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Commit 09ef257b authored by Carsten Lemmen's avatar Carsten Lemmen Committed by Ovidio Fernando Garcia Oliva
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Gmp

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# Dockerfile for development on Alpine linux with gfortran
#
# SPDX-FileContributor: Carsten Lemmen <carsten.lemmen@hereon.de>
# SPDX-FileCopyrightText: 2024-2025 Helmholtz-Zentrum hereon GmbH
# SPDX-License-Identifier: CC0-1.0
#
# Download base image alpine
FROM python:3.11-alpine AS base
LABEL maintainer="carsten.lemmen@hereon.de"
LABEL version="0.1a"
LABEL description="This is a custom Docker image for a development container"
# Install a development toolchain based on gnu/openmpi, git and build tools
RUN apk add --no-cache cmake make bash
RUN apk add --no-cache gcc
RUN apk add --no-cache gfortran
RUN apk add --no-cache g++
RUN apk add --no-cache netcdf-dev netcdf-fortran-dev
RUN apk add --no-cache git
RUN pip install editscenario
RUN pip install matplotlib
RUN pip install gotmgui
CMD ["/bin/bash"]
FROM base AS gotm
ENV GOTMDIR /home/gotm
RUN git clone --depth=1 --recurse-submodules https://github.com/gotm-model/code.git $GOTMDIR
RUN mkdir -p $GOTMDIR/build
RUN mkdir -p /opt
RUN cmake -B $GOTMDIR/build -S $GOTMDIR -DCMAKE_INSTALL_PREFIX=/opt -DGOTM_USE_FABM=OFF
RUN make -C $GOTMDIR/build
RUN make -C $GOTMDIR/build install
CMD ["/bin/bash"]
FROM gotm AS gotm-fabm
ENV GOTM_BASE=$GOTMDIR
RUN cmake -B $GOTMDIR/build -S $GOTMDIR -DCMAKE_INSTALL_PREFIX=/opt -DGOTM_USE_FABM=ON
RUN make -C $GOTMDIR/build
RUN make -C $GOTMDIR/build install
CMD ["/bin/bash"]
FROM gotm-fabm AS fabm
RUN cmake -B $GOTMDIR/build -S $GOTMDIR -DCMAKE_INSTALL_PREFIX=/opt -DGOTM_USE_FABM=ON -DFABM_DOBGCP_BASE=./src -DFABM_INSTITUTES=dobgcp
RUN make -C $GOTMDIR/build
RUN make -C $GOTMDIR/build install
CMD ["/bin/bash"]
FROM alpine:edge AS runtime
COPY --from=gotm /opt /opt
LABEL maintainer="carsten.lemmen@hereon.de"
LABEL version="0.1a"
LABEL description="This is a custom Docker image for a deployment container"
LABEL license="CC0-1.0"
LABEL copyright="2024-2025 Helmholtz-Zentrum hereon GmbH"
# Install a development toolchain based on gnu/openmpi, git and build tools
#RUN apk add --no-cache \
RUN apk add \
git \
netcdf \
netcdf-fortran \
openmpi \
shadow \
openssh \
bash
#RUN python3 -m venv /home/.pyenv && \
# . /home/.pyenv/bin/activate && \
# pip install editscenario && deactivate
ENV PATH ${PATH}:/opt/bin
ENV LD_LIBRARY_PATH ${PATH}:/opt/lib
RUN groupadd -g 1009 model
RUN useradd -d /home -s /bin/bash -m model -u 1009 -g 1009
USER model
ENV HOME /home
CMD ["/bin/bash"]
\ No newline at end of file
# SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
# SPDX-License-Identifier: CC0-1.0
# SPDX-FileContributor: Carsten Lemmen <carsten.lemmen@hereon.de>
.PHONY: default push fabm
default:
@echo Valid Makefile targets are fabm and push
fabm:
@docker image inspect platipodium/fabm > /dev/null 2>&1 || \
docker build -f ./Dockerfile-fabm -t platipodium/fabm \
..
push: fabm
docker login -u ${CI_REGISTRY_USER} -p ${CI_WRITE_REGISTRY_TOKEN} ${CI_REGISTRY} && \
@for V in "fabm"; do \
IMAGEID=docker images -q platipodium/$$V && \
docker tag ${IMAGEID} ${CI_REGISTRY}/dam-elbextreme/dobgcp/$$V && \
docker image push ${CI_REGISTRY}/dam-elbextreme/dobgcp/$$V && \
done
\ No newline at end of file
# SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
# SPDX-License-Identifier: CC0-1.0
# SPDX-FileContributor: Carsten Lemmen <carsten.lemmen@hereon.de>
#
include:
# - ".gitlab/zenodo.yaml" # enable once we have .zenodo.json
- ".gitlab/license.yaml"
- ".gitlab/joss.yaml"
- ".gitlab/fabm.yaml"
- template: Security/SAST.gitlab-ci.yml
- template: Security/Secret-Detection.gitlab-ci.yml
stages:
- lint
- run
- test
- deploy
- release
# Automated job for software security, provided by GitLab
sast:
stage: test
release_job:
stage: release
image: registry.gitlab.com/gitlab-org/release-cli:latest
rules:
- if: $CI_COMMIT_TAG # Run this job when a tag is created
script:
- echo "Running release_job"
release: # See https://docs.gitlab.com/ee/ci/yaml/#release for available properties
tag_name: "$CI_COMMIT_TAG"
description: "$CI_COMMIT_TAG"
# GitLab CI configuration file for providing a gotm/fabm environment
#
# SPDX-FileCopyrightText: 2023-2025 Helmholtz-Zentrum hereon GmbH
# SPDX-License-Identifier: CC0-1.0
# SPDX-FileContributor Carsten Lemmen <carsten.lemmen@hereon.de
.base-fabm-docker:
image: docker
tags: ["docker", "dind"]
services:
- docker:dind
stage: deploy
variables:
CONTAINER_REGISTRY_IMAGE: $CI_REGISTRY_IMAGE/fabm
allow_failure: false
interruptible: true
needs: []
build-fabm-docker:
extends: .base-fabm-docker
before_script:
- docker login -u $CI_REGISTRY_USER -p $CI_JOB_TOKEN $CI_REGISTRY
script:
- "docker build -t ${CONTAINER_REGISTRY_IMAGE}
-f .docker/Dockerfile-fabm ."
- docker push ${CONTAINER_REGISTRY_IMAGE}
test-fabm-docker:
extends: .base-fabm-docker
stage: deploy
before_script:
- docker login -u $CI_REGISTRY_USER -p $CI_JOB_TOKEN $CI_REGISTRY
script:
- docker pull ${CONTAINER_REGISTRY_IMAGE}
- docker run ${CONTAINER_REGISTRY_IMAGE} gotm -v
needs:
- build-fabm-docker
# GitLab CI configuration file for building the JOSS paper
#
# SPDX-FileCopyrightText: 2022-2025 Helmholtz-Zentrum hereon GmbH
# SPDX-License-Identifier: CC0-1.0
# SPDX-FileContributor Carsten Lemmen <carsten.lemmen@hereon.de
# The JOSS-provided workflow did not work for issues between inara docker
# and gitlab, see https://github.com/openjournals/inara/issues/34.
# This is resolved by resetting the container's entrypoint.
joss-inara:
stage: deploy
image:
name: openjournals/inara
entrypoint: ["/bin/sh", "-c"]
variables:
GIT_SHA: $CI_COMMIT_SHA
JOURNAL: joss
script:
- inara -o pdf,cff ./doc/joss/paper.md
allow_failure: false
artifacts:
paths:
- ./doc/joss/paper.pdf
needs: []
# SPDX-FileCopyrightText: 2022-2025 Helmholtz-Zentrum hereon GmbH
# SPDX-License-Identifier: CC0-1.0
# SPDX-FileContributor: Carsten Lemmen <carsten.lemmen@hereon.de>
reuse:
stage: lint
image:
name: fsfe/reuse:latest
entrypoint: [""]
script:
- reuse lint
# GitLab CI configuration file for pushing tagged versions
# of the code as archive to zenodo, based on documentation
# at https://pypi.org/project/gitlab2zenodo/
#
# SPDX-FileCopyrightText: 2023-2025 Helmholtz-Zentrum hereon GmbH
# SPDX-License-Identifier: CC0-1.0
# SPDX-FileContributor Carsten Lemmen <carsten.lemmen@hereon.de
image: python:3.11
send-snapshot:
stage: deploy
rules:
- if: $CI_COMMIT_TAG =~ /^v?[0-9]+\.[0-9]+/
script:
- pip install gitlab2zenodo
- git archive --format zip --output ${CI_COMMIT_TAG#v}.zip ${CI_COMMIT_TAG}
- g2z-send -i $zenodo_record -t $zenodo_token -s -m .zenodo.json ${CI_COMMIT_TAG#v}.zip
needs: []
allow_failure: false
interruptible: true
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<!---
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# DO+BGC (Dissolved Oxygen and BioGeoChemistry)
......
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# Contributing
We hope you can make good use of the software and find it useful and enjoyable.
## Bugs, vulnerabilities, improvements, feedback
We appreciate your feedback, bug or vulnerability reports and improvement suggestions on our [issue tracker](https://codebase.helmholtz.cloud/dam-elbextreme/dobgcp/-/issues).
## Code contributions
We also welcome your contributions, subject to our Contributor
Covenant [code of conduct](./code_of_conduct.md) and our [contributor license agreement](./contributing-license.md). Please adhere to the [codeing guidelines](./coding guidelines.md) when making a contribution.
The best way to contribute is by
1. creating a fork off our repository,
2. committing your changes on your fork and then
3. creating a pull request ("PR") to push your changes back to us.
## Registration
To file an issue or to contribute, you are asked (1) to authenticate and (2) to register: When asked, **scroll all the way down** and click `Sign in with Helmholtz AAI`. On the following page "Login to Helmholtz AAI OAuth2 Authorization Server", search for one of your existing authentication providers (this may be your university, company, ORCID, github, or many others) and log in. You are then asked to provide name and email address for registration on the HIFIS GitLab instance.
<!--
SPDX-FileContributor: Coraline Ada Ehmke.de>
SPDX-FileCopyrightText: 2014-2023 Organization for Ethical Source
SPDX-License-Identifier: CC-BY-4.0
-->
# Contributor Covenant Code of Conduct
## Our Pledge
We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.
We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.
## Our Standards
Examples of behavior that contributes to a positive environment for our
community include:
- Demonstrating empathy and kindness toward other people
- Being respectful of differing opinions, viewpoints, and experiences
- Giving and gracefully accepting constructive feedback
- Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
- Focusing on what is best not just for us as individuals, but for the overall
community
Examples of unacceptable behavior include:
- The use of sexualized language or imagery, and sexual attention or advances of
any kind
- Trolling, insulting or derogatory comments, and personal or political attacks
- Public or private harassment
- Publishing others' private information, such as a physical or email address,
without their explicit permission
- Other conduct which could reasonably be considered inappropriate in a
professional setting
## Enforcement Responsibilities
Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.
Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.
## Scope
This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the ombudspersons
markus.quante@hereon.de or sabine.mendach@hereon.de.
All complaints will be reviewed and investigated promptly and fairly.
All community leaders are obligated to respect the privacy and security of the
reporter of any incident.
## Enforcement Guidelines
Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:
### 1. Correction
**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.
**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.
### 2. Warning
**Community Impact**: A violation through a single incident or series of
actions.
**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or permanent
ban.
### 3. Temporary Ban
**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.
**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.
### 4. Permanent Ban
**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.
**Consequence**: A permanent ban from any sort of public interaction within the
community.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.1, available at
[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
For answers to common questions about this code of conduct, see the FAQ at
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
[https://www.contributor-covenant.org/translations][translations].
[homepage]: https://www.contributor-covenant.org
[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations
<!--
SPDX-FileContributor: Carsten Lemmen <carsten.lemmen@hereon.de>
SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
SPDX-License-Identifier: CC0-1.0
-->
# Coding standard
We hope you find it easy to read our code and understand its structure. When you contribute code to our project, we ask you to adhere to coding standards, the most important one is consistency with the current code.
## Coding rules
1. Consistency
: Whatever you do, be consistent in what you do. This is the guiding principle all other rules are subjected to
2. Line break
: Please break at 132 columns at the latest
3. Empty lines.
: Do not overuse empty lines, but reserve them for separating logical units or blocks of statements, just like
you would use paragraphs in a text. Separate procedures with one empty line.
4. Indentation
Use consistent and logical indentation to make the code more readable. Each level of indentation should consist of three spaces.
5. Naming conventions
: Use meaningful english names for variables, procedures, and functions. Names should be descriptive and use lowercase letters.
6. Comments:
: Use comments to explain complex sections of code, as well as to provide an overview of what the code does.
7. Error handling:
Always include error handling code to catch and handle unexpected exceptions. Preferably either halt the simulation with `stop`. Use appropriate error messages to help users diagnose and fix problems.
8. Documentation:
Provide documentation for the code, including a description of its purpose, its input and output parameters, and examples of its usage.
<!--
SPDX-FileCopyrightText: 2011 Project Harmony
SPDX-License-Identifier: CC-BY-3.0
-->
# Individual Contributor License Agreement
Thank you for your interest in contributing to our project ("We" or "Us").
This contributor agreement ("Agreement") documents the rights granted by contributors to Us. To make this document effective, please sign it and send it to Us by mail, email, fax, or electronic submission. This is a legally binding document, so please read it carefully before agreeing to it.
## Definitions
"You" means the individual who Submits a Contribution to Us; or the
any Legal Entity on behalf of whom a Contribution has been received by Us.
"Legal Entity" means an entity which is not a natural person. "Affiliates" means other Legal Entities that control, are controlled by, or under common control with that Legal Entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such Legal Entity, whether by contract or otherwise, (ii) ownership of fifty percent (50%) or more of the outstanding shares or securities which vote to elect the management or other persons who direct such Legal Entity or (iii) beneficial ownership of such entity.
"Contribution" means any work of authorship that is Submitted by You to Us in which You own or assert ownership of the Copy<!-- /-->right.
"Copy<!-- /-->right" means all rights protecting works of authorship owned or controlled by You, including copyright, moral and neighboring rights, as appropriate, for the full term of their existence including any extensions by You.
"Material" means the work of authorship which is made available by Us to third parties. When this Agreement covers more than one software project, the Material means the work of authorship to which the Contribution was Submitted. After You Submit the Contribution, it may be included in the Material.
"Submit" means any form of electronic, verbal, or written communication sent to Us or our representatives, including but not limited to electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, Us for the purpose of discussing and improving the Material, but excluding communication that is conspicuously marked or otherwise designated in writing by You as "Not a Contribution."
"Submission Date" means the date on which You Submit a Contribution to Us.
"Effective Date" means the date You execute this Agreement or the date You first Submit a Contribution to Us, whichever is earlier.
"Media" means any portion of a Contribution which is not software.
## Grant of Rights
### Copy<!-- /-->right and License
(a) You retain ownership of the Copy<!-- /-->right in Your Contribution and have the same rights to use or license the Contribution which You would have had without entering into the Agreement.
(b) To the maximum extent permitted by the relevant law, You grant to Us a perpetual, worldwide, non-exclusive, transferable, royalty-free, irrevocable license under the Copy<!-- /-->right covering the Contribution, with the right to sublicense such rights through multiple tiers of sublicensees, to reproduce, modify, display, perform and distribute the Contribution as part of the Material; provided that this license is conditioned upon compliance with Section 2.3.
### Outbound Licenses for non-open source Material
We agree to license the Contribution only under the terms of the license or licenses which We are using on the Submission Date for the Material (including any rights to adopt any future version of a license if permitted).
### Outbound Licenses for open source Material
We agree to license the Contribution only under the terms of the license or licenses which We are using on the Submission Date for the Material or any licenses which are approved by the Open Source Initiative on or after the Effective Date, including both permissive and copyleft licenses, whether or not such licenses are subsequently disapproved (including any right to adopt any future version of a license if permitted).
In addition, We may use the following licenses for Media in the Contribution: [CC0-1.0, CC-by-SA-4.0] (including any right to adopt any future version of a license if permitted).
### Moral Rights
If moral rights apply to the Contribution, to the maximum extent permitted by law, You waive and agree not to assert such moral rights against Us or our successors in interest, or any of our licensees, either direct or indirect.
### Our Rights
You acknowledge that We are not obligated to use Your Contribution as part of the Material and may decide to include any Contribution We consider appropriate.
### Reservation of Rights
Any rights not expressly [assigned or] licensed under this section are expressly reserved by You.
## Agreement
You confirm that:
(a) You have the legal authority to enter into this Agreement.
(b) You own the Copy<!-- /-->right and patent claims covering the Contribution which are required to the Grant of Rights.
(c)(Individual) The Grant of Rights does not violate any grant of rights which You have made to third parties, including Your employer. If You are an employee, You have had Your employer approve this Agreement or sign the Entity version of this document. If You are less than eighteen years old, please have Your parents or guardian sign the Agreement.
(c)(Entity) The Grant of Rights does not violate any grant of rights which You or Your Affiliates have made to third parties.
# Disclaimer
EXCEPT FOR THE EXPRESS WARRANTIES IN SECTION 3, THE CONTRIBUTION IS PROVIDED "AS IS". MORE PARTICULARLY, ALL EXPRESS OR IMPLIED WARRANTIES INCLUDING, WITHOUT LIMITATION, ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT ARE EXPRESSLY DISCLAIMED BY YOU TO US [AND BY US TO YOU]. TO THE EXTENT THAT ANY SUCH WARRANTIES CANNOT BE DISCLAIMED, SUCH WARRANTY IS LIMITED IN DURATION TO THE MINIMUM PERIOD PERMITTED BY LAW.
# Consequential Damage Waiver
TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL YOU [OR US] BE LIABLE FOR ANY LOSS OF PROFITS, LOSS OF ANTICIPATED SAVINGS, LOSS OF DATA, INDIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL AND EXEMPLARY DAMAGES ARISING OUT OF THIS AGREEMENT REGARDLESS OF THE LEGAL OR EQUITABLE THEORY (CONTRACT, TORT OR OTHERWISE) UPON WHICH THE CLAIM IS BASED.
# Miscellaneous
This Agreement will be governed by and construed in accordance with the laws of Germany excluding its conflicts of law provisions. Under certain circumstances, the governing law in this section might be superseded by the United Nations Convention on Contracts for the International Sale of Goods ("UN Convention") and the parties intend to avoid the application of the UN Convention to this Agreement and, thus, exclude the application of the UN Convention in its entirety to this Agreement.
This Agreement sets out the entire agreement between You and Us for Your Contributions to Us and overrides all other agreements or understandings.
If You or We assign the rights or obligations received through this Agreement to a third party, as a condition of the assignment, that third party must agree in writing to abide by all the rights and obligations in the Agreement.
The failure of either party to require performance by the other party of any provision of this Agreement in one situation shall not affect the right of a party to require such performance at any time in the future. A waiver of performance under a provision in one situation shall not be considered a waiver of the performance of the provision in the future or a waiver of the provision in its entirety.
If any provision of this Agreement is found void and unenforceable, such provision will be replaced to the extent possible with a provision that comes closest to the meaning of the original provision and which is enforceable. The terms and conditions set forth in this Agreement shall apply notwithstanding any failure of essential purpose of this Agreement or any limited remedy to the maximum extent possible under law.
## SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
## SPDX-License-Identifier: CC0-1.0
## SPDX-FileContributor Carsten Lemmen <carsten.lemmen@hereon.de>
CITATION.cff
paper.pdf
\ No newline at end of file
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