Merge branch 'master' into cookbook-solute-transport-in-homogeneous-medium

.gitignore

@@ -4,7 +4,8 @@ build-cmake/
 # Exclude generated files
 doc/manual/config-file.rst
 doc/default_files/config.ini
-doc/cookbook/tutorial-*/config.ini
+doc/cookbook/1-infiltration-sand/config.ini
+doc/cookbook/7-solute-transport/config.ini
 python/dorie/wrapper/pf_from_file.py
 python/dorie/wrapper/test_dorie.py
 python/dorie/dorie/cli/cmds.py

.gitlab-ci.yml

 variables:
-  DUNE_CONTROL_PATH: /opt/dune:$CI_PROJECT_DIR
+  DUNE_DIR: /opt/dune
+  DUNE_CONTROL_PATH: $DUNE_DIR:$CI_PROJECT_DIR
   DUNECONTROL: ./dune-common/bin/dunecontrol
   CPUS_MULTICORE: 4
   CPUS_DIND: 2
@@ -30,8 +31,9 @@ variables:
 
 image: $DUNE_ENV_IMAGE
 
+# Move into top-level DUNE directory
 before_script:
-  - cd /opt/dune
+  - cd $DUNE_DIR
 
 # Provide SSH access via the SSH_PRIVATE_KEY and SSH_KNOWN_HOSTS variables
 .ssh-access: &ssh_access
@@ -123,7 +125,7 @@ prep:update-dune-clang:
 build:system-tests: &build-tests
   stage: build
   script:
-    - CMAKE_FLAGS="$CMAKE_FLAGS"
+    - CMAKE_FLAGS="$CMAKE_FLAGS -DCOVERAGE_REPORT=On"
       $DUNECONTROL --only=dorie configure
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS dorie-rfg
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS build_system_tests
@@ -136,20 +138,22 @@ build:system-tests: &build-tests
 build:unit-tests:
   <<: *build-tests
   script:
-    - CMAKE_FLAGS="$CMAKE_FLAGS
-                   -DCMAKE_BUILD_TYPE=Debug"
+    - CMAKE_FLAGS="$CMAKE_FLAGS -DCOVERAGE_REPORT=On
+                   -DCMAKE_BUILD_TYPE=None"
       $DUNECONTROL --only=dorie configure
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS build_unit_tests
 
 build:debug: &debug
   stage: build
   allow_failure: true
-  script:
+  before_script:
+    - cd $DUNE_DIR
     - CMAKE_FLAGS="
         $CMAKE_FLAGS
         -DCMAKE_BUILD_TYPE=Debug
         -DCMAKE_CXX_FLAGS_DEBUG='-Werror'"
       $DUNECONTROL --only=dorie configure
+  script:
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS dorie-rfg
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS build_unit_tests
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS richards_d2_r1 transport_d2_r0_t0
@@ -157,7 +161,9 @@ build:debug: &debug
 build:debug-clang:
   <<: *debug
   image: ${DUNE_ENV_IMAGE}-clang
-  script:
+  before_script:
+    - cd $DUNE_DIR
+    # Choose Clang compiler explicitly
     - CMAKE_FLAGS="
         $CMAKE_FLAGS
         -DCMAKE_BUILD_TYPE=Debug
@@ -165,9 +171,6 @@ build:debug-clang:
         -DCMAKE_CXX_COMPILER=clang++
         -DCMAKE_CXX_FLAGS_DEBUG='-Werror'"
       $DUNECONTROL --only=dorie configure
-    - $DUNECONTROL --only=dorie make $MAKE_FLAGS dorie-rfg
-    - $DUNECONTROL --only=dorie make $MAKE_FLAGS build_unit_tests
-    - $DUNECONTROL --only=dorie make $MAKE_FLAGS transport_d2_r0_t0 transport_d2_r1_t0
 
 build:docs:
   stage: build
@@ -186,50 +189,53 @@ test:system-tests: &test
   stage: test
   dependencies:
     - build:system-tests
+  needs: ["build:system-tests"]
+  variables:
+    GCOVR_PATHS:
+      --root $CI_PROJECT_DIR
+      --exclude $CI_PROJECT_DIR/dune/dorie/test
+      --exclude $CI_PROJECT_DIR/plugins
   script:
     - $DUNECONTROL --only=dorie configure
     - $DUNECONTROL --only=dorie make system_tests
+  # Run coverage utility (will also run after failed job)
+  after_script:
+    - source $CI_PROJECT_DIR/build-cmake/activate
+    - pip3 install gcovr
+    - cd $CI_PROJECT_DIR/build-cmake
+    - mkdir coverage
+    - gcovr $GCOVR_PATHS --html --html-details -o coverage/report.html
+    # run again for coverage report in GitLab
+    - gcovr $GCOVR_PATHS
+  coverage: '/^TOTAL.*\s+(\d+\%)$/'
   artifacts:
     name: "$CI_JOB_NAME"
     paths:
       - $CI_PROJECT_DIR/build-cmake/test
+      - $CI_PROJECT_DIR/build-cmake/coverage
     expire_in: 1 day
 
 test:unit-tests:
   <<: *test
   dependencies:
     - build:unit-tests
+  needs: ["build:unit-tests"]
   script:
-    # install coverage reporter
-    - $DUNECONTROL --only=dorie bexec
-      "./run-in-dune-env python3 -m pip install gcovr"
-    # perform the tests
     - $DUNECONTROL --only=dorie configure
     - $DUNECONTROL --only=dorie make unit_tests
-    # report coverage
-    - cd $CI_PROJECT_DIR/build-cmake
-    - mkdir -p dune/dorie/test/coverage
-    - ./run-in-dune-env gcovr
-      --root ../
-      --exclude ../dune/dorie/test
-      --exclude ../plugins
-      --html --html-details
-      -o dune/dorie/test/coverage/coverage.html
-    # run again for coverage report in GitLab
-    - ./run-in-dune-env gcovr
-      --root ../
-      --exclude ../dune/dorie/test
-      --exclude ../plugins
-  coverage: '/^TOTAL.*\s+(\d+\%)$/'
   artifacts:
     name: "$CI_JOB_NAME"
     paths:
       - $CI_PROJECT_DIR/build-cmake/dune/dorie/test
+      - $CI_PROJECT_DIR/build-cmake/coverage
     expire_in: 1 day
 
 test:python-tests:
   <<: *test
   dependencies: []
+  # TODO: Make empty once https://gitlab.com/gitlab-org/gitlab/issues/30631
+  #       is resolved
+  needs: ["build:docs"] # Any quick job from previous stage
   script:
     - $DUNECONTROL --only=dorie configure
     - $DUNECONTROL --only=dorie make test_python

.gitlab/issue_templates/bug-report.md

-(One-sentence description of what kind of bug you would like to report)
+_One-sentence description of what kind of bug you would like to report_
 
-#### Summary
-(Summarise the encountered bug concisely)
+### Summary
+_Summarise the encountered bug concisely_
 
 
-#### Steps to reproduce
-(How can this be reproduced? If you can, point to specific files/configurations where the bug occurs)
+### Steps to reproduce
+_How can this be reproduced? If you can, point to specific files/configurations where the bug occurs_
 
 
-#### What is the current _bug_ behaviour?
-(More about the behaviour of the bug)
+### What is the current _bug_ behaviour?
+_More about the behaviour of the bug_
 
 
-#### What is the expected _correct_ behaviour?
-(Which behaviour would you have expected?)
+### What is the expected _correct_ behaviour?
+_Which behaviour would you have expected?_
 
 
-#### Relevant logs, screenshots, files...?
-(Anything that helps reproducing the bug)
+### Relevant logs, screenshots, files...?
+_Anything that helps reproducing the bug_
 
 <!-- Put very long log outputs within the <pre></pre> tags below -->
 <!-- If this doesn't apply, delete the whole <details></details> block -->
@@ -28,8 +28,21 @@
 </pre>
 </details>
 
+#### Reproducing input
+_Do you have input files reproducing the problem? Insert them here:_
 
-#### Ideas how to fix this?
-(Add them here, if you have any.)
+| Input data | |
+| - | - |
+| Simulation Case | _Description goes here_ |
+| PFG config file | _if any_ |
+| Grid mapping file | _if any_ |
+| GMSH grid file | _if any_ |
+| Boundary Condition file | |
+| Parameterization file | |
+| Run config file | |
 
-/label ~bug
\ No newline at end of file
+
+### Ideas how to fix this?
+_Add them here, if you have any._
+
+/label ~Bug

.gitlab/issue_templates/patch-release.md

+<!-- _Set the title to: "Patch Release: X.Y.Z" -->
+<!-- Replace X.Y.Z with the actual version numbers everywhere -->
+
+We're releasing patch version `X.Y.Z` for branch `X.Y-stable`! :tada:
+
+### 1 — List of MRs to be Included
+
+List the MRs and the commit SHA of their respective merge commits here.
+Placing them in chronological order here ensures fewer issues when
+cherry-picking them!
+
+The MRs are indicated by the ~"Pick into X.Y" label.
+
+| MR | Merge Commit SHA |
+| -- | ---------------- |
+| !  |  ...  |
+
+### 2 — On GitLab
+Use the "patch-release" template for creating a new Merge Request.
+
+- [ ] [Create a branch][new branch] `X.Y-patch` from `X.Y-stable`
+- [ ] [Create a Merge Request][new mr] with source branch `X.Y-patch` and
+   target branch `X.Y-stable`: !
+- [ ] Merge this MR: !
+- [ ] [Create tag][new tag] `X.Y.Z` from branch `X.Y-stable`
+   - Message:
+
+      ```
+      Version X.Y.Z (YYYY-MM-DD)
+      ```
+
+   - Release Notes:
+      ```
+      # Version X.Y.Z (YYYY-MM-DD)
+
+      -> Copy appropriate entries from MR changelog here <-
+      ```
+- [ ] Update "Release" [project badge][badge] <!-- only if applicable -->
+
+### 3 — On Docker Hub
+- [ ] Update [description on DockerHub][DockerHub description]
+- [ ] Push new `latest` tag to DockerHub <!-- only if applicable -->
+
+### 4 — All done? :white_check_mark:
+Close this issue!
+
+/label ~Release
+
+[new branch]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/-/branches/new
+[new mr]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/merge_requests/new
+[new tag]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/-/tags/new
+[DockerHub description]: https://hub.docker.com/r/dorie/dorie
+[badge]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/edit

.gitlab/issue_templates/task.md

@@ -8,7 +8,7 @@
 
 
 ### Related issues
-See #...
+See #
 
 <!--
 PLEASE READ THIS

.gitlab/issue_templates/version-rollout.md

+<!-- _Set the title to: "Release: X.Y.0" -->
+<!-- Replace X.Y with the actual version numbers everywhere -->
+
+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`.
+
+### 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`
+   - Message:
+
+      ```
+      Version X.Y.0 (YYYY-MM-DD)
+      ```
+
+   - Release Notes:
+      ```
+      # Version X.Y.0 (YYYY-MM-DD)
+
+      -> Insert version changelog here! <-
+      ```
+      Shortcut to the most up-to-date [CHANGELOG.md][changelog]
+- [ ] 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`.
+
+### 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
+
+[new branch]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/-/branches/new
+[new tag]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/-/tags/new
+[changelog]: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/blob/master/CHANGELOG.md
+[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

.gitlab/merge_request_templates/MR-from-task.md

 ### What does this MR do?
-
+_Fill this in_
 
 ### Is there something that needs to be double checked?
-
+<!-- Is there something a reviewer should look out for _especially_? -->
+_Fill this in_
 
 ### Can this MR be accepted?
 - [ ] Implemented ...
-- [ ] Added test to ...
-- ...
-- [ ] Pipeline passing
+   - [ ] ...
+- [ ] Added/Updated tests:
+   - [ ] ...
+- [ ] Added/Updated documentation
+- [ ] Pipeline passing <!-- please check for new warnings -->
+- [ ] Squash option set <!-- unless there's a good reason -->
+- [ ] Delete branch option set <!-- unless there's a good reason -->
 - [ ] Added entry to `CHANGELOG.md`
 
+_**Assignee:** If the Squash option is set, check/update the commit message right before merging!_
 
 ### Related issues
 
-Closes #, # and #
+Closes #
 <!-- For automatic closing, do not forget the commas between issue numbers-->
 
 

.gitlab/merge_request_templates/patch-release.md

+<!-- _Set the title to: "Resolve "Patch Release: X.Y.Z"" -->
+<!-- Replace X.Y.Z with the actual version numbers everywhere -->
+
+We're releasing patch version `X.Y.Z` for branch `X.Y-stable`! :tada:
+
+### Release Issue
+<!-- DO NOT use automatic Issue resolution here! -->
+The MRs to be considered in this update are listed in #
+
+### Tasks
+- [ ] Cherry-pick the listed commits into `X.Y-patch`
+- [ ] `CHANGELOG.md`: Move appropriate entries into new section
+- [ ] Update version numbers in `VERSION`, `CHANGELOG.md`, `dune.module`
+- [ ] Update `version="unreleased"` tags in the default config file XML
+    sources <!-- only if applicable -->
+- [ ] Update Sphinx version directives with version `unreleased` in the user
+    docs. <!-- only if applicable -->
+
+#### Help on Cherry-Picking
+Cherry-picking merge commits requires specifying the "mainline" parent, which
+should always be number 1. Append a line indicating a cherry-pick to the commit
+message with the `-x` argument. The following should do the trick:
+```bash
+git cherry-pick -m 1 -x <commits>
+```
+Replace `<commits>` with the Commit SHAs listed above, separated by a single
+whitespace each. Make sure they are in chronological order to reduce the
+number of merge conflicts! Fix such conflicts as unintrusively as possible.
+
+### Can this MR be merged?
+- [ ] Pipeline passing <!-- please check for new warnings -->
+- [ ] Delete branch option set <!-- unless there's a good reason -->
+
+### Related Issues

CHANGELOG.md

@@ -4,34 +4,14 @@
 ## Unreleased
 
 ### Added
-* DORiE now depends on [`yaml-cpp`](https://github.com/jbeder/yaml-cpp/), a
-    library for reading YAML files. The version required is >=5.2.0.
-* New classes representing parameterizations. Every parameterization must now
-    derive from `RichardsParameterization`, and return function objects
-    representing parameterization functions.
-* Added a abstract base class [`SimulationBase`](dune/dorie/interface/base_simulation.hh) 
-    that models the concept of simulation steps so that they 
-    can be later coupled with other simulations.
-* Added an abstract base class
-    [`SimulationBase`](dune/dorie/common/simulation_base.hh)
-    that models the concept of simulation steps so that they 
-    can be later coupled with other simulations.
-* New classes representing parameterizations. Every parameterization must now
-    derive from `RichardsParameterization`, and return function objects
-    representing parameterization functions.
-* CMake module `DorieTesting.cmake`. The module contains multiple functions
-    which facilitate registering tests in the two new testing categories:
-    System tests and Unit tests. Unit tests are compiled with appropriate flags
-    for code coverage reports.
-* Code coverage reports for unit tests. Detailed reports can be retrieved from
-    the artifacts of the `test:unit-tests` test in the folder
-    `build-cmake/test/coverage`. The total coverage is reported to GitLab.
-* New class [`SimulationTransport`](dune/dorie/interface/transport_simulation.hh)
-    which solves the transport equation with a finite volume scheme for give
-    grid functions of water content and velocity.
+* [`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
 * Grid function container to store transient grid functions !115
 * Infrastructure for the input of Miller scaling fields. !110
-* Add logging framework 'spdlog' as submodule !106
+* Logging framework [`spdlog`](https://github.com/gabime/spdlog) as
+    Git submodule for all terminal output !106
 * 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
@@ -39,113 +19,34 @@
     [muparser](http://beltoforion.de/article.php?a=muparser) !131
 * Coupling between transient models for water flow and solute transport !96
 * Initial conditions generated from H5 input data !130
-* Generic Python VTK file reader !143
 * Linear interpolator for initial conditions and scaling fields !145, !156
 * Parameterizations for hydrodynamic dispersion in solute transport !141
-* Generic Python VTK file reader !143, !150
+* Generic Python VTK file reader !143, !150, !178
 * 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
+* Cookbook tutorial on infiltration into homogeneous sand !157
+* GitLab Description Templates for Releases !166
+* ParaView tutorial for analyzing DORiE output files !173
+* Parameter XML files support tags for version changes !171
+* Unit test for Parameter XML file parser !171
+* CMake option to enable code coverage flags on all targets !172
+* Changes to config file parameters listed per version in user docs !175
 
 ### Changed
-* `Simulation` is renamed `RichardsSimulation` and moved to 
-	[richards.hh](dune/dorie/model/richards/richards.hh).
-* `RichardsSimulation` now has its own `RichardsSimulationTraits` derived from
-    `BaseTraits`, which defines all its member types. `BaseTraits` now have
-    reduced content and are intended to be shared between models/simulations.
-* Data structures for storing and accessing parameters. The new class
-    `FlowParameters` maps parameter sets and scaling factors to every grid cell
-    on the coarsest grid level, and only stores one set of parameters for
-    each soil layer. Before querying the parameterization functions, users need
-    to call `FlowParameters::bind` with a grid entity to cache the appropriate
-    data. All classes and functions querying parameter data have been updated.
-    
-    The old parameterization classes located in
-    [`param_base.hh`](dune/dorie/solver/param_base.hh),
-    [`param_factory.hh`](dune/dorie/solver/param_factory.hh), and
-    [`param_van_genuchten.hh`](dune/dorie/solver/param_van_genuchten.hh)
-    are still used for reading in data for the new storage scheme.
-    The respective objects are freed once a simulation commences.
-* Grid adaptation now is done in two steps: (1) mark entities of the grid to 
-    refine/coarse and (2) adapt the grid and project the degrees of freedom on 
-    the new grid.
-    The old parameterization classes have been removed.
-* `RichardsSimulation` now uses one vector of coefficients instead of two, which
-    now is a `shared_ptr` instead a `unique_ptr`.
-* Every `VTKAdapter` is now able to be used as `GridFunctionAdapter` of the
-    solution vector.
-* `GradientFluxAdapter` was reimplemented and renamed `WaterFluxAdapter`.
-* Every grid function adapter has its own file and are gathered in the 
-    subdirectory
-    [dune/dorie/model/richards/adapters](dune/dorie/model/richards/adapters).
-* `VTKAdapters` are now managed with `shared_ptr` instead of references.
-* `OutputWriter` class is deprecated in favor of an minimal extension of the 
-    usual `VTKSequenceWriter` for grid functions called
-    `GridFunctionVTKSequenceWriter`.
-* `RichardsSimulation` now models the `SimulationBase` class (See details in
-    https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/94). For this, 
-    several methods were renamed with basically no change in behaviour.
-* `RichardsSimulation` and `TimeController` are able to receive a suggestion for
-    the next timestep.
-* Static const `bool`s for adaptivity and output writing in `BaseTraits` were 
-    removed in favor of run-time policies (See details in
-    https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/94).
-* Swich to the stable release branch `releases/2.6` of `dune-testtools`.
-* The `build` CI stage now explicitly builds system tests and unit tests. The
-    job `build:main` has been removed. The `build:debug` jobs now build the
-    unit test targets.
-* Merge Python packages into single new package `dorie`.
-* Executables and files of unit-tests and system-tests are now located in 
-    [`dune/dorie/test/`](dune/dorie/test/) and [`test/`](test/) respectively.
-* The `dorie` CLI has been moved into the DORiE Python package. It can now only
-    be invoked after activating the DUNE virtual environment. The usage
-    instructions in docs and `README.md` have been updated accordingly.
-* Soil architecture and parameter input has been completely revised.
-
-    DORiE now expects a YAML file containing parameterization data and separate
-    domain mapping data which can be supplied through the input GMSH file, or as
-    H5 dataset. See the documentation for more information. Several keys in the
-    main routine config file have been changed.
-
-    See [#86](https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/86).
-
-* The Parameter Field Generator (PFG) module has been revised and does not
-    write parameterization data anymore.
-    
-    It can be used to create mappings for heterogeneous media through the
-    binary converter, or continuous scaling fields (feature pending).
-    Several keys in the PFG config file have been changed.
-
-    See [#86](https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/86).
-
-* Improved and refurbished `Dorie::H5File`.
-
-    The source file was renamed to `dune/dorie/common/util_h5file.hh`. The
-    `read_dataset` function is now capable of directly opening dataset paths
-    that contain groups.
-
-* The following changes were done in order to have a consistent API to support 
-    different models:
-
-    * Folder structure has changed to a model based structure: in the main
-        [C++ source directory](dune/dorie/) there now is a `common` folder, and
-        a folder for `model` containing the source files for each model.
-
-    * The API has been updated to support several models: from now, categories 
-        that  target a specific model has to be preceded by a keyword 
-        identifying the  corresponding model (e.g. `richards.initial`,
-        `richards.output`, etc.), while common categories stay with no prefix
-        at all (e.g. `grid`, `adaptivity`, etc.).
-
-    * The parameter scraper now accepts the argument `--model <model>` which
-        adds the prefix `<model>.` to every category in the scraper. This helps
-        to be able to use the method `sub()` from the `ParameterTree` object.
-        It dumps its data into a YAML file which is then loaded for writing
-        the default configuration files and the cheat sheet.
-
-* Use logging framework 'spdlog' for all terminal output !106
-* DORiE now writes vertex data by default. #129
+* 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
+* Rework VTK adapters and VTK output writer !64
+* `RichardsSimulation` now implements the abstract simulation base class !89
+* Switch to the stable release branch `releases/2.6` of `dune-testtools` !97
+* Merge Python packages into single new package `dorie` !100
+* Move `dorie` Command Line Interface script into Python package !102
+* Parameterization data input via YAML and H5 files !82
+* Simplify H5 reader to only read datasets !109
+* 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
@@ -156,27 +57,25 @@
 * 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
 
 ### Fixed
-* Solver in `RichardsSimulation` was using the wrong time variable.
-