Fix the CLI test runner

* Fix the clunky CLI test runner.
  * Update the README about it.
  * The `--plot` test requires installing matplotlib, in particular, one that's compatible with the installed numpy.
  * Moved the `analysis/` directory into the `test/` directory for the tests to import.
  * TODO: Fix the `--memory` test, which fails `assert memory_increases <= 10` on macOS.
  * TODO: Fix the `--plot` test, which raises `ValueError: x and y must have same first dimension, but have shapes (115,) and (114, 2469)` from matplotlib.
* Delete `release.sh` which would be risky to run now and has been supplanted by GitHub Actions. Actually my process was to copy/paste from this script rather than run it as is.

Q. Do *.pxd header files need `freethreading_compatible = True` or is it sufficient in the .pyx module?

Makefile

@@ -13,5 +13,8 @@ clean:
 compile:
 	USE_CYTHON=1 python -m pip install -e .
 
+test: clean compile
+	pytest test
+
 dist:
 	USE_CYTHON=1 python -m build --sdist

README.md

@@ -91,32 +91,43 @@ from stochastic_arrow import reenact_events
 history = reenact_events(stoichiometric_matrix, result['events'], state)
 ```
 
-## Testing
-
-`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
+## Building
 
     > make clean compile
-    > pytest
+
+This builds the extension package and installs it in editable mode.
 
 **NOTE:** `make compile` without an explicit `clean` might not fully build the extension.
 
-There are more command line features in test_arrow:
+## Testing
 
-    > python -m stochastic_arrow.test.test_arrow --complexation
+`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/).
+To run the main tests, in the source tree:
 
-    > python -m stochastic_arrow.test.test_arrow --plot
+    > make test
 
-    > python -m stochastic_arrow.test.test_arrow --obsidian
+or
 
-    > python -m stochastic_arrow.test.test_arrow --memory
+    > pytest
 
-    > python -m stochastic_arrow.test.test_arrow --time
+There are additional command line features in test_arrow:
 
-More examples:
+    > python -m test.test_arrow --help
+    > python -m test.test_arrow --complexation
+    > python -m test.test_arrow --complexation --runs 3
+    > python -m test.test_arrow --obsidian
+    > python -m test.test_arrow --memory
+    > python -m test.test_arrow --time
+    > python -m test.test_arrow --pickle
+    > python -m test.test_arrow --test-fail-flagella
+    > python -m test.test_arrow --test-fail-stdout
+    > python -m test.test_hang
 
-    > python -m stochastic_arrow.test.test_hang
+This test requires installing a version of matplotlib that's compatible with the installed numpy:
 
-    > pytest -m stochastic_arrow/test/test_arrow.py
+    > python -m test.test_arrow --plot
+
+More examples:
 
     > pytest -k flagella
 

optional_requirements.txt

@@ -1 +1 @@
-matplotlib==2.2.3
+matplotlib

analysis/distributions.py → test/analysis/distributions.py

@@ -96,7 +96,7 @@ def _last_where(bool_array):
 if __name__ == '__main__':
     import matplotlib.pyplot as plt
 
-    from stochastic_arrow.analysis.plotting import plot_full_history
+    from .plotting import plot_full_history
 
     (fig, axes) = plt.subplots(constrained_layout = True)
 

test/test_arrow.py

@@ -378,7 +378,7 @@ def check_gillespie_reference():
                 system()
     else:
         import matplotlib.pyplot as plt
-        from stochastic_arrow.analysis.plotting import plot_full_history
+        from .analysis.plotting import plot_full_history
 
         n_systems = len(systems)
 
@@ -412,9 +412,10 @@ def check_gillespie_reference():
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(
-        description='Run one of these tests')
+        description='Run the specified test or some default tests')
     parser.add_argument('--complexation', action='store_true')
-    parser.add_argument('--runs', type=int, default=1)
+    parser.add_argument('--runs', type=int, default=1,
+        help='an option for complexation')
     parser.add_argument('--plot', action='store_true')
     parser.add_argument('--obsidian', action='store_true')
     parser.add_argument('--memory', action='store_true')