Merge pull request #67 from boutproject/merge-boututils

Merge `boututils` into `boutdata`

Author: ZedThree

.github/workflows/formatting.yml

@@ -0,0 +1,38 @@
+name: Formatting (black & isort)
+on:
+  push:
+    branches: master
+    paths:
+      - '**.py'
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.x
+    - name: Install black
+      run: |
+        python -m pip install --upgrade pip
+        pip install black isort
+    - name: Version
+      run: |
+        python --version
+        black --version
+        isort --version
+    - name: Run black
+      run: |
+        black boututils
+    - name: Run isort
+      run: |
+        isort boututils
+    - uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: "[skip ci] Apply black/isort changes"

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Test
+name: Test and lint
 
 on:
   # Run each time we push and pull requests
@@ -10,10 +10,8 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  # As we are running on different environments, we are splitting the jobs
-  # https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#jobs
-  local:
-    runs-on: ${{ matrix.os }}
+  test:
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: true
       matrix:

.gitignore

@@ -127,4 +127,5 @@ dmypy.json
 .idea/
 *.sw[po]
 
-boutdata/_version.py
+src/boutdata/_version.py
+src/boututils/_version.py

README.md

@@ -7,21 +7,15 @@
 [![PEP8](https://img.shields.io/badge/code%20style-PEP8-brightgreen.svg)](https://www.python.org/dev/peps/pep-0008/)
 [![License](https://img.shields.io/badge/license-LGPL--3.0-blue.svg)](https://github.com/boutproject/boutdata/blob/master/LICENSE)
 
-pip-package of what is found in `BOUT-dev/tools/pylib/boutdata`.
-Note that `BOUT-dev/tools/pylib/boutdata` will likely be replaced by this repo
-in `BOUT++ v4.3.0`.
-See [this issue](https://github.com/boutproject/BOUT-dev/issues/1347),
-[this pull request](https://github.com/boutproject/BOUT-dev/pull/1766) and
-[this pull request](https://github.com/boutproject/BOUT-dev/pull/1740) for details.
+Python tools for working with [BOUT++](https://github.com/boutproject/BOUT-dev.git).
 
 > **NOTE**: This package will likely be superseded by
   [`xBOUT`](https://github.com/boutproject/xBOUT) in the near future
 
 # Dependencies
 
-`boutdata` depends on `boututils` which again depends on
-[`netcfd4`](https://github.com/Unidata/netcdf4-python) which requires
-[`HDF5`](https://www.h5py.org) and
+`boutdata` uses [`netcfd4`](https://github.com/Unidata/netcdf4-python)
+which requires [`HDF5`](https://www.h5py.org) and
 [`netcdf-4`](https://github.com/Unidata/netcdf-c/releases) are
 installed, and that the `nc-config` utility is in your `PATH`. This
 can be install with

pyproject.toml

@@ -28,15 +28,15 @@ keywords = [
     "data-visualization",
 ]
 license = {text = "GNU Lesser General Public License v3 or later (LGPLv3+)"}
-authors = [{name = "Ben Dudson", email = "benjamin.dudson@york.ac.uk"}]
+authors = [{name = "Ben Dudson", email = "benjamin.dudson@york.ac.uk"}, {name = "BOUT++ team"}]
 urls = {project = "https://github.com/boutproject/boutdata"}
 dependencies = [
     "sympy>=1.5.1",
     "numpy>=1.22.0",
     "matplotlib>=3.2.1",
     "natsort>=8.1.0",
     "scipy>=1.4.1",
-    "boututils>=0.1.9",
+    "netCDF4",
 ]
 dynamic = ["version"]
 
@@ -52,14 +52,11 @@ docs = [
 [project.scripts]
 bout-squashoutput = "boutdata.scripts.bout_squashoutput:main"
 
-[tool.setuptools]
-packages = ["boutdata"]
-
 [tool.setuptools.dynamic]
 version = { attr = "setuptools_scm.get_version" }
 
 [tool.setuptools_scm]
-write_to = "boutdata/_version.py"
+write_to = "src/boutdata/_version.py"
 
 [tool.pytest.ini_options]
 addopts = "--cov=boutdata"

boutdata/__init__.py src/boutdata/__init__.pyboutdata/__init__.py renamed to src/boutdata/__init__.py

@@ -1,9 +1,32 @@
 """ Routines for exchanging data to/from BOUT++ """
 
-# Import this, as this almost always used when calling this package
 from boutdata.collect import collect, attributes
+from boututils.boutarray import BoutArray
+from boututils.boutwarnings import alwayswarn
+from boututils.run_wrapper import (
+    launch,
+    launch_safe,
+    shell,
+    shell_safe,
+    determineNumberOfCPUs,
+    build_and_log,
+)
 
-__all__ = ["attributes", "collect", "gen_surface", "pol_slice"]
+
+__all__ = [
+    "attributes",
+    "collect",
+    "gen_surface",
+    "pol_slice",
+    "BoutArray",
+    "alwayswarn",
+    "launch",
+    "launch_safe",
+    "shell",
+    "shell_safe",
+    "determineNumberOfCPUs",
+    "build_and_log",
+]
 
 __name__ = "boutdata"