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Initial work towards demonstration code and documentation #1

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merged 33 commits into from
Jul 7, 2023
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b20fb3d
add some example code and env
d33bs Jun 28, 2023
7b54774
add alpine diags and descriptions, begin slurm sec
d33bs Jun 28, 2023
6f26541
implementation diagram and init content; run scrpt
d33bs Jun 29, 2023
2d659f3
step 0 access content
d33bs Jun 29, 2023
d3b50fc
add data transfer + prepare data on alpine content
d33bs Jun 30, 2023
1792b17
add comments to run script
d33bs Jun 30, 2023
3a3b450
quotes display tweaks
d33bs Jun 30, 2023
4ab7765
replace fontawesome with emoji symbols
d33bs Jun 30, 2023
784cc82
add args
d33bs Jun 30, 2023
4086483
Update run_script.sh
d33bs Jun 30, 2023
27cbb86
Update run_script.sh
d33bs Jun 30, 2023
542985a
Update run_script.sh
d33bs Jun 30, 2023
b2daf69
add env variable
d33bs Jun 30, 2023
fd5ae48
yml file ext
d33bs Jun 30, 2023
b0c0705
remove the environment if it exists
d33bs Jun 30, 2023
0bd36a1
yes remove env
d33bs Jun 30, 2023
c00c333
linting; named variable use in python
d33bs Jun 30, 2023
61f51c6
adding logging for stdout from sbatch run
d33bs Jun 30, 2023
8435b0f
implementation process and modified logging file
d33bs Jun 30, 2023
c9e6481
add globus transfer directions
d33bs Jul 5, 2023
28409bb
Update README.md
d33bs Jul 5, 2023
4569e70
spacing
d33bs Jul 5, 2023
f96786e
more descriptive text
d33bs Jul 6, 2023
7460127
appropriate product naming capitalizations
d33bs Jul 6, 2023
b3ada82
simplifying code preparation description
d33bs Jul 6, 2023
eaa5cfe
more descriptive slurm directive documentation
d33bs Jul 6, 2023
5e39224
write instead of send
d33bs Jul 6, 2023
95659db
simplify run script python docs
d33bs Jul 6, 2023
400eba8
capitalizations and sentence endings
d33bs Jul 6, 2023
6e582d7
docstring sentence
d33bs Jul 6, 2023
839c1e4
Apply suggestions from code review
d33bs Jul 7, 2023
5c1a8fe
linting
d33bs Jul 7, 2023
5c932d3
add authorship team / department links
d33bs Jul 7, 2023
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4 changes: 4 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -158,3 +158,7 @@ cython_debug/
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/

# data ignores

*.csv
60 changes: 60 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,60 @@
# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
default_language_version:
python: python3.10
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-yaml
- id: check-added-large-files
- id: check-toml
- repo: https://github.com/codespell-project/codespell
rev: v2.2.5
hooks:
- id: codespell
exclude: >
(?x)^(
.*\.lock|.*\.csv|.*\.ipynb
)$
additional_dependencies:
- tomli
- repo: https://github.com/executablebooks/mdformat
rev: 0.7.16
hooks:
- id: mdformat
- repo: https://github.com/nbQA-dev/nbQA
rev: 1.7.0
hooks:
- id: nbqa-black
- id: nbqa-isort
- repo: https://github.com/psf/black
rev: 23.3.0
hooks:
- id: black
- repo: https://github.com/asottile/blacken-docs
rev: 1.14.0
hooks:
- id: blacken-docs
- repo: https://github.com/PyCQA/isort
rev: 5.12.0
hooks:
- id: isort
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.4.0
hooks:
- id: mypy
- repo: https://github.com/PyCQA/pylint
rev: v3.0.0a6
hooks:
- id: pylint
name: pylint
entry: pylint
language: python
types: [python]
# args: ["--disable=X"]
additional_dependencies:
- "numpy"
- "pandas"
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