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Module 5 updates #109

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merged 7 commits into from
Aug 8, 2022
Merged

Module 5 updates #109

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c447261
:label: py.test -> pytest
jack89roberts Jul 16, 2022
d8cfe96
:sparkles: replace nose decorator with pytest skip
jack89roberts Jul 16, 2022
a2c5d05
:heavy_minus_sign: Remove use of nose
jack89roberts Jul 16, 2022
ccefa61
:adhesive_bandage: update test framework links
jack89roberts Jul 16, 2022
e19225a
:pencil2: typos, fix old links
jack89roberts Jul 16, 2022
86734a1
edit test to pass
helendduncan Aug 8, 2022
50b2201
fix broken link
helendduncan Aug 8, 2022
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66 changes: 42 additions & 24 deletions module01_introduction_to_python/01_01_data_analysis_example.ipynb
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4 changes: 2 additions & 2 deletions module05_testing_your_code/05_00_introduction.ipynb
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Expand Up @@ -105,7 +105,7 @@
"```\n",
"\n",
"* Does not test correctness of code\n",
"* Checks code is a similarly wrong on day N as day 0"
"* Checks code is as similarly wrong on day N as day 0"
]
},
{
Expand Down Expand Up @@ -174,7 +174,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.9.9"
}
},
"nbformat": 4,
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32 changes: 13 additions & 19 deletions module05_testing_your_code/05_01_how_to_test.ipynb
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Expand Up @@ -784,25 +784,12 @@
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"tags": [
"raises-exception"
]
},
"outputs": [
{
"ename": "SyntaxError",
"evalue": "invalid syntax (3187101134.py, line 1)",
"output_type": "error",
"traceback": [
"\u001b[0;36m File \u001b[0;32m\"/var/folders/q7/nl3w6z854711jwsdy0hj7sxhwypcgh/T/ipykernel_66962/3187101134.py\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m assert I_only_accept_positive_numbers(-5) == # Gives a value error\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
]
}
],
"cell_type": "markdown",
"metadata": {},
"source": [
"assert I_only_accept_positive_numbers(-5) == # Gives a value error"
"```python\n",
"assert I_only_accept_positive_numbers(-5) == # Gives a value error\n",
"```"
]
},
{
Expand All @@ -811,6 +798,13 @@
"source": [
"But to do that, we need to learn about more sophisticated testing tools, called \"test frameworks\"."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -832,7 +826,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.9.9"
}
},
"nbformat": 4,
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47 changes: 22 additions & 25 deletions module05_testing_your_code/05_02_testing_frameworks.ipynb
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Expand Up @@ -38,43 +38,40 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"* Language agnostic: [CTest](http://www.cmake.org/cmake/help/v2.8.12/ctest.html)\n",
"* Language agnostic: [CTest](https://cmake.org/cmake/help/latest/manual/ctest.1.html)\n",
" * Test runner for executables, bash scripts, etc...\n",
" * Great for legacy code hardening\n",
" \n",
"* C unit-tests:\n",
" * all c++ frameworks,\n",
" * [Check](http://check.sourceforge.net/),\n",
" * [Check](https://libcheck.github.io/check/),\n",
" * [CUnit](http://cunit.sourceforge.net)\n",
"\n",
"* C++ unit-tests:\n",
" * [CppTest](http://cpptest.sourceforge.net/),\n",
" * [Boost::Test](http://www.boost.org/doc/libs/1_55_0/libs/test/doc/html/index.html),\n",
" * [google-test](https://code.google.com/p/googletest/),\n",
" * [Catch](https://github.com/philsquared/Catch) (best)\n",
" * [Boost::Test](https://www.boost.org/doc/libs/1_79_0/libs/test/doc/html/index.html),\n",
" * [google-test](https://google.github.io/googletest/),\n",
" * [Catch](https://github.com/catchorg/Catch2)\n",
"\n",
"* Python unit-tests:\n",
" * [nose](https://nose.readthedocs.org/en/latest/) includes test discovery, coverage, etc\n",
" * [unittest](http://docs.python.org/2/library/unittest.html) comes with standard python library\n",
" * [py.test](http://pytest.org/latest/), branched off of nose\n",
" * [unittest](https://docs.python.org/3/library/unittest.html) comes with standard python library\n",
" * [pytest](http://pytest.org/latest/), includes test discovery, coverage, etc\n",
"\n",
"* R unit-tests:\n",
" * [RUnit](http://cran.r-project.org/web/packages/RUnit/index.html),\n",
" * [svUnit](http://cran.r-project.org/web/packages/svUnit/index.html)\n",
" * (works with [SciViews](http://www.sciviews.org/) GUI)\n",
" * [RUnit](https://cran.r-project.org/web/packages/RUnit/index.html),\n",
" * [testthat](https://testthat.r-lib.org/)\n",
"\n",
"* Fortran unit-tests:\n",
" * [funit](http://nasarb.rubyforge.org/funit/),\n",
" * [pfunit](http://sourceforge.net/projects/pfunit/)(works with MPI)"
" * [pfunit](https://github.com/Goddard-Fortran-Ecosystem/pFUnit)(works with MPI)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## py.test framework: usage\n",
"## pytest framework: usage\n",
"\n",
"[py.test](https://docs.pytest.org/en/latest/) is a recommended python testing framework."
"[pytest](https://docs.pytest.org/en/latest/) is a recommended python testing framework."
]
},
{
Expand Down Expand Up @@ -211,9 +208,9 @@
"output_type": "stream",
"text": [
"============================= test session starts ==============================\n",
"platform darwin -- Python 3.8.13, pytest-7.1.2, py-1.10.0, pluggy-1.0.0\n",
"rootdir:/home/turingdev/projects/research-software/rse-course/ch03tests/saskatchewan\n",
"plugins: anyio-3.3.0\n",
"platform darwin -- Python 3.9.9, pytest-7.1.2, pluggy-1.0.0\n",
"rootdir: /Users/jroberts/GitHub/rse-course/module05_testing_your_code/saskatchewan\n",
"plugins: anyio-3.6.1, cov-3.0.0\n",
"collected 3 items\n",
"\n",
"test_overlap.py ..F [100%]\n",
Expand All @@ -229,7 +226,7 @@
"test_overlap.py:13: AssertionError\n",
"=========================== short test summary info ============================\n",
"FAILED test_overlap.py::test_no_overlap - assert 0.25 == 0.0\n",
"========================= 1 failed, 2 passed in 0.11s ==========================\n",
"========================= 1 failed, 2 passed in 0.07s ==========================\n",
"Tests failed\n"
]
}
Expand All @@ -238,7 +235,7 @@
"%%bash\n",
"#%%cmd #(windows)\n",
"cd saskatchewan\n",
"py.test || echo \"Tests failed\""
"pytest || echo \"Tests failed\""
]
},
{
Expand Down Expand Up @@ -272,8 +269,8 @@
"source": [
"Some options:\n",
"\n",
"* help: `py.test --help`\n",
"* run only tests for a given feature: `py.test -k foo` # tests with 'foo' in the test name"
"* help: `pytest --help`\n",
"* run only tests for a given feature: `pytest -k foo` # tests with 'foo' in the test name"
]
},
{
Expand Down Expand Up @@ -476,13 +473,13 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Numpy ships with a number of assertions (in ``numpy.testing``) to make\n",
"Numpy ships with a number of assertions (in `numpy.testing`) to make\n",
"comparison easy:"
]
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 8,
"metadata": {
"attributes": {
"classes": [
Expand Down Expand Up @@ -529,7 +526,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.9.9"
}
},
"nbformat": 4,
Expand Down
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