Deleted gmsh, meshio dependencies.

Also replaced the last few files in the benchmark folder with a version compatible with the recusive remesh. Finally also unpinned sphinx and slightly cleaned conda_env.yml.

dependencies/conda_env.yml

@@ -8,17 +8,14 @@ channels:
 dependencies:
   - python>=3.9
   - cmake
-  - k3d
-  # - numpy=1.23 #Temporary error with numba calling numpy calling ufunc with no exceptions in latest numpy; see https://github.com/numba/numba/issues/8615
-  - vtk
+  - numpy
   - jupyterlab
   - yt
   - scipy<=1.13
   - mpi4py
   - plotly
   - pyyaml
   - ipywidgets
-  - meshio=5.2
   - tqdm
   - palettable
   - h5py
@@ -31,8 +28,11 @@ dependencies:
   - pandas
   - nodejs
   - twine
-  - sphinx=4.4.0
-  - breathe
+  - sphinx #=4.4.0
+  - pip
+  - pip:
+    - breathe
+  # - breathe #install with pip, otherwise it will install the wrong version, not compatible with sphinx
   - sphinx-copybutton
   - nbsphinx
   - sphinx_rtd_theme

docs/src/0_getting_started/0_prerequisites.rst

@@ -11,11 +11,11 @@ Below is a list of the software required to be able to compile and run Magritte.
 * `GCC <https://gcc.gnu.org/>`_ (version :literal:`5.0.0` or later): to compile the C++ part of Magritte.
 * `CMake <https://cmake.org/>`_ (version :literal:`3.18.0` or later): for building Magritte, organising compilation and linking;
 * `Anaconda <https://www.anaconda.com/blog/individual-edition-2020-11>`_ (optional): for managing the required Python packages;
-* `Gmsh <https://gmsh.info/>`_ (optional): for constructing geometric meshes for the models;
+.. * `Gmsh <https://gmsh.info/>`_ (optional): for constructing geometric meshes for the models;
 
 Although Anaconda is optional and you could, in priciple, use any other way of installing the required Python dependencies, we recommend and assume the use of Anaconda.
 The list of required Python packages can be found in the `conda environment file <https://github.com/Magritte-code/Magritte/blob/stable/dependencies/conda_env.yml>`_.
-Also Gmsh is optional, however, it will be used in most examples in this documentation to create models.
+.. Also Gmsh is optional, however, it will be used in most examples in this documentation to create models.
 
 Once these prerequisites are in place, Magritte can be installed following the :ref:`quickstart <link-quickstart>`.
 
@@ -25,9 +25,8 @@ Once these prerequisites are in place, Magritte can be installed following the :
 
 
 .. Hint::
-    Although we recommend to first try to install the required software in your preferred usual way, the folder `Magritte/dependencies/ <https://github.com/Magritte-code/Magritte/tree/stable/dependencies>`_ contains a set of bash scripts: :literal:`get_conda.sh`, :literal:`get_cmake.sh`,
-    and :literal:`get_gmsh.sh`, to quickly obtain the appropriate versions of miniconda3 (for Anaconda), CMake, and
-    Gmsh respectively. However, these scripts don't properly install the software, but rather download an executable binary, which is useful, e.g. if you don't have root access.
+    Although we recommend to first try to install the required software in your preferred usual way, the folder `Magritte/dependencies/ <https://github.com/Magritte-code/Magritte/tree/stable/dependencies>`_ contains a set of bash scripts: :literal:`get_conda.sh` and :literal:`get_cmake.sh`,
+    to quickly obtain the appropriate versions of miniconda3 (for Anaconda) and CMake respectively. However, these scripts don't properly install the software, but rather download an executable binary, which is useful, e.g. if you don't have root access.
 
     To use these, first clone the Magritte `GitHub <https://github.com/Magritte-code/Magritte>`_ repository
 
@@ -44,10 +43,6 @@ Once these prerequisites are in place, Magritte can be installed following the :
     .. code-block:: shell
     
         bash dependencies/get_cmake.sh
-        
-    .. code-block:: shell
-    
-        bash dependencies/get_gmsh.sh
 
     ⚠️  Don't forget to include the relevant paths to your shell's :literal:`$PATH` variable!
     (For convenience, the scripts will print the relevant path.)

docs/src/0_getting_started/2_installation.rst

@@ -49,7 +49,6 @@ Magritte has several dependencies, some of which are optional.
 **Optional**
 
 * `Anaconda <https://www.anaconda.com/blog/individual-edition-2020-11>`_, for managing the required Python packages;
-* `Gmsh <https://gmsh.info/>`_, version :literal:`4.6.0` or later, for meshing model geometries.
 
 
 Please note that :literal:`Paracabs` might have further dependencies depending
@@ -71,8 +70,6 @@ the model files.
 * :mod:`scipy`, for interpolation and spatial functions such as nearest neighbour calculations;
 * :mod:`healpy`, to sample directions from a discretized unit sphere;
 * :mod:`astropy`, for unit conversions and physical constants;
-* :mod:`meshio`, for reading and writing several types of mesh data structures;
-* :mod:`vtk`, for reading and writing vtk files;
 * :mod:`pyyaml`, for reading and writing yaml files;
 * :mod:`mpi4py`, for MPI (Message Passing Interface) functionality in Python;
 * :mod:`tqdm`, for progress bars;