Docs: Fix commands given in the examples (#11)

.github/workflows/run-tox.yml

@@ -30,13 +30,8 @@ jobs:
     - name: Get current month
       id: date
       run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
-    - name: Cache APT Packages
-      # This action should only be used when you need extra system packages
-      uses: awalsh128/cache-apt-pkgs-action@latest
-      with:
-        packages: graphviz poppler-utils
-        version: 1.0
-        execute_install_scripts: true
+    - name: Install APT Packages
+      run: sudo apt-get install graphviz poppler-utils imagemagick
     - name: Cache tox and precommit environments
       uses: actions/cache@v4
       with:

README.rst

@@ -27,14 +27,14 @@ The usual command is the following:
 
 .. code::
 
-    synthesis_workflow <workflow>
+    synthesis-workflow <workflow>
 
 You can get help and complete parameter description with the following commands:
 
 .. code::
 
-    synthesis_workflow --help
-    synthesis_workflow <workflow> --help
+    synthesis-workflow --help
+    synthesis-workflow <workflow> --help
 
 You can also run a complete ``luigi`` command in order to fine-control task parameters:
 
@@ -46,7 +46,7 @@ You can also run a complete ``luigi`` command in order to fine-control task para
 
 .. note::
 
-	The ``synthesis_workflow`` command (or the complete ``luigi`` command) must be
+	The ``synthesis-workflow`` command (or the complete ``luigi`` command) must be
 	executed from a directory containing a ``luigi.cfg`` file.
 	A simple example of such file is given in the ``examples`` directory.
 
@@ -57,13 +57,13 @@ The usual command is the following:
 
 .. code::
 
-    morph_validation -t <path to reference data> -r <path to test data> -o <output path> -c <YAML config file> --bio-compare
+    morph-validation -t <path to reference data> -r <path to test data> -o <output path> -c <YAML config file> --bio-compare
 
 You can get help and complete parameter description with the following command:
 
 .. code::
 
-    morph_validation --help
+    morph-validation --help
 
 Funding & Acknowledgment
 ~~~~~~~~~~~~~~~~~~~~~~~~

requirements/test.pip

@@ -9,4 +9,5 @@ pytest-xdist>=3.0.2
 
 # Pin versions for tests
 matplotlib==3.6.*
+pynrrd==0.4.3
 seaborn==0.12.*

src/morphval/cli.py

@@ -4,13 +4,19 @@
 
 import pkg_resources
 
+import morphval
 from morphval import config
 from morphval.validation_main import Validation
 
 
 def get_parser():
     """Return the argument parser."""
     parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--version",
+        action="version",
+        version=f"%(prog)s, version {morphval.__version__}",
+    )
     parser.add_argument(
         "-t", "--test-dir", required=True, help="full path to directory with test data"
     )

tests/data/in_small_O1/out/synthesis/apical_points.yaml

@@ -2,49 +2,49 @@
 216363698b529b4a97b750923ceb3ffd: null
 4462ebfc5f915ef09cfbac6e7687a66e: null
 48f165d57b00c7f4781ef86f5c8cc1ab:
-- -14.394819259643555
-- 194.89781188964844
-- 9.01955795288086
+- -14.394821166992188
+- 194.8978271484375
+- 9.019556999206543
 4dad2986ce8349606a06e9ab85a0bcc1:
-- -1.07305908203125
+- -1.0730547904968262
 - 195.03805541992188
-- -7.569953918457031
+- -7.569961071014404
 5bc8fbbcbde5c0994164d8399f767c45: null
 6018366cf658f7a75ed34fe53a096533: null
 6513270e269e0d37f2a74de452e6b438: null
 72e63ac7a95383221f70d5dc2e675fc7:
-- 4.626476764678955
-- 194.84230041503906
-- 20.284626007080078
+- 4.6264824867248535
+- 194.84231567382812
+- 20.28464126586914
 7b89296c6dcbac5008577eb1924770d3:
-- -8.819189071655273
-- 194.1275177001953
-- -14.387084007263184
+- -8.819184303283691
+- 194.12750244140625
+- -14.38708782196045
 8575062102fbcd4f357fbc5af71a1bfc:
-- -1.843111515045166
+- -1.8431235551834106
 - 195.61419677734375
-- 12.465193748474121
+- 12.46518611907959
 87751d4ca8501e2c44dcda6a797d76de:
-- -3.984039545059204
+- -3.9840335845947266
 - 197.0111541748047
-- -6.497995376586914
+- -6.498000144958496
 b8a1abcd1a6916c74da4f9fc3c6da5d7: null
 c15521b1b3dca50a9daa37e51b591d75:
-- -0.25705447793006897
-- 199.17787170410156
-- 11.141695022583008
+- -0.2570788562297821
+- 199.17788696289062
+- 11.141693115234375
 cd613e30d8f16adf91b7584a2265b1f5: null
 d95bafc8f2a4d27bdcf4bb99f4bea973: null
 db5b5fab8f4d3e27dda1494c73cf256d:
 - 26.932884216308594
-- 195.74429321289062
-- -1.293025255203247
+- 195.74427795410156
+- -1.2930362224578857
 e3e70682c2094cac629f6fbed82c07cd: null
 e539a78bc8eff3460b12ae6ead581e57:
-- 9.035844802856445
-- 195.72015380859375
-- 7.5418572425842285
+- 9.035848617553711
+- 195.7201690673828
+- 7.5418620109558105
 e8d79f49af6d114c4a6f188a424e617b:
-- 21.528072357177734
+- 21.5280704498291
 - 197.24026489257812
-- 9.389350891113281
+- 9.38935661315918

tests/test_O1_workflow.py

@@ -50,6 +50,9 @@ def test_ValidateSynthesis(small_O1_working_directory, data_dir):
                 "tolerance": 2e-3,
                 "absolute_tolerance": 1e-15,
             },
+            "synthesis/apical_points.yaml": {
+                "tolerance": 1e-3,
+            },
             "validation/morphology_validation_reports/validation_results.json": {
                 "tolerance": 2e-3,
                 "absolute_tolerance": 1e-12,

tests/test_cli.py

@@ -40,9 +40,17 @@ def test_dependency_graph(self, vacuum_working_directory):
         assert (root_dir / "dependency_graph.png").exists()
 
 
-def test_entry_point(script_runner):
-    """Test the entry point."""
+def test_entry_point_synthesis_workflow(script_runner):
+    """Test the entry point of synthesis-workflow."""
     ret = script_runner.run("synthesis-workflow", "--version")
     assert ret.success
     assert ret.stdout.startswith("synthesis-workflow, version ")
     assert ret.stderr == ""
+
+
+def test_entry_point_morph_validation(script_runner):
+    """Test the entry point of MorphVal."""
+    ret = script_runner.run("morph-validation", "--version")
+    assert ret.success
+    assert ret.stdout.startswith("morph-validation, version ")
+    assert ret.stderr == ""