Update devel tiny 20250901

.github/workflows/documentation.yml.disabled

@@ -1,10 +1,19 @@
-name: documentation
+name: Documentation
 
 on:
   push:
     branches: [ devel ]
+    paths:
+      - 'docs/**'
+      - 'psydac/**.py'
+
   pull_request:
     branches: [ devel ]
+    paths:
+      - 'docs/**'
+      - 'psydac/**.py'
+
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -29,7 +38,7 @@ jobs:
         sudo apt install graphviz
     - name: Install Python dependencies
       run: |
-        python -m pip install -r docs_requirements.txt
+        python -m pip install -r docs/requirements.txt
     - name: Make the sphinx doc
       run: |
         rm -rf docs/source/modules/STUBDIR
@@ -44,7 +53,7 @@ jobs:
         path: 'docs/build/html'
 
   deploy_docs:
-    if: github.event_name != 'pull_request'
+    if: github.event_name == 'push' && github.ref == 'refs/heads/devel'
     needs: build_docs
     runs-on: ubuntu-latest
     environment:

.github/workflows/testing.yml

@@ -146,10 +146,6 @@ jobs:
           python -m pip install wheel Cython numpy
           python -m pip install src/binding/petsc4py
 
-      - name: Install Python dependencies
-        run: |
-          python -m pip install -r requirements.txt --no-cache-dir
-          python -m pip list
       # - name: Check parallel h5py installation
       #   run: |
       #       python -c "
@@ -323,11 +319,6 @@ jobs:
           python -m pip install wheel Cython numpy
           python -m pip install src/binding/petsc4py
 
-      - name: Install Python dependencies
-        run: |
-          python -m pip install -r requirements.txt --no-cache-dir
-          python -m pip list
-
       # - name: Check parallel h5py installation
       #   run: |
       #       python -c "

.gitignore

@@ -35,3 +35,5 @@ __test__/
 env/
 env*/
 *env/
+# Visual Studio Code workspace files
+*.code-workspace

.travis.yml

@@ -24,7 +24,6 @@ before_install:
   - python -m pip uninstall -y sympde
   - python -m pip uninstall -y pyccel
   - python -m pip uninstall -y gelato
-  - python -m pip install -r requirements.txt
 
 # command to install project
 install:

CITATION.bib

@@ -0,0 +1,10 @@
+@inproceedings{Guclu2022,
+  title = {{{PSYDAC}}: A High-Performance {{IGA}} Library in {{Python}}},
+  booktitle = {8th {{European Congress}} on {{Computational Methods}} in {{Applied Sciences}} and {{Engineering}}},
+  author = {Güçlü, Y. and Hadjout, S. and Ratnani, A.},
+  year = {2022},
+  publisher = {CIMNE},
+  doi = {10.23967/eccomas.2022.227},
+  url = {https://www.scipedia.com/public/Guclu_et_al_2022a},
+  eventtitle = {8th {{European Congress}} on {{Computational Methods}} in {{Applied Sciences}} and {{Engineering}}},
+}

docs/installation.md

@@ -0,0 +1,202 @@
+# Installation
+
+-   [Requirements](#requirements)
+-   [Python setup and project download](#python-setup-and-project-download)
+-   [Installing the library](#installing-the-library)
+-   [Optional PETSc installation](#optional-petsc-installation)
+-   [Uninstall](#uninstall)
+
+## Requirements
+
+Psydac requires a certain number of components to be installed on the machine:
+
+-   Fortran and C compilers with OpenMP support
+-   OpenMP library
+-   BLAS and LAPACK libraries
+-   MPI library
+-   HDF5 library with MPI support
+
+The installation instructions depend on the operating system and on the packaging manager used.
+
+### Linux Debian-Ubuntu-Mint
+
+To install all requirements on a Linux Ubuntu operating system, just use APT, the Advanced Packaging Tool:
+```sh
+sudo apt update
+sudo apt install python3 python3-dev python3-pip
+sudo apt install gcc gfortran
+sudo apt install libblas-dev liblapack-dev
+sudo apt install libopenmpi-dev openmpi-bin
+sudo apt install libomp-dev libomp5
+sudo apt install libhdf5-openmpi-dev
+```
+
+### macOS
+
+To install all the requirements on a macOS operating system we recommend using [Homebrew](https://brew.sh/):
+
+```eh
+brew update
+brew install gcc
+brew install openblas
+brew install lapack
+brew install open-mpi
+brew install libomp
+brew install hdf5-mpi
+```
+
+### Other operating systems
+
+Please see the [instructions for the pyccel library](https://github.com/pyccel/pyccel#Requirements) for further details.
+
+### High-performance computers using Environment Modules
+
+Many high-performance computers use [Environment Modules](https://modules.sourceforge.net/).
+On those systems one typically needs to load the correct versions (i.e. compatible with each other) of the modules `gcc`, `openmpi`, and `hdf5-mpi`, e.g.
+
+```sh
+module load gcc/15
+module load openmpi/5.0
+module load hdf5-mpi/1.14.1
+```
+OpenMP instructions should work out of the box.
+For access to BLAS and LAPACK routines there are usually different options, we refer therefore to any documentation provided by the supercomputer's maintainers.
+
+## Python setup and project download
+
+We recommend creating a clean Python virtual environment using [venv](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/#creating-a-virtual-environment):
+```sh
+python3 -m venv <ENV-PATH>
+```
+where `<ENV-PATH>` is the location to create the virtual environment.
+(A new directory will be created at the required location.)
+In order to activate the environment just run the command
+```sh
+source <ENV-PATH>/bin/activate
+```
+At this point the commands `python` and [`pip`](https://pip.pypa.io/en/stable/) will refer to the Python 3 interpreter and package manager of the virtual environment, respectively.
+Additionally, the command `deactivate` closes the environment.
+It is good practice to keep `pip` up to date with
+```sh
+pip install --upgrade pip
+```
+
+One can clone the Psydac repository at any location `<ROOT-PATH>` in the filesystem which does not require administrator privileges, using either
+```sh
+git clone https://github.com/pyccel/psydac.git
+```
+or
+```sh
+git clone [email protected]:pyccel/psydac.git
+```
+The latter command requires a GitHub account.
+
+## Installing the library
+
+Psydac depends on several Python packages, which should be installed in the newly created virtual environment.
+Almost all of these dependencies will be automatically installed by `pip` at the time of installing the `psydac` package later on.
+
+The single exception is the `h5py` package, which needs to be installed in parallel mode.
+This means that a wheel will be built from sources and linked to the local parallel HDF5 library.
+
+To this end, we first set the environment variable `HDF5_DIR` s.t. the path `$HDF5_DIR/lib/` will correspond to the folder containing the dynamic library `libhdf5.so` (on Ubuntu/Debian) or `libhdf5.dylib` (on macOS).
+This path can be obtained with a command which depends on your system.
+
+-   **Ubuntu/Debian**:
+    ```sh
+    export HDF5_DIR=$(dpkg -L libhdf5-openmpi-dev | grep "libhdf5.so" | xargs dirname)
+    ```
+
+-   **macOS**:
+    ```sh
+    export HDF5_DIR=$(brew list hdf5-mpi | grep "libhdf5.dylib" | xargs dirname | xargs dirname)
+    ```
+
+- **High-performance computers using [Environment Modules](https://modules.sourceforge.net/)**:
+
+    The correct location of the HDF5 library can be found using the `module show` command, which reveals any environment variables after the `setenv` keyword.
+    For example, on this system both `HDF5_HOME` and `HDF5_ROOT` contain the information we need:
+
+    ```sh
+    > module show hdf5-mpi/1.14.1
+
+    -------------------------------------------------------------------
+    /mpcdf/soft/SLE_15/sub/gcc_15/sub/openmpi_5_0/modules/libs/hdf5-mpi/1.14.1:
+
+    module-whatis   {HDF5 library 1.14.1 with MPI support, built for openmpi_5_0_7_gcc_15_1}
+    conflict        hdf5-serial
+    conflict        hdf5-mpi
+    setenv          HDF5_HOME /mpcdf/soft/SLE_15/packages/skylake/hdf5/gcc_15-15.1.0-openmpi_5.0-5.0.7/1.14.1
+    setenv          HDF5_ROOT /mpcdf/soft/SLE_15/packages/skylake/hdf5/gcc_15-15.1.0-openmpi_5.0-5.0.7/1.14.1
+    prepend-path    PATH /mpcdf/soft/SLE_15/packages/skylake/hdf5/gcc_15-15.1.0-openmpi_5.0-5.0.7/1.14.1/bin
+    -------------------------------------------------------------------
+    ```
+
+    Therefore it is sufficient to set
+
+    ```sh
+    export HDF5_DIR=$HDF5_HOME
+    ```
+
+Next, install `h5py` in parallel mode using `pip`:
+```sh
+export CC="mpicc"
+export HDF5_MPI="ON"
+
+pip install h5py --no-cache-dir --no-binary h5py
+```
+
+At this point the Psydac library may be installed from the cloned directory `<ROOT-PATH>/psydac` in **standard mode**, which copies the relevant files to the correct locations of the virtual environment, or in **development mode**, which only installs symbolic links to the Psydac directory. The latter mode allows one to affect the behavior of Psydac by modifying the source files.
+
+-   **Standard mode**:
+    ```bash
+    pip install .
+    ```
+
+-   **Development mode**:
+    ```bash
+    pip install --editable .
+    ```
+
+## Optional PETSc installation
+
+Although Psydac provides several iterative linear solvers which work with our native matrices and vectors, it is often useful to access a dedicated library like [PETSc](https://petsc.org). To this end, our matrices and vectors have the method `topetsc()`, which converts them to the corresponding `petsc4py` objects.
+(`petsc4py` is a Python package which provides Python bindings to PETSc.) After solving the linear system with a PETSc solver, the function `petsc_to_psydac` allows converting the solution vector back to the Psydac format.
+
+In order to use these additional feature, PETSc and petsc4py must be installed as follows.
+First, we download the latest release of PETSc from its [official Git repository](https://gitlab.com/petsc/petsc):
+```sh
+git clone --depth 1 --branch v3.21.4 https://gitlab.com/petsc/petsc.git
+```
+Next, we specify a configuration for complex numbers, and install PETSc in a local directory:
+```sh
+cd petsc
+
+export PETSC_DIR=$(pwd)
+export PETSC_ARCH=petsc-cmplx
+
+./configure --with-scalar-type=complex --with-fortran-bindings=0 --have-numpy=1
+
+make all check
+
+cd -
+```
+Finally, we install the Python package `petsc4py` which is included in the `PETSc` source distribution:
+```sh
+pip install wheel Cython numpy
+pip install petsc/src/binding/petsc4py
+```
+
+## Uninstall
+
+-   **Whichever the install mode**:
+    ```bash
+    pip uninstall psydac
+    ```
+-   **If PETSc was installed**:
+    ```bash
+    pip uninstall petsc4py
+    ```
+
+The non-Python dependencies can be uninstalled manually using the package manager.
+In the case of PETSc, it is sufficient to remove the cloned source directory given that the installation has been performed locally.

docs/psydac-mesh.md

@@ -0,0 +1,9 @@
+# Mesh Generation
+
+After installation, the command `psydac-mesh` will be available.
+
+## Example of usage
+
+```bash
+psydac-mesh -n='16,16' -d='3,3' square mesh.h5
+```

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 64.0", "wheel", "numpy", "pyccel >= 1.11.2"]
+requires = ["setuptools >= 64.0, != 67.2.0", "wheel", "numpy", "pyccel >= 2.0.1"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -8,7 +8,7 @@ version         = "2.4.5.dev0"
 description     = "Python package for isogeometric analysis (IGA)"
 readme          = "README.md"
 requires-python = ">= 3.10"
-license         = "MIT"
+license         = {file = "LICENSE"}
 authors         = [
     {name = "Psydac development team", email = "[email protected]"}
 ]
@@ -30,13 +30,7 @@ dependencies = [
     'pyevtk',
 
     # Our packages from PyPi
-    'pyccel >= 2.0',
-
-    # In addition, we depend on mpi4py and h5py (MPI version).
-    # Since h5py must be built from source, we run the commands
-    #
-    # python3 -m pip install requirements.txt
-    # python3 -m pip install .
+    'pyccel >= 2.0.1',
     'mpi4py >= 4',
     'h5py',