From c34ea668ab02ba989b49356bd9118163914c8549 Mon Sep 17 00:00:00 2001 From: "Eric T. Johnson" Date: Sun, 14 Apr 2024 17:27:33 -0400 Subject: [PATCH] Simplify pytest usage * fix some old code under `examples/mesh/experiments` that was breaking pytest discovery * update `presentations/pyro_intro.ipynb` to the new package layout and ignore a cell that prints its run time * move the pytest ignores to pyproject.toml This allows us to simply run `pytest` from the repository root, and not have to pass a bunch of `--ignore` arguments. --- .github/workflows/pytest.yml | 2 +- README.md | 2 +- docs/source/testing.rst | 2 +- examples/mesh/experiments/test_indexer.py | 2 +- examples/mesh/experiments/test_mask.py | 4 ++-- examples/mesh/experiments/test_subclass.py | 8 +++---- presentations/pyro_intro.ipynb | 26 ++++++++-------------- pyproject.toml | 8 +++++++ 8 files changed, 27 insertions(+), 27 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 79479bda1..14b153b45 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -36,4 +36,4 @@ jobs: run: pip install . - name: Run tests with pytest - run: pytest -v --cov=pyro --nbval --ignore=docs --ignore=./pyro/multigrid/derive_analytic_solutions.ipynb --ignore=examples/mesh --ignore=examples/multigrid --ignore=presentations + run: pytest -v --cov=pyro --nbval --color=yes diff --git a/README.md b/README.md index b86f90abf..3ec3878e5 100644 --- a/README.md +++ b/README.md @@ -268,7 +268,7 @@ with their data. Unit tests are controlled by pytest and can be run simply via ``` - pytest pyro + pytest ``` ## Acknowledgements diff --git a/docs/source/testing.rst b/docs/source/testing.rst index 8e54bfc5d..1d0b3bd15 100644 --- a/docs/source/testing.rst +++ b/docs/source/testing.rst @@ -13,7 +13,7 @@ pyro implements unit tests using ``pytest``. These can be run via: .. prompt:: bash - pytest -v --nbval pyro + pytest -v --nbval Regression tests diff --git a/examples/mesh/experiments/test_indexer.py b/examples/mesh/experiments/test_indexer.py index 906d282b8..8fdbcaddb 100644 --- a/examples/mesh/experiments/test_indexer.py +++ b/examples/mesh/experiments/test_indexer.py @@ -3,7 +3,7 @@ import numpy as np -import mesh.patch as patch +from pyro.mesh import patch myg = patch.Grid2d(8, 8, ng=2) a = myg.scratch_array() diff --git a/examples/mesh/experiments/test_mask.py b/examples/mesh/experiments/test_mask.py index 0916726ae..408fcdf16 100644 --- a/examples/mesh/experiments/test_mask.py +++ b/examples/mesh/experiments/test_mask.py @@ -4,8 +4,8 @@ import numpy as np -import mesh.boundary as bnd -from mesh import patch +import pyro.mesh.boundary as bnd +from pyro.mesh import patch class Mask(object): diff --git a/examples/mesh/experiments/test_subclass.py b/examples/mesh/experiments/test_subclass.py index 7df48d1f7..5877af453 100644 --- a/examples/mesh/experiments/test_subclass.py +++ b/examples/mesh/experiments/test_subclass.py @@ -19,9 +19,9 @@ import numpy as np -import mesh.array_indexer as ai -import mesh.patch as patch -from util import msg +import pyro.mesh.array_indexer as ai +from pyro.mesh import patch +from pyro.util import msg _buf_split = ai._buf_split @@ -121,7 +121,7 @@ def pretty_print(self): a different color, to make things stand out """ - if self.dtype == np.int: + if self.dtype == int: fmt = "%4d" elif self.dtype == np.float64: fmt = "%10.5g" diff --git a/presentations/pyro_intro.ipynb b/presentations/pyro_intro.ipynb index b7b89a20e..b499737bb 100644 --- a/presentations/pyro_intro.ipynb +++ b/presentations/pyro_intro.ipynb @@ -184,8 +184,8 @@ }, "outputs": [], "source": [ - "import mesh.patch as patch\n", - "import mesh.boundary as bnd\n", + "import pyro.mesh.patch as patch\n", + "import pyro.mesh.boundary as bnd\n", "import numpy as np" ] }, @@ -344,7 +344,10 @@ "metadata": { "slideshow": { "slide_type": "fragment" - } + }, + "tags": [ + "nbval-ignore-output" + ] }, "outputs": [ { @@ -393,7 +396,7 @@ } ], "source": [ - "from pyro import Pyro\n", + "from pyro.pyro_sim import Pyro\n", "pyro_sim = Pyro(\"advection\")\n", "pyro_sim.initialize_problem(\"tophat\", \"inputs.tophat\",\n", " other_commands=[\"mesh.nx=8\", \"mesh.ny=8\",\n", @@ -474,22 +477,11 @@ } }, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/alice/Documents/pyro2/advection/simulation.py:121: MatplotlibDeprecationWarning: Since 3.2, mpl_toolkits's own colorbar implementation is deprecated; it will be removed two minor releases later. Set the 'mpl_toolkits.legacy_colorbar' rcParam to False to use Matplotlib's default colorbar implementation and suppress this deprecation warning.\n", - " cb = axes.cbar_axes[0].colorbar(img)\n", - "/home/alice/anaconda3/lib/python3.7/site-packages/mpl_toolkits/axes_grid1/axes_grid.py:51: MatplotlibDeprecationWarning: \n", - "The mpl_toolkits.axes_grid1.colorbar module was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use matplotlib.colorbar instead.\n", - " from .colorbar import Colorbar\n" - ] - }, { "data": { "image/png": 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\n", "text/plain": [ - "
" + "
" ] }, "metadata": { @@ -500,7 +492,7 @@ { "data": { "text/plain": [ - "
" + "
" ] }, "metadata": {}, diff --git a/pyproject.toml b/pyproject.toml index 03edffa53..e32c50477 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,3 +49,11 @@ ignore-words-list = "pres" [tool.isort] known_first_party = ["pyro"] + +[tool.pytest.ini_options] +# docs: symlinks to notebooks we're already testing +# derive_analytic_solutions.ipynb: sympy derivations, doesn't use any pyro code +addopts = """\ + --ignore=docs/ \ + --ignore=pyro/multigrid/derive_analytic_solutions.ipynb \ + """