@@ -7,7 +7,7 @@ be tested via [`pytest`][pytest] up to a certain level, some (most?) of them
77should even work in a Python 3 environment.
88
99To perform those tests, the packges otherwise provided by ImageJ need to be
10- mocked using the ` imcf-fiji-mocks ` package. For seting up a _ venv _ use the steps
10+ mocked using the ` imcf-fiji-mocks ` package. For seting up a * venv * use the steps
1111described here:
1212
1313``` bash
@@ -37,7 +37,7 @@ pip install --upgrade \
3737pip install -e .
3838```
3939
40- Using this _ venv _ , tests can be triggered just the usual way. To run only
40+ Using this * venv * , tests can be triggered just the usual way. To run only
4141specific tests, use e.g.
4242
4343``` bash
@@ -48,12 +48,12 @@ pytest tests/bdv/test_processingoptions.py
4848
4949For running [ ` pytest ` ] [ pytest ] in a C-Python 2 environment, things are slightly
5050more complicated than the approach described for Python 3 above as ` pip ` for
51- Python 2 cannot install a project in _ editable _ mode unless it has a ` setup.py `
51+ Python 2 cannot install a project in * editable * mode unless it has a ` setup.py `
5252file (which we don't have and don't want).
5353
5454Therefore, a wheel needs to be built (e.g. using [ ` poetry ` ] [ poetry ] ) and
5555installed (every time) into the corresponding virtualenv when performing the
56- tests. Assuming you're having a working _ poetry _ setup on your machine, you can
56+ tests. Assuming you're having a working * poetry * setup on your machine, you can
5757simply use the provided ` scripts/py2-pytest.sh ` wrapper that will create the
5858virtualenv, build and install the ` imcflibs ` wheel and launch ` pytest ` with the
5959parameters specified, e.g.
@@ -68,35 +68,35 @@ Unfortunately there is nothing like `pytest` available for the parts that are
6868running exclusively in a ImageJ2 / Fiji context. So in order to provide at least
6969some basic, semi-interactive tests the following conventions are being used:
7070
71- * Each _ ** function** _ in any of the ` imcflibs.imagej ` submodules should have its
71+ * Each *** function*** in any of the ` imcflibs.imagej ` submodules should have its
7272 own directory underneath ` /tests/interactive-imagej/ ` , using their fully
7373 qualified name as the path (only skipping the ` imcflibs. ` prefix). For example
7474 test scripts for ` imcflibs.imagej.bioformats.import_image() ` will be placed in
7575 the directory ` /tests/interactive-imagej/bioformats/import_image/ ` .
7676* The scripts inside those directories are intended to be run interactively /
7777 manually in a (freshly started) Fiji instance. Yes, really. Any other
7878 suggestions are highly welcome!
79- * To facilitate this, a collection of _ test images _ (and possibly other input
79+ * To facilitate this, a collection of * test images * (and possibly other input
8080 data) should be cloned to the local file system. Currently this ` sample-data `
81- repository is _ NOT _ publicly available due to legal β uncertainties. A repo
81+ repository is * NOT * publicly available due to legal β uncertainties. A repo
8282 containing test data π that can be published should be assembled over time
8383 though!
84- * Any _ interactive _ test script should start with a header similar to the one
85- described below. Paths to input data _ inside _ the test scripts ** has** to be
84+ * Any * interactive * test script should start with a header similar to the one
85+ described below. Paths to input data * inside * the test scripts ** has** to be
8686 relative to the location of the ` sample-data ` repository mentioned above. This
8787 will allow for a fairly okayish testing workflow like this:
8888 * Make your changes in VS Code, then trigger a build by pressing ` Shift ` +
89- ` Ctrl ` + ` B ` . If things are configured as described in the _ DEVELOPMENT _
89+ ` Ctrl ` + ` B ` . If things are configured as described in the * DEVELOPMENT *
9090 document, the resulting ` .jar ` file will be automatically placed in Fiji's
9191 ` jars/ ` folder.
9292 * Next, start a fresh instance of the Fiji that received the newly built JAR.
9393 * After Fiji has started, simply drag and drop the desired test script onto
94- the main window. This will open the _ Script Editor _ , then press ` Ctrl ` + ` R `
94+ the main window. This will open the * Script Editor * , then press ` Ctrl ` + ` R `
9595 to launch the script.
9696 * Only on the first run on the machine being used you will have to select the
9797 base location of the ` sample-data ` repository.
98- * All subsequent runs of _ ** any** _ test script using the defined _ Script
99- Parameter _ ` IMCF_TESTDATA ` will remember this selection, so it will be
98+ * All subsequent runs of *** any*** test script using the defined * Script
99+ Parameter * ` IMCF_TESTDATA ` will remember this selection, so it will be
100100 sufficient to just confirm the dialog by pressing ` Enter ` .
101101
102102### Quick Workflow Summary
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