Skip to content

Commit

Permalink
Resolving merge conflicts merging 'development' into 'tj2016'.
Browse files Browse the repository at this point in the history
  • Loading branch information
mwaxmonsky committed Jul 23, 2024
2 parents 223f3fe + 4609b76 commit 3f58522
Show file tree
Hide file tree
Showing 192 changed files with 3,211 additions and 9,944 deletions.
4 changes: 2 additions & 2 deletions .github/scripts/pr_mod_file_tests.py
Original file line number Diff line number Diff line change
Expand Up @@ -197,10 +197,10 @@ def _main_prog():
#PR itself, so don't check its file type:
if os.path.exists(file_obj.filename):

#Don't analyze 'manage_externals' files,
#Don't analyze 'git-fleximod' files,
#as they are an external repo and thus
#not our responsibility:
if 'manage_externals' not in file_obj.filename:
if 'git-fleximod' not in file_obj.filename:

#Check if it is a python file:
if _file_is_python(file_obj.filename):
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/python_unit_tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,8 @@ jobs:
# Run "checkout_externals":
- name: Checkout externals
run: |
manage_externals/checkout_externals --externals Externals_CAM.cfg ccpp-framework
manage_externals/checkout_externals --externals Externals.cfg cime
bin/git-fleximod update ccpp-framework
bin/git-fleximod update cime
# Run python unit and doctests:
- name: python unit tests
run: |
Expand Down
17 changes: 0 additions & 17 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,20 +1,3 @@
# Ignore externals
ccpp_framework
ccs_config
chem_proc
cime
components
libraries
manage_externals.log
share
src/dynamics/mpas/dycore
src/physics/carma/base
src/physics/clubb
src/physics/cosp2/src
src/physics/ncar_ccpp
src/physics/silhs
src/utils/history_output

# Ignore compiled python
*.pyc
buildnmlc
Expand Down
103 changes: 103 additions & 0 deletions .gitmodules
Original file line number Diff line number Diff line change
@@ -0,0 +1,103 @@
[submodule "ccpp-framework"]
path = ccpp_framework
url = https://github.com/NCAR/ccpp-framework
fxtag = 2024-07-11-dev
fxrequired = AlwaysRequired
fxDONOTUSEurl = https://github.com/NCAR/ccpp-framework
[submodule "mpas"]
path = src/dynamics/mpas/dycore
url = https://github.com/MPAS-Dev/MPAS-Model.git
fxsparse = ../.mpas_sparse_checkout
fxtag = ed6f8e39ec0a811b6d079ca0fc6f9fb6e30bad23
fxrequired = AlwaysRequired
fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
[submodule "ncar-physics"]
path = src/physics/ncar_ccpp
url = https://github.com/ESCOMP/atmospheric_physics
fxtag = atmos_phys0_03_000
fxrequired = AlwaysRequired
fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
[submodule "ccs_config"]
path = ccs_config
url = https://github.com/ESMCI/ccs_config_cesm.git
fxtag = ccs_config_cesm0.0.106
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
[submodule "cdeps"]
path = components/cdeps
url = https://github.com/ESCOMP/CDEPS.git
fxtag = cdeps1.0.34
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
[submodule "cice"]
path = components/cice
url = https://github.com/ESCOMP/CESM_CICE
fxtag = cesm_cice6_5_0_10
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
[submodule "cime"]
path = cime
url = https://github.com/ESMCI/cime
fxtag = cime6.0.246
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESMCI/cime
[submodule "cism"]
path = components/cism
url = https://github.com/ESCOMP/CISM-wrapper
fxtag = cismwrap_2_2_001
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
[submodule "clm"]
path = components/clm
url = https://github.com/ESCOMP/CTSM
fxtag = ctsm5.2.007
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
[submodule "cmeps"]
path = components/cmeps
url = https://github.com/ESCOMP/CMEPS.git
fxtag = cmeps0.14.67
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
[submodule "fms"]
path = libraries/FMS
url = https://github.com/ESCOMP/FMS_interface
fxtag = fi_240516
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
[submodule "mct"]
path = libraries/mct
url = https://github.com/MCSclimate/MCT
fxtag = MCT_2.11.0
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/MCSclimate/MCT
[submodule "mizuRoute"]
path = components/mizuRoute
url = https://github.com/ESCOMP/mizuRoute
fxtag = cesm-coupling.n02_v2.1.2
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
[submodule "mosart"]
path = components/mosart
url = https://github.com/ESCOMP/MOSART
fxtag = mosart1_0_49
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
[submodule "parallelio"]
path = libraries/parallelio
url = https://github.com/NCAR/ParallelIO
fxtag = pio2_6_2
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
[submodule "rtm"]
path = components/rtm
url = https://github.com/ESCOMP/RTM
fxtag = rtm1_0_79
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/RTM
[submodule "share"]
path = share
url = https://github.com/ESCOMP/CESM_share
fxtag = share1.0.19
fxrequired = ToplevelRequired
fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
13 changes: 13 additions & 0 deletions .lib/git-fleximod/.github/workflows/pre-commit
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
name: pre-commit
on:
pull_request:
push:
branches: [main]

jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v3
- uses: pre-commit/[email protected]
77 changes: 77 additions & 0 deletions .lib/git-fleximod/.github/workflows/pytest.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,77 @@
# Run this job on pushes to `main`, and for pull requests. If you don't specify
# `branches: [main], then this actions runs _twice_ on pull requests, which is
# annoying.

on:
push:
branches: [main]
pull_request:
branches: [main]

jobs:
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4

# If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
# reference the matrixe python version here.
- uses: actions/setup-python@v5
with:
python-version: '3.9'

# Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
# from installing Poetry every time, which can be slow. Note the use of the Poetry version
# number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
# manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
# mildly cleaner by using an environment variable, but I don't really care.
- name: cache poetry install
uses: actions/cache@v4
with:
path: ~/.local
key: poetry-1.7.1

# Install Poetry. You could do this manually, or there are several actions that do this.
# `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
# Poetry's default install script, which feels correct. I pin the Poetry version here
# because Poetry does occasionally change APIs between versions and I don't want my
# actions to break if it does.
#
# The key configuration value here is `virtualenvs-in-project: true`: this creates the
# venv as a `.venv` in your testing directory, which allows the next step to easily
# cache it.
- uses: snok/install-poetry@v1
with:
version: 1.7.1
virtualenvs-create: true
virtualenvs-in-project: true

# Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
# key: if you're using multiple Python versions, or multiple OSes, you'd need to include
# them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
- name: cache deps
id: cache-deps
uses: actions/cache@v4
with:
path: .venv
key: pydeps-${{ hashFiles('**/poetry.lock') }}

# Install dependencies. `--no-root` means "install all dependencies but not the project
# itself", which is what you want to avoid caching _your_ code. The `if` statement
# ensures this only runs on a cache miss.
- run: poetry install --no-interaction --no-root
if: steps.cache-deps.outputs.cache-hit != 'true'

# Now install _your_ project. This isn't necessary for many types of projects -- particularly
# things like Django apps don't need this. But it's a good idea since it fully-exercises the
# pyproject.toml and makes that if you add things like console-scripts at some point that
# they'll be installed and working.
- run: poetry install --no-interaction

# And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
# so this line is super-simple. But it could be as complex as you need.
- run: |
git config --global user.name "${GITHUB_ACTOR}"
git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
poetry run pytest
18 changes: 18 additions & 0 deletions .lib/git-fleximod/.pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
exclude: ^utils/.*$

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.0.1
hooks:
- id: end-of-file-fixer
- id: trailing-whitespace
- repo: https://github.com/psf/black
rev: 22.3.0
hooks:
- id: black
- repo: https://github.com/PyCQA/pylint
rev: v2.11.1
hooks:
- id: pylint
args:
- --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member
107 changes: 107 additions & 0 deletions .lib/git-fleximod/CODE_OF_CONDUCT.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,107 @@
# Contributor Code of Conduct
_The Contributor Code of Conduct is for participants in our software projects and community._

## Our Pledge
We, as contributors, creators, stewards, and maintainers (participants), of **git-fleximod** pledge to make participation in
our software, system or hardware project and community a safe, productive, welcoming and inclusive experience for everyone.
All participants are required to abide by this Code of Conduct.
This includes respectful treatment of everyone regardless of age, body size, disability, ethnicity, gender identity or expression,
level of experience, nationality, political affiliation, veteran status, pregnancy, genetic information, physical appearance, race,
religion, or sexual orientation, as well as any other characteristic protected under applicable US federal or state law.

## Our Standards
Examples of behaviors that contribute to a positive environment include:

* All participants are treated with respect and consideration, valuing a diversity of views and opinions
* Be considerate, respectful, and collaborative
* Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism
* Acknowledging the contributions of others
* Avoid personal attacks directed toward other participants
* Be mindful of your surroundings and of your fellow participants
* Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress
* Respect the rules and policies of the project and venue

Examples of unacceptable behavior include, but are not limited to:

* Harassment, intimidation, or discrimination in any form
* Physical, verbal, or written abuse by anyone to anyone, including repeated use of pronouns other than those requested
* Unwelcome sexual attention or advances
* Personal attacks directed at other guests, members, participants, etc.
* Publishing others' private information, such as a physical or electronic address, without explicit permission
* Alarming, intimidating, threatening, or hostile comments or conduct
* Inappropriate use of nudity and/or sexual images
* Threatening or stalking anyone, including a participant
* Other conduct which could reasonably be considered inappropriate in a professional setting

## Scope
This Code of Conduct applies to all spaces managed by the Project whether they be physical, online or face-to-face.
This includes project code, code repository, associated web pages, documentation, mailing lists, project websites and wiki pages,
issue tracker, meetings, telecons, events, project social media accounts, and any other forums created by the project team which the
community uses for communication.
In addition, violations of this Code of Conduct outside these spaces may affect a person's ability to participate within them.
Representation of a project may be further defined and clarified by project maintainers.

## Community Responsibilities
Everyone in the community is empowered to respond to people who are showing unacceptable behavior.
They can talk to them privately or publicly.
Anyone requested to stop unacceptable behavior is expected to comply immediately.
If the behavior continues concerns may be brought to the project administrators or to any other party listed in the
[Reporting](#reporting) section below.

## Project Administrator Responsibilities
Project administrators are responsible for clarifying the standards of acceptable behavior and are encouraged to model appropriate
behavior and provide support when people in the community point out inappropriate behavior.
Project administrator(s) are normally the ones that would be tasked to carry out the actions in the [Consequences](#consequences)
section below.

Project administrators are also expected to keep this Code of Conduct updated with the main one housed at UCAR, as listed below in
the [Attribution](#attribution) section.

## Reporting
Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as
outlined in the [Consequences](#consequences) section below.
However, making a report to a project administrator is not considered an 'official report' to UCAR.

Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint
Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's
EthicsPoint Hotline](https://www2.fin.ucar.edu/ethics/anonymous-reporting).

Complaints received by UCAR will be handled pursuant to the procedures outlined in UCAR's Harassment Reporting and Complaint
Procedure.
Complaints to UCAR will be held as confidential as practicable under the circumstances, and retaliation against a person who
initiates a complaint or an inquiry about inappropriate behavior will not be tolerated.

Any Contributor can use these reporting methods even if they are not directly affiliated with UCAR.
The Frequently Asked Questions (FAQ) page for reporting is [here](https://www2.fin.ucar.edu/procedures/hr/reporting-faqs).

## Consequences
Upon receipt of a complaint, the project administrator(s) may take any action deemed necessary and appropriate under the
circumstances.
Such action can include things such as: removing, editing, or rejecting comments, commits, code, wiki edits, email, issues, and
other contributions that are not aligned to this Code of Conduct, or banning temporarily or permanently any contributor for other
behaviors that are deemed inappropriate, threatening, offensive, or harmful.
Project administrators also have the right to report violations to UCAR HR and/or UCAR's Office of Diversity, Equity and Inclusion
(ODEI), as well as a participant's home institution and/or law enforcement.
In the event an incident is reported to UCAR, UCAR will follow its Harassment Reporting and Complaint Procedure.

## Process for Changes
All UCAR managed projects are required to adopt this Contributor Code of Conduct.
Adoption is assumed even if not expressly stated in the repository.
Projects should fill in sections where prompted with project-specific information, including, project name and adoption date.

Projects that adopt this Code of Conduct need to stay up to date with UCAR's Contributor Code of Conduct, linked with a DOI in the
[Attribution](#attribution) section below.
Projects can make limited substantive changes to the Code of Conduct, however, the changes must be limited in scope and may not
contradict the UCAR Contributor Code of Conduct.

## Attribution
This Code of Conduct was originally adapted from the [Contributor Covenant](http://contributor-covenant.org/version/1/4), version
1.4.
We then aligned it with the UCAR Participant Code of Conduct, which also borrows from the American Geophysical Union (AGU) Code of
Conduct.
The UCAR Participant Code of Conduct applies to both UCAR employees as well as participants in activities run by UCAR.
The original version of this for all software projects that have strong management from UCAR or UCAR staff is available on the UCAR
website at https://doi.org/10.5065/6w2c-a132.
The date that it was adopted by this project was **Feb/13/2018**.
When responding to complaints, UCAR HR and ODEI will do so based on the latest published version.
Therefore, any project-specific changes should follow the [Process for Changes](#process-for-changes) section above.
20 changes: 20 additions & 0 deletions .lib/git-fleximod/License
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR)

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
“Software”), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Loading

0 comments on commit 3f58522

Please sign in to comment.