pangeo-data/escience-2022

eScience 2022 course on Tools in Climate Science: Linking Observations with Modelling

Pangeo 101 Tutorial for eScience Course 2022

This repository contains the documentation and jupyter notebooks used for delivering the tutorial on Pangeo during the eScience Course 2022.

The content of this repository (folder tutorial) is rendered as an online document using Jupyter Book. You can access it here.

eScience Course 2022

The eScience course is taking place 31 October to 11 November 2022 at Tjärnö Marine Laboratory (plus 28-30 November for remote presentations of final results).

Contributors ✨

Thanks goes to these wonderful people (emoji key):

Alejandro © 🤔 🎨 💻 🖋 📖 ✅	Anne Fouilloux 🤔 🎨 💻 🖋 📖 ✅	Guillaume Eynard-Bontemps 🤔 👀 📓 🖋 🚇	Miguel Caballer 📦 🚇	Rich Signell 🤔	Sebastian Luna-Valero 📦 🚇	Tina Odaka 🤔 🎨 💻 🖋 📖 ✅
Zdeněk Šustr 📦 🚇	j34ni 📦 🚇	pl.marasco 🤔 🎨 💻 🖋 📖 ✅

This project follows the all-contributors specification. Contributions of any kind welcome!

This work used advanced computing resources from the CESNET resource centre of the EGI federation. The services are co-funded by the EGI-ACE project (https://www.egi.eu/project/egi-ace/, grant number 101017567).

We also would like to thank the Pangeo Europe Team and in particular Guillaume Eynard-Bontemps and Jean Iaquinta for the Pangeo deployment, and Anne Fouilloux and Tina Odaka for the training material content and delivery.

escience-2022's Issues

403: Forbidden issue

Hi,

I have tried to sign up for an EGI account to get access to the jupyter notebooks for the escience course. I followed the instructions at https://pangeo-data.github.io/escience-2022/before/setup.html, and got emails saying that my requests to join have been approved.
However, for some reason, when trying to access the jupyter notebook through the link on the setup page, I get redirected to a webpage that gives me an issue 403: forbidden.
How can I fix this?
-Mateusz

403 : Forbidden

When I do the following step "To access the Pangeo EOSC JupyterHub, you need to click on this link to open a Jupyterlab on the correct folder for the tutorial." I get the error message "403 : Forbidden" when signing in with the EGI account on JupyterHub

Recommendations on how to authenticate in Github

Thanks for an amazing tutorial with so many great resources! I was wondering what would be the recommendation on authentication for github and maybe in general workflow if we are using the egi notebook (jupyter hub?) during the course?

pip install fedcloudclient does not work

@annefou
After conda activate egi

pip install fedcloudclient

does not work and results in error output::

Building wheels for collected packages: psutil, netifaces
Building wheel for psutil (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for psutil (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [43 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/psutil
copying psutil/init.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_pssunos.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_psposix.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_psosx.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_pswindows.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_psaix.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_compat.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_psbsd.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_common.py -> build/lib.linux-x86_64-cpython-311/psutil
copying psutil/_pslinux.py -> build/lib.linux-x86_64-cpython-311/psutil
creating build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/init.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_process.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_system.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/main.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_memleaks.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/runner.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_testutils.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-cpython-311/psutil/tests
running build_ext
building 'psutil._psutil_linux' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/psutil
gcc -pthread -B /srv/conda/envs/egi/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /srv/conda/envs/egi/include -fPIC -O2 -isystem /srv/conda/envs/egi/include -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=593 -DPSUTIL_LINUX=1 -DPSUTIL_ETHTOOL_MISSING_TYPES=1 -I/srv/conda/envs/egi/include/python3.11 -c psutil/_psutil_common.c -o build/temp.linux-x86_64-cpython-311/psutil/_psutil_common.o
C compiler or Python headers are not installed on this system. Try to run:
sudo apt-get install gcc python3-dev
error: command 'gcc' failed: No such file or directory
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for psutil
Building wheel for netifaces (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [17 lines of output]
/srv/conda/envs/egi/lib/python3.11/site-packages/setuptools/config/setupcfg.py:508: SetuptoolsDeprecationWarning: The license_file parameter is deprecated, use license_files instead.
warnings.warn(msg, warning_class)
running bdist_wheel
running build
running build_ext
checking for getifaddrs...not found.
checking for getnameinfo...not found.
checking for socket IOCTLs...not found.
checking for optional header files...none found.
checking whether struct sockaddr has a length field...no.
checking which sockaddr_xxx structs are defined...none!
checking for routing socket support...no.
checking for sysctl(CTL_NET...) support...no.
checking for netlink support...no.
building 'netifaces' extension
gcc -pthread -B /srv/conda/envs/egi/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /srv/conda/envs/egi/include -fPIC -O2 -isystem /srv/conda/envs/egi/include -fPIC -DNETIFACES_VERSION=0.11.0 -I/srv/conda/envs/egi/include/python3.11 -c netifaces.c -o build/temp.linux-x86_64-cpython-311/netifaces.o
error: command 'gcc' failed: No such file or directory
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for netifaces
Running setup.py clean for netifaces
Failed to build psutil netifaces
ERROR: Could not build wheels for psutil, which is required to install pyproject.toml-based projects

403 forbidden

Hi,
I cannot login to jupyterHub even though I have followed all the steps from 1 to 4. I get 403 forbidden when it opens that page.
Any help? Am I approved?
Best regards,
maher.