v0.8.1 release (#110)

* Revert 0.8 API changes for release

* Test against 0.7.3 image

* Update citation file and pyproject.toml

* Update workflows

* Correct version in readme

* Test redhat installation (#111)

* Test package on redhat

* Remove default build from matrix as redhat image does not have adios2 installed

* Re-introduce type hints from typing

* Add back adios2 to the Python dependencies

* Try setting working directory in test

* Remove petsc arch

* try fixing petsc dir again

* Install adios2 from source as it requires MPI build. Set pythonpath in parent workflow

* Add notes about adios2 installation

* Use newest install-dolfinx action

* Remove adios2 from deps as the pypi version is incompatible with package (no MPI support)

.github/workflows/build_docs.yml

@@ -19,7 +19,7 @@ jobs:
       DEB_PYTHON_INSTALL_LAYOUT: deb_system
 
     runs-on: ubuntu-22.04
-    container: ghcr.io/fenics/dolfinx/dolfinx:nightly
+    container: ghcr.io/fenics/dolfinx/dolfinx:v0.8.0
     steps:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v4

.github/workflows/check_formatting.yml

@@ -9,7 +9,7 @@ jobs:
       DEB_PYTHON_INSTALL_LAYOUT: deb_system
 
     runs-on: ubuntu-22.04
-    container: ghcr.io/fenics/dolfinx/dolfinx:nightly
+    container: ghcr.io/fenics/dolfinx/dolfinx:v0.8.0
     steps:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v4

.github/workflows/test_package.yml

@@ -33,7 +33,7 @@ jobs:
   test-code:
     runs-on: "ubuntu-22.04"
     needs: [create-datasets, create-legacy-datasets, check-formatting]
-    container: ghcr.io/fenics/dolfinx/dolfinx:nightly
+    container: ghcr.io/fenics/dolfinx/dolfinx:v0.8.0
     env:
       DEB_PYTHON_INSTALL_LAYOUT: deb_system
 

.github/workflows/test_package_openmpi.yml

@@ -37,6 +37,7 @@ jobs:
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
       PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe
+      working-directory: ./src
 
     strategy:
       matrix:
@@ -48,11 +49,15 @@ jobs:
         run: python3 -m pip install --upgrade pip setuptools
 
       - name: Install DOLFINx
-        uses: jorgensd/actions/install-dolfinx@v0.2.0
+        uses: jorgensd/actions/install-dolfinx@v0.3.0
         with:
           adios2: ${{ matrix.adios2 }}
           petsc_arch: ${{ env.PETSC_ARCH }}
-          dolfinx: main
+          dolfinx: v0.8.0
+          basix: v0.8.0
+          ufl: 2024.1.0.post0
+          ffcx: v0.8.0
+          working-directory: ${{ env.working-directory}}
 
       - name: Download legacy data
         uses: actions/download-artifact@v4

.github/workflows/test_redhat.yml

@@ -0,0 +1,83 @@
+name: Test package with redhat
+
+on:
+  push:
+    # The CI is executed on every push on every branch
+    branches:
+      - "**"
+  pull_request:
+    # The CI is executed on every pull request to the main branch
+    branches:
+      - main
+
+  workflow_call:
+  workflow_dispatch:
+  schedule:
+    # The CI is executed every day at 8am
+    - cron: "0 8 * * *"
+
+jobs:
+  create-datasets:
+    uses: ./.github/workflows/create_legacy_data.yml
+    with:
+      artifact_name: "legacy_ompi"
+
+  create-legacy-datasets:
+    uses: ./.github/workflows/create_legacy_checkpoint.yml
+    with:
+      artifact_name: "legacy_checkpoint_ompi"
+
+  test-code:
+    runs-on: "ubuntu-22.04"
+    needs: [create-datasets, create-legacy-datasets]
+    container: docker.io/fenicsproject/test-env:current-redhat
+    env:
+      DEB_PYTHON_INSTALL_LAYOUT: deb_system
+      PETSC_ARCH: ""
+      PETSC_DIR: "/usr/local/"
+      PYTHONPATH: "/usr/local/lib/:${PYTHONPATH}"
+      working-directory: ./src
+
+    strategy:
+      matrix:
+        adios2: ["v2.10.0"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Update pip
+        run: python3 -m pip install --upgrade pip setuptools
+
+      - name: Install DOLFINx
+        uses: jorgensd/actions/[email protected]
+        with:
+          adios2: ${{ matrix.adios2 }}
+          petsc_arch: ${{ env.PETSC_ARCH }}
+          petsc_dir: ${{ env.PETSC_DIR }}
+          dolfinx: v0.8.0
+          basix: v0.8.0
+          ufl: 2024.1.0.post0
+          ffcx: v0.8.0
+          working-directory: ${{ env.working-directory}}
+
+      - name: Download legacy data
+        uses: actions/download-artifact@v4
+        with:
+          name: legacy_ompi
+          path: ./legacy
+
+      - name: Download legacy data
+        uses: actions/download-artifact@v4
+        with:
+          name: legacy_checkpoint_ompi
+          path: ./legacy_checkpoint
+
+      - name: Install package
+        run: python3 -m pip install .[test]
+
+      - name: Run tests
+        run: |
+          coverage run --rcfile=.coveragerc -m mpi4py -m pytest -xvs ./tests
+
+      - name: Run tests in parallel
+        run: |
+          mpirun -n 4 coverage run --rcfile=.coveragerc -m mpi4py -m pytest -xvs ./tests

CITATION.cff

@@ -1,9 +1,9 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 authors:
-- family-names: "Dokken"
-  given-names: "Jørgen S."
-  orcid: "0000-0001-6489-8858"
+  - family-names: "Dokken"
+    given-names: "Jørgen S."
+    orcid: "0000-0001-6489-8858"
 title: "ADIOS2Wrappers"
-version: "0.7.2"
-date-released: "2023-02-07"
+version: "0.8.1"
+date-released: "2023-04-25"

README.md

@@ -3,7 +3,6 @@
 ![MIT](https://img.shields.io/github/license/jorgensd/adios4dolfinx)
 [![status](https://joss.theoj.org/papers/7866cb142db8a803e32d79a109573d25/status.svg)](https://joss.theoj.org/papers/7866cb142db8a803e32d79a109573d25)
 
-
 ADIOS4DOLFINx is an extension for [DOLFINx](https://github.com/FEniCS/dolfinx/) to checkpoint meshes, meshtags and functions using [ADIOS 2](https://adios2.readthedocs.io/en/latest/).
 
 The code uses the ADIOS2 Python-wrappers to write DOLFINx objects to file, supporting N-to-M (_recoverable_) and N-to-N (_snapshot_) checkpointing.
@@ -12,40 +11,53 @@ See: [Checkpointing in DOLFINx - FEniCS 23](https://jsdokken.com/checkpointing-p
 For scalability, the code uses [MPI Neighbourhood collectives](https://www.mpi-forum.org/docs/mpi-3.1/mpi31-report/node200.htm) for communication across processes.
 
 ## Statement of Need
+
 As the usage of high performance computing clusters increases, more and more large-scale, long-running simulations are deployed.
 The need for storing intermediate solutions from such simulations are crucial, as the HPC system might crash, or the simulation might crash or exceed the alloted computational budget.
 Having a checkpoint of related variables, such as the solutions to partial differential equations (PDEs) is therefore essential.
 The `adios4dolfinx` library extends the [DOLFINx](https://github.com/FEniCS/dolfinx/) computational framework for solving PDEs with checkpointing functionality, such that immediate solutions and mesh information can be stored and re-used in another simulation.
 
-
 ## Installation
+
 Compatibility with DOLFINx:
+
 - ADIOS4DOLFINx v0.7.3 is compatible with DOLFINx v0.7.x
-- ADIOS4DOLFINx v0.8.x is compatible with the main branch of DOLFINx
+- ADIOS4DOLFINx v0.8.1 is compatible with DOLFINx v0.8.x
+
+### Dependencies
+
+The library depends on the Python-interface of [DOLFINx](https://github.com/) and an MPI-build of [ADIOS2](https://adios2.readthedocs.io/en/latest/setting_up/setting_up.html#as-package) and can therefore not be installed through PyPi, but has to be installed through Conda, Spack or from source.
 
 ### Docker
 
-ADIOS2 is installed in the official DOLFINx containers, and thus there are no additional dependencies required to install `adios4dolfinx`
+An MPI build of ADIOS2 is installed in the official DOLFINx containers, and thus there are no additional dependencies required to install `adios4dolfinx`
 on top of DOLFINx in these images.
 
 Create a Docker container, named for instance `dolfinx-checkpoint`.
-Use the `nightly` tag to get the main branch of DOLFINx, or `stable` to get the lastest stable release
+Use the `nightly` tag to get the main branch of DOLFINx, or `stable` to get the latest stable release
+
 ```bash
 docker run -ti -v $(pwd):/root/shared -w /root/shared --name=dolfinx-checkpoint ghcr.io/fenics/dolfinx/dolfinx:nightly
 ```
+
 For the latest version compatible with nightly (with the ability to run the test suite), use
+
 ```bash
 python3 -m pip install adios4dolfinx[test]@git+https://github.com/jorgensd/adios4dolfinx@main
 ```
+
 If you are using the `stable` image, you can install `adios4dolfinx` from [PYPI](https://pypi.org/project/adios4dolfinx/) with
+
 ```bash
 python3 -m pip install adios4dolfinx[test]
 ```
 
 This docker container can be opened with
+
 ```bash
 docker container start -i dolfinx-checkpoint
 ```
+
 at a later instance
 
 ### Conda
@@ -54,18 +66,21 @@ at a later instance
 > Conda supports the stable release of DOLFINx, and thus the appropriate version should be installed, see the section above for more details.
 
 Following is a minimal recipe of how to install adios4dolfinx, given that you have conda installed on your system.
+
 ```bash
 conda create -n dolfinx-checkpoint python=3.10
 conda activate dolfinx-checkpoint
-conda install -c conda-forge fenics-dolfinx pip adios2
-python3 -m pip install adios4dolfinx[test]@git+https://github.com/jorgensd/adios4dolfinx@v0.7.3
+conda install -c conda-forge fenics-dolfinx pip adios2=*=mpi_*
+python3 -m pip install adios4dolfinx[test]@git+https://github.com/jorgensd/adios4dolfinx@v0.8.1
 ```
 
 > [!NOTE]
 > To run the tests or demos associated with the code, install `ipyparallel` in your environment, for instance by calling
+>
 > ```bash
-> python3 -m pip install adios4dolfinx[test]@git+https://github.com/jorgensd/adios4dolfinx@v0.7.3
+> python3 -m pip install adios4dolfinx[test]@git+https://github.com/jorgensd/adios4dolfinx@v0.8.1
 > ```
+
 ## Functionality
 
 ### DOLFINx
@@ -86,13 +101,15 @@ python3 -m pip install adios4dolfinx[test]@git+https://github.com/jorgensd/adios
 > Only one mesh per file is allowed
 
 ## Example Usage
+
 The repository contains many documented examples of usage, in the `docs`-folder, including
+
 - [Reading and writing mesh checkpoints](./docs/writing_mesh_checkpoint.py)
 - [Storing mesh partitioning data](./docs/partitioned_mesh.py)
 - [Writing mesh-tags to a checkpoint](./docs/meshtags.py)
 - [Reading and writing function checkpoints](./docs/writing_functions_checkpoint.py)
 - [Checkpoint on input mesh](./docs/original_checkpoint.py)
-Further examples can be found at [ADIOS4DOLFINx examples](https://jsdokken.com/adios4dolfinx/)
+  Further examples can be found at [ADIOS4DOLFINx examples](https://jsdokken.com/adios4dolfinx/)
 
 ### Backwards compatibility
 
@@ -113,30 +130,39 @@ See the [API](./docs/api) for more information.
 
 This library uses `pytest` for testing.
 To execute the tests, one should first install the library and its dependencies, as listed above.
-Then, can execute all tests by calling 
+Then, can execute all tests by calling
+
 ```bash
 python3 -m pytest .
 ```
 
 ### Testing against data from legacy dolfin
+
 Some tests check the capability of reading data created with the legacy version of DOLFIN.
-To create this dataset, start a docker container with legacy DOLFIN, for instance: 
+To create this dataset, start a docker container with legacy DOLFIN, for instance:
+
 ```bash
 docker run -ti -v $(pwd):/root/shared -w /root/s
 hared --rm ghcr.io/scientificcomputing/fenics:2024-02-19
 ```
+
 Then, inside this container, call
+
 ```bash
 python3 ./tests/create_legacy_data.py --output-dir=legacy
 ```
 
 ### Testing against data from older versions of ADIOS4DOLFINx
+
 Some tests check the capability to read data generated by `adios4dolfinx<0.7.2`.
 To generate data for these tests use the following commands:
+
 ```bash
 docker run -ti -v $(pwd):/root/shared -w /root/shared --rm ghcr.io/fenics/dolfinx/dolfinx:v0.7.3
 ```
+
 Then, inside the container, call
+
 ```bash
 python3 -m pip install adios4dolfinx==0.7.1
 python3 ./tests/create_legacy_checkpoint.py --output-dir=legacy_checkpoint

pyproject.toml

@@ -3,12 +3,12 @@ requires = ["setuptools>=61.0.0", "wheel"]
 
 [project]
 name = "adios4dolfinx"
-version = "0.8.0.dev0"
+version = "0.8.1"
 description = "Checkpointing functionality for DOLFINx meshes/functions with ADIOS2"
 authors = [{ name = "Jørgen S. Dokken", email = "[email protected]" }]
 license = { file = "LICENSE" }
 readme = "README.md"
-dependencies = ["fenics-dolfinx>=0.8.0.dev0"]
+dependencies = ["fenics-dolfinx>=0.8.0"]
 
 [project.optional-dependencies]
 test = ["pytest", "coverage", "ipyparallel"]

src/adios4dolfinx/adios2_helpers.py

@@ -2,7 +2,7 @@
 
 from contextlib import contextmanager
 from pathlib import Path
-from typing import NamedTuple
+from typing import NamedTuple, Union
 
 from mpi4py import MPI
 
@@ -44,7 +44,7 @@ class AdiosFile(NamedTuple):
 @contextmanager
 def ADIOSFile(
     adios: adios2.ADIOS,
-    filename: Path | str,
+    filename: Union[Path, str],
     engine: str,
     mode: adios2.Mode,
     io_name: str,
@@ -62,7 +62,7 @@ def ADIOSFile(
 def read_cell_perms(
     adios: adios2.ADIOS,
     comm: MPI.Intracomm,
-    filename: Path | str,
+    filename: Union[Path, str],
     variable: str,
     num_cells_global: np.int64,
     engine: str,
@@ -126,12 +126,12 @@ def read_cell_perms(
 def read_adjacency_list(
     adios: adios2.ADIOS,
     comm: MPI.Intracomm,
-    filename: Path | str,
+    filename: Union[Path, str],
     dofmap: str,
     dofmap_offsets: str,
     num_cells_global: np.int64,
     engine: str,
-) -> dolfinx.cpp.graph.AdjacencyList_int64 | dolfinx.cpp.graph.AdjacencyList_int32:
+) -> Union[dolfinx.cpp.graph.AdjacencyList_int64, dolfinx.cpp.graph.AdjacencyList_int32]:
     """
     Read an adjacency-list from an ADIOS file with given communicator.
     The adjancency list is split in to a flat array (data) and its corresponding offset.
@@ -205,7 +205,7 @@ def read_adjacency_list(
 
 def read_array(
     adios: adios2.ADIOS,
-    filename: Path | str,
+    filename: Union[Path, str],
     array_name: str,
     engine: str,
     comm: MPI.Intracomm,