GitLab

Fix issues from Python package updates

See merge request !224

* base64.decodestring() was previously deprecated and recently removed.
* PyYAML 6 now requires a `loader` argument when loading.
* numpy.dtype only understands lowercase type strings now.
* Update CHANGELOG.md

Run pipelines on any branch

See merge request !221

Resolve "Flux reconstruction on FV does not work with alpha volumes"

Closes #206

See merge request !219

Santiago Ospina De Los Ríos authored Oct 12, 2020 and Lukas Riedel committed Oct 12, 2020

This only serves to make the current flux reconstruction implementation
compatible with finite volume operators which implement an `alpha_volume()`
method.

Make PVDReader initialize VTKReaders lazily

See merge request !216

PVDReader now only stores the paths to VTK files and initializes
VTKReader instances when they are explicitly accessed. Users can choose
if missing VTK files should result in exceptions or warnings.

Additionally:

* Add time as argument for VTKReader.
* Make PVDReader raise more exceptions.
* Switch to FileNotFoundError exceptions where suitable.
* Update tests to check PVDReader initialization.
* Update docs and docstrings.

This fixes the issue that pipelines are not run for branches with a
single commit.

Resolve "Update C++ standard requirement"

Closes #198

See merge request !218

Lukas Riedel authored Aug 27, 2020 and Santiago Ospina De Los Ríos committed Aug 27, 2020

* Explicitly sets the C++ standard version for the compiled DORiE libraries and document the standard we use.

Add JOSS publication

Closes #199

See merge request !198

Lukas Riedel authored Aug 24, 2020 and Santiago Ospina De Los Ríos committed Aug 24, 2020

Include the binary random fields and GMSH files to ensure that the same
simulations can be run on any system.

Improve GitLab CI pipeline

See merge request !214

Lukas Riedel authored Aug 20, 2020 and Santiago Ospina De Los Ríos committed Aug 20, 2020

This is achieved by moving the dune-env into the project build
directory which is propagated as artifact.

Resolve "Use more recent version of Ubuntu in Docker"

Closes #178

See merge request !189

Santiago Ospina De Los Ríos authored Aug 11, 2020 and Lukas Riedel committed Aug 11, 2020

This updates the Docker base image and testing system to the most
recent Ubuntu with LTS. Accordingly, the software requirements have
been updated.

* Update Docker base image to Ubuntu `focal`.
* Switch to Ubuntu version based tagging scheme of base image.
* Update CMake configuration to CMake v3.16.
* Use spdlog as external dependency and remove Git Submodule.
* Update installation instructions in README.md
* Make code compliant to recent Python and compiler versions.

Fix installation stage

See merge request !207

This will install the executables of DORiE into the target install
directory.

Resolve "setting of [grid]extensions seems to not work with gmsh grids"

Closes #193

See merge request !215

* Stop passing grid extensions into model config sections.
* Clean up FlowSource, removing the storage of grid extensions.
* Clarify usage of grid related keys in config file.
* Update CHANGELOG.md.

Resolve "Use more elaborate "rules" in GitLab CI/CD configuration"

Closes #203

See merge request !213

Lukas Riedel authored Jul 21, 2020 and Santiago Ospina De Los Ríos committed Jul 21, 2020

* Switch to 'rules' for specifying when certain CI jobs are executed.
* Execute 'setup' and 'prep' jobs when respective Dockerfiles change.

Add .clang-format file and instructions

Closes #180

See merge request !203

Lukas Riedel authored Jul 20, 2020 and Santiago Ospina De Los Ríos committed Jul 20, 2020

Use 'Mozilla' style with slight modifications:

* Break before binary operators, except assignment operators.
* Usually break before braces ('Allman' style).

Fix warning about unused HD5 status file valriable on release mode

See merge request !206

Santiago Ospina De Los Ríos authored Jul 15, 2020 and Lukas Riedel committed Jul 15, 2020

H5File will now log warnings if non-critical assertions fail.

Fix "Available Models" table in user docs

See merge request !211

This reverts commit 358ed887.

Fix Python encoding error in Docker image

See merge request !210

Upgrading the "locale" package invalidates previous locale definitions.

Advertise features in README and docs

See merge request !209

add extended miller scaling adapter

See merge request !122

Hannes Bauser authored Jul 03, 2020 and Santiago Ospina De Los Ríos committed Jul 03, 2020

* Port test to Google Test.
* Add meta-ini config file to build grid in test fixture.
* Add Python script for creating scaling datasets before testing.
* Add test case for non-cubic dataset.

Resolve "Simplify cloning DUNE modules and executing dunecontrol script"

Closes #197

See merge request !205

Lukas Riedel authored Jul 03, 2020 and Santiago Ospina De Los Ríos committed Jul 03, 2020

* Update Dockerfiles to clone and build DUNE modules using the
  `clone_dune` script and `build.opts` file.
* Set compiler environment variables in base image (only).

Resolve "Use BCGS_AMG_SSOR solver for finite volume methods"

Closes #169

See merge request !204

Lukas Riedel authored Jun 30, 2020 and Santiago Ospina De Los Ríos committed Jun 30, 2020

This selects the BCGS_AMG_SSOR linear solver backend for FV computations
in both the Richards and the Transport model.