Provide new package: MOAB by KineticTheory · Pull Request #938 · spack/spack

KineticTheory · 2016-05-11T18:40:36Z

This commit provides a basic MOAB installation. MOAB has many optional features that I did not setup or test. I will leave the addition of those variants to someone who is actually using them.

Information on MOAB: https://bitbucket.org/fathomteam/moab

MOAB is a component for representing and evaluating mesh data. MOAB can store structured and unstructured mesh, consisting of elements in the finite element 'zoo.' The functional interface to MOAB is simple yet powerful, allowing the representation of many types of metadata commonly found on the mesh. MOAB is optimized for efficiency in space and time, based on access to mesh in chunks rather than through individual entities, while also versatile enough to support individual entity access

tgamblin · 2016-05-11T19:05:24Z

@KineticTheory: Thanks!

We added flake8 checking to Spack recently -- this one is hitting some pep8 checks. From the Travis output:

var/spack/repos/builtin/packages/moab/package.py:5: [E302] expected 2 blank lines, found 1
var/spack/repos/builtin/packages/moab/package.py:6: [E501] line too long (504 > 79 characters)
var/spack/repos/builtin/packages/moab/package.py:14: [E501] line too long (98 > 79 characters)
var/spack/repos/builtin/packages/moab/package.py:15: [E501] line too long (88 > 79 characters)
var/spack/repos/builtin/packages/moab/package.py:27: [E231] missing whitespace after ','
var/spack/repos/builtin/packages/moab/package.py:29: [E261] at least two spaces before inline comment
var/spack/repos/builtin/packages/moab/package.py:45: [E202] whitespace before ']'
var/spack/repos/builtin/packages/moab/package.py:50: [E202] whitespace before ')'

KineticTheory · 2016-05-11T19:57:16Z

@tgamblin Can you point me to a formatting guide or a properly formatted package.py? How do I run flake8 locally before pushing my files to github?

tgamblin · 2016-05-11T20:03:22Z

Oh, sorry -- it's in the README but onyx since yesterday. There is a script (share/spack/qa/run-flake8), which will do the same thing as Travis, only locally. It must be run from the top-level repo directory. Working on a spack command, but not there yet.

adamjstewart · 2016-05-11T20:06:18Z

You can see further comments left for me by @alalazo and @tgamblin here

But yeah, this should definitely be in the documentation...

adamjstewart · 2016-05-11T20:07:31Z

Ah, just saw the README. That may be sufficient?

KineticTheory · 2016-05-11T22:36:19Z

@adamjstewart Thanks for the pointer to the README. I haven't looked at that recently, but I will be sure to follow the recommendations in the Contributions section from now on.

Also - Since I don't have an easy way to install flake8 on my target system (I don't have root), I added it as a spack package.

tgamblin · 2016-05-12T00:14:27Z

@KineticTheory: thanks for doing that! I was hoping someone would 😄

* update bglibpy to 4.4.6 * updated to bglpy 4.4.10 v 4.4.10 does not have the pandas, pyrsistent or the bluepy-configfile dependencies

* Update bbp-packages.yaml Adding my currentscape module to bbp-packages. * Update modules.yaml Adding my currentscape package to the whitelist. * Create package.py Added my currentscape package. * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update package.py Modified the version. Is it better now? * update bglibpy to 4.4.6 (spack#937) * Update package.py Changing tag to match the one from source on gerrit. * Bglibpy 4.4.10 (spack#938) * update bglibpy to 4.4.6 * updated to bglpy 4.4.10 v 4.4.10 does not have the pandas, pyrsistent or the bluepy-configfile dependencies * Updates Libsonata package to include readers improvements (spack#940) * update glm to 0.9.9.3 (spack#943) * Bump neurodamus for most recent patches (spack#942) Bump neurodamus-py 2.0.0 to 2.0.2: - Fixing replay to work with multiple populations - Ensure data dir when skipping model build - Fix skipping synapse creation when weight is 0 (BBPBGLIB-673) - Fix deadlock when an exception is thrown from NEURON (BBPBGLIB-678) - Logging colors only for tty Bump neurodamus-core 3.0.0 to 3.0.1: - Avoid getting nilSecRef from objects (HPCTM-1381) * Update py-sonata-network-reduction dependencies: [email protected], [email protected] (spack#930) * Update bbp-packages.yaml Updated currentscape version. * Update package.py Updated version & tag. * Brion and Brayns are dependent on GLM (spack#944) * Steps updates (spack#941) * gmsh: add version 4.6.0 * omega-h: new version 9.32.5.dev3 * steps: new test requirements * libsonata-report: Improves initialization performance (spack#945) * adapt brion test to a new python module name (spack#946) * Adding nvidia-hpc-sdk based on upstream PR (spack#935) * New compiler: nvhpc (NVIDIA HPC SDK) (spack#19294) * Add nvhpc compiler definition: "spack compiler add" will now look for instances of the NVIDIA HPC SDK compiler executables (nvc, nvc++, nvfortran) in supplied paths * Add the nvhpc package which installs the nvhpc compiler * Add testing for nvhpc detection and C++-standard/pic flags Based on spack#19294 * Add CUDA@11 required for latest NVIDIA-HPC-SDK * Fix legacy apis : setup_environment to setup_run_environment * NEURON and CoreNEURON should use legacy units for BBP/HBP deployment (spack#947) * Update bbp-packages.yaml Adding my currentscape module to bbp-packages. * Update modules.yaml Adding my currentscape package to the whitelist. * Create package.py Added my currentscape package. * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update var/spack/repos/builtin/packages/py-currentscape/package.py Co-authored-by: Matthias Wolf <[email protected]> * Update package.py Modified the version. Is it better now? * Update package.py Changing tag to match the one from source on gerrit. * Update bbp-packages.yaml Updated currentscape version. * Update package.py Updated version & tag. Co-authored-by: Matthias Wolf <[email protected]> Co-authored-by: anilbey <[email protected]> Co-authored-by: Sergio <[email protected]> Co-authored-by: ppodhajski <[email protected]> Co-authored-by: Fernando Pereira <[email protected]> Co-authored-by: asanin-epfl <[email protected]> Co-authored-by: Nadir Román Guerrero <[email protected]> Co-authored-by: Tristan Carel <[email protected]> Co-authored-by: Pramod Kumbhar <[email protected]> Co-authored-by: Jaquier Aurélien Tristan <[email protected]>

KineticTheory added 2 commits May 11, 2016 12:34

New package MOAB.

e200a41

Remove some extraneous comments.

9482ce1

Attempt to fix formatting issues (flake8).

8bec127

Clean up formatting.

c5a19b5

tgamblin merged commit 2dc49ee into spack:develop May 12, 2016

KineticTheory deleted the pkg-moab branch April 18, 2017 15:06

olupton pushed a commit to olupton/spack that referenced this pull request Feb 7, 2022

Bglibpy 4.4.10 (spack#938)

ab4da7d

* update bglibpy to 4.4.6 * updated to bglpy 4.4.10 v 4.4.10 does not have the pandas, pyrsistent or the bluepy-configfile dependencies

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Provide new package: MOAB#938

Provide new package: MOAB#938
tgamblin merged 4 commits intospack:developfrom
KineticTheory:pkg-moab

KineticTheory commented May 11, 2016

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KineticTheory commented May 11, 2016

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tgamblin commented May 11, 2016

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KineticTheory commented May 11, 2016

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tgamblin commented May 11, 2016

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adamjstewart commented May 11, 2016

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KineticTheory commented May 11, 2016

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