Rename package

Author: finsberg

.coveragerc

@@ -1,6 +1,6 @@
 [run]
 parallel = true
-source = adios4dolfinx
+source = io4dolfinx
 
 [html]
 directory= htmlcov

docs/backends/adios2.rst

@@ -1,6 +1,6 @@
 ADIOS2-backend
 --------------
 
-.. automodule:: adios4dolfinx.backends.adios2.backend
+.. automodule:: io4dolfinx.backends.adios2.backend
     :members:
     :exclude-members: read_point_data

docs/backends/h5py.rst

@@ -1,6 +1,6 @@
 H5PY-backend
 -------------
 
-.. automodule:: adios4dolfinx.backends.h5py.backend
+.. automodule:: io4dolfinx.backends.h5py.backend
     :members:
     :exclude-members: read_point_data

docs/backends/pyvista.rst

@@ -1,6 +1,6 @@
 PyvVsta-backend
 ----------------
 
-.. automodule:: adios4dolfinx.backends.pyvista.backend
+.. automodule:: io4dolfinx.backends.pyvista.backend
     :members:
     :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array

docs/backends/xdmf.rst

@@ -1,6 +1,6 @@
 XDMF-backend
 -------------
 
-.. automodule:: adios4dolfinx.backends.xdmf.backend
+.. automodule:: io4dolfinx.backends.xdmf.backend
     :members:
     :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array

docs/original_checkpoint.py

@@ -1,6 +1,6 @@
 # # Checkpoint on input mesh
 # As we have discussed earlier, one can choose to store function data in a way that
-# is N-to-M compatible by using {py:func}`adios4dolfinx.write_checkpoint`.
+# is N-to-M compatible by using {py:func}`io4dolfinx.write_checkpoint`.
 # This stores the distributed mesh in it's current (partitioned) ordering, and does
 # use the original input data ordering for the cells and connectivity.
 # This means that you cannot use your original mesh (from `.xdmf` files) or mesh tags
@@ -10,7 +10,7 @@
 # An optional way of store an N-to-M checkpoint is to store the function data in the same
 # ordering as the mesh. The write operation will be more expensive, as it requires data
 # communication to ensure contiguous data being written to the checkpoint.
-# The method is exposed as {py:func}`adios4dolfinx.write_function_on_input_mesh`.
+# The method is exposed as {py:func}`io4dolfinx.write_function_on_input_mesh`.
 # Below we will demonstrate this method.
 
 # +
@@ -65,18 +65,18 @@ def write_function(
 
     import dolfinx
 
-    import adios4dolfinx
+    import io4dolfinx
 
     with dolfinx.io.XDMFFile(MPI.COMM_WORLD, mesh_filename, "r") as xdmf:
         mesh = xdmf.read_mesh()
     V = dolfinx.fem.functionspace(mesh, element)
     u = dolfinx.fem.Function(V)
     u.interpolate(f)
 
-    adios4dolfinx.write_function_on_input_mesh(
+    io4dolfinx.write_function_on_input_mesh(
         function_filename.with_suffix(".bp"),
         u,
-        mode=adios4dolfinx.FileMode.write,
+        mode=io4dolfinx.FileMode.write,
         time=0.0,
         name="Output",
     )
@@ -112,13 +112,13 @@ def verify_checkpoint(
     import dolfinx
     import numpy as np
 
-    import adios4dolfinx
+    import io4dolfinx
 
     with dolfinx.io.XDMFFile(MPI.COMM_WORLD, mesh_filename, "r") as xdmf:
         in_mesh = xdmf.read_mesh()
     V = dolfinx.fem.functionspace(in_mesh, element)
     u_in = dolfinx.fem.Function(V)
-    adios4dolfinx.read_function(function_filename.with_suffix(".bp"), u_in, time=0.0, name="Output")
+    io4dolfinx.read_function(function_filename.with_suffix(".bp"), u_in, time=0.0, name="Output")
 
     # Compute exact interpolation
     u_ex = dolfinx.fem.Function(V)

docs/snapshot_checkpoint.py

@@ -12,7 +12,7 @@
 # does not require extra RAM.
 
 # In this example, we will demonstrate how to write a
-# {py:func}`snapshot checkpoint<adios4dolfinx.snapshot_checkpoint>` to disk.
+# {py:func}`snapshot checkpoint<io4dolfinx.snapshot_checkpoint>` to disk.
 
 # First we define a {py:class}`function<dolfinx.fem.Function>` `f` that we want to represent in
 # the {py:class}`function space<dolfinx.fem.FunctionSpace>`.
@@ -33,7 +33,7 @@ def f(x):
 # -
 
 # Next, we create a mesh and an appropriate function space and read and write from file.
-# Note that for both these operations, we use {py:func}`adios4dolfinx.snapshot_checkpoint`,
+# Note that for both these operations, we use {py:func}`io4dolfinx.snapshot_checkpoint`,
 # with different read and write modes.
 
 
@@ -43,20 +43,20 @@ def read_write_snapshot(filename: Path):
     import dolfinx
     import numpy as np
 
-    import adios4dolfinx
+    import io4dolfinx
 
     mesh = dolfinx.mesh.create_unit_cube(MPI.COMM_WORLD, 3, 7, 4)
     V = dolfinx.fem.functionspace(mesh, ("Lagrange", 5))
     u = dolfinx.fem.Function(V)
     u.interpolate(f)
     u.name = "Current_solution"
     # Next, we store the solution to file
-    adios4dolfinx.snapshot_checkpoint(u, filename, adios4dolfinx.FileMode.write)
+    io4dolfinx.snapshot_checkpoint(u, filename, io4dolfinx.FileMode.write)
 
     # Next, we create a new function and load the solution into it
     u_new = dolfinx.fem.Function(V)
     u_new.name = "Read_solution"
-    adios4dolfinx.snapshot_checkpoint(u_new, filename, adios4dolfinx.FileMode.read)
+    io4dolfinx.snapshot_checkpoint(u_new, filename, io4dolfinx.FileMode.read)
 
     # Next, we verify that the solution is correct
     np.testing.assert_allclose(u_new.x.array, u.x.array, atol=np.finfo(float).eps)

docs/time_dependent_mesh.py

@@ -16,7 +16,7 @@
 
 import ipyparallel as ipp
 
-import adios4dolfinx
+import io4dolfinx
 
 
 def compute_volume(mesh, time_stamp):
@@ -39,7 +39,7 @@ def write_meshes(filename: Path):
     import dolfinx
     import numpy as np
 
-    import adios4dolfinx
+    import io4dolfinx
 
     # Create a unit cube
     mesh = dolfinx.mesh.create_unit_cube(
@@ -52,15 +52,15 @@ def write_meshes(filename: Path):
     )
 
     # Write mesh to file, associated with time stamp 1.5
-    adios4dolfinx.write_mesh(filename, mesh, time=1.5)
+    io4dolfinx.write_mesh(filename, mesh, time=1.5)
     compute_volume(mesh, 1.5)
     mesh.geometry.x[:, 0] += 0.1 * mesh.geometry.x[:, 0]
     mesh.geometry.x[:, 1] += 0.3 * mesh.geometry.x[:, 1] * np.sin(mesh.geometry.x[:, 2])
     compute_volume(mesh, 3.3)
     # Write mesh to file, associated with time stamp 3.3
     # Note that we set the mode to append, as we have already created the file
     # and we do not want to overwrite the existing data
-    adios4dolfinx.write_mesh(filename, mesh, time=3.3, mode=adios4dolfinx.FileMode.append)
+    io4dolfinx.write_mesh(filename, mesh, time=3.3, mode=io4dolfinx.FileMode.append)
 
 
 # -
@@ -82,14 +82,14 @@ def write_meshes(filename: Path):
 
 # # Reading a time dependent mesh
 # The only thing we need to do to read the mesh is to send in the associated time stamp,
-# which we do by adding `time=time_stamp` when calling {py:func}`adios4dolfinx.read_mesh`.
+# which we do by adding `time=time_stamp` when calling {py:func}`io4dolfinx.read_mesh`.
 
-second_mesh = adios4dolfinx.read_mesh(
+second_mesh = io4dolfinx.read_mesh(
     mesh_file, comm=MPI.COMM_WORLD, backend="adios2", backend_args={"engine": "BP4"}, time=3.3
 )
 compute_volume(second_mesh, 3.3)
 
-first_mesh = adios4dolfinx.read_mesh(
+first_mesh = io4dolfinx.read_mesh(
     mesh_file, comm=MPI.COMM_WORLD, backend="adios2", backend_args={"engine": "BP4"}, time=1.5
 )
 compute_volume(first_mesh, 1.5)

pyproject.toml

@@ -2,7 +2,7 @@
 requires = ["setuptools>=61.0.0", "wheel"]
 
 [project]
-name = "adios4dolfinx"
+name = "io4dolfinx"
 version = "0.11.0.dev0"
 description = "Checkpointing functionality for DOLFINx meshes/functions with ADIOS2"
 authors = [{ name = "Jørgen S. Dokken", email = "dokken@simula.no" }]
@@ -15,9 +15,9 @@ test = [
     "pytest", 
     "coverage", 
     "ipyparallel", 
-    "adios4dolfinx[h5py]", 
-    "adios4dolfinx[pyvista]", 
-    "adios4dolfinx[xdmf]"
+    "io4dolfinx[h5py]", 
+    "io4dolfinx[pyvista]", 
+    "io4dolfinx[xdmf]"
 ]
 dev = ["pdbpp", "ipython", "mypy", "ruff"]
 h5py = ["h5py"]
@@ -30,10 +30,10 @@ docs = [
     "jupytext",
     "ipykernel<7.0.0",     # Note: Remove once https://github.com/ipython/ipykernel/issues/1450 is in a release
     "sphinx-codeautolink",
-    "adios4dolfinx[h5py]",
+    "io4dolfinx[h5py]",
     "sphinx_external_toc<1.1.0",
 ]
-all = ["adios4dolfinx[test,dev,docs]"]
+all = ["io4dolfinx[test,dev,docs]"]
 
 [tool.pytest.ini_options]
 addopts = ["--import-mode=importlib"]
@@ -64,7 +64,7 @@ select = [
 
 
 [tool.ruff.lint.isort]
-known-first-party = ["adios4dolfinx"]
+known-first-party = ["io4dolfinx"]
 known-third-party = [
     "basix",
     "dolfinx",

tests/conftest.py

@@ -12,7 +12,7 @@
 import numpy.typing as npt
 import pytest
 
-import adios4dolfinx
+import io4dolfinx
 
 
 def find_backends():
@@ -71,7 +71,7 @@ def _write_function(
         uh.interpolate(f)
         uh.name = name
         el_hash = (
-            adios4dolfinx.utils.element_signature(V)
+            io4dolfinx.utils.element_signature(V)
             .replace(" ", "")
             .replace(",", "")
             .replace("(", "")
@@ -90,13 +90,13 @@ def _write_function(
         filename = (f_path / f"mesh_{file_hash}").with_suffix(suffix)
         if mesh.comm.size != 1:
             if not append:
-                adios4dolfinx.write_mesh(filename, mesh, backend=backend)
-            adios4dolfinx.write_function(filename, uh, time=0.0, backend=backend)
+                io4dolfinx.write_mesh(filename, mesh, backend=backend)
+            io4dolfinx.write_function(filename, uh, time=0.0, backend=backend)
         else:
             if MPI.COMM_WORLD.rank == 0:
                 if not append:
-                    adios4dolfinx.write_mesh(filename, mesh, backend=backend)
-                adios4dolfinx.write_function(filename, uh, time=0.0, backend=backend)
+                    io4dolfinx.write_mesh(filename, mesh, backend=backend)
+                io4dolfinx.write_function(filename, uh, time=0.0, backend=backend)
 
         return filename
 
@@ -108,7 +108,7 @@ def read_function():
     def _read_function(
         comm, el, f, path, dtype, backend: typing.Literal["adios2", "h5py"], name="uh"
     ):
-        mesh = adios4dolfinx.read_mesh(
+        mesh = io4dolfinx.read_mesh(
             path,
             comm,
             ghost_mode=dolfinx.mesh.GhostMode.shared_facet,
@@ -117,7 +117,7 @@ def _read_function(
         V = dolfinx.fem.functionspace(mesh, el)
         v = dolfinx.fem.Function(V, dtype=dtype)
         v.name = name
-        adios4dolfinx.read_function(path, v, backend=backend)
+        io4dolfinx.read_function(path, v, backend=backend)
         v_ex = dolfinx.fem.Function(V, dtype=dtype)
         v_ex.interpolate(f)
 
@@ -157,7 +157,7 @@ def _write_function_time_dep(
         uh = dolfinx.fem.Function(V, dtype=dtype)
         uh.interpolate(f0)
         el_hash = (
-            adios4dolfinx.utils.element_signature(V)
+            io4dolfinx.utils.element_signature(V)
             .replace(" ", "")
             .replace(",", "")
             .replace("(", "")
@@ -174,17 +174,17 @@ def _write_function_time_dep(
             suffix = ".h5"
         filename = (f_path / f"mesh_{file_hash}").with_suffix(suffix)
         if mesh.comm.size != 1:
-            adios4dolfinx.write_mesh(filename, mesh, backend=backend)
-            adios4dolfinx.write_function(filename, uh, time=t0, backend=backend)
+            io4dolfinx.write_mesh(filename, mesh, backend=backend)
+            io4dolfinx.write_function(filename, uh, time=t0, backend=backend)
             uh.interpolate(f1)
-            adios4dolfinx.write_function(filename, uh, time=t1, backend=backend)
+            io4dolfinx.write_function(filename, uh, time=t1, backend=backend)
 
         else:
             if MPI.COMM_WORLD.rank == 0:
-                adios4dolfinx.write_mesh(filename, mesh, backend=backend)
-                adios4dolfinx.write_function(filename, uh, time=t0, backend=backend)
+                io4dolfinx.write_mesh(filename, mesh, backend=backend)
+                io4dolfinx.write_function(filename, uh, time=t0, backend=backend)
                 uh.interpolate(f1)
-                adios4dolfinx.write_function(filename, uh, time=t1, backend=backend)
+                io4dolfinx.write_function(filename, uh, time=t1, backend=backend)
 
         return filename
 
@@ -196,7 +196,7 @@ def read_function_time_dep():
     def _read_function_time_dep(
         comm, el, f0, f1, t0, t1, path, dtype, backend: typing.Literal["adios2", "h5py"]
     ):
-        mesh = adios4dolfinx.read_mesh(
+        mesh = io4dolfinx.read_mesh(
             path,
             comm,
             ghost_mode=dolfinx.mesh.GhostMode.shared_facet,
@@ -205,14 +205,14 @@ def _read_function_time_dep(
         V = dolfinx.fem.functionspace(mesh, el)
         v = dolfinx.fem.Function(V, dtype=dtype)
 
-        adios4dolfinx.read_function(path, v, time=t1, backend=backend)
+        io4dolfinx.read_function(path, v, time=t1, backend=backend)
         v_ex = dolfinx.fem.Function(V, dtype=dtype)
         v_ex.interpolate(f1)
 
         res = np.finfo(dtype).resolution
         assert np.allclose(v.x.array, v_ex.x.array, atol=10 * res, rtol=10 * res)
 
-        adios4dolfinx.read_function(path, v, time=t0, backend=backend)
+        io4dolfinx.read_function(path, v, time=t0, backend=backend)
         v_ex = dolfinx.fem.Function(V, dtype=dtype)
         v_ex.interpolate(f0)