Merge branch 'master' into fix-build_models_mva

cta-observatory · Mar 30, 2021 · 9198cec · 9198cec
2 parents 4a16c42 + 0dc958c
commit 9198cec
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diff --git a/docs/contribute/beforepushing.rst b/docs/contribute/beforepushing.rst
@@ -35,8 +35,27 @@ You will have to fix any warning that appears during documentation building,
 because the documentation also runs on `readthedocs <https://readthedocs.org/>`__
 with an option to treat warnings as errors.
 
+Testing
+-------
+
+All testing code is called by issuing the ``pytest`` command.
+
+This command can be called from any place within the cloned repository and it
+will always run from the root directory of the project.
+
+For debugging purposes you can add the ``-s`` option which will allow to 
+visualise any ``print`` statement within the test module(s).
+
+Testing is automatically triggered by the CI every time a new
+pull-request is pushed to the repository, and its correct
+execution is one of the mandatory condition for merging.
+
 Unit tests
-----------
+^^^^^^^^^^
+
+You can follow 
+`these guidelines <https://cta-observatory.github.io/ctapipe/development/code-guidelines.html#unit-tests>`__
+to understand what a unit-test is supposed to do.
 
 .. note::
   This is a maintenance activity which has being long overdue and we need
@@ -65,6 +84,12 @@ Same for *pyirf*.
 Integration tests
 ^^^^^^^^^^^^^^^^^
 
+These are neither unit-tests nor benchmarks, but rather functions that tests
+whole functionalities and not just single API functions.
+
+In the case of the pipeline, such functionalities are the scripts/tools
+that make up its workflow.
+
 .. note::
   For more information on how to contribute to this effort check
   `this issue <https://github.com/cta-observatory/protopipe/issues/70>`__.
@@ -79,13 +104,7 @@ CTAN and CTAS produced with the following Corsika settings,
 - protons, ``NSHOW=10 ESLOPE=-2.0 EMIN=100 EMAX=200 NSCAT=1 CSCAT=200 VIEWCONE=3``
 - electrons, ``NSHOW=10 ESLOPE=-2.0 EMIN=10 EMAX=20 NSCAT=1 CSCAT=200 VIEWCONE=3``
 
-in the same proportions as a standard full-scale analysis.
-
-The pipeline integration testing can be executed directly from the main folder 
-of *protopipe* by launching ``pytest``.
-It is also automatically triggered by the CI every time a new
-pull-request is pushed to the repository, and its correct
-execution is a mandatory condition for merging.
+and it is analysed using the same workflow as in a standard full-scale analysis.
 
 Benchmarks
 ----------

diff --git a/protopipe/scripts/tests/test_pipeline.py b/protopipe/scripts/tests/test_pipeline.py
@@ -48,15 +48,23 @@ def test_GET_GAMMAS_FOR_ENERGY_MODEL_WITH_IMAGES(test_case, pipeline_testdir):
 
     outpath = pipeline_testdir / f"test_training_withImages_{test_case}.h5"
 
-    exit_status = system(
-        f"python {data_training.__file__}\
-        --config_file {input_data[test_case]['config']}\
-        -o {outpath}\
-        --save_images\
-        -i {input_data[test_case]['gamma1'].parent}\
-        -f {input_data[test_case]['gamma1'].name}"
+    command = f"python {data_training.__file__}\
+    --config_file {input_data[test_case]['config']}\
+    -o {outpath}\
+    --save_images\
+    -i {input_data[test_case]['gamma1'].parent}\
+    -f {input_data[test_case]['gamma1'].name}"
+
+    print(  # only with "pytest -s"
+        f'''
+        /n You can reproduce this test by running the following command,
+
+        {command}
+        '''
     )
 
+    exit_status = system(command)
+
     # check that the script ends without crashing
     assert exit_status == 0
 
@@ -73,14 +81,22 @@ def test_GET_GAMMAS_FOR_ENERGY_MODEL(test_case, pipeline_testdir):
 
     outpath = pipeline_testdir / f"test_gamma1_noImages_{test_case}.h5"
 
-    exit_status = system(
-        f"python {data_training.__file__}\
-        --config_file {input_data[test_case]['config']}\
-        -o {outpath}\
-        -i {input_data[test_case]['gamma1'].parent}\
-        -f {input_data[test_case]['gamma1'].name}"
+    command = f"python {data_training.__file__}\
+    --config_file {input_data[test_case]['config']}\
+    -o {outpath}\
+    -i {input_data[test_case]['gamma1'].parent}\
+    -f {input_data[test_case]['gamma1'].name}"
+
+    print(  # only with "pytest -s"
+        f'''
+        /n You can reproduce this test by running the following command,
+
+        {command}
+        '''
     )
 
+    exit_status = system(command)
+
     # check that the script ends without crashing
     assert exit_status == 0
 
@@ -103,13 +119,21 @@ def test_BUILD_ENERGY_MODEL_AdaBoost_DecisionTreeRegressor(test_case, pipeline_t
 
     config = resource_filename("protopipe", "scripts/tests/test_regressor.yaml")
 
-    exit_status = system(
-        f"python {build_model.__file__}\
-        --config_file {config}\
-        --infile_signal {infile}\
-        --outdir {outdir}\
-        --cameras_from_file"
+    command = f"python {build_model.__file__}\
+    --config_file {config}\
+    --infile_signal {infile}\
+    --outdir {outdir}\
+    --cameras_from_file"
+
+    print(  # only with "pytest -s"
+        f'''
+        /n You can reproduce this test by running the following command,
+
+        {command}
+        '''
     )
+
+    exit_status = system(command)
     assert exit_status == 0
 
 
@@ -124,16 +148,24 @@ def test_GET_GAMMAS_FOR_CLASSIFICATION_MODEL(test_case, pipeline_testdir):
     modelpath = pipeline_testdir / f"energy_model_{test_case}"
     outpath = pipeline_testdir / f"test_gamma2_noImages_{test_case}.h5"
 
-    exit_status = system(
-        f"python {data_training.__file__}\
-        --config_file {input_data[test_case]['config']}\
-        -o {outpath}\
-        -i {input_data[test_case]['gamma2'].parent}\
-        -f {input_data[test_case]['gamma2'].name}\
-        --estimate_energy True\
-        --regressor_dir {modelpath}"
+    command = f"python {data_training.__file__}\
+    --config_file {input_data[test_case]['config']}\
+    -o {outpath}\
+    -i {input_data[test_case]['gamma2'].parent}\
+    -f {input_data[test_case]['gamma2'].name}\
+    --estimate_energy True\
+    --regressor_dir {modelpath}"
+
+    print(  # only with "pytest -s"
+        f'''
+        /n You can reproduce this test by running the following command,
+
+        {command}
+        '''
     )
 
+    exit_status = system(command)
+
     # check that the script ends without crashing
     assert exit_status == 0
 
@@ -153,17 +185,25 @@ def test_GET_PROTONS_FOR_CLASSIFICATION_MODEL(test_case, pipeline_testdir):
     modelpath = pipeline_testdir / f"energy_model_{test_case}"
     outpath = pipeline_testdir / f"test_proton1_noImages_{test_case}.h5"
 
-    exit_status = system(
-        f"python {data_training.__file__}\
-        --config_file {input_data[test_case]['config']}\
-        -o {outpath}\
-        -m 10\
-        -i {input_data[test_case]['proton1'].parent}\
-        -f {input_data[test_case]['proton1'].name}\
-        --estimate_energy True\
-        --regressor_dir {modelpath}"
+    command = f"python {data_training.__file__}\
+    --config_file {input_data[test_case]['config']}\
+    -o {outpath}\
+    -m 10\
+    -i {input_data[test_case]['proton1'].parent}\
+    -f {input_data[test_case]['proton1'].name}\
+    --estimate_energy True\
+    --regressor_dir {modelpath}"
+
+    print(  # only with "pytest -s"
+        f'''
+        /n You can reproduce this test by running the following command,
+
+        {command}
+        '''
     )
 
+    exit_status = system(command)
+
     # check that the script ends without crashing
     assert exit_status == 0
 
@@ -187,12 +227,20 @@ def test_BUILD_CLASSIFICATION_MODEL_RandomForest(test_case, pipeline_testdir):
 
     config = resource_filename("protopipe", "scripts/tests/test_regressor.yaml")
 
-    exit_status = system(
-        f"python {build_model.__file__}\
-        --config_file {config}\
-        --infile_signal {infile_signal}\
-        --infile_background {infile_background}\
-        --outdir {outdir}\
-        --cameras_from_file"
+    command = f"python {build_model.__file__}\
+    --config_file {config}\
+    --infile_signal {infile_signal}\
+    --infile_background {infile_background}\
+    --outdir {outdir}\
+    --cameras_from_file"
+
+    print(  # only with "pytest -s"
+        f'''
+        /n You can reproduce this test by running the following command,
+
+        {command}
+        '''
     )
+
+    exit_status = system(command)
     assert exit_status == 0