.0 snowballstemmer 2.2.0 sortedcontainers 2.4.0 soupsieve 2.4.1 Sphinx 5.3.0 sphinx-rtd-theme 1.1.1 sphinxcontrib-applehelp 1.0.2 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 2.0.0 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.5 starfile 0.4.12 tblib 1.7.0 threadpoolctl 3.1.0 tifffile 2023.4.12 toolz 0.12.0 tornado 6.3.2 tqdm 4.65.0 types-pytz 2023.3.0.0 types-tabulate 0.9.0.2 typing_extensions 4.5.0 tzdata 2023.3 urllib3 1.26.15 virtualenv 20.23.0 virtualenv-clone 0.5.7 w3lib 2.1.1 websockets 10.4 wheel 0.38.4 zict 3.0.0 zipp 3.15.0
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JatGreer
This error is apparent on my latest git clone of the doppio repo - my first since the doppio beta tag was introduced. The full error trace and list of potentially useful commands is below. The commit of parakeet that I am trying to install is
git checkout 17a0c864f6cfd84b5fd56b60fa446f7b021d338cand has been checkout out. I have also pre-installed python-multem and guanaco according to the version numbers which can be found below.Please could you let me know if you can replicate this error? If necessary to quickly fix things, it's fine with me to remove the doppio beta tag. Looks like maybe pypi cannot not happily recognise
'v0.4.3-doppio-beta'as a version identifier and needs a boring X.X.X identifier instead?