From 227bc6ea182964ecac9cdc313434eb82b07a12ae Mon Sep 17 00:00:00 2001
From: Remy Prechelt <prechelt@hawaii.edu>
Date: Fri, 2 Oct 2020 21:00:30 -1000
Subject: [PATCH] Add `read_hist` method with coverage info.
---
.gitlab-ci.yml | 4 +-
Python/Makefile | 2 +-
Python/corsika/__init__.py | 7 ++++
Python/corsika/io/__init__.py | 14 +++++++
Python/corsika/io/hist.py | 70 +++++++++++++++++++++++++++++++++++
Python/setup.cfg | 4 ++
Python/setup.py | 2 +-
Python/tests/test_hist.py | 36 ++++++++++++++++++
8 files changed, 135 insertions(+), 4 deletions(-)
create mode 100644 Python/corsika/io/__init__.py
create mode 100644 Python/corsika/io/hist.py
create mode 100644 Python/tests/test_hist.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 464ce2402..bf5ccd361 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -622,8 +622,8 @@ sanity:
- cd ${CI_PROJECT_DIR}/Python # change into the Python directory
- pip install --user -e '.[test]' # install the package + test deps
- make all 2&>1 | tee python-test.log # this runs all of the Python tests
- - echo "finished" >> python-test.log # create even an empty file...
- - cd ${CI_PROJECT_DIR} # reset the directory
+ - cd ${CI_PROJECT_DIR} # reset the directory
+ coverage: '/^TOTAL\s*\d+\s*\d+\s*(.*\%)/'
artifacts:
when: always
expire_in: 1 year
diff --git a/Python/Makefile b/Python/Makefile
index 59a1613fd..ccc13257f 100644
--- a/Python/Makefile
+++ b/Python/Makefile
@@ -16,7 +16,7 @@ tests:
${PYTHON} -m pytest --cov=corsika tests
flake:
- ${PYTHON} -m flake8 corsika
+ ${PYTHON} -m flake8 corsika tests
black:
${PYTHON} -m black -t py37 corsika tests
diff --git a/Python/corsika/__init__.py b/Python/corsika/__init__.py
index cf4f1519e..f5331efad 100644
--- a/Python/corsika/__init__.py
+++ b/Python/corsika/__init__.py
@@ -1,4 +1,6 @@
"""
+ A Python interface to CORSIKA 8.
+
(c) Copyright 2018 CORSIKA Project, corsika-project@lists.kit.edu
This software is distributed under the terms of the GNU General Public
@@ -6,4 +8,9 @@
the license.
"""
+from . import io
+
+# all imported objects
+__all__ = ["io"]
+
__version__: str = "8.0.0-alpha"
diff --git a/Python/corsika/io/__init__.py b/Python/corsika/io/__init__.py
new file mode 100644
index 000000000..bd8a0d8bc
--- /dev/null
+++ b/Python/corsika/io/__init__.py
@@ -0,0 +1,14 @@
+"""
+ 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.
+"""
+
+from .hist import read_hist
+
+# all exported objects
+__all__ = ["read_hist"]
diff --git a/Python/corsika/io/hist.py b/Python/corsika/io/hist.py
new file mode 100644
index 000000000..e12dcfd1b
--- /dev/null
+++ b/Python/corsika/io/hist.py
@@ -0,0 +1,70 @@
+"""
+ 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 `save_hist()` 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 histogram
+ if at == b"c":
+ axes.append(
+ bh.axis.Variable(
+ d[f"binedges_{i}"], overflow=has_overflow, underflow=has_underflow
+ )
+ )
+ # discrete histogram
+ 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
+ h = bh.Histogram(*axes)
+ h.view(flow=True)[:] = d["data"]
+
+ return h
diff --git a/Python/setup.cfg b/Python/setup.cfg
index d318235ee..2544189ca 100644
--- a/Python/setup.cfg
+++ b/Python/setup.cfg
@@ -59,3 +59,7 @@ ignore_missing_imports = True
# ignore missing types for matplotlib
[mypy-matplotlib.*]
ignore_missing_imports = True
+
+# ignore missing types for boost_histogram
+[mypy-boost_histogram.*]
+ignore_missing_imports = True
diff --git a/Python/setup.py b/Python/setup.py
index 36360358f..350fbe9fa 100644
--- a/Python/setup.py
+++ b/Python/setup.py
@@ -32,7 +32,7 @@ setup(
keywords=["cosmic ray", "physics", "astronomy", "simulation"],
packages=["corsika"],
python_requires=">=3.6*, <4",
- install_requires=["numpy", "pyyaml",],
+ install_requires=["numpy", "pyyaml", "boost_histogram"],
extras_require={
"test": [
"pytest",
diff --git a/Python/tests/test_hist.py b/Python/tests/test_hist.py
new file mode 100644
index 000000000..0ad70b734
--- /dev/null
+++ b/Python/tests/test_hist.py
@@ -0,0 +1,36 @@
+"""
+ 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 pytest
+
+import corsika
+
+
+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`.
+ """
+
+ # try and read in a continuous histogram
+
+ # try and read in a discrete histogram
+
+
+def test_corsika_read_hist_fail() -> None:
+ """
+ Check that an exception is thrown when reading
+ an incorrectly formatted histogram.
+ """
--
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