unable to load server, rdkit mismatch in pip
JenkeScheen opened this issue · 7 comments
it seems like there might be an issue with rdkit versioning specified in requirements_devel.txt (technically in requirements.txt). When doing a fresh install as per README.md instructions, I get the following:
(qfepweb) (mbp) jscheen@macbook:$ pip install -r requirements.txt
Collecting Django==3.2.5
Using cached Django-3.2.5-py3-none-any.whl (7.9 MB)
Collecting Pillow==8.2.0
Using cached Pillow-8.2.0-cp37-cp37m-macosx_10_10_x86_64.whl (2.8 MB)
Collecting django-crispy-forms==1.11.0
Using cached django_crispy_forms-1.11.0-py3-none-any.whl (108 kB)
Collecting django-extensions==3.1.3
Using cached django_extensions-3.1.3-py3-none-any.whl (223 kB)
Collecting django-environ==0.4.5
Using cached django_environ-0.4.5-py2.py3-none-any.whl (21 kB)
Collecting gunicorn==20.1.0
Using cached gunicorn-20.1.0-py3-none-any.whl (79 kB)
Collecting networkx==2.5.1
Using cached networkx-2.5.1-py3-none-any.whl (1.6 MB)
Collecting pandas==1.2.4
Using cached pandas-1.2.4-cp37-cp37m-macosx_10_9_x86_64.whl (10.4 MB)
ERROR: Could not find a version that satisfies the requirement rdkit-pypi==2021.3.1.4 (from versions: 2021.3.1.5, 2021.3.2, 2021.3.2.1, 2021.3.2.2, 2021.3.2.3, 2021.3.3)
ERROR: No matching distribution found for rdkit-pypi==2021.3.1.4
pip version:
pip 21.1.3 from /Users/jscheen/projects/modsim/qfepweb/qfepweb/lib/python3.7/site-packages/pip (python 3.7)
Mauricio and I discussed this a while ago. RDKit releases often (once a month or more).
But in this case, I cannot reproduce:
$ pip install rdkit-pypi==2021.3.1.4
Collecting rdkit-pypi==2021.3.1.4
Using cached rdkit_pypi-2021.3.1.4-cp39-cp39-manylinux2014_x86_64.whl (33.0 MB)
Installing collected packages: rdkit-pypi
Successfully installed rdkit-pypi-2021.3.1.4
We can always update to the latests, but first you should check why you can't install. Any of the wheels are compatible with your system?
https://pypi.org/project/rdkit-pypi/2021.3.1.4/#files
Are you on Python 3.6 to 3.9? Linux?
python 3.7 on macos big sur. I'll test on linux.
different dependency error on linux, ugh.. system is ubuntu 18.04, Python 3.6.6.
(qfepweb) jscheen@yoko:qfepweb$ pip install -r requirements_devel.txt
Collecting Django==3.2.5 (from -r requirements.txt (line 1))
Downloading https://files.pythonhosted.org/packages/37/a1/790e01bf4348dd68090d47108052a8130954d473d54b4ea7924f5bb154de/Django-3.2.5-py3-none-any.whl (7.9MB)
100% |████████████████████████████████| 7.9MB 279kB/s
Collecting Pillow==8.2.0 (from -r requirements.txt (line 2))
Using cached https://files.pythonhosted.org/packages/89/d2/942af29f8494a1a3f4bc4f483d520f7c02ccae677f5f50cf76c6b3d827d8/Pillow-8.2.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting django-crispy-forms==1.11.0 (from -r requirements.txt (line 4))
Downloading https://files.pythonhosted.org/packages/78/d9/33b4707afcb099bebedca3b3b7ce71085e9b0facd7c5ac45ba767fea24ea/django_crispy_forms-1.11.0-py3-none-any.whl (108kB)
100% |████████████████████████████████| 112kB 7.5MB/s
Collecting django-extensions==3.1.3 (from -r requirements.txt (line 5))
Downloading https://files.pythonhosted.org/packages/a1/40/c94fde79735d0c3578ed7d595593bd52c5633d8a02e53a2ef9346f93e2db/django_extensions-3.1.3-py3-none-any.whl (223kB)
100% |████████████████████████████████| 225kB 4.4MB/s
Collecting django-environ==0.4.5 (from -r requirements.txt (line 6))
Downloading https://files.pythonhosted.org/packages/9f/32/76295a1a5d00bf556c495216581c6997e7fa5f533b2229e0a9d6cbaa95ae/django_environ-0.4.5-py2.py3-none-any.whl
Collecting gunicorn==20.1.0 (from -r requirements.txt (line 7))
Downloading https://files.pythonhosted.org/packages/e4/dd/5b190393e6066286773a67dfcc2f9492058e9b57c4867a95f1ba5caf0a83/gunicorn-20.1.0-py3-none-any.whl (79kB)
100% |████████████████████████████████| 81kB 7.3MB/s
Collecting networkx==2.5.1 (from -r requirements.txt (line 9))
Downloading https://files.pythonhosted.org/packages/f3/b7/c7f488101c0bb5e4178f3cde416004280fd40262433496830de8a8c21613/networkx-2.5.1-py3-none-any.whl (1.6MB)
100% |████████████████████████████████| 1.6MB 1.2MB/s
Collecting pandas==1.2.4 (from -r requirements.txt (line 10))
Cache entry deserialization failed, entry ignored
Could not find a version that satisfies the requirement pandas==1.2.4 (from -r requirements.txt (line 10)) (from versions: 0.1, 0.2b0, 0.2b1, 0.2, 0.3.0b0, 0.3.0b2, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.6.0, 0.6.1, 0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.8.0rc1, 0.8.0, 0.8.1, 0.9.0, 0.9.1, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 0.19.2, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21.0, 0.21.1, 0.22.0, 0.23.0, 0.23.1, 0.23.2, 0.23.3, 0.23.4, 0.24.0, 0.24.1, 0.24.2, 0.25.0, 0.25.1, 0.25.2, 0.25.3, 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.1.0, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5)
No matching distribution found for pandas==1.2.4 (from -r requirements.txt (line 10))
I'd rather fix the issue on the macbook though as that's my local workstation.
What happens if you install directly?
$ pip install pandas==1.2.4
$ pip install rdkit-pypi==2021.3.1.4
Same error. Sorry, I'm much more used to conda for this sort of development. Version-less installing works OK and seems to be installing an even newer version of rdkit:
(qfepweb) (mbp) jscheen@macbook:$ pip install rdkit-pypi
Collecting rdkit-pypi
Downloading rdkit_pypi-2021.3.3-cp37-cp37m-macosx_10_9_x86_64.whl (15.9 MB)
|████████████████████████████████| 15.9 MB 2.4 MB/s
Collecting numpy>=1.19
Downloading numpy-1.21.0-cp37-cp37m-macosx_10_9_x86_64.whl (16.8 MB)
|████████████████████████████████| 16.8 MB 1.2 MB/s
Installing collected packages: numpy, rdkit-pypi
Successfully installed numpy-1.21.0 rdkit-pypi-2021.3.3
Presumably this isn't how we would want to deploy.. but I'd be happy to work like this on my side, it's most likely a MacOS issue. I'll try to be careful not to commit the change to requirements.txt.
We are going to upgrade RDKit sooner or later anyways.
The idea behind version pinning is to reproduce the environment and avoid "Works in my Machine (TM)" events due to different versions doing different things. It's not usual, but it happens from time to time.
Closing issue then?
yep, thanks for the feedback!