Commit 10c6c9db authored by Lukas Riedel's avatar Lukas Riedel

Merge branch 'master' into 127-add-data-assimilation-interface-to-richardssimulation

parents 5acbc9f1 350d6a57
---
BasedOnStyle: Mozilla
# Break before braces, except for one-line statements
BreakBeforeBraces: Allman
# Do not break before assignment operators
BreakBeforeBinaryOperators: NonAssignment
......@@ -11,6 +11,7 @@ variables:
BASE_IMAGE: dorie/dune-env
# Use semantic versioning (not the version of DUNE) and bump according to
# to whether changes are backwards-compatible or not.
# NOTE: Update the default value in the Dockerfiles accordingly!
IMAGE_VERSION: "1.3"
DUNE_ENV_IMAGE: ${BASE_IMAGE}:img-v${IMAGE_VERSION}
......@@ -31,6 +32,10 @@ variables:
image: $DUNE_ENV_IMAGE
# Run pipelines on branches
include:
- template: 'Workflows/Branch-Pipelines.gitlab-ci.yml'
# Move into top-level DUNE directory
before_script:
- cd $DUNE_DIR
......@@ -63,13 +68,8 @@ stages:
- test
- deploy
# --- Preparation of Docker Images ---
setup:dune-env: &setup
stage: setup
only:
variables:
- $REBUILD_BASE_IMAGE # must be defined and have non-empty value
# --- Job Template for Docker in Docker (DinD) Runner Setup ---
.dind:
tags:
- dind
image: docker:stable
......@@ -79,6 +79,14 @@ setup:dune-env: &setup
DOCKER_DRIVER: overlay2
before_script:
- $DOCKER_LOGIN
# --- Preparation of Docker Images ---
setup:dune-env: &setup
stage: setup
extends: .dind
rules:
- changes:
- docker/dune-env.dockerfile
script:
- docker build -f docker/dune-env.dockerfile
--build-arg PROCNUM=$CPUS_DIND
......@@ -96,12 +104,17 @@ setup:dune-env-clang:
- docker push ${DUNE_ENV_IMAGE}-clang
prep:update-dune: &update
<<: *setup
stage: prep
extends: .dind
allow_failure: true
only:
- master
- tags
rules:
# Run after pushes to master and tags in original repo, not forks
- if: '$CI_COMMIT_BRANCH == "master" && $CI_PROJECT_PATH == "dorie/dorie"'
- if: '$CI_COMMIT_TAG && $CI_PROJECT_PATH == "dorie/dorie"'
# Run after Dockerfile changed. Do not allow failure then.
- changes:
- docker/dune-env-update.dockerfile
allow_failure: false
script:
- docker build -f docker/dune-env-update.dockerfile
--build-arg DUNE_ENV_IMAGE=$DUNE_ENV_IMAGE
......@@ -114,8 +127,6 @@ prep:update-dune-clang:
script:
- docker build -f docker/dune-env-update.dockerfile
--build-arg DUNE_ENV_IMAGE=${DUNE_ENV_IMAGE}-clang
--build-arg CC=clang
--build-arg CXX=clang++
--build-arg PROCNUM=$CPUS_DIND
-t ${DUNE_ENV_IMAGE}-clang .
- docker push ${DUNE_ENV_IMAGE}-clang
......@@ -124,6 +135,8 @@ prep:update-dune-clang:
# --- Build jobs ---
build:system-tests: &build-tests
stage: build
tags:
- multicore
# Reduce concurrent jobs due to RAM limitations
variables:
MAKE_FLAGS: -j 2
......@@ -153,6 +166,8 @@ build:unit-tests:
build:debug: &debug
stage: build
tags:
- multicore
allow_failure: true
before_script:
- cd $DUNE_DIR
......@@ -257,10 +272,9 @@ test:examples:
test:python-tests:
<<: *test
# May run immediately
dependencies: []
# TODO: Make empty once https://gitlab.com/gitlab-org/gitlab/issues/30631
# is resolved
needs: ["build:docs"] # Any quick job from previous stage
needs: []
script:
- $DUNECONTROL --only=dorie configure
- $DUNECONTROL --only=dorie make test_python
......@@ -268,18 +282,10 @@ test:python-tests:
# --- Deploy jobs ---
deploy:dockerhub-devel: &deploy
stage: deploy
only:
- master@dorie/dorie
tags:
- dind
image: docker:stable
services:
- docker:dind
variables:
DOCKER_DRIVER: overlay2
dependencies: []
before_script:
- $DOCKER_LOGIN
extends: .dind
rules:
# Run after pushes to master in original repo, not forks
- if: '$CI_COMMIT_BRANCH == "master" && $CI_PROJECT_PATH == "dorie/dorie"'
script:
- docker build -f docker/dorie.dockerfile
--build-arg BASE_IMG_VERSION=$IMAGE_VERSION --build-arg PROCNUM=$CPUS_DIND
......@@ -291,8 +297,9 @@ deploy:dockerhub-devel: &deploy
deploy:dockerhub-stable:
<<: *deploy
only:
- tags@dorie/dorie
rules:
# Run after pushes to tags in original repo, not forks
- if: '$CI_COMMIT_TAG && $CI_PROJECT_PATH == "dorie/dorie"'
script:
- docker build -f docker/dorie.dockerfile
--build-arg BASE_IMG_VERSION=$IMAGE_VERSION --build-arg PROCNUM=$CPUS_DIND
......
......@@ -4,14 +4,13 @@
We're rolling out version `X.Y.0`! :tada:
### 1 — In the Code
- [ ] `master`: Update version numbers in `VERSION`, `CHANGELOG.md`,
`dune.module` to `X.Y.0`.
- [ ] `master`: Update all `version="unreleased"` tags in the default config
file XML sources to `version="X.Y.0"`.
- [ ] `master`: Update all [version directives][sphinx-ver-dir] with version
`unreleased` in the user docs to `X.Y.0`.
- [ ] [Create branch][new branch] `X.Y-release` from `master`.
- [ ] *(Insert MR here)*: Merge `X.Y-release` into `master`. Use the
`pre-release` MR description template.
### 2 — On GitLab
- [ ] [Create branch][new branch] `X.Y-stable` from `master`
- [ ] [Create label][new label] ~"Pick into X.Y"
- [ ] [Create tag][new tag] `X.Y.0` from branch `X.Y-stable`
......@@ -31,14 +30,17 @@ We're rolling out version `X.Y.0`! :tada:
- [ ] Update "Release" [project badge][badge] <!-- only if applicable -->
### 3 — In the Code
- [ ] `master`: Update version numbers in `VERSION`, `CHANGELOG.md`,
`dune.module` to `X.Y+1-pre`.
- [ ] *(Insert MR here)*: Merge `X.Y-release` into `master`. Use the
`post-release` description template.
### 4 — On Docker Hub
- [ ] Update [description on DockerHub][DockerHub description]
- [ ] Push new `latest` tag to DockerHub <!-- only if applicable -->
### 5 — All done? :white_check_mark:
Close this issue!
/label ~Release
......@@ -49,4 +51,3 @@ Close this issue!
[new label]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/-/labels/new
[DockerHub description]: https://hub.docker.com/r/dorie/dorie
[badge]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/edit
[sphinx-ver-dir]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-versionadded
<!-- _Set the title to: "Post Release: X.Y.0" -->
<!-- Replace X.Y with the actual version numbers everywhere -->
We're updating the repository after Release `X.Y.0` 🧹
### Release Issue
<!-- DO NOT use automatic Issue resolution here! -->
The release is coordinated in issue #
### Tasks
- [ ] Update version numbers in `VERSION` and `dune.module` to `X.Y+1-pre`
- [ ] Add new "Unreleased" section in `CHANGELOG.md`
### Can this MR be merged?
- [ ] Pipeline passing <!-- please check for new warnings -->
- [ ] Delete branch option set
### Related Issues
<!-- _Set the title to: "Pre Release: X.Y.0" -->
<!-- Replace X.Y.0 with the actual version numbers everywhere -->
We're gearing up for Release `X.Y.0` 🎉
### Release Issue
<!-- DO NOT use automatic Issue resolution here! -->
The release is coordinated in issue #
### Tasks
- [ ] Update version numbers in `VERSION`, `CHANGELOG.md`, `dune.module` to
`X.Y.0`.
- [ ] Update all `version="unreleased"` tags in the default config file XML
sources to `version="X.Y.0"`.
- [ ] Update all [version directives][sphinx-ver-dir] with version `unreleased`
in the user docs to `X.Y.0`.
- [ ] Trigger re-build of Docker base image,
see [`docker/README.md`][docker_readme]
### Can this MR be merged?
- [ ] Pipeline passing <!-- please check for new warnings -->
- [ ] Delete branch option **not set**
### Related Issues
[docker_readme]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/blob/master/docker/README.md
[sphinx-ver-dir]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-versionadded
......@@ -4,3 +4,6 @@
[submodule "plugins/vendor/googletest"]
path = plugins/vendor/googletest
url = https://github.com/google/googletest.git
[submodule "plugins/vendor/clang-format-hooks"]
path = plugins/vendor/clang-format-hooks
url = https://github.com/barisione/clang-format-hooks.git
# DORiE Changelog
## Unreleased
### Added
* Extended Miller scaling adapter with additional porosity scaling !122
* Coding style tools and instructions.
[`clang-format-hook`](https://github.com/barisione/clang-format-hooks)
as Git submodule !203
* Automatically trigger DUNE Docker image builds using `rules` !213
### Changed
* Linerar solver for finite volumes changed from `AMG_4_DG` to
`BCGS_AMG_SSOR` !204
* Simplify installation instructions !205
### Fixed
* Compiler warnings for unused variables in `dune/dorie/common/h5file.hh` !206
* Ensure UTF-8 locale definition in Docker images !210
## 2.0.0 (2020-05-14)
### Added
* [`yaml-cpp`](https://github.com/jbeder/yaml-cpp/) v5.2.0 or greater as
dependency !81
* Abstract base class for Models !87
* Finite volume solver for passive transport model !93 !88
* Abstract base class for Models !87 !159
* Finite volume solver for passive transport model !93 !88 !179 !180 !181
* Grid function container to store transient grid functions !115
* Infrastructure for the input of Miller scaling fields. !110
* Infrastructure for the input of Miller scaling fields !110 !124 !133
* Logging framework [`spdlog`](https://github.com/gabime/spdlog) as
Git submodule for all terminal output !106
Git submodule for all terminal output !106 !192
* Support input of boundary segmentations !119
* Reconstruction of continuous fluxes using RT finite elements !105
* Custom DG finite element map for simplices based on Pk polynomials !125
......@@ -25,7 +46,7 @@
* Define compile-time settings via CPP macros !144
* [Google Test](https://github.com/google/googletest) unit test framework
as Git Submodule !159
* Upwinding options for Richards finite volume local operator !161
* Finite volume solver for the Richards equation !132 !161
* Cookbook tutorial on infiltration into homogeneous sand !157
* GitLab Description Templates for Releases !166
* ParaView tutorial for analyzing DORiE output files !173
......@@ -34,12 +55,15 @@
* CMake option to enable code coverage flags on all targets !172
* Steady state initial condition in Richards model !176
* Changes to config file parameters listed per version in user docs !175
* Control negative transport solution by a check policy !181
* DG solver for solute transport model !112
* Cookbook tutorial on using the random field generator !184
* Outflow boundary condition for Richards model !191
* Specify water content as initial condition in Richards model !187
* Documentation about model solver loop and time step adaptation schemes !190
* Documentation about the parallel features of several classes and methods !197
### Changed
* Data structures for storing and accessing parameter information !55
* Split unit tests into separate CI job with coverage reports !98
* Split grid adaptivity process into marking and actual adaptation !91
......@@ -53,43 +77,41 @@
* Extend run config file to contain data on multiple models !103
* DORiE now writes vertex data by default. !128
* Switch license from MIT to GPLv3 !135
* Specifying scaling field `extensions` and `offset` is now optional !133
* Generalized initial condition specification in config file !129
* Structure and setup of Sphinx user docs !126
* Switch to stable `dune-randomfield` release branch !151, !153
* System tests for executing `dorie pfg` module !153
* Finite volume solver for the Richards equation !132
* Build independent library and executable for each compile-time setting !144
* `SimulationBase` unit test now uses Google Test !159
* Deploy online documentation for each branch to private server !163
* Use YAML (instead of muPhi `.bcdat`) files for specifying BCs !121
* Unit and system tests report code coverage separately !172
* Improve docs on config file parameters and make default ones executable !183
* Update the contribution guidelines and the code of conduct !194
### Fixed
* Allow meta-ini files for unit tests !101
* Allow meta-ini files for unit tests #105
* Solver in `RichardsSimulation` was using the wrong time variable !116
* Shape of input datasets was flipped when loading scaling factors !124
* `dune_add_system_test` requires target with location after bugfix !165
* `make all` would not build the solver application target `dorie` !167
* Allow Neumman BC to be applied on a different direction other than gravity !121
* Transport model option `dirichletMode` was not working properly !121
* `dune_add_system_test` requires target with location after bugfix #161
* `make all` would not build the solver application target `dorie` #162
* Allow Neumman BC to be applied on a different direction than gravity #136
* Use unsafe loader of PyYAML v5.2 for loading parameter scraper data !177
* CFL condition in explicit Transport model serves as time step upper limit !179
* Use apparent solute velocity instead of water flux in CFL condition !180
* Steps were not synchronized when timestep suggestions differed in parallel #187
### Deprecated
### Removed
* Boundary conditions `evaporation` and `limitedInflux` !120
* Boundary conditions `evaporation` and `limitedInflux` !120
## 1.1.1 (2018-08-21)
### Added
* Documentation of Docker images and their usage in the CI/CD pipeline.
### Changed
* Rebuilds of the DUNE environment Docker image are now triggered by setting the
CI variable `REBUILD_BASE_IMAGE` to a non-empty value. Previously, the
builds in stage `setup` where triggered by any manual pipeline run.
......@@ -98,6 +120,7 @@
[`richards_operator_DG.hh`](dune/dorie/solver/richards_operator_DG.hh)
### Fixed
* Removed VTK output from `dorie_mass_conservation` executable, which would
cause the corresponding test to fail if the designated output directory did
not exist.
......@@ -115,10 +138,10 @@
* Re-introduced deployment of the documentation which can now be found online
at https://dorie-doc.netlify.com/.
## 1.1.0 (2018-07-27)
### Added
* DORiE now employs a `SubsamplingVTKWriter` for higher output precision.
Subsampling levels are controlled via the new key `output.subsamplingLevel`.
* Automatic deployment of `devel` and stable DORiE Docker Images to Docker Hub.
......@@ -129,6 +152,7 @@
* Public API definition in documentation.
### Changed
* Update code base to *DUNE v2.6*.
* Raise software requirements to versions available on Ubuntu 18.04 LTS
(Bionic Beaver).
......@@ -139,24 +163,26 @@
sequential ones. This significantly improves performance for large problems.
* Change compilation order which reduces RAM usage when compiling in parallel.
* Decentralization of the header system so that in most of the header files are
independent of each other.
independent of each other.
### Deprecated
* `output.subsamplingLevel` is optional and defaults to 0 if not given
explicitly in the config file. The key will become mandatory in future
versions.
### Removed
* Complete doxygen documentation from Sphinx docs.
### Fixed
* The source code is now compatible to the Clang LLVM compiler.
DORiE can now be compiled with the onboard compiler on macOS.
* Fix finite element map used for simplex grids. The old one did not implement
a discontinuous function space.
* Allow warnings on ParMETIS not being available for parallel computations.
## 1.0.0 (2018-03-28)
First stable version.
......@@ -43,12 +43,10 @@ set(DORIE_EXE_PATH ${PROJECT_BINARY_DIR}/dune/dorie/
# add subdirectories
add_subdirectory("plugins/vendor")
add_subdirectory("m4")
add_subdirectory("cmake/modules")
add_subdirectory("python")
add_subdirectory("doc")
add_subdirectory("dune")
add_subdirectory("lib")
if(DORIE_TESTING)
add_subdirectory("test")
add_subdirectory("doc/cookbook")
......
......@@ -2,74 +2,127 @@
## Our Pledge
In the interest of fostering an open and welcoming environment, we as
contributors and maintainers pledge to making participation in our project and
our community a harassment-free experience for everyone, regardless of age, body
size, disability, ethnicity, gender identity and expression, level of experience,
education, socio-economic status, nationality, personal appearance, race,
religion, or sexual identity and orientation.
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, 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 creating a positive environment
include:
Examples of behavior that contributes to a positive environment for our
community include:
* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
* 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 by participants include:
Examples of unacceptable behavior include:
* The use of sexualized language or imagery and unwelcome sexual attention or
advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* 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 electronic
address, without explicit permission
* 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
## Our Responsibilities
## Enforcement Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable
behavior and are expected to take appropriate and fair corrective action in
response to any instances of unacceptable behavior.
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.
Project maintainers 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, or to ban temporarily or
permanently any contributor for other behaviors 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 both within project spaces and in public spaces
when an individual is representing the project or its community. Examples of
representing a project or community include using an official project e-mail
address, posting via an official social media account, or acting as an appointed
representative at an online or offline event. Representation of a project may be
further defined and clarified by project maintainers.
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 by contacting the project team at
[dorieteam@iup.uni-heidelberg.de](mailto:dorieteam@iup.uni-heidelberg.de). All
complaints will be reviewed and investigated and will result in a response that
is deemed necessary and appropriate to the circumstances. The project team is
obligated to maintain confidentiality with regard to the reporter of an incident.
Further details of specific enforcement policies may be posted separately.
reported to the community leaders responsible for enforcement at
[dorieteam@iup.uni-heidelberg.de](mailto:dorieteam@iup.uni-heidelberg.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
Project maintainers who do not follow or enforce the Code of Conduct in good
faith may face temporary or permanent repercussions as determined by other
members of the project's leadership.
**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 1.4,
available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.0, available at
https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
Community Impact Guidelines were inspired by [Mozilla's code of conduct
enforcement ladder](https://github.com/mozilla/diversity).
[homepage]: https://www.contributor-covenant.org
For answers to common questions about this code of conduct, see the FAQ at
https://www.contributor-covenant.org/faq. Translations are available at
https://www.contributor-covenant.org/translations.
# Contributing to DORiE
**Thank you for taking your time and contributing to DORiE!** :+1:
**Thank you for taking your time and contributing to DORiE!** 👍
## License and Distribution
DORiE is licensed under the
[GNU General Public License Version 3](https://www.gnu.org/licenses/gpl-3.0.en.html).
Contributors to the DORiE project and source code agree that their contributions
are published and may be distributed according to this license. All contributors
will be acknowledged in the [authors list](COPYING.md#copyright-holders).