diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 24b12ee57447094bec3d20ea77940cf6c7091e56..6a5606c681ea6fd39476929d9034592d65fdd4d8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -65,6 +65,25 @@ check-clang-format:
- if: $CI_COMMIT_BRANCH
allow_failure: true
+check-python-quality:
+ image: corsika/devel:u-22.04
+ stage: quality
+ tags:
+ - corsika
+ script:
+ - cd ${CI_PROJECT_DIR}/python # change into the Python directory
+ - pip3 install --user -e '.[test]' # install the package + test deps
+ - python3 --version
+ - python3 -m black -t py37 --check corsika tests
+ - python3 -m flake8 -v corsika tests
+ - python3 -m isort --atomic --check-only corsika tests
+ - python3 -m mypy corsika
+ rules:
+ - if: $CI_MERGE_REQUEST_ID
+ - if: $CI_COMMIT_TAG
+ - if: $CI_COMMIT_BRANCH
+ allow_failure: true
+
### CodeQuality tool ####
#include:
# - template: Code-Quality.gitlab-ci.yml
@@ -76,7 +95,8 @@ check-clang-format:
# when: never
# - if: '$CI_PIPELINE_SOURCE == "merge_request_event"' # Run code quality job in merge request pipelines
# - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH' # Run code quality job in pipelines on the master branch (but not in other branch pipelines)
-# - if: '$CI_COMMIT_TAG' # Run code quality job in pipelines for tags
+# - if: '$CI_COMMIT_TAG'
+
####### CONFIG ##############
@@ -163,13 +183,11 @@ build_test-clang-14:
artifacts: false
-
####### BUILD-TEST-EXAMPLE (only non-Draft/non-WIP) ##############
##########################################################
# generic example template job
# normal pipeline for each commit
-# artefacts are needed as input for python jobs
.build_test_example:
stage: build_test_example
tags:
@@ -204,8 +222,10 @@ build_test-clang-14:
junit:
- ${CI_PROJECT_DIR}/build/test_outputs/junit*.xml
paths:
- - ${CI_PROJECT_DIR}/build/build_examples/example_outputs
+ - ${CI_PROJECT_DIR}/build/build_examples/example_outputs #python tests need this
- ${CI_PROJECT_DIR}/build/test_outputs/junit*.xml
+ - ${CI_PROJECT_DIR}/build/CMakeCache.txt #python tests need this
+ - ${CI_PROJECT_DIR}/build/bin #python tests need this
# build_test_example for gcc
build_test_example-u-22_04:
@@ -225,9 +245,6 @@ build_test_example-clang-14:
artifacts: false
-
-
-
####### OPTIONAL ##############
##########################################################
@@ -288,7 +305,7 @@ release-full-clang-14:
artifacts: false
-
+###### COVERAGE ##########
##########################################################
# the coverage generation should either run when manually requested, OR always on the master
@@ -330,7 +347,7 @@ coverage:
-
+###### SANITY ##########
##########################################################
sanity:
@@ -378,19 +395,17 @@ sanity:
- python3 -m black -t py37 corsika tests
- python3 -m flake8 corsika tests
- python3 -m pytest --cov=corsika tests
- - cd ${CI_PROJECT_DIR} # reset the directory
coverage: '/^TOTAL\s*\d+\s*\d+\s*(.*\%)/'
-# the default Python version Ubuntu 22.04 is Python3.8
-python-3.8:
+python-tests:
extends: .python
- image: corsika/analysis:python-3.9.5
+ image: corsika/devel:u-22.04
needs:
- job: build_test_example-u-22_04
artifacts: true
artifacts:
when: always
- expire_in: 3 month
+ expire_in: 1 month
paths:
- - ${CI_PROJECT_DIR}/Python/python-test.log
- allow_failure: true
+ - ${CI_PROJECT_DIR}/python/python-test.log
+ allow_failure: false
diff --git a/modules/data b/modules/data
index 331c0aad7c6c17fe456c4a80f8b2575ef341ce90..aa320e6a1203436766a374878e83e3685eae78e4 160000
--- a/modules/data
+++ b/modules/data
@@ -1 +1 @@
-Subproject commit 331c0aad7c6c17fe456c4a80f8b2575ef341ce90
+Subproject commit aa320e6a1203436766a374878e83e3685eae78e4
diff --git a/python/corsika/io/__init__.py b/python/corsika/io/__init__.py
index 296572d6dee46a4b95a61b8ef18c549f120a1205..7c8d197d724ed4a45e6f51b2a6ae31e8c064ee27 100644
--- a/python/corsika/io/__init__.py
+++ b/python/corsika/io/__init__.py
@@ -8,8 +8,7 @@
the license.
"""
-from .hist import read_hist
from .library import Library
# all exported objects
-__all__ = ["read_hist", "Library"]
+__all__ = ["Library"]
diff --git a/python/corsika/io/converters/__init__.py b/python/corsika/io/converters/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..034aa1d4643e1cf19fe728e21790c4862b0626e3
--- /dev/null
+++ b/python/corsika/io/converters/__init__.py
@@ -0,0 +1,9 @@
+"""
+ The 'io' module provides for reading CORSIKA8 output files.
+
+ (c) Copyright 2018 CORSIKA Project, corsika-project@lists.kit.edu
+
+ This software is distributed under the terms of the GNU General Public
+ Licence version 3 (GPL Version 3). See file LICENSE for a full version of
+ the license.
+"""
diff --git a/python/corsika/io/converters/arrow_to_numpy.py b/python/corsika/io/converters/arrow_to_numpy.py
new file mode 100644
index 0000000000000000000000000000000000000000..dddb34b8a740633755d38e055dd2c5e507a8df3d
--- /dev/null
+++ b/python/corsika/io/converters/arrow_to_numpy.py
@@ -0,0 +1,59 @@
+"""
+ Converter for the pyarrow data types to numpy ones
+
+ (c) Copyright 2020 CORSIKA Project, corsika-project@lists.kit.edu
+
+ This software is distributed under the terms of the GNU General Public
+ Licence version 3 (GPL Version 3). See file LICENSE for a full version of
+ the license.
+"""
+
+import numpy as np
+import pyarrow
+
+
+def convert_to_numpy(pyarrow_table: pyarrow.lib.Table) -> np.ndarray:
+ """
+ Converts a pyarrow Table to a numpy structured array
+
+ Parameters
+ ----------
+ pyarrow_table: pyarrow.lib.Table
+ PyArrow table of any dimension to be sliced
+
+ Returns
+ -------
+ np.ndarray:
+ converted table with the same column labels and data types
+
+ """
+
+ # Type conversions for pyarrow data types to numpy ones
+ # https://arrow.apache.org/docs/python/data.html
+ # https://numpy.org/doc/stable/reference/arrays.dtypes.html#arrays-dtypes-constructing
+ type_conversions = {
+ pyarrow.int8(): "int8",
+ pyarrow.int16(): "int16",
+ pyarrow.int32(): "int32",
+ pyarrow.int64(): "int64",
+ pyarrow.uint8(): "uint8",
+ pyarrow.uint16(): "uint16",
+ pyarrow.uint32(): "uint32",
+ pyarrow.uint64(): "uint64",
+ pyarrow.float16(): "float16",
+ pyarrow.float32(): "float32",
+ pyarrow.float64(): "float64",
+ }
+
+ # Perform type conversion of all fields
+ column_types = [
+ type_conversions[pyarrow_table[key].type] for key in pyarrow_table.column_names
+ ]
+ dtypes = [(x, y) for (x, y) in zip(pyarrow_table.column_names, column_types)]
+
+ # Make an empty array and then fill the values
+ np_table = np.zeros(pyarrow_table.num_rows, dtype=dtypes)
+ for key in pyarrow_table.column_names:
+ np_table[key] = pyarrow_table[key]
+
+ return np_table
diff --git a/python/corsika/io/hist.py b/python/corsika/io/hist.py
deleted file mode 100644
index afa1418418f636eac2f00d77c58d58b5808c4875..0000000000000000000000000000000000000000
--- a/python/corsika/io/hist.py
+++ /dev/null
@@ -1,76 +0,0 @@
-"""
- This file supports reading boost_histograms from CORSIKA8.
-
- (c) Copyright 2018 CORSIKA Project, corsika-project@lists.kit.edu
-
- This software is distributed under the terms of the GNU General Public
- Licence version 3 (GPL Version 3). See file LICENSE for a full version of
- the license.
-"""
-
-import boost_histogram as bh
-import numpy as np
-
-
-def read_hist(filename: str) -> bh.Histogram:
- """
- Read a histogram produced with CORSIKA8's `SaveBoostHistogram()` function.
-
- Parameters
- ----------
- filename: str
- The filename of the .npy file containing the histogram.
-
- Returns
- -------
- hist: bh.Histogram
- An initialized bh.Histogram instance.
-
- Throws
- ------
- ValueError:
- If the histogram type is not supported.
- """
-
- # load the filenames
- d = np.load(filename)
-
- # extract the axis and overflows information
- axistypes = d["axistypes"].view("c")
- overflow = d["overflow"]
- underflow = d["underflow"]
-
- # this is where we store the axes that we extract from the file.
- axes = []
-
- # we now loop over the axes
- for i, (at, has_overflow, has_underflow) in enumerate(
- zip(axistypes, overflow, underflow)
- ):
-
- # continuous axis
- if at == b"c":
- axes.append(
- bh.axis.Variable(
- d[f"binedges_{i}"], overflow=has_overflow, underflow=has_underflow
- )
- )
- # discrete axis
- elif at == b"d":
- axes.append(bh.axis.IntCategory(d[f"bins_{i}"], growth=(not has_overflow)))
-
- # and unknown histogram type
- else:
- raise ValueError(f"'{at}' is not a valid C8 histogram axistype.")
-
- # create the histogram and fill it in
- data = d["data"]
- if data.dtype.names: # structured array -> mean and variance
- h = bh.Histogram(*axes, storage=bh.storage.Weight())
- h.view(flow=True)[:]['value'] = data['mean']
- h.view(flow=True)[:]['variance'] = data['variance']
- else:
- h = bh.Histogram(*axes)
- h.view(flow=True)[:] = data
-
- return h
diff --git a/python/corsika/io/library.py b/python/corsika/io/library.py
index 1c2ff38e025e9a728bde4b9c7a5e0cad5982deb1..486181e5a7422e811721370955383385e8165526 100644
--- a/python/corsika/io/library.py
+++ b/python/corsika/io/library.py
@@ -58,13 +58,6 @@ class Library(object):
"""
return list(self.__outputs.keys())
- @property
- def modules(self) -> Dict[str, str]:
- """
- Return the list of registered outputs.
- """
- pass
-
def get(self, name: str) -> Optional[outputs.Output]:
"""
Return the output with a given name.
@@ -73,7 +66,7 @@ class Library(object):
return self.__outputs[name]
else:
msg = f"Output with name '{name}' not available in this library."
- logging.getLogger("corsika").warn(msg)
+ logging.getLogger("corsika").warning(msg)
return None
@staticmethod
@@ -181,7 +174,6 @@ class Library(object):
# loop over the subdirectories
for subdir in dirs:
-
# read the config file for this output
config = Library.load_config(op.join(path, subdir))
@@ -197,13 +189,12 @@ class Library(object):
f"'{subdir}' does not contain a valid config."
"Missing 'type' or 'name' keyword."
)
- logging.getLogger("corsika").warn(msg)
+ logging.getLogger("corsika").warning(msg)
continue # skip to the next output, don't error
# we now have a valid component type, get the corresponding
# type from the proccesses subdirectory
try:
-
# instantiate the output and store it in our dict
component = getattr(outputs, out_type)(op.join(path, subdir))
@@ -213,7 +204,7 @@ class Library(object):
f"'{name}' encountered an error while reading. "
"This process will be not be loaded."
)
- logging.getLogger("corsika").warn(msg)
+ logging.getLogger("corsika").warning(msg)
else:
components[name] = component
@@ -222,8 +213,8 @@ class Library(object):
f"Unable to instantiate an instance of '{out_type}' "
f"for a process called '{name}'"
)
- logging.getLogger("corsika").warn(msg)
- logging.getLogger("corsika").warn(e)
+ logging.getLogger("corsika").warning(msg)
+ logging.getLogger("corsika").warning(e)
continue # skip to the next output, don't error
# and we are done building - return the constructed outputs
diff --git a/python/corsika/io/outputs/__init__.py b/python/corsika/io/outputs/__init__.py
index 81ecd786e25aef93a2b84cea6e6419b133078518..54731dd42d775073d5d15e3d21e914706b5a7755 100644
--- a/python/corsika/io/outputs/__init__.py
+++ b/python/corsika/io/outputs/__init__.py
@@ -7,16 +7,15 @@
the license.
"""
-from .observation_plane import ObservationPlane
-from .track_writer import TrackWriter
-from .longitudinal_profile import LongitudinalProfile
from .bethe_bloch import BetheBlochPDG
-from .particle_cut import ParticleCut
from .energy_loss import EnergyLoss
+from .longitudinal_profile import LongitudinalProfile
+from .observation_plane import ObservationPlane
from .output import Output
+from .particle_cut import ParticleCut
+from .primary import Particle, PrimaryParticle
from .radio_process import RadioProcess
from .track_writer import TrackWriter
-from .primary import PrimaryParticle, Particle
__all__ = [
"Output",
@@ -25,7 +24,8 @@ __all__ = [
"LongitudinalProfile",
"BetheBlochPDG",
"ParticleCut",
- "EnergyLoss" "RadioProcess",
+ "EnergyLoss",
+ "RadioProcess",
"PrimaryParticle",
"Particle",
]
diff --git a/python/corsika/io/outputs/bethe_bloch.py b/python/corsika/io/outputs/bethe_bloch.py
index b12d29036de5553d139c9cee0f7c8120f4fd4f7b..42e65943c4a2ac5e82752534a996e2d018edf089 100644
--- a/python/corsika/io/outputs/bethe_bloch.py
+++ b/python/corsika/io/outputs/bethe_bloch.py
@@ -13,6 +13,7 @@ from typing import Any
import pyarrow.parquet as pq
+from ..converters import arrow_to_numpy
from .output import Output
@@ -72,11 +73,13 @@ class BetheBlochPDG(Output):
return self.__data
elif dtype == "pandas":
return self.__data.to_pandas()
+ elif dtype == "numpy":
+ return arrow_to_numpy.convert_to_numpy(self.__data)
else:
raise ValueError(
(
f"Unknown format '{dtype}' for BetheBlochPDG. "
- "We currently only support ['arrow', 'pandas']."
+ "We currently only support ['arrow', 'pandas', 'numpy']."
)
)
diff --git a/python/corsika/io/outputs/energy_loss.py b/python/corsika/io/outputs/energy_loss.py
index 76846dd2c83d497f68aaf38d3f3e4823b91ee8a3..82b98b0fe2d02530b10231890341359161d4c418 100644
--- a/python/corsika/io/outputs/energy_loss.py
+++ b/python/corsika/io/outputs/energy_loss.py
@@ -13,6 +13,7 @@ from typing import Any
import pyarrow.parquet as pq
+from ..converters import arrow_to_numpy
from .output import Output
@@ -72,11 +73,13 @@ class EnergyLoss(Output):
return self.__data
elif dtype == "pandas":
return self.__data.to_pandas()
+ elif dtype == "numpy":
+ return arrow_to_numpy.convert_to_numpy(self.__data)
else:
raise ValueError(
(
f"Unknown format '{dtype}' for EnergyLoss. "
- "We currently only support ['arrow', 'pandas']."
+ "We currently only support ['arrow', 'pandas', 'numpy']."
)
)
@@ -84,4 +87,4 @@ class EnergyLoss(Output):
"""
Return a string representation of this class.
"""
- return f"EnergyLess('{self.config['name']}')"
+ return f"EnergyLoss('{self.config['name']}')"
diff --git a/python/corsika/io/outputs/longitudinal_profile.py b/python/corsika/io/outputs/longitudinal_profile.py
index 00000567d827a12e94c198a0ef1102b1c010a74e..f4126c05a30d2460bdb3c1e1534a01b57a38d8fb 100644
--- a/python/corsika/io/outputs/longitudinal_profile.py
+++ b/python/corsika/io/outputs/longitudinal_profile.py
@@ -13,6 +13,7 @@ from typing import Any
import pyarrow.parquet as pq
+from ..converters import arrow_to_numpy
from .output import Output
@@ -72,11 +73,13 @@ class LongitudinalProfile(Output):
return self.__data
elif dtype == "pandas":
return self.__data.to_pandas()
+ elif dtype == "numpy":
+ return arrow_to_numpy.convert_to_numpy(self.__data)
else:
raise ValueError(
(
f"Unknown format '{dtype}' for LongitudinalProfile. "
- "We currently only support ['arrow', 'pandas']."
+ "We currently only support ['arrow', 'pandas', 'numpy']."
)
)
diff --git a/python/corsika/io/outputs/observation_plane.py b/python/corsika/io/outputs/observation_plane.py
index 271d145b4f076f1c7d747d6cc5e05b4a183d3655..d98c31646d73dad382e23e17070a0aa4b27df0c2 100644
--- a/python/corsika/io/outputs/observation_plane.py
+++ b/python/corsika/io/outputs/observation_plane.py
@@ -13,6 +13,7 @@ from typing import Any
import pyarrow.parquet as pq
+from ..converters import arrow_to_numpy
from .output import Output
@@ -72,11 +73,13 @@ class ObservationPlane(Output):
return self.__data
elif dtype == "pandas":
return self.__data.to_pandas()
+ elif dtype == "numpy":
+ return arrow_to_numpy.convert_to_numpy(self.__data)
else:
raise ValueError(
(
f"Unknown format '{dtype}' for ObservationPlane. "
- "We currently only support ['arrow', 'pandas']."
+ "We currently only support ['arrow', 'pandas', 'numpy']."
)
)
diff --git a/python/corsika/io/outputs/particle_cut.py b/python/corsika/io/outputs/particle_cut.py
index a55b5fe718cf788fdba051dfa891e77b2d75ede7..d797923374febd1098126dc04f9d9541e886285d 100644
--- a/python/corsika/io/outputs/particle_cut.py
+++ b/python/corsika/io/outputs/particle_cut.py
@@ -13,6 +13,7 @@ from typing import Any
import pyarrow.parquet as pq
+from ..converters import arrow_to_numpy
from .output import Output
@@ -72,11 +73,13 @@ class ParticleCut(Output):
return self.__data
elif dtype == "pandas":
return self.__data.to_pandas()
+ elif dtype == "numpy":
+ return arrow_to_numpy.convert_to_numpy(self.__data)
else:
raise ValueError(
(
f"Unknown format '{dtype}' for ParticleCut. "
- "We currently only support ['arrow', 'pandas']."
+ "We currently only support ['arrow', 'pandas', 'numpy']."
)
)
diff --git a/python/corsika/io/outputs/radio_process.py b/python/corsika/io/outputs/radio_process.py
index 62ceb3f1905ccaf938b1a6f8fba799e655eb7750..152b6d6347a5803481bb519f016c9f10deeebc1c 100644
--- a/python/corsika/io/outputs/radio_process.py
+++ b/python/corsika/io/outputs/radio_process.py
@@ -10,8 +10,9 @@
import logging
import os.path as op
from typing import Any
-import pyarrow.parquet as pq
+
import pandas as pd
+import pyarrow.parquet as pq
from .output import Output
@@ -47,8 +48,7 @@ class RadioProcess(Output):
f"An error occured loading a RadioProcess: {e}"
)
-
- def load_data(self, path: str):
+ def load_data(self, path: str) -> dict:
"""
Load the data associated with this radio process.
@@ -59,7 +59,7 @@ class RadioProcess(Output):
"""
data = pq.read_table(op.join(path, "antennas.parquet"))
- nshowers = data.to_pandas()['shower'].iloc[-1] + 1
+ nshowers = data.to_pandas()["shower"].iloc[-1] + 1
antennas = list(self.config["antennas"].keys())
# check that we got some events
@@ -78,13 +78,17 @@ class RadioProcess(Output):
# loop over each of the antennas
for name in antennas:
sampling_period = self.config["antennas"][name]["number of bins"]
- antenna_data = data[ant_nr*sampling_period:(ant_nr+1)*sampling_period].to_pandas()
+ start = ant_nr * sampling_period
+ stop = (ant_nr + 1) * sampling_period
+ antenna_data = data[start:stop].to_pandas()
times = antenna_data["Time"]
Ex = antenna_data["Ex"]
Ey = antenna_data["Ey"]
Ez = antenna_data["Ez"]
- dictionary[name] = pd.DataFrame({'time': times, 'Ex': Ex, 'Ey': Ey, 'Ez': Ez})
- ant_nr = ant_nr+ 1
+ dictionary[name] = pd.DataFrame(
+ {"time": times, "Ex": Ex, "Ey": Ey, "Ez": Ez}
+ )
+ ant_nr = ant_nr + 1
dataset[str(i)] = dictionary
@@ -126,14 +130,14 @@ class RadioProcess(Output):
)
)
- def get_antenna_list(self):
+ def get_antenna_list(self) -> list:
"""
Return a list with the names of the antennas of this RadioProcess.
"""
antennas = list(self.config["antennas"].keys())
return antennas
- def get_antennas(self):
+ def get_antennas(self) -> dict:
"""
Return a pandas dataframe with all the information for the antennas
of this RadioProcess. This information is shower number, antenna
@@ -150,13 +154,22 @@ class RadioProcess(Output):
nr_bins = self.config["antennas"][name]["number of bins"]
sampling_frequency = self.config["antennas"][name]["sampling frequency"]
location = self.config["antennas"][name]["location"]
- dictionary[name] = pd.DataFrame({'type': type, 'start time': start_time, 'duration': duration,
- 'number of bins': nr_bins, 'sampling frequency': sampling_frequency,
- 'x': [location[0]], 'y': [location[1]], 'z': [location[2]]})
+ dictionary[name] = pd.DataFrame(
+ {
+ "type": type,
+ "start time": start_time,
+ "duration": duration,
+ "number of bins": nr_bins,
+ "sampling frequency": sampling_frequency,
+ "x": [location[0]],
+ "y": [location[1]],
+ "z": [location[2]],
+ }
+ )
return dictionary
- def get_units(self):
+ def get_units(self) -> dict:
"""
Return the units of the antennas of this RadioProcess.
"""
diff --git a/python/corsika/io/outputs/track_writer.py b/python/corsika/io/outputs/track_writer.py
index 0859660d590182578e08ad4beaef5bb9a5c53498..7b4fd4f414d56f6716817ddb78c688806f5d9f56 100644
--- a/python/corsika/io/outputs/track_writer.py
+++ b/python/corsika/io/outputs/track_writer.py
@@ -13,6 +13,7 @@ from typing import Any
import pyarrow.parquet as pq
+from ..converters import arrow_to_numpy
from .output import Output
@@ -72,11 +73,13 @@ class TrackWriter(Output):
return self.__data
elif dtype == "pandas":
return self.__data.to_pandas()
+ elif dtype == "numpy":
+ return arrow_to_numpy.convert_to_numpy(self.__data)
else:
raise ValueError(
(
f"Unknown format '{dtype}' for TrackWriter. "
- "We currently only support ['arrow', 'pandas']."
+ "We currently only support ['arrow', 'pandas', 'numpy']."
)
)
diff --git a/python/setup.cfg b/python/setup.cfg
index 2c8d668ffdf9a3a8135dc52fc6e4c79b66c06e72..e0a574a473491369997c050a47a5fc51c9a9e570 100644
--- a/python/setup.cfg
+++ b/python/setup.cfg
@@ -67,3 +67,7 @@ ignore_missing_imports = True
# ignore missing types for pyarow
[mypy-pyarrow.*]
ignore_missing_imports = True
+
+# ignore missing types for pandas
+[mypy-pandas.*]
+ignore_missing_imports = True
diff --git a/python/setup.py b/python/setup.py
index c1460c9d6cb5f759b50abd609e31061ef0d1751b..20da6eaa249c572540bd66ba574a4995705d5578 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -32,7 +32,7 @@ setup(
keywords=["cosmic ray", "physics", "air shower", "simulation"],
packages=find_packages(),
python_requires=">=3.6, <4",
- install_requires=["numpy", "pyyaml", "pyarrow", "boost_histogram", "xarray"],
+ install_requires=["numpy", "pyyaml", "pyarrow", "pandas"],
extras_require={
"test": [
"pytest",
@@ -42,8 +42,9 @@ setup(
"coverage",
"pytest-cov",
"flake8",
+ "types-PyYAML",
+ "pandas-stubs",
],
- "pandas": ["pandas"],
},
scripts=[],
project_urls={"code": "https://gitlab.iap.kit.edu/AirShowerPhysics/corsika"},
diff --git a/python/tests/__init__.py b/python/tests/__init__.py
index c7d9b672b4c1bde7cc7725c619c0390a79e682c7..4e71ff9c93bb28bec001dad43656772ca9709fef 100644
--- a/python/tests/__init__.py
+++ b/python/tests/__init__.py
@@ -29,25 +29,34 @@ def find_build_directory() -> str:
If the build directory cannot be found or it is empty.
"""
- # check if we are running on Gitlab
- gitlab_build_dir = os.getenv("CI_BUILDS_DIR")
-
# if we are running on Gitlab
- if gitlab_build_dir is not None:
- build_dir = op.abspath(gitlab_build_dir)
+ is_on_CI = os.getenv("CI_PROJECT_DIR") is not None
+ if is_on_CI:
+ build_dir = op.abspath(op.join(os.getenv("CI_PROJECT_DIR"), "build"))
+
else: # otherwise, we are running locally
- build_dir = op.abspath(
- op.join(
- op.dirname(__file__),
- op.pardir,
- op.pardir,
- "build",
+ here = op.dirname(os.path.realpath(__file__))
+ for name in ["build", "corsika-build"]:
+ build_dir = op.realpath(
+ op.join(
+ here,
+ op.pardir,
+ op.pardir,
+ op.pardir,
+ "corsika-build",
+ )
)
- )
+ if op.isdir(build_dir):
+ break
# check that the build directory contains 'CMakeCache.txt'
if not op.exists(op.join(build_dir, "CMakeCache.txt")):
- raise RuntimeError("Python tests cannot find C8 build directory.")
+ msg = "Python tests cannot find C8 build dir.\n"
+ msg += f"Is on CI: {is_on_CI}\n"
+ msg += f"Path for CI: {os.getenv('CI_PROJECT_DIR')}\n"
+ msg += f"Checked in {build_dir}\n"
+ msg += f"Contents: {os.listdir(build_dir)}"
+ raise RuntimeError(msg)
return build_dir
diff --git a/python/tests/io/test_hist.py b/python/tests/io/test_hist.py
deleted file mode 100644
index 3bd11003ca663337f322ed9fea4a7f7559e75d03..0000000000000000000000000000000000000000
--- a/python/tests/io/test_hist.py
+++ /dev/null
@@ -1,70 +0,0 @@
-"""
- Tests for `corsika.io.hist`
-
- (c) Copyright 2018 CORSIKA Project, corsika-project@lists.kit.edu
-
- This software is distributed under the terms of the GNU General Public
- Licence version 3 (GPL Version 3). See file LICENSE for a full version of
- the license.
-"""
-import os
-import os.path as op
-import subprocess
-
-import corsika
-
-from .. import build_directory
-
-# the directory containing 'testSaveBoostHistogram'
-bindir = op.join(build_directory, "bin")
-
-
-def generate_hist() -> str:
- """
- Generate a test with `testSaveBoostHistogram`.
-
- Returns
- -------
- str
- The path to the generated histogram.
- bool
- If True, this file was regenerated.
- """
-
- # we construct the name of the bin
- bin = op.join(bindir, "testFramework")
-
- # check if a histogram already exists
- if op.exists(op.join(bin, "hist.npz")):
- return op.join(bin, "hist.npz"), False
- else:
- # run the program - this generates "hist.npz" in the CWD
- subprocess.call([bin, "saveHistogram"])
-
- return op.join(os.getcwd(), "hist.npz"), True
-
-
-def test_corsika_io() -> None:
- """
- Test I can corsika.io without a further import.
- """
- corsika.io.read_hist
-
-
-def test_corsika_read_hist() -> None:
- """
- Check that I can read in the test histograms with `read_hist`.
- """
-
- # generate a test histogram
- filename, delete = generate_hist()
-
- # and try and read in a histogram
- h = corsika.io.read_hist(filename)
-
- # and delete the generated histogram
- if delete:
- os.remove(filename)
-
- # and check that it isn't empty
- assert not h.empty()
diff --git a/python/tests/io/test_library.py b/python/tests/io/test_library.py
new file mode 100644
index 0000000000000000000000000000000000000000..d029c59e33f889724a47806a40b7cfdd7fc50339
--- /dev/null
+++ b/python/tests/io/test_library.py
@@ -0,0 +1,72 @@
+"""
+ Tests for `corsika.io.outputs.energy_loss`
+
+ (c) Copyright 2018 CORSIKA Project, corsika-project@lists.kit.edu
+
+ This software is distributed under the terms of the GNU General Public
+ Licence version 3 (GPL Version 3). See file LICENSE for a full version of
+ the license.
+"""
+import os
+import os.path as op
+import subprocess
+
+import pytest
+
+from corsika.io import Library
+
+from .. import build_directory
+
+bindir = op.join(build_directory, "bin")
+
+
+def generate_data() -> str:
+ """
+ Generate a test with `testOutput`.
+
+ Returns
+ -------
+ str
+ The path to the generated data.
+ """
+
+ # Expected output directory that is made from the testOutput binary
+ output_dir = op.join(os.getcwd(), "out_test/check")
+
+ if not op.exists(output_dir): # only make if not already run
+ binary = op.join(bindir, "testOutput")
+
+ # ensure that the binary exists (not trivial on the CI)
+ if not op.exists(binary):
+ msg = f"Could not find testOutput binary at {binary}\n"
+ msg += f"Binary dir contains {os.listdir(bindir)}"
+ raise RuntimeError(msg)
+
+ subprocess.call([binary, "OutputManager"])
+
+ # Check if it still doesn't exist
+ if not op.exists(output_dir):
+ msg = "After running binary, could not find expected"
+ msg += f" output dir {output_dir}\n"
+ msg += "The binary did not execute successfully or the"
+ msg += " OutputManager tests have changed"
+ raise RuntimeError(msg)
+
+ return output_dir
+
+
+def test_basic_Library() -> None:
+ dir_to_test = generate_data()
+ lib = Library(dir_to_test)
+
+ assert 0 == len(lib.names)
+ assert len(lib.summary)
+ assert len(lib.config)
+
+ # Check what happens for an unknown output subdir
+ assert lib.get("Does not exits") is None
+
+
+def test_bad_Library() -> None:
+ with pytest.raises(ValueError):
+ Library("This does not exist")